https://www.cazypedia.org/api.php?action=feedcontributions&user=Gideon+Davies&feedformat=atomCAZypedia - User contributions [en-ca]2024-03-28T22:27:54ZUser contributionsMediaWiki 1.35.10https://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_164&diff=14670Glycoside Hydrolase Family 1642020-04-08T13:07:43Z<p>Gideon Davies: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: ^^^Zachary Armstrong^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH164'''<br />
|-<br />
|'''Clan''' <br />
|GH-A<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH164.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
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[[Image:BS164_AB.png|thumb|right|400px|'''Figure 1. '''The trimeric structure of Bs164 is shown in panel''' A'''. All three protomers are shown with a surface and each chain is displayed as a cartoon diagram coloured by domain.''' B '''shows the structure of one protomer. Domain A, which has a (β/α)8 fold, is shown in green with subdomain H is shown in magenta, domain B, containing a mixed β-sheet, is shown in red and the β-sandwich of domain C is shown in blue.''' ''']]<br />
== Substrate specificities ==<br />
The defining member of [[glycoside hydrolase]] family 164, a β-mannosidase from ''Bacteroidetes salyersiae'' (''Bs''164, GenbankID: EIY59668.1), was identified initially identified through rational bioinformatic selection of enzyme targets <cite>Helbert2019</cite>. Although ''Bs''164 was initially reported as an α-mannosidase, subsequent detailed biochemical characterization and structure determination revealed that was instead a β-mannosidase <cite>Armstrong2020</cite>. This enzyme is an exo-acting and is capable of cleaving mannooligos and β-mannosides<cite>Armstrong2020</cite>. <br />
<br />
== Kinetics and Mechanism ==<br />
''Bs''164 β-mannosidase is a [[retaining]] enzyme, as first shown by NMR <cite>Armstrong2020</cite>, and follows the [[classical Koshland double-displacement mechanism]]. <br />
<br />
== Catalytic Residues ==<br />
The catalytic nucleophile of ''Bs''164 was identified as glutamate 297 through mutational analysis<cite>Armstrong2020</cite>. A structural complex with 2,4-dinitrophenyl 2-deoxy-2-fluoro-β-D-mannopyranoside showed a covalent attachment of the inhibitor to glutamate 297, reinforcing the assignment of Glu297 as the catalytic nucleophile. The acid/base residue, Glu160 is positioned to perform ''anti''-protonation of the leaving group, typical of clan GH-A glycoside hydrolases. This residue forms hydrogen bonding interactions with both the endocyclic nitrogen in noeuromycin and imidazole nitrogen in mannoimidazole. Complete loss of activity by the E160Q variant confirmed the assignment of Glu160 as the acid/base residue<cite>Armstrong2020</cite>.<br />
<br />
== Three-dimensional structures ==<br />
To date only the structure of ''Bs''164 has been solved. ''Bs''164 was solved using multi-wavelength anomalous diffraction of a seleno-methionine labeled protein<cite>Armstrong2020</cite>. The structure of ''Bs''164 has been solved in an uncomplexed state and in complex with mannoimidazole, noeuromycin and 2-deoxy-2-fluoromannose. Bs164 exists as a donut shaped trimer, see figure 1A. Each trimer-donut has an outer diameter of approximately 100 Å and an internal diameter of between 30 and 35 Å. The individual Bs164 chains contain three clearly defined domains: a modified (β/α)<sub>8</sub> barrel, a domain containing a seven membered mixed β-sheet sandwiched between α-helices, and a β-sheet domain (Figure 1B). The catalytic residues are present on strands 4 (acid/base) and 7<br />
(nucleophile) of the (β/α)<sub>8</sub> barrel indicating that GH164 belongs to clan GH-A glycoside hydrolases. This domain architecture is quite similar to that seen for family [[GH42]] enzymes <cite>Hidaka2002</cite>, but is previously unseen for β-mannosidases. <br />
<br />
<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: ''Bacteroides salyersiae'' β-mannosidase by NMR <cite>Armstrong2020</cite><br />
;First [[catalytic nucleophile]] identification: ''Bacteroides salyersiae'' β-mannosidase by 2-fluoromannose labeling and kinetic analysis of mutants <cite>Armstrong2020</cite><br />
;First [[general acid/base]] residue identification: ''Bacteroides salyersiae'' β-mannosidase by kinetic analysis of mutants <cite>Armstrong2020</cite><br />
;First 3-D structure of a GH1 enzyme: ''Bacteroides salyersiae'' β-mannosidase <cite>Armstrong2020</cite><br />
== References ==<br />
<biblio><br />
#Helbert2019 pmid=30850540<br />
#Hidaka2002 pmid=12215416<br />
#Armstrong2020 pmid=31871050<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH164]]<br />
<!-- ATTENTION: Make sure to replace "nnn" with a three digit family number, e.g. "032" or "105" etc., for proper sorting of the page by family number. --></div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Auxiliary_Activity_Family_13&diff=13559Auxiliary Activity Family 132019-02-22T10:58:00Z<p>Gideon Davies: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: ^^^Glyn Hemsworth^^^ & ^^^Leila LoLeggio^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
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<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
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{| {{Prettytable}}<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Auxiliary Activity Family 13'''<br />
|-<br />
|'''Clan''' <br />
|Structurally related to [[AA9]], [[AA10]] & [[AA11]]<br />
|-<br />
|'''Mechanism'''<br />
|lytic oxidase<br />
|-<br />
|'''Active site residues'''<br />
|mononuclear copper ion coordinated by the “histidine brace”<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}AA13.html<br />
|}<br />
</div><br />
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<br />
== Substrate specificities ==<br />
The AA13 family represents the fourth family of (Lytic) Polysaccharide Monooxygenases (LPMOs / sometimes called PMOs) that has been identified. Found in fungi, the first member of this family to be identified and characterised in the academic literature was isolated from <i>Neurospora crassa</i> by Vu et al <cite>Vu2014</cite>. While searching the <i>Neurospora crassa</i> genome for new putative LPMO sequences, they identified a sequence that appeared to code for an LPMO with a C-terminal [[CBM20]] domain but lacked significant overall sequence similarity to other [[AA9]], [[AA10]] or [[AA11]] LPMOs. Subsequently, Lo Leggio et al <cite>LoLeggio2015</cite> also identified and characterised AA13 family members from <i>Aspergilllus nidulans</i> and <i>Aspergillus oryzae</i> using a similar approach. Prior to this, genes now known to code for AA13s were demonstrated to produce proteins capable of boosting &alpha; and &beta;-amylase activity during starch, amylose and amylopectin degradation ([{{PatentLink}}WO2014197705A1 WO2014197705A1]).<br />
<br />
Of the AA13s that have been biochemically characterised to date, activity has only been demonstrate on starch and related substrates <cite>Vu2014 LoLeggio2015</cite>. The expression of these enzymes has also been shown to be heavily unregulated during growth of <i>A. nidulans</i> on starch <cite>Nekiunaite2016a</cite>. As for other LPMOs, AA13s utilise copper and an electron donor to oxidatively introduce chain breaks into the &alpha;-1,4-linked glucose polymers that form starch <cite>Vu2014 LoLeggio2015</cite>. AA13s specifically attack at the C1 position of the sugar ring forming oligosaccharide products with lactones at the reducing end which are then additionally hydrated to form aldonic acid terminated maltodextrins <cite>LoLeggio2015</cite>. The C1 specificity suggests that these LPMOs should be able to oxidatively attack both the &alpha;-1,4- and &alpha;-1,6-linkages found in amylopectin <cite>Vu2015</cite>. Interestingly, AA13s are currently the only LPMOs characterised to date that act on a glucan polymer formed from anything other than &beta;-1,4-linkages <cite>Vu2016</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
All LPMOs ([[AA9]], [[AA10]], [[AA11]], & AA13) are copper dependent monooxygenases and there is considerable work ongoing in trying to elucidate their detailed reaction mechanism <cite>Walton2017</cite>. Starch, being an &alpha;-1,4-linked substrate, poses a different challenge for AA13s to be able to oxidatively attack at the C1 carbon. Whether there is a significant difference in mechanism required in order to oxidise starch is currently unclear.<br />
<br />
[[File:AA13_Cazypedia_Small.gif|thumb|right|450x356px|'''Figure 1. Structure of AA13 from <i>Aspergillus oryzae</i> (PDB ID [{{PDBlink}}4opb 4OPB] <cite>LoLeggio2015</cite>).''' In the above animation the structure is shown initially in cartoon representation coloured by secondary structure and the transparent surface shown in grey. The active site is shown at the top of the structure with the copper ion shown as a sphere and surrounding active site residues shown as sticks with green carbon atoms. As the animation proceeds the surface surrounding the active site is shown to illustrate the presence of a groove that passes over the active site. This groove is thought to accommodate the helical structure of an &alpha;-1,4-linked amylopectin substrate.]]<br />
<br />
Performing kinetic measurements on LPMOs has been notoriously difficult. Several key aspects of AA13 biochemistry have been observed however. The <i>A. nidulans</i> AA13 showed significant synergy with a &beta;-amylase during degradation assays using retrograded starch as the substrate. The combined action of these enzymes resulted in >100-fold increase in the release of maltose compared to &beta;-amylase acting alone, representing one of the most significant boosting activities observed so far for any LPMO <cite>LoLeggio2015</cite>. Also highlighted in this study was the importance of the reducing agent used to activate the enzyme with cysteine providing greater activity than ascorbate which is typically used to activate LPMOs. Vu et al <cite>Vu2014</cite> also showed that cellobiose dehydrogenase (CDH composed of [[AA3]] and [[AA8]] domains) represents a good activating partner for AA13s as has been observed for [[AA9]]s. The importance of the [[CBM20]] module for AA13 activity has also been highlighted. The <i>A. oryzae</i> AA13, which naturally lacks a CBM, did not appear to be active in assays on starch while the [[CBM20]] appended A.nidulans enzyme showed clear activity <cite>LoLeggio2015</cite>. Indeed the presence of the [[CBM20]] domain has been demonstrated to confer typical starch and &beta;-cyclodextrin binding properties to AA13s and is suggested to mediate most of the substrate binding properties of this family of enzymes <cite>Nekiunaite2017b</cite>.<br />
<br />
[[File:AA13_Active_Site.png|thumb|right|331x654px|'''Figure 2. The active site architecture observed for the AA13 from <i>A. oryzae</i> (PDB ID [{{PDBlink}}4opb 4OPB] <cite>LoLeggio2015</cite>).''' '''Top:''' the active site residues surrounding the copper ion are shown. The Cu is shown as a sphere and is in the Cu(I) state due to photo reduction from the X-ray beam. '''Bottom:''' EPR spectrum observed for the AA13 from <i>A. oryzae</i> revealing super hyperfine coupling. The raw data are shown in black with the simulated data in red.]]<br />
<br />
== Three-dimensional structures ==<br />
The core fold of the AA13 structure is similar to all other LPMOs ([[AA9]], [[AA10]], & [[AA11]]) representing a &beta;-sandwich immunoglobulin like fold <cite>LoLeggio2015</cite>. There are some significant structural differences compared to the other families however. Firstly, the AA13 structure reveals additional helical secondary structure elements that are not found in other LPMOs (Figure 1). The most prominent difference however is surrounding the copper active site. Where in other LPMOs, the copper histidine brace is found at the centre of a flat or slightly concave surface ([[AA9]], [[AA10]], & [[AA11]]), a distinct groove can be observed passing over the active site of AA13 (Figure 1). This is an adaptation that is thought to be necessary to accommodate the helical structure of an amylopectin substrate. Despite significant efforts, it has not been possible to determine an oligosaccharide bound structure for an AA13 which would be particularly beneficial to delineating the adaptions necessary to allow activity on an &alpha;-1,4-linked substrate <cite>Frandsen2017</cite>.<br />
<br />
== Catalytic Residues ==<br />
The “histidine brace” motif is used to bind the active site copper in AA13 <cite>LoLeggio2015</cite>, as it is for all other LPMOs studied to date ([[AA9]], [[AA10]] & [[AA11]]) <cite>Vaaje-Kolstad2017</cite>. This motif sees the amino group and imidazole side chain of the N-terminal histidine, together with the imidazole group of a second histidine, directly coordinate the copper ion in a T-shaped geometry. For AA13s, one axial position is occupied by a tyrosine on one side of the copper ion, with a loop containing a glycine approaching near to the copper on the other side (Figure 2, top) <cite>LoLeggio2015</cite>. In [[AA10]]s and [[AA11]]s alanine in this position has been suggested as a possible important factor in distorting the arrangement of water molecules around the active site which may have mechanistic consequences in these families <cite>Hemsworth2013 Hemsworth2014</cite>. An interesting feature of the electron paramagnetic resonance (EPR) spectrum observed for the <i>A. nidulans</i> and <i>A. oryzae</i> AA13s was the presence of superhyperfine coupling in the spectrum (Figure 2, bottom) <cite>LoLeggio2015</cite>.<br />
<br />
== Family Firsts ==<br />
;First family member identified: AA13 from <i>N. crassa</i> <cite>Vu2014</cite>.<br />
;First demonstration of oxidative cleavage: The <i>N. crassa</i> AA13 was shown to produce oxidised malto-oligosaccharides in the presence of oxygen and reducing agents <cite>Vu2014</cite>.<br />
;First 3-D structure: AA13 from ''A. oryzae'' with Cu+ [{{PDBlink}}4opb 4OPB] <cite>LoLeggio2015</cite><br />
<br />
== References ==<br />
<biblio><br />
#Vu2014 pmid=25201969<br />
#LoLeggio2015 pmid=25608804<br />
#Nekiunaite2016a Nekiunaite, L., Arntzen, M.Ø., Svensson, B., Vaaje-Kolstad, G., Abou Hachem, M. (2016) Lytic polysaccharide monooxygenases and other oxidative enzymes are abundantly secreted by <i>Aspergillus nidulans</i> grown on different starches. Biotechnology for Biofuels. 9, 187 [http://dx.doi.org/10.1186/s13068-016-0604-0]<br />
#Vu2016 pmid=27170366<br />
#Walton2017 pmid=27094791<br />
#Nekiunaite2017b pmid=27397613<br />
#Vaaje-Kolstad2017 pmid=28086105<br />
#Frandsen2017 pmid=28045386<br />
<br />
#Hemsworth2013 pmid=23769965<br />
<br />
#Hemsworth2014 pmid=24362702<br />
</biblio><br />
<br />
[[Category:Auxiliary Activity Families|AA13]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Auxiliary_Activity_Family_11&diff=9857Auxiliary Activity Family 112014-02-06T10:49:21Z<p>Gideon Davies: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: ^^^Glyn Hemsworth^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Auxiliary Activity Family 11'''<br />
|-<br />
|'''Clan''' <br />
|Structurally related to [[AA9]] & [[AA10]]<br />
|-<br />
|'''Mechanism'''<br />
|lytic oxidase<br />
|-<br />
|'''Active site residues'''<br />
|mononuclear copper ion<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}AA11.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
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<br />
== Substrate specificities ==<br />
The AA11 family of Lytic Polysaccharide Mono-oxygenases (LPMOs; first described in <cite>Eijsink2010</cite>) was identified using a bioinformatic 'module walking' approach <cite>Hemsworth2013</cite>. Many [[AA9]] proteins have C-terminal domains, which are often cellulose binding CBMs (eg. [[CBM1]]), but some have no known function (also see <cite>Horn2012</cite>). Sequence searches using one of these domains (termed X278) returned hits where the domain was fused with [[GH18]] family members and another set of domains of unknown function. Closer examination of these domains revealed that they had a likely signal peptide followed by a histidine, typical of LPMOs, though they otherwise lacked significant sequence similarity to either [[AA9]] or [[AA10]] family members.<br />
<br />
The only AA11 to be isolated to to date is from ''Aspergillus oryzae'' which showed copper dependent oxidase activity on chitin in the presence of ascorbate. The observed products were a mixture of mainly aldonic acids and unmodified oligosaccharides with a small amount of a -2Da species, which may be C4 oxidation or the C1 lactone prior to ring opening. It is unknown at this stage whether AA11 family members will show any activity towards other substrates, whether they oxidise at positions other than C1 on the sugar ring or what the role of the X278 domain often found at the C-terminus is (although a chitin binding function would seem logical given its presence on GH18 chitinases and AA11).<br />
<br />
== Kinetics and Mechanism ==<br />
AA11s, like [[AA9]]s and [[AA10]]s, are copper dependent mono-oxygenases but the chemical mechanism by which these enzymes perform the reaction is yet to be elucidated. Recent quantum mechanical simulations suggest that [[AA9]]s are likely to oxidise cellulose using a copper-oxyl, oxygen rebound mechanism <cite>Kim2013</cite> but further work is needed in this area. The differences in the copper coordination geometries between the families might further hint that they might use different mechanisms (Reviewed in <cite>Hemsworth2013c</cite>). As is the case for [[AA10]]s, the natural electron donor for AA11s is unknown, with no equivalent of cellobiose dehydrogenase yet discovered that is active on chitobiose. It is also unknown whether the N-terminal histidine in AA11s is N-methylated (as the enzyme in the published study was expressed in ''E. coli'' and not a filamentous fungi)as is seen in [[AA9]]s and what effect this will have on the reaction performed by the enzyme. <br />
<br />
== Catalytic Residues ==<br />
Like [[AA9]] and [[AA10]], AA11 utilises copper, which it binds through the "histidine brace" consisting of the N-terminal histidine's amino and imidazole groups together with the imidazole sidechain of another histidine. It is unknown at this stage whether AA11s possess the methylated N-terminal histidine observed in [[AA9]]s as the protein was produced recombinantly in ''E. coli'' which does not carry out this modification. Like [[AA9]], a tyrosine sidechain is in close proximity to the copper ion but it does not directly coordinate the metal in this case. [[AA9]]s typically leave the opposite side to the tyrosine open to solvent where water molecules are observed coordinating the metal ion <cite>Harris2010 Karkehabadi2008 Li2012 Quinlan2011</cite>. In [[AA10]]s there is an alanine in this position, which causes a distortion in the copper coordination geometry away from octahedral <cite>Hemsworth2013b Vaaje-Kolstad2012 Vaaje-Kolstad2005 Aachmann2012</cite>. Interestingly AA11 has an alanine in a very similar position giving an active site structure somewhere between that of [[AA9]]s and [[AA10]]s. The structure was only determined with Cu(I) in the active site so the coordination geometry of Cu(II) was not directly observed but electron paramagnetic resonance spectroscopy confirmed that the copper coordination geometry lies somewhere between that of [[AA9]]s and [[AA10]]s <cite>Hemsworth2013</cite>.<br />
<br />
== Three-dimensional structures ==<br />
[[Image:AoAA11_Cazypedia.png|thumb|right|486x332px|'''Figure 1. Structure of AA11 from ''Aspergillus oryzae'' (PDB ID [{{PDBlink}}4mai 4MAI] <cite>Hemsworth2013</cite>).''' On the left the overall structure is shown in cartoon representation with the surface of the protein shown in gray. The active site is shown at the top of the structure with the copper ion shown as a sphere and surrounding active site residues shown as sticks with green carbon atoms. On the right; at the top is a view of the active site showing the coordinatiuon of the copper ion by the “histidine brace”. Below are shown the active sites of ''Thermoascus aurantiacus'' [[AA9]] (PDB ID [{{PDBlink}}2yet 2YET] <cite>Quinlan2011</cite>) and ''Bacillus amyloliquefaciens'' [[AA10]] (PDB ID [{{PDBlink}}2yoy 2YOY] <cite>Hemsworth2013b</cite>) in the same orientation showing how the AA11 forms a hybrid active site between the two families.]]<br />
<br />
Though AA11 does not share significant sequence similarity to [[AA9]] and [[AA10]] proteins, the core fold of the protein is remarkably similar forming a typical ß-sandwich immunoglobulin like fold <cite>Hemsworth2013</cite>. The active site is at the centre of a slightly concave surface which, consistent with observations in [[AA10]]s <cite>Aachmann2012 Vaaje-Kolstad2012</cite>, has very few aromatic residues suggesting that it also primarily interacts with chitin via H-bonding interactions. Given that LPMOs are oxidoreductases there is increasing interest in the role of electron transport chains within these proteins <cite>Li2012</cite>. Internal tyrosine and tryptophan residues have been implicated in these roles in [[AA9]]s <cite>Li2012</cite> and [[AA10]]s <cite>Hemsworth2013c</cite> respectively. Similarly in AA11s it is possible to trace a path through the core of the protein using tryptophans, methionine and other hydrophilic residues to the distal face of the enzyme from the active site suggesting that there may be a similar electron transport path in AA11s though these are yet to be experimentally verified in LPMOs.<br />
<br />
== Family Firsts ==<br />
;First family member identified: AA11 from ''A. oryzae'' <cite>Hemsworth2013</cite>.<br />
;First demonstration of oxidative cleavage: ''Ao''AA11 was shown to oxidatively cleave squid pen chitin producing a mixture of aldonic acids, unmodified oligosaccharides and undistinguishable lactone/C4 oxidation products <cite>Hemsworth2013</cite>.<br />
;First 3-D structure: AA11 from ''A. oryzae'' with Zn2+ [{{PDBlink}}4mah 4MAH] & Cu(I) [{{PDBlink}}4mai 4MAI] <cite>Hemsworth2013</cite><br />
<br />
== References ==<br />
<biblio><br />
#Eijsink2010 pmid=20929773<br />
#Hemsworth2013 pmid=24362702<br />
#Horn2012 pmid=22747961<br />
#Kim2013 pmid=24344312<br />
#Hemsworth2013c pmid=23769965<br />
#Harris2010 pmid=20230050<br />
#Karkehabadi2008 pmid=18723026<br />
#Li2012 pmid=22578542<br />
#Quinlan2011 pmid=21876164<br />
#Hemsworth2013b pmid=23540833<br />
#Aachmann2012 pmid=23112164<br />
#Vaaje-Kolstad2012 pmid=22210154<br />
#Vaaje-Kolstad2005 pmid=15590674<br />
<br />
</biblio><br />
<br />
[[Category:Auxiliary Activity Families|AA11]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_18&diff=8794Glycoside Hydrolase Family 182013-06-04T19:22:59Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]s: ^^^Gideon Davies^^^, ^^^Nathalie Juge^^^, ^^^Vincent Eijsink^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH18'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known (acid/neighbouring group)<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH18.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Family GH18 is unusual in having [[glycoside hydrolases]] that are both catalytically active chitinases (EC 3.2.1.14) and endo-β-N-acetylglucosaminidases (EC 3.2.1.96) and also sub-families of non-hydrolytic proteins that function as carbohydrate binding modules / "lectins" or as xylanase inhibitors.<br />
<br />
The active chitinases comprise non-processive endo-acting enzymes as well as processive enzymes with exo- and endo-binding preferences <cite>Horn2006a,Hult2005</cite>. Most enzymes primarily produce chitobiose, but some endo-acting family 18 chitinases are not capable of cleaving trimers or tetramers and thus yield longer products. Note that in older literature the endo-/exo-character of these enzymes often is assessed by studying the degradation of oligomeric substrates, and that several recent studies have shown this method to be invalid.<br />
<br />
Family 18 chitinases break down all forms of chitin at varying rates depending on the enzyme and the substrate. They also act on chitosan with degrees of acetylation as low as 13 % <cite>Sorbotten2005</cite> and some are known to degrade peptidoglycan <cite>Bokma1997</cite>. Studies on family 18 chitinases from ''Serratia marcescens'' have suggested that most subsites for sugar binding show some promiscuity with the notable exception of subsite -1 <cite>Horn2006a</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH18 enzymes perform enzymic catalysis with [[retaining|retention]] of anomeric configuration. They belong to a group of enzymes (including GH families 18, [[Glycoside Hydrolase Family 20|20]], [[Glycoside Hydrolase Family 25|25]], [[Glycoside Hydrolase Family 56|56]], [[Glycoside Hydrolase Family 84|84]], and [[Glycoside Hydrolase Family 85|85]]) that perform catalysis using a double-displacement reaction but instead of the more common enzyme-derived nucleophile they utilize the ''N''-acetamido carbonyl oxygen in what is termed [[neighboring group participation]] (or substrate participation or anchimeric assistance). Figures showing such a mechanism date back to Koshland's 1953 review <cite>Koshland1953</cite>; indeed they frequent the chemical literature of participating groups long before that, but it is primarily through the work on GH18 <cite>TerwisschavanScheltinga1995</cite> and soon after [[GH20]] <cite>Tews1996,Armand1997</cite> that such a mechanism became well established. In such a mechanism, which occurs with (net) retention of anomeric configuration, the enzyme provides a [[general acid]] function to protonate the leaving group to facilitate its departure with the substrate carbonyl oxygen playing the role of nucleophile to generate a bicyclic "[[oxazolinium ion]]" [[intermediate]], which subsequently breaks down following the microscopic reverse ''via'' hydrolysis or occasionally transglycosylation). Such a mechanism has a number of facets, one of which is its potential inhibition using thiazolines <cite>Macdonald</cite>. Allosamidin, a pseudotrisaccharide consisting of two ''N''-acetylallosamine sugars linked to an allosamizoline moiety <cite>Sakuda1987</cite>, is a well known natural compound that is a high affinity inhibitor of family 18 chitinases (see Figure).<br />
<br />
[[Image:Ligands.PNG|thumb|right|300px|'''Trisaccharide oxazolinium ion intermediate (upper panel), allosamidin (middle panel), and trisaccharide thiazoline (lower panel).''']] Like in many other enzymes acting on polysaccharides the substrate-binding clefts of processive family 18 chitinases are lined with aromatic residues. Family 18 chitinases have proven very useful to gain insight into the structural basis of a processive mechanism and in the importance of such a mechanism for biomass-converting efficiency <cite>Eijsink2008,Zakariassen2009</cite>. As previously suggested for cellulases in e.g. <cite>Varrot2003</cite>, aromatic residues close to the catalytic center play a crucial role in processivity <cite>Horn2006b</cite>.<br />
<br />
== Catalytic Residues ==<br />
The catalytically-active GH18 enzymes use a double displacement reaction mechanism with [[neighboring group participation]](see Figure). In this mechanism the carbonyl oxygen of the substrate acts as a nucleophile, with assistance from a carboxylate (Asp) that acts to deprotonate the ''N''-acetamido nitrogen during [[oxazolinium ion]] formation/breakdown. A second catalytic acid residue (glutamate in family GH18, but often also Asp in other families using this mechanism) acts as a general acid/base to protonate the glycosidic oxygen to assist in the departure of the aglycon, and to deprotonate the nucleophilic water molecule during the hydrolysis of the [[oxazolinium ion]] [[intermediate]]. In family GH18 the two catalytic carboxylates are found in an D-X-E motif whereas in other families the carboxylates may be adjacent, such as the DD motif in family [[GH84]] (for example see <cite>He2010</cite>). The physical separation of the two catalytic residues (with the second not in a position to act as a nucleophile itself) has led to confusion in some literature that GH18 and other enzymes (notably [[GH25]]) may be inverting enzymes; this is certainly not the case for GH18 and is unlikely to be the case for [[GH25]].[[Image:mechanism.jpg|thumb|right|600px|'''Catalytic mechanism of family 18 chitinases.''' The picture shows the mechanism proposed for ChiB from ''Serratia marcescens''. Panel c shows the oxazolium ion intermediate which is to be hydrolyzed by an incoming water molecule. The picture is taken from<cite>Daan2001</cite>.]] <br />
<br />
The D-X-E motif (Asp140-Glu144 in the Figure) is part of a diagnostic D-X-X-''D''-X-D-X-E motif that includes two more aspartates of which the one in italics (Asp140 in the Figure) is known to be essential for catalytic activity. There are several other conserved residues in the catalytic center that play important roles during catalysis, related to distortion of the -1 sugar, activation of the acetamido group and/or cycling of the p''K''a of the catalytic glutamate <cite>Synstad2004</cite>. The O6 of the –1 sugar interacts with the side chain of yet another semi-conserved aspartate (Asp215 in the Figure). In enzymes with an acidic pH optimum this residue is an asparagine.<br />
<br />
=== Catalytically inactive members ===<br />
One unusual of feature of plant members of the GH18 family is the large number of sequences that encode catalytically-inactive proteins that function as enzyme inhibitors or lectins. Phylogenetic analysis of the plant GH18 family reveals clear distinction between hevamine-type chitinases, putative chitinases and narbonins <cite>Durand2005</cite>. Out of the major subfamilies, only the one that contains hevamine contains enzymes of demonstrated activity <cite> TerwisschavanScheltinga1996</cite>. The subfamily of GH18 that contains xylanase inhibitor proteins (XIP) emerged from the hevamine cluster along with concanavalin B. All have non-conservative substitutions of one of the acidic amino acid residues in the catalytic region. In the structure of concanavalin B the catalytic Glu residue is replaced by Gln <cite>Henniga1995</cite>, which mostly accounts for the lack of chitinase activity reported for this protein. The XIP-type inhibitors all have the third aspartic acid DxxDxDxE mutated into an aromatic residue whereas the catalytic glutamate residue is only conserved in the prototype of cereal xylanase inhibitors, XIP-I (isolated from ''Triticum aetivum'') <cite>Juge2004</cite>. In XIP-I and narbonin, the glutamic acid residues are present in an equivalent position to the catalytic residue in hevamine, but their side chain is fully engaged in salt bridges with neighbouring arginine residues <cite>Hennigb1995 Payan2003</cite>, preventing chitinase activity despite the presence of the catalytic residue. Furthermore in both XIP-I and narbonin, the position equivalent to residue Asp in hevamine, which has been proposed to stabilize the positively charged [[oxazolinium ion]] reaction [[intermediate]] <cite>TerwisschavanScheltinga1996</cite>, is occupied by a bulky residue <cite>Hennigb1995 Payan2003</cite>. The mutation of this Asp residue in alanine in hevamine led to a mutant with approx. 2% residual activity <cite>Bokma2002</cite>. The most striking disruption of the cleft in XIP-I and narbonin is caused by the mutation of subsite -1 Gly which participates in the hydrogen-bonding network with the ligand <cite>ATVA1 TerwisschavanScheltinga1995</cite>, resulting in complete obstruction of subsite -1 and preventing access to the catalytic residue <cite>Payan2003</cite>. Xylanase inhibitors appeared after the emergence of the various subfamilies of chitinases from their common ancestor. In this respect, the xylanase inhibitors are a relatively new acquisition, and so far no protein has been reported to display both xylanase inhibition and chitinase activities. GH18 XIP-type inhibitors can inhibit xylanases from [[GH10]] and [[GH11]] families <cite>Juge2004</cite>. The inhibition specificity of the GH18 xylanase inhibitors can be explained on the basis of the solved 3-D structure of XIP-I in complex with a [[GH10]] xylanase from ''A. nidulans'' and a [[GH11]] xylanase from ''P. funiculosum'' <cite>Payan2004</cite>.<br />
<br />
== Three-dimensional structures ==<br />
[[Image:FIGURE ChiA_ChiB.jpg|thumb|right|500px|'''Structures of ChiA (left) and ChiB (right) from ''Serratia marcescens''.''' Panels A and B show C-alpha traces of the complete two-domain enzymes, with a substrate-binding non-catalytic domain pointing to the upper left (A) or lower right (B). The side chains of aromatic residues (possibly) involved in polysaccharide binding are shown in dark blue, whereas the side chain of the acid/base catalytic glutamate is shown in green. Panel C shows details of ChiA in complex with an chito-octamer (PDB ID[{{PDBlink}}1ehn 1ehn]) and panel D shows details of ChiB in complex with a chito-pentamer (PDB ID[{{PDBlink}}1e6n 1e6n]). Subsites are numbered. This picture was taken from <cite>Zakariassen2009</cite>.]]<br />
Although these enzymes are frequently multi-modular, the catalytic domains are &alpha; / &beta; barrels <cite>Perrakis,ATVA1</cite>. While several structures for complete bi-modular chitinases are available <cite>Perrakis,Aalten2000</cite> (see Figure), available structural information for multi-modular enzymes is often limited to the isolated catalytic domain.<br />
Work on the conformational itinerary of catalysis which is extremely similar to other [[retaining]] enzymes active on ''gluco''-configured substrates, was provided by the van Aalten group <cite>Daan2001</cite> in 2001 through the trapping of a distorted Michaelis complex in <sup>1,4</sup>''B'' conformation and thus extremely similar to the <sup>1</sup>''S''<sub>3</sub> skew boats observed in [[GH5]] <cite>Davies1998</cite> for example or the <sup>4</sup>E conformation originally seen for a "neighboring group" enzyme in [[GH20]] <cite>Tews1996</cite>. More recently, a similar conformation has been observed for the Michaelis complex of another neighboring group enzyme, the [[GH84]] O-GlcNAcase <cite>He2010</cite>. Fungal GH18 enzymes are considered as possible therapeutic targets and a number of programmes are probing this area (for example <cite>Housten2002</cite>).<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: Sometimes '''incorrectly''' reported as inverting, this family performs catalysis with '''retention''' of anomeric configuration as first shown on the ''Bacillus ciculans'' enzyme <cite>Armand1994</cite>.<br />
;First [[catalytic nucleophile]] identification: This family is one of many that uses neighbouring group participation for catalysis with the N-acetyl carbonyl group acting as the nucleophile; first proposed (we believe) for this family in <cite>TerwisschavanScheltinga1995</cite>.<br />
;First [[general acid/base]] residue identification: On the basis of 3-D structure <cite>Perrakis</cite>.<br />
;First 3-D structure: The first two 3-D structures for catalytically active GH18 members were the ''Serratia marcescens'' chitinase A and the plant defence protein hevamine published "back-to-back" in ''Structure'' in 1994 <cite>Perrakis,ATVA1</cite>. In retrospect, however, the non-catalytic "narbonin" structure was arguably the first GH18 3-D structure, although it is has no enzymatic activity <cite>Hennig1993</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Perrakis pmid=7704527<br />
#ATVA1 pmid=7704528<br />
#Armand1994 pmid=8168626<br />
#Koshland1953 Koshland, D. (1953) Biol. Rev. 28, 416.<br />
#Armand1997 pmid=9396742<br />
#Housten2002 pmid=12093900<br />
#Tews1996 pmid=8673609<br />
#Daan2001 pmid=11481469<br />
#Macdonald pmid=20209544<br />
#He2010 pmid=20067256<br />
#Davies1998 pmid=9718293<br />
#Daan2003 pmid=12775711<br />
#Henniga1995 pmid=7490746<br />
#Hennig1993 pmid=1628747<br />
#Hennigb1995 pmid=15299319<br />
#TerwisschavanScheltinga1996 pmid=8831791<br />
#Bokma2002 pmid=11846790<br />
#Payan2003 pmid=12617724<br />
#Payan2004 pmid=15181003<br />
#Juge2004 pmid=14871661<br />
#Durand2005 pmid=15794761<br />
#TerwisschavanScheltinga1995 pmid=7495789<br />
#Horn2006a pmid=16420473<br />
#Horn2006b pmid=17116887<br />
#Sorbotten2005 pmid=15654891<br />
#Varrot2003 pmid=12842048<br />
#Bokma1997 pmid=9271197<br />
#Eijsink2008 pmid=18367275<br />
#Hult2005 pmid=15717865<br />
#Aalten2000 pmid=7675786<br />
#Zakariassen2009 pmid=19244232<br />
#Synstad2004 pmid=14717693<br />
#Sakuda1987 pmid=3570982<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH018]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_6&diff=6100Glycoside Hydrolase Family 62010-12-03T12:35:26Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: ^^^Kathleen Piens^^^ and ^^^Gideon Davies^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}}<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH6'''<br />
|-<br />
|'''Clan'''<br />
|none<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|acid known, base debated<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH6.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
[[Glycoside hydrolases]] of family GH6 cleave &beta;-1,4 glycosidic bonds in cellulose / &beta;-1,4-glucans. Only endoglucanase (EC [{{EClink}}3.2.1.4 3.2.1.4]) and cellobiohydrolase (EC [{{EClink}}3.2.1.91 3.2.1.91]) activity has been reported for the bacterial and eukaryotic members of this family. <br />
<br />
== Kinetics and Mechanism ==<br />
GH6 enzymes perform catalysis with [[inverting|inversion]] of anomeric stereochemistry, as first shown by NMR <cite>Knowles1988</cite> on Cellobiohydrolase II (CBH II; Cel6A) from the fungus ''Trichoderma reesei'' (a clonal derivative of ''Hypocrea jecorina'' <cite>Kuhls1996</cite>).<br />
<br />
== Catalytic Residues ==<br />
The first 3-D structure of CBHII provided a strong clue as to the identification of the catalytic [[general acid]] in the [[inverting]] mechanism (Asp 221 in the case of this ''Trichoderma reesei'' Cel6A enzyme). This assigment has withstood the tests of time with strong kinetic support (from kinetics as a function of leaving group ability for a series of enzyme variants) <cite>Damude1995</cite> as well as from all subsequent 3-D analyses of enzyme-ligand complexes (for example <cite>Zou1999 Varrot2005 Varrot2002</cite> ). The identification of the catalytic [[general base]] is, however, far less clear. Simply put this is because there is no clear potential base within hydrogen-bonding distance of a water molecule that could act as the nucleophile in the [[inverting]] mechanism. Thus, although there are mutagenesis / kinetic proposals for a base <cite>Damude1995</cite>, the current 'Zeitgeist' is that the attacking water is deprotonated via a string of water molecules in what Sinnott has descibed as a "Grotthuss" mechanism; for which there is solvent kinetic isotope effect support <cite>Koivula2002</cite>. On the basis of structure the residue most likely to act as the [[general base]] is Asp175 on the ''Trichoderma reesei'' Cel6A, although Asp401 may also play a role (see Table 1).<br />
<br />
<br />
----<br />
{| {{Prettytable}} style="text-align:left"<br />
|+ Table 1. Putative catalytic residues of some representatives in GH family 6<br>(with biochemical characterization of wt and mutant enzymes).<br />
! Proposed role<br />
! ''Cf''Cel6A (endo)<br />
! ''Hi''Cel6A (exo)<br />
! ''Hj''Cel6A (exo)<br />
! ''Tf''Cel6A (endo)<br />
! ''Tf''Cel6B (exo)<br />
|-<br />
| Substrate distortion<br />
| Tyr210<br />
| Tyr174<br />
| Tyr169<br />
| Tyr73<br />
| Tyr220<br />
|-<br />
| Increase in pKa acid/Catalytic base<br />
| Asp216<br />
| Asp180<br />
| Asp175<br />
| Asp79<br />
| Asp226<br />
|-<br />
| Proton network<br />
| Gly222?<br />
| Ser186<br />
| Ser181<br />
| Ser85<br />
| Ser232<br />
|-<br />
| Catalytic acid<br />
| Asp252<br />
| Asp226<br />
| Asp221<br />
| Asp117<br />
| Asp274<br />
|-<br />
| Catalytic base/substrate binding<br />
| Asp392<br />
| Asp405<br />
| Asp401<br />
| Asp265<br />
| Asp497<br />
|}<br />
----<br />
<br />
<br />
== Three-dimensional structures ==<br />
The first crystal structures of cellobiohydrolases and endoglucanases from family [[GH6]] revealed modified &alpha;/&beta; barrel folds which, unlike the classical (&beta;/&alpha;)<sub>8</sub> "TIM" barrel has just seven &beta;-strands forming the central &beta;-barrel. The CBHII structure revealed an active centre (see above) enclosed in a tunnel formed primarily by two surface loops. When, subsequently, the first endoglucanase from GH6 was solved, the active center was observed in a long open groove. The comparison of these two structures thus provided the first insight into how endo or processive activity was modulated, through display of the active centre in a in an open grove, or loop-enclosed tunnel, respectively. In 1995 the UBC group were able to truncate the extended loops of a cellobiohydrolase resulting in an enzyme with more endo-activity <cite>Meinke1995</cite>. To this day the debate continues about the possibilities of loop conformational change in moderating the activity of cellobiohydrolases between exo and endo. Ståhlberg was perhaps the first to explicitly state that ''T. reesei'' "has no true exo-cellulases" <cite>Stberg1993</cite>. It is clear that there is no absolute steric demand for the ''exo'' activity of cellobiohydrolases; the enzymes have a viable "-3" subsite <cite>Varrot1999, Varrot2003</cite>, the loops of the cellobiohydrolases are clearly mobile and show multiple conformations (consistent with occasional opening to support ''endo''-activity, and are also able to act on artificial substrates in which both ends have large appended groups (for example <cite>Armand1997</cite>).<br />
<br />
The nature of how catalysis was achived, and the conformational itinerary of catalysis was first provided by the Uppsala, Grenoble and Gent groups in 1999 <cite>Zou1999</cite> was a trapped Michaelis complex of a thio-oligosaccharide was observed spanning the active centre with the -1 subsite sugar in <sup>2</sup>''S''<sub>O</sub> conformation, which suggested a pathway around the <sup>2,5</sup>''B'' [[transition state]] conformation. Subsequent structural <cite>Varrot2005 Varrot2002</cite> and modelling <cite>Koivula2002</cite> support for these proposals comes from similarly distorted species on other GH6 enzymes and from the observation of a "cellobiosyl isofagomine" in <sup>2,5</sup>''B'' conformation <cite>Varrot2003</cite>.<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: ''Hypocrea jecorina'' cellobiohydrolase Cel6A by NMR <cite>Knowles1988</cite>.<br />
;First [[general acid]] residue identification: The role of Asp221 as the potential catalytic acid was first proposed on the basis of 3-D structure of the ''Hypocrea jecorina'' cellobiohydrolase CBHII / Cel6A <cite>Rouvinen1990</cite>. Enzyme kinetics of variants, in conjunction with leaving groups requiring provided strong confirmation <cite>Damude1995</cite>. <br />
;First [[general base]] residue identification: The existence / identification of the catalytic base is less clear and current beliefs are that the water is deprotonated through a "solvent wire" through to one of the conserved aspartates near the active centre.<br />
;First 3-D structure: The catalytic core domain of the ''Trichoderma reesei'' (the organism now known as ''Hypocrea jecorina'') cellobiohydrolase II by the Jones group <cite>Rouvinen1990</cite>. The first endoglucanase in this family was the ''Thermomonospora fusca'' E2 enzyme (catalytic core) solved by the Wilson/Karplus groups<cite>Spezio1993</cite><br />
<br />
== References ==<br />
<biblio><br />
#Knowles1988 Knowles, J.K.C., Lehtovaara, P., Murray, M. and Sinnott, M.L. (1988) Stereochemical course of the action of the cellobioside hydrolases I and II of ''Trichoderma reesei''. J. Chem. Soc., Chem. Commun., 1988, 1401-1402. [http://dx.doi.org/10.1039/C39880001401 DOI: 10.1039/C39880001401]<br />
#Kuhls1996 pmid=8755548<br />
#Rouvinen1990 pmid=2377893<br />
#Spezio1993 pmid=8399160<br />
#Koivula2002 pmid=12188666<br />
#Zou1999 pmid=10508787 <br />
#Varrot2003 pmid=12744312<br />
#Varrot2005 pmid=15824123<br />
#Varrot2002 pmid=12454501<br />
#Varrot1999 pmid=10413461<br />
#Damude1995 pmid=7857933<br />
#Meinke1995 pmid=7876202<br />
#Armand1997 pmid=9006908<br />
#Stberg1993 pmid=8499476<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH006]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_18&diff=5940Glycoside Hydrolase Family 182010-10-22T18:01:50Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]s: ^^^Gideon Davies^^^, ^^^Nathalie Juge^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH18'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known (acid/neighbouring group)<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH18.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Family GH18 is unusual in having [[glycoside hydrolases]] that are both catalytically active chitinases (EC 3.2.1.14) and endo-β-N-acetylglucosaminidases (EC 3.2.1.96) and also sub-families of non-hydrolytic proteins that function as carbohydrate binding modules / "lectins" or as xylanase inhibitors.<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
GH18 enzymes perform enzymic catalysis with [[retaining|retention]] of anomeric configuration. They belong to a growing group of enzymes (now including GH families 18, [[Glycoside Hydrolase Family 20|20]], [[Glycoside Hydrolase Family 25|25]], [[Glycoside Hydrolase Family 56|56]], [[Glycoside Hydrolase Family 84|84]], and [[Glycoside Hydrolase Family 85|85]]) that perform catalysis using a double-displacement reaction but instead of the more common enzyme-derived nucleophile they utilize the ''N''-acetamido carbonyl oxygen in what is termed [[neighboring group participation]] (or substrate participation or anchimeric assistance). Figures showing such a mechanism date back to Koshland's 1953 review <cite>Koshland1953</cite>; indeed they frequent the chemical literature of participating groups long before that, but it is primarily through the work on GH18 <cite>TerwisschavanScheltinga1995</cite> and soon after [[GH20]] <cite>Tews1996,Armand1997</cite> that such a mechanism became well established. In such a mechanism, which occurs with (net) retention of anomeric configuration, the enzyme provides a [[general acid]] function to protonate the leaving group to facilitate its departure with the substrate carbonyl oxygen playing the role of nucleophile to generate a bicyclic "[[oxazolinium ion]]" [[intermediate]], which subsequently breaks down following the microscopic reverse ''via'' hydrolysis or occasionally transglycosylation). Such a mechanism has a number of facets, one of which is its potential inhibition using thiazolines <cite>Macdonald</cite>.<br />
<br />
== Catalytic Residues ==<br />
The catalytically-active GH18 enzymes use a double displacement reaction mechanism with [[neighboring group participation]]. In this mechanism the carbonyl oxygen of the substrate acts as a nucleophile, with assistance from a carboxylate (Asp) that acts to deprotonate the ''N''-acetamido nitrogen during [[oxazolinium ion]] formation/breakdown. A second catalytic acid residue (glutamate in family GH18, but often also Asp in other families using this mechanism, except for [[GH85]] where this residue is an amide) acts as a general acid/base to protonate the glycosidic oxygen to assist in the departure of the aglycon, and to deprotonate the nucleophilic water molecule during the hydrolysis of the [[oxazolinium ion]] [[intermediate]]. In family GH18 the two catalytic carboxylates are found in an D-X-E motif whereas in other families the carboxylates may be adjacent, such as the DD motif in family [[GH84]] (for example see <cite>He2010</cite>). The physical separation of the two catalytic residues (with the second not in a position to act as a nucleophile itself) has led to confusion in some literature that GH18 and other enzymes (notably [[GH25]]) may be inverting enzymes; this is certainly not the case for GH18 and is unlikely to be the case for [[GH25]].<br />
<br />
=== Catalytically inactive members ===<br />
One unusual of feature of plant members of the GH18 family is the large number of sequences that encode catalytically-inactive proteins that function as enzyme inhibitors or lectins. Phylogenetic analysis of the plant GH18 family reveals clear distinction between hevamine-type chitinases, putative chitinases and narbonins <cite>Durand2005</cite>. Out of the major subfamilies, only the one that contains hevamine contains enzymes of demonstrated activity <cite> TerwisschavanScheltinga1996</cite>. The subfamily of GH18 that contains xylanase inhibitor proteins (XIP) emerged from the hevamine cluster along with concanavalin B. All have non-conservative substitutions of one of the acidic amino acid residues in the catalytic region. In the structure of concanavalin B the catalytic Glu residue is replaced by Gln <cite>Henniga1995</cite>, which mostly accounts for the lack of chitinase activity reported for this protein. The XIP-type inhibitors all have the third aspartic acid DxxDxDxE mutated into an aromatic residue whereas the catalytic glutamate residue is only conserved in the prototype of cereal xylanase inhibitors, XIP-I (isolated from ''Triticum aetivum'') <cite>Juge2004</cite>. In XIP-I and narbonin, the glutamic acid residues are present in an equivalent position to the catalytic residue in hevamine, but their side chain is fully engaged in salt bridges with neighbouring arginine residues <cite>Hennigb1995 Payan2003</cite>, preventing chitinase activity despite the presence of the catalytic residue. Furthermore in both XIP-I and narbonin, the position equivalent to residue Asp in hevamine, which has been proposed to stabilize the positively charged [[oxazolinium ion]] reaction [[intermediate]] <cite>TerwisschavanScheltinga1996</cite>, is occupied by a bulky residue <cite>Hennigb1995 Payan2003</cite>. The mutation of this Asp residue in alanine in hevamine led to a mutant with approx. 2% residual activity <cite>Bokma2002</cite>. The most striking disruption of the cleft in XIP-I and narbonin is caused by the mutation of subsite -1 Gly which participates in the hydrogen-bonding network with the ligand <cite>ATVA1 TerwisschavanScheltinga1995</cite>, resulting in complete obstruction of subsite -1 and preventing access to the catalytic residue <cite>Payan2003</cite>. Xylanase inhibitors appeared after the emergence of the various subfamilies of chitinases from their common ancestor. In this respect, the xylanase inhibitors are a relatively new acquisition, and so far no protein has been reported to display both xylanase inhibition and chitinase activities. GH18 XIP-type inhibitors can inhibit xylanases from [[GH10]] and [[GH11]] families <cite>Juge2004</cite>. The inhibition specificity of the GH18 xylanase inhibitors can be explained on the basis of the solved 3-D structure of XIP-I in complex with a [[GH10]] xylanase from ''A. nidulans'' and a [[GH11]] xylanase from ''P. funiculosum'' <cite>Payan2004</cite>.<br />
<br />
== Three-dimensional structures ==<br />
Although these enzymes are frequently multi-modular, the catalytic domains are &alpha; / &beta; barrels <cite>Perrakis,ATVA</cite>.<br />
<br />
Work on the conformational itinerary of catalysis which is extremely similar to other [[retaining]] enzymes active on ''gluco''-configured substrates, was provided by the van Aalten group <cite>Daan2001</cite> in 2001 through the trapping of a distorted Michaelis complex in <sup>1,4</sup>''B'' conformation and thus extremely similar to the <sup>1</sup>''S''<sub>3</sub> skew boats observed in [[GH5]] <cite>Davies1998</cite> for example or the <sup>4</sup>E conformation originally seen for a "neighboring group" enzyme in [[GH20]] <cite>Tews1996</cite>. More recently, a similar conformation has been observed for the Michaelis complex of another neighboring group enzyme, the [[GH84]] O-GlcNAcase <cite>He2010</cite>. Fungal GH18 enzymes are considered as possible therapeutic targets and a number of programmes are probing this area (for example <cite>Housten2002</cite>).<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: Sometimes '''incorrectly''' reported as inverting, this family performs catalysis with '''retention''' of anomeric configuration as first shown on the ''Bacillus ciculans'' enzyme <cite>Armand1994</cite>.<br />
;First [[catalytic nucleophile]] identification: This family is one of many that uses neighbouring group participation for catalysis with the N-acetyl carbonyl group acting as the nucleophile; first proposed (we believe) for this family in <cite>TerwisschavanScheltinga1995</cite>.<br />
;First [[general acid/base]] residue identification: On the basis of 3-D structure <cite>Perrakis</cite>.<br />
;First 3-D structure: The first two 3-D structures for catalytically active GH18 members were the ''Serratia marcescens'' chitinase A and the plant defence protein hevamine published "back-to-back" in ''Structure'' in 1994 <cite>Perrakis,ATVA1</cite>. In retrospect, however, the non-catalytic "narbonin" structure was arguably the first GH18 3-D structure, although it is has no enzymatic activity <cite>Hennig1993</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Perrakis pmid=7704527<br />
#ATVA1 pmid=7704528<br />
#Armand1994 pmid=8168626<br />
#Koshland1953 Koshland, D. (1953) Biol. Rev. 28, 416.<br />
#Armand1997 pmid=9396742<br />
#Housten2002 pmid=12093900<br />
#Tews1996 pmid=8673609<br />
#Daan2001 pmid=11481469<br />
#Macdonald pmid=20209544<br />
#He2010 pmid=20067256<br />
#Davies1998 pmid=9718293<br />
#Daan2003 pmid=12775711<br />
#Henniga1995 pmid=7490746<br />
#Hennig1993 pmid=1628747<br />
#Hennigb1995 pmid=15299319<br />
#TerwisschavanScheltinga1996 pmid=8831791<br />
#Bokma2002 pmid=11846790<br />
#Payan2003 pmid=12617724<br />
#Payan2004 pmid=15181003<br />
#Juge2004 pmid=14871661<br />
#Durand2005 pmid=15794761<br />
#TerwisschavanScheltinga1995 pmid=7495789<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH018]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_18&diff=5919Glycoside Hydrolase Family 182010-10-13T11:59:35Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]s: ^^^Gideon Davies^^^, ^^^Nathalie Juge^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH18'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known (acid/neighbouring group)<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH18.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Family GH18 is unusual in having [[glycoside hydrolases]] that are both catalytically active chitinases (EC 3.2.1.14) and endo-β-N-acetylglucosaminidases (EC 3.2.1.96) and also sub-families of non-hydrolytic proteins that function as carbohydrate binding modules / "lectins" or as xylanase inhibitors.<br />
<br />
=== Catalytically inactive members ===<br />
One unusual of feature of plant members of the GH18 family is the large number of sequences that encode catalytically-inactive proteins that function as enzyme inhibitors or lectins. Phylogenetic analysis of the plant GH18 family reveals clear distinction between hevamine-type chitinases, putative chitinases and narbonins <cite>Durand2005</cite>. Out of the major subfamilies, only the one that contains hevamine contains enzymes of demonstrated activity <cite> TerwisschavanScheltinga1996</cite>. The subfamily of GH18 that contains xylanase inhibitor proteins (XIP) emerged from the hevamine cluster along with concanavalin B. All have non-conservative substitutions of one of the acidic amino acid residues in the catalytic region. In the structure of concanavalin B the catalytic Glu residue is replaced by Gln <cite>Henniga1995</cite>, which mostly accounts for the lack of chitinase activity reported for this protein. The XIP-type inhibitors all have the third aspartic acid DxxDxDxE mutated into an aromatic residue whereas the catalytic glutamate residue is only conserved in the prototype of cereal xylanase inhibitors, XIP-I (isolated from ''Triticum aetivum'') <cite>Juge2004</cite>. In XIP-I and narbonin, the glutamic acid residues are present in an equivalent position to the catalytic residue in hevamine, but their side chain is fully engaged in salt bridges with neighbouring arginine residues <cite>Hennigb1995 Payan2003</cite>, preventing chitinase activity despite the presence of the catalytic residue. Furthermore in both XIP-I and narbonin, the position equivalent to residue Asp in hevamine, which has been proposed to stabilize the positively charged [[oxazolinium ion]] reaction [[intermediate]] <cite>TerwisschavanScheltinga1996</cite>, is occupied by a bulky residue <cite>Hennigb1995 Payan2003</cite>. The mutation of this Asp residue in alanine in hevamine led to a mutant with approx. 2% residual activity <cite>Bokma2002</cite>. The most striking disruption of the cleft in XIP-I and narbonin is caused by the mutation of subsite -1 Gly which participates in the hydrogen-bonding network with the ligand <cite>ATVA1 TerwisschavanScheltinga1995</cite>, resulting in complete obstruction of subsite -1 and preventing access to the catalytic residue <cite>Payan2003</cite>. Xylanase inhibitors appeared after the emergence of the various subfamilies of chitinases from their common ancestor. In this respect, the xylanase inhibitors are a relatively new acquisition, and so far no protein has been reported to display both xylanase inhibition and chitinase activities. GH18 XIP-type inhibitors can inhibit xylanases from [[GH10]] and [[GH11]] families <cite>Juge2004</cite>. The inhibition specificity of the GH18 xylanase inhibitors can be explained on the basis of the solved 3-D structure of XIP-I in complex with a [[GH10]] xylanase from ''A. nidulans'' and a [[GH11]] xylanase from ''P. funiculosum'' <cite>Payan2004</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH18 enzymes perform enzymic catalysis with [[retaining|retention]] of anomeric configuration. They belong to a growing group of enzymes (now including GH families 18, [[Glycoside Hydrolase Family 20|20]], [[Glycoside Hydrolase Family 25|25]], [[Glycoside Hydrolase Family 56|56]], [[Glycoside Hydrolase Family 84|84]], and [[Glycoside Hydrolase Family 85|85]]) that perform catalysis using a double-displacement reaction but instead of the more common enzyme-derived nucleophile they utilize the ''N''-acetamido carbonyl oxygen in what is termed [[neighboring group participation]] (or substrate participation or anchimeric assistance). Figures showing such a mechanism date back to Koshland's 1953 review <cite>Koshland1953</cite>; indeed they frequent the chemical literature of participating groups long before that, but it is primarily through the work on GH18 <cite>TerwisschavanScheltinga1995</cite> and soon after [[GH20]] <cite>Tews1996,Armand1997</cite> that such a mechanism became well established. In such a mechanism, which occurs with (net) retention of anomeric configuration, the enzyme provides a [[general acid]] function to protonate the leaving group to facilitate its departure with the substrate carbonyl oxygen playing the role of nucleophile to generate a bicyclic "[[oxazolinium ion]]" [[intermediate]], which subsequently breaks down following the microscopic reverse ''via'' hydrolysis or occasionally transglycosylation). Such a mechanism has a number of facets, one of which is its potential inhibition using thiazolines <cite>Macdonald</cite>.<br />
<br />
== Catalytic Residues ==<br />
The catalytically-active GH18 enzymes use a double displacement reaction mechanism with [[neighboring group participation]]. In this mechanism the carbonyl oxygen of the substrate acts as a nucleophile, with assistance from a carboxylate (Asp) that acts to deprotonate the ''N''-acetamido nitrogen during [[oxazolinium ion]] formation/breakdown. A second catalytic acid residue (glutamate in family GH18, but often also Asp in other families using this mechanism, except for [[GH85]] where this residue is an amide) acts as a general acid/base to protonate the glycosidic oxygen to assist in the departure of the aglycon, and to deprotonate the nucleophilic water molecule during the hydrolysis of the [[oxazolinium ion]] [[intermediate]]. In family GH18 the two catalytic carboxylates are found in an D-X-G motif whereas in other families the carboxylates may be adjacent, such as the DD motif in family [[GH84]] (for example see <cite>He2010</cite>). The physical separation of the two catalytic residues (with the second not in a position to act as a nucleophile itself) has led to confusion in some literature that GH18 and other enzymes (notably [[GH25]]) may be inverting enzymes; this is certainly not the case for GH18 and is unlikely to be the case for [[GH25]].<br />
<br />
== Three-dimensional structures ==<br />
Although these enzymes are frequently multi-modular, the catalytic domains are &alpha; / &beta; barrels <cite>Perrakis,ATVA</cite>.<br />
<br />
Work on the conformational itinerary of catalysis which is extremely similar to other [[retaining]] enzymes active on ''gluco''-configured substrates, was provided by the van Aalten group <cite>Daan2001</cite> in 2001 through the trapping of a distorted Michaelis complex in <sup>1,4</sup>''B'' conformation and thus extremely similar to the <sup>1</sup>''S''<sub>3</sub> skew boats observed in [[GH5]] <cite>Davies1998</cite> for example or the <sup>4</sup>E conformation originally seen for a "neighboring group" enzyme in [[GH20]] <cite>Tews1996</cite>. More recently, a similar conformation has been observed for the Michaelis complex of another neighboring group enzyme, the [[GH84]] O-GlcNAcase <cite>He2010</cite>. Fungal GH18 enzymes are considered as possible therapeutic targets and a number of programmes are probing this area (for example <cite>Housten2002</cite>).<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: Sometimes '''incorrectly''' reported as inverting, this family performs catalysis with '''retention''' of anomeric configuration as first shown on the ''Bacillus ciculans'' enzyme <cite>Armand1994</cite>.<br />
;First [[catalytic nucleophile]] identification: This family is one of many that uses neighbouring group participation for catalysis with the N-acetyl carbonyl group acting as the nucleophile; first proposed (we believe) for this family in <cite>TerwisschavanScheltinga1995</cite>.<br />
;First [[general acid/base]] residue identification: On the basis of 3-D structure <cite>Perrakis</cite>.<br />
;First 3-D structure: The first two 3-D structures for catalytically active GH18 members were the ''Serratia marcescens'' chitinase A and the plant defence protein hevamine published "back-to-back" in ''Structure'' in 1994 <cite>Perrakis,ATVA1</cite>. In retrospect, however, the non-catalytic "narbonin" structure was arguably the first GH18 3-D structure, although it is has no enzymatic activity <cite>Hennig1993</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Perrakis pmid=7704527<br />
#ATVA1 pmid=7704528<br />
#Armand1994 pmid=8168626<br />
#Koshland1953 Koshland, D. (1953) Biol. Rev. 28, 416.<br />
#Armand1997 pmid=9396742<br />
#Housten2002 pmid=12093900<br />
#Tews1996 pmid=8673609<br />
#Daan2001 pmid=11481469<br />
#Macdonald pmid=20209544<br />
#He2010 pmid=20067256<br />
#Davies1998 pmid=9718293<br />
#Daan2003 pmid=12775711<br />
#Henniga1995 pmid=7490746<br />
#Hennig1993 pmid=1628747<br />
#Hennigb1995 pmid=15299319<br />
#TerwisschavanScheltinga1996 pmid=8831791<br />
#Bokma2002 pmid=11846790<br />
#Payan2003 pmid=12617724<br />
#Payan2004 pmid=15181003<br />
#Juge2004 pmid=14871661<br />
#Durand2005 pmid=15794761<br />
#TerwisschavanScheltinga1995 pmid=7495789<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH018]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_18&diff=5918Glycoside Hydrolase Family 182010-10-13T11:58:29Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]s: ^^^Gideon Davies^^^, ^^^Nathalie Juge^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH18'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known (acid/neighbouring group)<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH18.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Family GH18 is unusual in having [[glycoside hydrolases]] that are both catalytically active chitinases (EC 3.2.1.14) and endo-β-N-acetylglucosaminidases (EC 3.2.1.96) and also sub-families of non-hydrolytic proteins that function as carbohydrate binding modules / "lectins" or as xylanase inhibitors.<br />
<br />
=== Catalytically inactive members ===<br />
One unusual of feature of plant members of the GH18 family is the large number of sequences that encode catalytically-inactive proteins that function as enzyme inhibitors or lectins. Phylogenetic analysis of the plant GH18 family reveals clear distinction between hevamine-type chitinases, putative chitinases and narbonins <cite>Durand2005</cite>. Out of the major subfamilies, only the one that contains hevamine contains enzymes of demonstrated activity <cite> TerwisschavanScheltinga1996</cite>. The subfamily of GH18 that contains xylanase inhibitor proteins (XIP) emerged from the hevamine cluster along with concanavalin B. All have non-conservative substitutions of one of the acidic amino acid residues in the catalytic region. In the structure of concanavalin B the catalytic Glu residue is replaced by Gln <cite>Henniga1995</cite>, which mostly accounts for the lack of chitinase activity reported for this protein. The XIP-type inhibitors all have the third aspartic acid DxxDxDxE mutated into an aromatic residue whereas the catalytic glutamate residue is only conserved in the prototype of cereal xylanase inhibitors, XIP-I (isolated from ''Triticum aetivum'') <cite>Juge2004</cite>. In XIP-I and narbonin, the glutamic acid residues are present in an equivalent position to the catalytic residue in hevamine, but their side chain is fully engaged in salt bridges with neighbouring arginine residues <cite>Hennigb1995 Payan2003</cite>, preventing chitinase activity despite the presence of the catalytic residue. Furthermore in both XIP-I and narbonin, the position equivalent to residue Asp in hevamine, which has been proposed to stabilize the positively charged [[oxazolinium ion]] reaction [[intermediate]] <cite>TerwisschavanScheltinga1996</cite>, is occupied by a bulky residue <cite>Hennigb1995 Payan2003</cite>. The mutation of this Asp residue in alanine in hevamine led to a mutant with approx. 2% residual activity <cite>Bokma2002</cite>. The most striking disruption of the cleft in XIP-I and narbonin is caused by the mutation of subsite -1 Gly which participates in the hydrogen-bonding network with the ligand <cite>ATVA1 TerwisschavanScheltinga1995</cite>, resulting in complete obstruction of subsite -1 and preventing access to the catalytic residue <cite>Payan2003</cite>. Xylanase inhibitors appeared after the emergence of the various subfamilies of chitinases from their common ancestor. In this respect, the xylanase inhibitors are a relatively new acquisition, and so far no protein has been reported to display both xylanase inhibition and chitinase activities. GH18 XIP-type inhibitors can inhibit xylanases from [[GH10]] and [[GH11]] families <cite>Juge2004</cite>. The inhibition specificity of the GH18 xylanase inhibitors can be explained on the basis of the solved 3-D structure of XIP-I in complex with a [[GH10]] xylanase from ''A. nidulans'' and a [[GH11]] xylanase from ''P. funiculosum'' <cite>Payan2004</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH18 enzymes perform enzymic catalysis with [[retaining|retention]] of anomeric configuration. They belong to a growing group of enzymes (now including GH families 18, [[Glycoside Hydrolase Family 20|20]], [[Glycoside Hydrolase Family 25|25]], [[Glycoside Hydrolase Family 56|56]], [[Glycoside Hydrolase Family 84|84]], and [[Glycoside Hydrolase Family 85|85]]) that perform catalysis using a double-displacement reaction but instead of the more common enzyme-derived nucleophile they utilize the ''N''-acetamido carbonyl oxygen in what is termed [[neighboring group participation]] (or substrate participation or anchimeric assistance). Figures showing such a mechanism date back to Koshland's 1953 review <cite>Koshland1953</cite>; indeed they frequent the chemical literature of participating groups long before that, but it is primarily through the work on GH18 <cite>TerwisschavanScheltinga1995</cite> and soon after [[GH20]] <cite>Tews1996,Armand1997</cite> that such a mechanism became well established. In such a mechanism, which occurs with (net) retention of anomeric configuration, the enzyme provides a [[general acid]] function to protonate the leaving group to facilitate its departure with the substrate carbonyl oxygen playing the role of nucleophile to generate a bicyclic "[[oxazolinium ion]]" [[intermediate]], which subsequently breaks down following the microscopic reverse ''via'' hydrolysis or occasionally transglycosylation). Such a mechanism has a number of facets, one of which is its potential inhibition using thiazolines <cite>Macdonald</cite>.<br />
<br />
== Catalytic Residues ==<br />
The catalytically-active GH18 enzymes use a double displacement reaction mechanism with [[neighboring group participation]]. In this mechanism the carbonyl oxygen of the substrate acts as a nucleophile, with assistance from a carboxylate (Asp) that acts to deprotonate the ''N''-acetamido nitrogen during [[oxazolinium ion]] formation/breakdown. A second catalytic acid residue (glutamate in family GH18, but often also Asp in other families using this mechanism, except for [[GH85]] where this residue is an amide) acts as a general acid/base to protonate the glycosidic oxygen to assist in the departure of the aglycon, and to deprotonate the nucleophilic water molecule during the hydrolysis of the [[oxazolinium ion]] [[intermediate]]. In family GH18 the two catalytic carboxylates are found in an D-X-G motif whereas in other families the carboxylates may be adjacent, such as the DD motif in family [[GH84]] (for example see <cite>He2010</cite>). The physical separation of the two catalytic residues (with the second not in a position to act as a nucleophile itself) has led to confusion in some literature that GH18 and other enzymes (notably [[GH25]]) may be inverting enzymes; this is certainly not the case for GH18 and is unlikely to be the case for [[GH25]].<br />
<br />
== Three-dimensional structures ==<br />
Although these enzymes are frequently multi-modular, the catalytic domains are &alpha; / &beta; barrels <cite>Perrakis,ATVA</cite>.<br />
<br />
Work on the conformational itinerary of catalysis which is extremely similar to other [[retaining]] enzymes active on ''gluco''-configured substrates, was provided by the van Aalten group <cite>Daan2001</cite> in 2001 through the trapping of a distorted Michaelis complex in <sup>1,4</sup>''B'' conformation and thus extremely similar to the <sup>1</sup>''S''<sub>3</sub> skew boats observed in [[GH5]] <cite>Davies1998</cite> for example or the <sup>4</sup>E conformation originally seen for a "neighboring group" enzyme in [[GH20]] <cite>Tews1996</cite>. More recently, a similar conformation has been observed for the Michaelis complex of another neighboring group enzyme, the [[GH84]] O-GlcNAcase <cite>He2010</cite>. Fungal GH18 enzymes are considered as possible therapeutic targets and a number of programmes are probing this area (for example <cite>Housten2002</cite>).<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: Sometimes '''incorrectly''' reported as inverting, this family performs catalysis with '''retention''' of anomeric configuration as first shown on the ''Bacillus ciculans'' enzyme <cite>Armand1994</cite>.<br />
;First [[catalytic nucleophile]] identification: This family is one of many that uses neighbouring group participation for catalysis with the N-acetyl carbonyl group acting as the nucleophile; first proposed (I believe) for this family in <cite>AVTA2</cite>.<br />
;First [[general acid/base]] residue identification: On the basis of 3-D structure <cite>Perrakis</cite>.<br />
;First 3-D structure: The first two 3-D structures for catalytically active GH18 members were the ''Serratia marcescens'' chitinase A and the plant defence protein hevamine published "back-to-back" in ''Structure'' in 1994 <cite>Perrakis,ATVA1</cite>. In retrospect, however, the non-catalytic "narbonin" structure was arguably the first GH18 3-D structure, although it is has no enzymatic activity <cite>Hennig1993</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Perrakis pmid=7704527<br />
#ATVA1 pmid=7704528<br />
#Armand1994 pmid=8168626<br />
#Koshland1953 Koshland, D. (1953) Biol. Rev. 28, 416.<br />
#Armand1997 pmid=9396742<br />
#Housten2002 pmid=12093900<br />
#Tews1996 pmid=8673609<br />
#Daan2001 pmid=11481469<br />
#Macdonald pmid=20209544<br />
#He2010 pmid=20067256<br />
#Davies1998 pmid=9718293<br />
#Daan2003 pmid=12775711<br />
#Henniga1995 pmid=7490746<br />
#Hennig1993 pmid=1628747<br />
#Hennigb1995 pmid=15299319<br />
#TerwisschavanScheltinga1996 pmid=8831791<br />
#Bokma2002 pmid=11846790<br />
#Payan2003 pmid=12617724<br />
#Payan2004 pmid=15181003<br />
#Juge2004 pmid=14871661<br />
#Durand2005 pmid=15794761<br />
#TerwisschavanScheltinga1995 pmid=7495789<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH018]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_18&diff=5891Glycoside Hydrolase Family 182010-10-12T21:24:21Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]s: ^^^Gideon Davies^^^, ^^^Nathalie Juge^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH18'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known (acid/neighbouring group)<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH18.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
GH18 is unusual in having both catalytically active chitinase (EC 3.2.1.14) and endo-β-N-acetylglucosaminidases (EC 3.2.1.96) but there are also sub-families of non-hydrolytic proteins that function as carbohydrate binding modules / "lectins" or as xylanase inhibitors.<br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
GH18 enzymes belong to a growing group of enzymes (now including GH families [[Glycoside Hydrolase Family 18|18]], [[Glycoside Hydrolase Family 20|20]],[[Glycoside Hydrolase Family 25|25]], [[Glycoside Hydrolase Family 56|56]], [[Glycoside Hydrolase Family 84|84]], and [[Glycoside Hydrolase Family 85|85]]) that perform a double-displacement reaction but instead of the more common enzyme-derived nucleophile they utlize the N-acetamido carbonyl oxygen in what is termed "neighbouring group participation" / "substrate participation" or "anchimeric assistance". Figures showing such a mechanism date back to Koshland's 1953 review <cite>Koshland1953</cite>, indeed they frequent the chemical literature of participating groups long before that, but it is primarily through the work on GH18 <cite>AVTA2</cite> and soon after GH20 <cite>Tews1996,Armand1997</cite> that such a mechanism became well established. In such a mechanism, which occurs with (net) retention of anomeric configuration, the enzyme provides a catalytic acid function to protonate the leaving group to facilitate its departure with the substrate carbonyl oxygen playing the role of nucleophile to generate a bicyclic "oxazoline" intermediate (which subsequently breaks down following the microscopic reverse ''via'' hydrolysis or occasionally transglycosylation). Such a mechanism has a number of facets, one of which is its potential inhibition using thiazolines <cite>Macdonald</cite>.<br />
<br />
<br />
== Catalytic Residues ==<br />
The catalytically active GH18 enzymes use a double displacement reaction mechanism with "neighbouring group participation". Hence there is a catalytic acid residue (glutamate in family GH18, but often also Asp in other families using this mechanism) and in all families apart from GH[[Glycoside Hydrolase Family 85|85]] (where this residue is an amide), a second carboxylate (here Asp) acts to deprotonate the N-acetamido nitrogen during oxazoline formation/breakdown. In family GH18 the two catalytic carboxylates are found in an D-X-G motif whereas in some families the carboxylates may be adjacent such as the DD motif in family GH84 (for example see <cite>He2010</cite>). The physical separation of the two catalytic residues (with the second not in a position to act as a nucleophile itself) has led to confusion in some literature that GH18 and other enzymes (notably GH25) may be inverting enzymes; this is certainly not the case for GH18 and is unlikely to be the case for GH25.<br />
<br />
<br />
== Three-dimensional structures ==<br />
Although these enzymes are frequently multi-modular, the catalytic domains are &alpha; / &beta; barrels <cite>Perrakis,ATVA</cite>.<br />
<br />
Work on the conformational itinerary of catalysis which is extremely similar to other retaining enzymes active on ''gluco''-configured substrates, was provided by the van Aalten group <cite>Daan2001</cite> in 2001 through the trapping of a distorted Michaelis complex in <sup>1,4</sup>B conformation and thus extremely similar to the <sup>1</sup>S<sub>3</sub> skew boats oberserved in GH[[Glycoside Hydrolase Family 5|5]] <cite>Davies1998</cite> for example or the <sup>4</sup>E conformation originally seen for a "neighboring group" enzyme in GH[[Glycoside Hydrolase Family 20|20]] <cite>Tews1996</cite>. More recently, a similar conformation has been observed for the Michaelis complex of another neighboring group enzyme, the GH84 O-GlcNAcase <cite>He2010</cite>. Fungal GH18 enzymes are considered as possible therapeutic targets and a number of programmes are probing this area (for example <cite>Housten2002</cite>).<br />
<br />
One unusual of feature of plant members of the GH18 family is the large number of sequences that encode catalytically-inactive proteins that function as enzyme inhibitors or lectins. Phylogenetic analysis of the plant GH18 family reveals clear distinction between hevamine-type chitinases, putative chitinases and narbonins <cite>Durand2005</cite>. Out of the major subfamilies, only the one that contains hevamine actually contains enzymes of demonstrated activity <cite> TerwisschavanScheltinga1996</cite>. The subfamily of GH18 coding for xylanase inhibitor proteins (XIP) emerged from the hevamine cluster along with concanavalin B. All have nonconservative substitutions of one of the acidic amino acid residues in the catalytic region. In the structure of concanavalin B the catalytic Glu residue is replaced by Gln <cite>Henniga1995</cite>, which mostly account for the lack of chitinase activity reported for this protein. The XIP-type inhibitors all have the third aspartic acid DxxDxDxE mutated into an aromatic residue whereas the catalytic glutamate residue is only conserved in the prototype of cereal xylanase inhibitors, XIP-I (isolated from ''Triticum aetivum'') <cite>Juge2004</cite>. In XIP-I and narbonin, the glutamic acid residues are present in an equivalent position to the catalytic residue in hevamine, but their side chain is fully engaged in salt bridges with neighbouring arginine residues <cite>Hennigb1995Payan2003</cite>, preventing chitinase activity despite the presence of the catalytic residue. Furthermore in both XIP-I and narbonin, the position equivalent to residue Asp in hevamine, which has been proposed to stabilize the positively charged oxazoline reaction intermediate (<cite>TerwisschavanScheltinga1996</cite>), is occupied by a bulky residue<cite>Hennigb1995Payan2003</cite>. The mutation of this Asp residue in alanine in hevamine led to a mutant with approx. 2% residual activity <cite> Bokma2002</cite>. The most striking disruption of the cleft in XIP-I and narbonin is caused by the mutation of subsite -1 Gly which participates in the hydrogen-bonding network with the ligand <cite>AVTA2</cite>, resulting in complete obstruction of subsite -1 and preventing access to the catalytic residue <cite>Payan2003</cite>. Xylanase inhibitors appeared after the emergence of the various subfamilies of chitinases from their common ancestor. In this respect, the xylanase inhibitors are a relatively new invention, and so far no protein has been reported to display both xylanase inhibition and chitinase activities. GH18 XIP-type inhibitors can inhibit xylanases from GH10 and GH11 families <cite>Juge2004</cite>. The inhibition specificity of the GH18 xylanase inhibitors can be explained on the basis of the solved 3-D structure of XIP-I in complex with a GH10 xylanase from ''A. nidulans'' and a GH11 xylanase from ''P. funiculosum'' <cite>Payan2004</cite>. <br />
<br />
<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: Sometimes '''incorrectly''' reported as inverting, this family performs catalysis with '''retention''' of anomeric configuration as first shown on the ''Bacillus ciculans'' enzyme <cite>Armand1994</cite>.<br />
;First catalytic nucleophile identification: This family is one of many that uses neighbouring group participation for catalysis with the N-acetyl carbonyl group acting as the nucleophile; first proposed (I believe) for this family in <cite>AVTA2</cite>.<br />
;First general acid/base residue identification: On the basis of 3-D structure <cite>Perrakis</cite>.<br />
;First 3-D structure: The first two 3-D structures for catalytically active GH18 members were the ''Serratia marcescens'' chitinase A and the plant defence protein hevamine published "back-to-back" in ''Structure'' in 1994 <cite>Perrakis,ATVA1</cite>. In retrospect, however, the non-catalytic "Narbonin" structure was arguably the first GH18 3-D structure, although it is has no enzymatic activity <cite>Hennig1993</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Perrakis pmid=7704527<br />
#ATVA1 pmid=7704528<br />
#AVTA2 pmid=7495789 <br />
#Armand1994 pmid=8168626<br />
#Koshland1953 Koshland, D. (1953) Biol. Rev. 28, 416.<br />
#Armand1997 pmid=9396742<br />
#Housten2002 pmid=12093900<br />
#Tews1996 pmid=8673609<br />
#Daan2001 pmid=11481469<br />
#Macdonald pmid=20209544<br />
#He2010 pmid=20067256<br />
#Davies1998 pmid=9718293<br />
#Daan2003 pmid=12775711<br />
#Henniga1995 pmid=7490746<br />
#Hennig1993 pmid=1628747<br />
#Hennigb1995 pmid=15299319<br />
#TerwisschavanScheltinga1996 pmid=8831791<br />
#Bokma2002 pmid=11846790<br />
#Payan2003 pmid=12617724<br />
#Payan2004 pmid=15181003<br />
#Juge2004 pmid=14871661<br />
#Durand2005 pmid=15794761<br />
<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH018]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_18&diff=5890Glycoside Hydrolase Family 182010-10-12T21:23:29Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]s: ^^^Gideon Davies^^^, ^^^Nathalie Juge^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH18'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known (acid/neighbouring group)<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH18.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
GH18 is unusual in having both catalytically active chitinase (EC 3.2.1.14) and endo-β-N-acetylglucosaminidases (EC 3.2.1.96) but there are also sub-families of non-hydrolytic proteins that function as carbohydrate binding modules / "lectins" or as xylanase inhibitors.<br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
GH18 enzymes belong to a growing group of enzymes (now including GH families [[Glycoside Hydrolase Family 18|18]], [[Glycoside Hydrolase Family 20|20]],[[Glycoside Hydrolase Family 25|25]], [[Glycoside Hydrolase Family 56|56]], [[Glycoside Hydrolase Family 84|84]], and [[Glycoside Hydrolase Family 85|85]]) that perform a double-displacement reaction but instead of the more common enzyme-derived nucleophile they utlize the N-acetamido carbonyl oxygen in what is termed "neighbouring group participation" / "substrate participation" or "anchimeric assistance". Figures showing such a mechanism date back to Koshland's 1953 review <cite>Koshland1953</cite>, indeed they frequent the chemical literature of participating groups long before that, but it is primarily through the work on GH18 <cite>AVTA2</cite> and soon after GH20 <cite>Tews1996,Armand1997</cite> that such a mechanism became well established. In such a mechanism, which occurs with (net) retention of anomeric configuration, the enzyme provides a catalytic acid function to protonate the leaving group to facilitate its departure with the substrate carbonyl oxygen playing the role of nucleophile to generate a bicyclic "oxazoline" intermediate (which subsequently breaks down following the microscopic reverse ''via'' hydrolysis or occasionally transglycosylation). Such a mechanism has a number of facets, one of which is its potential inhibition using thiazolines <cite>Macdonald</cite>.<br />
<br />
<br />
== Catalytic Residues ==<br />
The catalytically active GH18 enzymes use a double displacement reaction mechanism with "neighbouring group participation". Hence there is a catalytic acid residue (glutamate in family GH18, but often also Asp in other families using this mechanism) and in all families apart from GH[[Glycoside Hydrolase Family 85|85]] (where this residue is an amide), a second carboxylate (here Asp) acts to deprotonate the N-acetamido nitrogen during oxazoline formation/breakdown. In family GH18 the two catalytic carboxylates are found in an D-X-G motif whereas in some families the carboxylates may be adjacent such as the DD motif in family GH84 (for example see <cite>He2010</cite>). The physical separation of the two catalytic residues (with the second not in a position to act as a nucleophile itself) has led to confusion in some literature that GH18 and other enzymes (notably GH25) may be inverting enzymes; this is certainly not the case for GH18 and is unlikely to be the case for GH25.<br />
<br />
<br />
== Three-dimensional structures ==<br />
Although these enzymes are frequently multi-modular, the catalytic domains are &alpha; / &beta; barrels <cite>Perrakis,ATVA</cite>.<br />
<br />
Work on the conformational itinerary of catalysis which is extremely similar to other retaining enzymes active on ''gluco''-configured substrates, was provided by the van Aalten group <cite>Daan2001</cite> in 2001 through the trapping of a distorted Michaelis complex in <sup>1,4</sup>B conformation and thus extremely similar to the <sup>1</sup>S<sub>3</sub> skew boats oberserved in GH[[Glycoside Hydrolase Family 5|5]] <cite>Davies1998</cite> for example or the <sup>4</sup>E conformation originally seen for a "neighboring group" enzyme in GH[[Glycoside Hydrolase Family 20|20]] <cite>Tews1996</cite>. More recently, a similar conformation has been observed for the Michaelis complex of another neighboring group enzyme, the GH84 O-GlcNAcase <cite>He2010</cite>. Fungal GH18 enzymes are considered as possible therapeutic targets and a number of programmes are probing this area (for example <cite>Housten2002</cite>).<br />
<br />
One unusual of feature of plant members of the GH18 family is the large number of sequences that encode catalytically-inactive proteins that function as enzyme inhibitors or lectins. Phylogenetic analysis of the plant GH18 family reveals clear distinction between hevamine-type chitinases, putative chitinases and narbonins <cite>Durand2005</cite>. Out of the major subfamilies, only the one that contains hevamine actually contains enzymes of demonstrated activity <cite> TerwisschavanScheltinga1996</cite>. The subfamily of GH18 coding for xylanase inhibitor proteins (XIP) emerged from the hevamine cluster along with concanavalin B. All have nonconservative substitutions of one of the acidic amino acid residues in the catalytic region. In the structure of concanavalin B the catalytic Glu residue is replaced by Gln <cite>Henniga1995</cite>, which mostly account for the lack of chitinase activity reported for this protein. The XIP-type inhibitors all have the third aspartic acid DxxDxDxE mutated into an aromatic residue whereas the catalytic glutamate residue is only conserved in the prototype of cereal xylanase inhibitors, XIP-I (isolated from ''Triticum aetivum'') <cite>Juge2004</cite>. In XIP-I and narbonin, the glutamic acid residues are present in an equivalent position to the catalytic residue in hevamine, but their side chain is fully engaged in salt bridges with neighbouring arginine residues <cite>Hennigb1995Payan2003</cite>, preventing chitinase activity despite the presence of the catalytic residue. Furthermore in both XIP-I and narbonin, the position equivalent to residue Asp in hevamine, which has been proposed to stabilize the positively charged oxazoline reaction intermediate (<cite>TerwisschavanScheltinga1996</cite>), is occupied by a bulky residue<cite>Hennigb1995Payan2003</cite>. The mutation of this Asp residue in alanine in hevamine led to a mutant with approx. 2% residual activity <cite> Bokma2002</cite>. The most striking disruption of the cleft in XIP-I and narbonin is caused by the mutation of subsite -1 Gly which participates in the hydrogen-bonding network with the ligand <cite>AVTA2</cite>, resulting in complete obstruction of subsite -1and preventing access to the catalytic residue <cite>Payan2003</cite>. Xylanase inhibitors appeared after the emergence of the various subfamilies of chitinases from their common ancestor. In this respect, the xylanase inhibitors are a relatively new invention, and so far no protein has been reported to display both xylanase inhibition and chitinase activities. GH18 XIP-type inhibitors can inhibit xylanases from GH10 and GH11 families <cite>Juge2004</cite>. The inhibition specificity of the GH18 xylanase inhibitors can be explained on the basis of the solved 3-D structure of XIP-I in complex with a GH10 xylanase from ''A. nidulans'' and a GH11 xylanase from ''P. funiculosum'' <cite>Payan2004</cite>. <br />
<br />
<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: Sometimes '''incorrectly''' reported as inverting, this family performs catalysis with '''retention''' of anomeric configuration as first shown on the ''Bacillus ciculans'' enzyme <cite>Armand1994</cite>.<br />
;First catalytic nucleophile identification: This family is one of many that uses neighbouring group participation for catalysis with the N-acetyl carbonyl group acting as the nucleophile; first proposed (I believe) for this family in <cite>AVTA2</cite>.<br />
;First general acid/base residue identification: On the basis of 3-D structure <cite>Perrakis</cite>.<br />
;First 3-D structure: The first two 3-D structures for catalytically active GH18 members were the ''Serratia marcescens'' chitinase A and the plant defence protein hevamine published "back-to-back" in ''Structure'' in 1994 <cite>Perrakis,ATVA1</cite>. In retrospect, however, the non-catalytic "Narbonin" structure was arguably the first GH18 3-D structure, although it is has no enzymatic activity <cite>Hennig1993</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Perrakis pmid=7704527<br />
#ATVA1 pmid=7704528<br />
#AVTA2 pmid=7495789 <br />
#Armand1994 pmid=8168626<br />
#Koshland1953 Koshland, D. (1953) Biol. Rev. 28, 416.<br />
#Armand1997 pmid=9396742<br />
#Housten2002 pmid=12093900<br />
#Tews1996 pmid=8673609<br />
#Daan2001 pmid=11481469<br />
#Macdonald pmid=20209544<br />
#He2010 pmid=20067256<br />
#Davies1998 pmid=9718293<br />
#Daan2003 pmid=12775711<br />
#Henniga1995 pmid=7490746<br />
#Hennig1993 pmid=1628747<br />
#Hennigb1995 pmid=15299319<br />
#TerwisschavanScheltinga1996 pmid=8831791<br />
#Bokma2002 pmid=11846790<br />
#Payan2003 pmid=12617724<br />
#Payan2004 pmid=15181003<br />
#Juge2004 pmid=14871661<br />
#Durand2005 pmid=15794761<br />
<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH018]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_18&diff=5889Glycoside Hydrolase Family 182010-10-12T21:22:06Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]s: ^^^Gideon Davies^^^, ^^^Nathalie Juge^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH18'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known (acid/neighbouring group)<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH18.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
GH18 is unusual in having both catalytically active chitinase (EC 3.2.1.14) and endo-β-N-acetylglucosaminidases (EC 3.2.1.96) but there are also sub-families of non-hydrolytic proteins that function as carbohydrate binding modules / "lectins" or as xylanase inhibitors.<br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
GH18 enzymes belong to a growing group of enzymes (now including GH families [[Glycoside Hydrolase Family 18|18]], [[Glycoside Hydrolase Family 20|20]],[[Glycoside Hydrolase Family 25|25]], [[Glycoside Hydrolase Family 56|56]], [[Glycoside Hydrolase Family 84|84]], and [[Glycoside Hydrolase Family 85|85]]) that perform a double-displacement reaction but instead of the more common enzyme-derived nucleophile they utlize the N-acetamido carbonyl oxygen in what is termed "neighbouring group participation" / "substrate participation" or "anchimeric assistance". Figures showing such a mechanism date back to Koshland's 1953 review <cite>Koshland1953</cite>, indeed they frequent the chemical literature of participating groups long before that, but it is primarily through the work on GH18 <cite>AVTA2</cite> and soon after GH20 <cite>Tews1996,Armand1997</cite> that such a mechanism became well established. In such a mechanism, which occurs with (net) retention of anomeric configuration, the enzyme provides a catalytic acid function to protonate the leaving group to facilitate its departure with the substrate carbonyl oxygen playing the role of nucleophile to generate a bicyclic "oxazoline" intermediate (which subsequently breaks down following the microscopic reverse ''via'' hydrolysis or occasionally transglycosylation). Such a mechanism has a number of facets, one of which is its potential inhibition using thiazolines <cite>Macdonald</cite>.<br />
<br />
<br />
== Catalytic Residues ==<br />
The catalytically active GH18 enzymes use a double displacement reaction mechanism with "neighbouring group participation". Hence there is a catalytic acid residue (glutamate in family GH18, but often also Asp in other families using this mechanism) and in all families apart from GH[[Glycoside Hydrolase Family 85|85]] (where this residue is an amide), a second carboxylate (here Asp) acts to deprotonate the N-acetamido nitrogen during oxazoline formation/breakdown. In family GH18 the two catalytic carboxylates are found in an D-X-G motif whereas in some families the carboxylates may be adjacent such as the DD motif in family GH84 (for example see <cite>He2010</cite>). The physical separation of the two catalytic residues (with the second not in a position to act as a nucleophile itself) has led to confusion in some literature that GH18 and other enzymes (notably GH25) may be inverting enzymes; this is certainly not the case for GH18 and is unlikely to be the case for GH25.<br />
<br />
<br />
== Three-dimensional structures ==<br />
Although these enzymes are frequently multi-modular, the catalytic domains are &alpha; / &beta; barrels <cite>Perrakis,ATVA</cite>.<br />
<br />
Work on the conformational itinerary of catalysis which is extremely similar to other retaining enzymes active on ''gluco''-configured substrates, was provided by the van Aalten group <cite>Daan2001</cite> in 2001 through the trapping of a distorted Michaelis complex in <sup>1,4</sup>B conformation and thus extremely similar to the <sup>1</sup>S<sub>3</sub> skew boats oberserved in GH[[Glycoside Hydrolase Family 5|5]] <cite>Davies1998</cite> for example or the <sup>4</sup>E conformation originally seen for a "neighboring group" enzyme in GH[[Glycoside Hydrolase Family 20|20]] <cite>Tews1996</cite>. More recently, a similar conformation has been observed for the Michaelis complex of another neighboring group enzyme, the GH84 O-GlcNAcase <cite>He2010</cite>. Fungal GH18 enzymes are considered as possible therapeutic targets and a number of programmes are probing this area (for example <cite>Housten2002</cite>).<br />
<br />
One unusual of feature of plant members of the GH18 family is the large number of sequences that encode catalytically-inactive proteins that function as enzyme inhibitors or lectins. Phylogenetic analysis of the plant GH18 family reveals clear distinction between hevamine-type chitinases, putative chitinases and narbonins <cite>Durand2005</cite>. Out of the major subfamilies, only the one that contains hevamine actually contains enzymes of demonstrated activity <cite> TerwisschavanScheltinga1996</cite>. The subfamily of GH18 coding for xylanase inhibitor proteins (XIP) emerged from the hevamine cluster along with concanavalin B. All have nonconservative substitutions of one of the acidic amino acid residues in the catalytic region. In the structure of concanavalin B the catalytic Glu residue is replaced by Gln <cite>Henniga1995</cite>, which mostly account for the lack of chitinase activity reported for this protein. The XIP-type inhibitors all have the third aspartic acid DxxDxDxE mutated into an aromatic residue whereas the catalytic glutamate residue is only conserved in the prototype of cereal xylanase inhibitors, XIP-I (isolated from ''Triticum aetivum'') <cite>Juge2004</cite>. In XIP-I and narbonin, the glutamic acid residues are present in an equivalent position to the catalytic residue in hevamine, but their side chain is fully engaged in salt bridges with neighbouring arginine residues <cite>Hennigb1995Payan2003</cite>, preventing chitinase activity despite the presence of the catalytic residue. Furthermore in both XIP-I and narbonin, the position equivalent to residue Asp in hevamine, which has been proposed to stabilize the positively charged oxazoline reaction intermediate (<cite>TerwisschavanScheltinga1996</cite>), is occupied by a bulky residue<cite>Hennigb1995Payan2003</cite>. The mutation of this Asp residue in alanine in hevamine led to a mutant with approx. 2% residual activity <cite> Bokma2002</cite>. The most striking disruption of the cleft in XIP-I and narbonin is caused by the mutation of subsite -1 Gly which participates in the hydrogen-bonding network with the ligand <cite>ATVA2</cite>, resulting in complete obstruction of subsite -1and preventing access to the catalytic residue <cite>Payan2003</cite>. Xylanase inhibitors appeared after the emergence of the various subfamilies of chitinases from their common ancestor. In this respect, the xylanase inhibitors are a relatively new invention, and so far no protein has been reported to display both xylanase inhibition and chitinase activities. GH18 XIP-type inhibitors can inhibit xylanases from GH10 and GH11 families <cite>Juge2004</cite>. The inhibition specificity of the GH18 xylanase inhibitors can be explained on the basis of the solved 3-D structure of XIP-I in complex with a GH10 xylanase from ''A. nidulans'' and a GH11 xylanase from ''P. funiculosum'' <cite>Payan2004</cite>. <br />
<br />
<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: Sometimes '''incorrectly''' reported as inverting, this family performs catalysis with '''retention''' of anomeric configuration as first shown on the ''Bacillus ciculans'' enzyme <cite>Armand1994</cite>.<br />
;First catalytic nucleophile identification: This family is one of many that uses neighbouring group participation for catalysis with the N-acetyl carbonyl group acting as the nucleophile; first proposed (I believe) for this family in <cite>AVTA2</cite>.<br />
;First general acid/base residue identification: On the basis of 3-D structure <cite>Perrakis</cite>.<br />
;First 3-D structure: The first two 3-D structures for catalytically active GH18 members were the ''Serratia marcescens'' chitinase A and the plant defence protein hevamine published "back-to-back" in ''Structure'' in 1994 <cite>Perrakis,ATVA1</cite>. In retrospect, however, the non-catalytic "Narbonin" structure was arguably the first GH18 3-D structure, although it is has no enzymatic activity <cite>Hennig1993</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Perrakis pmid=7704527<br />
#ATVA1 pmid=7704528<br />
#AVTA2 pmid=7495789 <br />
#Armand1994 pmid=8168626<br />
#Koshland1953 Koshland, D. (1953) Biol. Rev. 28, 416.<br />
#Armand1997 pmid=9396742<br />
#Housten2002 pmid=12093900<br />
#Tews1996 pmid=8673609<br />
#Daan2001 pmid=11481469<br />
#Macdonald pmid=20209544<br />
#He2010 pmid=20067256<br />
#Davies1998 pmid=9718293<br />
#Daan2003 pmid=12775711<br />
#Henniga1995 pmid=7490746<br />
#Hennig1993 pmid=1628747<br />
#Hennigb1995 pmid=15299319<br />
#TerwisschavanScheltinga1996 pmid=8831791<br />
#Bokma2002 pmid=11846790<br />
#Payan2003 pmid=12617724<br />
#Payan2004 pmid=15181003<br />
#Juge2004 pmid=14871661<br />
#Durand2005 pmid=15794761<br />
<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH018]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_18&diff=5888Glycoside Hydrolase Family 182010-10-12T21:20:20Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]s: ^^^Gideon Davies^^^, ^^^Nathalie Juge^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH18'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known (acid/neighbouring group)<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH18.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
GH18 is unusual in having both catalytically active chitinase (EC 3.2.1.14) and endo-β-N-acetylglucosaminidases (EC 3.2.1.96) but there are also sub-families of non-hydrolytic proteins that function as carbohydrate binding modules / "lectins" or as xylanase inhibitors.<br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
GH18 enzymes belong to a growing group of enzymes (now including GH families [[Glycoside Hydrolase Family 18|18]], [[Glycoside Hydrolase Family 20|20]],[[Glycoside Hydrolase Family 25|25]], [[Glycoside Hydrolase Family 56|56]], [[Glycoside Hydrolase Family 84|84]], and [[Glycoside Hydrolase Family 85|85]]) that perform a double-displacement reaction but instead of the more common enzyme-derived nucleophile they utlize the N-acetamido carbonyl oxygen in what is termed "neighbouring group participation" / "substrate participation" or "anchimeric assistance". Figures showing such a mechanism date back to Koshland's 1953 review <cite>Koshland1953</cite>, indeed they frequent the chemical literature of participating groups long before that, but it is primarily through the work on GH18 <cite>AVTA2</cite> and soon after GH20 <cite>Tews1996,Armand1997</cite> that such a mechanism became well established. In such a mechanism, which occurs with (net) retention of anomeric configuration, the enzyme provides a catalytic acid function to protonate the leaving group to facilitate its departure with the substrate carbonyl oxygen playing the role of nucleophile to generate a bicyclic "oxazoline" intermediate (which subsequently breaks down following the microscopic reverse ''via'' hydrolysis or occasionally transglycosylation). Such a mechanism has a number of facets, one of which is its potential inhibition using thiazolines <cite>Macdonald</cite>.<br />
<br />
<br />
== Catalytic Residues ==<br />
The catalytically active GH18 enzymes use a double displacement reaction mechanism with "neighbouring group participation". Hence there is a catalytic acid residue (glutamate in family GH18, but often also Asp in other families using this mechanism) and in all families apart from GH[[Glycoside Hydrolase Family 85|85]] (where this residue is an amide), a second carboxylate (here Asp) acts to deprotonate the N-acetamido nitrogen during oxazoline formation/breakdown. In family GH18 the two catalytic carboxylates are found in an D-X-G motif whereas in some families the carboxylates may be adjacent such as the DD motif in family GH84 (for example see <cite>He2010</cite>). The physical separation of the two catalytic residues (with the second not in a position to act as a nucleophile itself) has led to confusion in some literature that GH18 and other enzymes (notably GH25) may be inverting enzymes; this is certainly not the case for GH18 and is unlikely to be the case for GH25.<br />
<br />
<br />
== Three-dimensional structures ==<br />
Although these enzymes are frequently multi-modular, the catalytic domains are &alpha; / &beta; barrels <cite>Perrakis,ATVA</cite>.<br />
<br />
Work on the conformational itinerary of catalysis which is extremely similar to other retaining enzymes active on ''gluco''-configured substrates, was provided by the van Aalten group <cite>Daan2001</cite> in 2001 through the trapping of a distorted Michaelis complex in <sup>1,4</sup>B conformation and thus extremely similar to the <sup>1</sup>S<sub>3</sub> skew boats oberserved in GH[[Glycoside Hydrolase Family 5|5]] <cite>Davies1998</cite> for example or the <sup>4</sup>E conformation originally seen for a "neighboring group" enzyme in GH[[Glycoside Hydrolase Family 20|20]] <cite>Tews1996</cite>. More recently, a similar conformation has been observed for the Michaelis complex of another neighboring group enzyme, the GH84 O-GlcNAcase <cite>He2010</cite>. Fungal GH18 enzymes are considered as possible therapeutic targets and a number of programmes are probing this area (for example <cite>Housten2002</cite>).<br />
<br />
One unusual of feature of plant members of the GH18 family is the large number of sequences that encode catalytically-inactive proteins that function as enzyme inhibitors or lectins. Phylogenetic analysis of the plant GH18 family reveals clear distinction between hevamine-type chitinases, putative chitinases and narbonins <cite>Durand2005</cite>. Out of the major subfamilies, only the one that contains hevamine actually contains enzymes of demonstrated activity <cite> TerwisschavanScheltinga1996</cite>. The subfamily of GH18 coding for xylanase inhibitor proteins (XIP) emerged from the hevamine cluster along with concanavalin B. All have nonconservative substitutions of one of the acidic amino acid residues in the catalytic region. In the structure of concanavalin B the catalytic Glu residue is replaced by Gln <cite>Henniga1995</cite>, which mostly account for the lack of chitinase activity reported for this protein. The XIP-type inhibitors all have the third aspartic acid DxxDxDxE mutated into an aromatic residue whereas the catalytic glutamate residue is only conserved in the prototype of cereal xylanase inhibitors, XIP-I (isolated from ''Triticum aetivum'') <cite>Juge2004</cite>. In XIP-I and narbonin, the glutamic acid residues are present in an equivalent position to the catalytic residue in hevamine, but their side chain is fully engaged in salt bridges with neighbouring arginine residues <cite>Hennigb1995Payan2003</cite>, preventing chitinase activity despite the presence of the catalytic residue. Furthermore in both XIP-I and narbonin, the position equivalent to residue Asp in hevamine, which has been proposed to stabilize the positively charged oxazoline reaction intermediate (<cite>TerwisschavanScheltinga1996</cite>), is occupied by a bulky residue<cite>Hennigb1995Payan2003</cite>. The mutation of this Asp residue in alanine in hevamine led to a mutant with approx. 2% residual activity <cite> Bokma2002</cite>. The most striking disruption of the cleft in XIP-I and narbonin is caused by the mutation of subsite -1 Gly which participates in the hydrogen-bonding network with the ligand <cite>ATVA2,</cite>, resulting in complete obstruction of subsite -1and preventing access to the catalytic residue <cite>Payan2003</cite>. Xylanase inhibitors appeared after the emergence of the various subfamilies of chitinases from their common ancestor. In this respect, the xylanase inhibitors are a relatively new invention, and so far no protein has been reported to display both xylanase inhibition and chitinase activities. GH18 XIP-type inhibitors can inhibit xylanases from GH10 and GH11 families <cite>Juge2004</cite>. The inhibition specificity of the GH18 xylanase inhibitors can be explained on the basis of the solved 3-D structure of XIP-I in complex with a GH10 xylanase from ''A. nidulans'' and a GH11 xylanase from ''P. funiculosum'' <cite>Payan2004</cite>. <br />
<br />
<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: Sometimes '''incorrectly''' reported as inverting, this family performs catalysis with '''retention''' of anomeric configuration as first shown on the ''Bacillus ciculans'' enzyme <cite>Armand1994</cite>.<br />
;First catalytic nucleophile identification: This family is one of many that uses neighbouring group participation for catalysis with the N-acetyl carbonyl group acting as the nucleophile; first proposed (I believe) for this family in <cite>AVTA2</cite>.<br />
;First general acid/base residue identification: On the basis of 3-D structure <cite>Perrakis</cite>.<br />
;First 3-D structure: The first two 3-D structures for catalytically active GH18 members were the ''Serratia marcescens'' chitinase A and the plant defence protein hevamine published "back-to-back" in ''Structure'' in 1994 <cite>Perrakis,ATVA1</cite>. In retrospect, however, the non-catalytic "Narbonin" structure was arguably the first GH18 3-D structure, although it is has no enzymatic activity <cite>Hennig1993</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Perrakis pmid=7704527<br />
#ATVA1 pmid=7704528<br />
#AVTA2 pmid=7495789 <br />
#Armand1994 pmid=8168626<br />
#Koshland1953 Koshland, D. (1953) Biol. Rev. 28, 416.<br />
#Armand1997 pmid=9396742<br />
#Housten2002 pmid=12093900<br />
#Tews1996 pmid=8673609<br />
#Daan2001 pmid=11481469<br />
#Macdonald pmid=20209544<br />
#He2010 pmid=20067256<br />
#Davies1998 pmid=9718293<br />
#Daan2003 pmid=12775711<br />
#Henniga1995 pmid=7490746<br />
#Hennig1993 pmid=1628747<br />
#Hennigb1995 pmid=15299319<br />
#TerwisschavanScheltinga1996 pmid=8831791<br />
#Bokma2002 pmid=11846790<br />
#Payan2003 pmid=12617724<br />
#Payan2004 pmid=15181003<br />
#Juge2004 pmid=14871661<br />
#Durand2005 pmid=15794761<br />
<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH018]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_18&diff=5887Glycoside Hydrolase Family 182010-10-12T21:18:01Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]s: ^^^Gideon Davies^^^, ^^^Nathalie Juge^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH18'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known (acid/neighbouring group)<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH18.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
GH18 is unusual in having both catalytically active chitinase (EC 3.2.1.14) and endo-β-N-acetylglucosaminidases (EC 3.2.1.96) but there are also sub-families of non-hydrolytic proteins that function as carbohydrate binding modules / "lectins" or as xylanase inhibitors.<br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
GH18 enzymes belong to a growing group of enzymes (now including GH families [[Glycoside Hydrolase Family 18|18]], [[Glycoside Hydrolase Family 20|20]],[[Glycoside Hydrolase Family 25|25]], [[Glycoside Hydrolase Family 56|56]], [[Glycoside Hydrolase Family 84|84]], and [[Glycoside Hydrolase Family 85|85]]) that perform a double-displacement reaction but instead of the more common enzyme-derived nucleophile they utlize the N-acetamido carbonyl oxygen in what is termed "neighbouring group participation" / "substrate participation" or "anchimeric assistance". Figures showing such a mechanism date back to Koshland's 1953 review <cite>Koshland1953</cite>, indeed they frequent the chemical literature of participating groups long before that, but it is primarily through the work on GH18 <cite>AVTA2</cite> and soon after GH20 <cite>Tews1996,Armand1997</cite> that such a mechanism became well established. In such a mechanism, which occurs with (net) retention of anomeric configuration, the enzyme provides a catalytic acid function to protonate the leaving group to facilitate its departure with the substrate carbonyl oxygen playing the role of nucleophile to generate a bicyclic "oxazoline" intermediate (which subsequently breaks down following the microscopic reverse ''via'' hydrolysis or occasionally transglycosylation). Such a mechanism has a number of facets, one of which is its potential inhibition using thiazolines <cite>Macdonald</cite>.<br />
<br />
<br />
== Catalytic Residues ==<br />
The catalytically active GH18 enzymes use a double displacement reaction mechanism with "neighbouring group participation". Hence there is a catalytic acid residue (glutamate in family GH18, but often also Asp in other families using this mechanism) and in all families apart from GH[[Glycoside Hydrolase Family 85|85]] (where this residue is an amide), a second carboxylate (here Asp) acts to deprotonate the N-acetamido nitrogen during oxazoline formation/breakdown. In family GH18 the two catalytic carboxylates are found in an D-X-G motif whereas in some families the carboxylates may be adjacent such as the DD motif in family GH84 (for example see <cite>He2010</cite>). The physical separation of the two catalytic residues (with the second not in a position to act as a nucleophile itself) has led to confusion in some literature that GH18 and other enzymes (notably GH25) may be inverting enzymes; this is certainly not the case for GH18 and is unlikely to be the case for GH25.<br />
<br />
<br />
== Three-dimensional structures ==<br />
Although these enzymes are frequently multi-modular, the catalytic domains are &alpha; / &beta; barrels <cite>Perrakis,ATVA</cite>.<br />
<br />
Work on the conformational itinerary of catalysis which is extremely similar to other retaining enzymes active on ''gluco''-configured substrates, was provided by the van Aalten group <cite>Daan2001</cite> in 2001 through the trapping of a distorted Michaelis complex in <sup>1,4</sup>B conformation and thus extremely similar to the <sup>1</sup>S<sub>3</sub> skew boats oberserved in GH[[Glycoside Hydrolase Family 5|5]] <cite>Davies1998</cite> for example or the <sup>4</sup>E conformation originally seen for a "neighboring group" enzyme in GH[[Glycoside Hydrolase Family 20|20]] <cite>Tews1996</cite>. More recently, a similar conformation has been observed for the Michaelis complex of another neighboring group enzyme, the GH84 O-GlcNAcase <cite>He2010</cite>. Fungal GH18 enzymes are considered as possible therapeutic targets and a number of programmes are probing this area (for example <cite>Housten2002</cite>).<br />
<br />
One unusual of feature of plant members of the GH18 family is the large number of sequences that encode catalytically-inactive proteins that function as enzyme inhibitors or lectins. Phylogenetic analysis of the plant GH18 family reveals clear distinction between hevamine-type chitinases, putative chitinases and narbonins <cite>Durand2005</cite>. Out of the major subfamilies, only the one that contains hevamine actually contains enzymes of demonstrated activity <cite> TerwisschavanScheltinga1996</cite>. The subfamily of GH18 coding for xylanase inhibitor proteins (XIP) emerged from the hevamine cluster along with concanavalin B. All have nonconservative substitutions of one of the acidic amino acid residues in the catalytic region. In the structure of concanavalin B the catalytic Glu residue is replaced by Gln <cite>Henniga1995</cite>, which mostly account for the lack of chitinase activity reported for this protein. The XIP-type inhibitors all have the third aspartic acid DxxDxDxE mutated into an aromatic residue whereas the catalytic glutamate residue is only conserved in the prototype of cereal xylanase inhibitors, XIP-I (isolated from ''Triticum aetivum'') <cite>Juge2004</cite>. In XIP-I and narbonin, the glutamic acid residues are present in an equivalent position to the catalytic residue in hevamine, but their side chain is fully engaged in salt bridges with neighbouring arginine residues <cite>Hennigb1995Payan2003</cite>, preventing chitinase activity despite the presence of the catalytic residue. Furthermore in both XIP-I and narbonin, the position equivalent to residue Asp in hevamine, which has been proposed to stabilize the positively charged oxazoline reaction intermediate (<cite>TerwisschavanScheltinga1996</cite>), is occupied by a bulky residue<cite>Hennigb1995Payan2003</cite>. The mutation of this Asp residue in alanine in hevamine led to a mutant with approx. 2% residual activity <cite> Bokma2002</cite>. The most striking disruption of the cleft in XIP-I and narbonin is caused by the mutation of subsite -1 Gly which participates in the hydrogen-bonding network with the ligand <cite>ATVA1, TerwisschavanScheltinga1995</cite>, resulting in complete obstruction of subsite -1and preventing access to the catalytic residue <cite>Payan2003</cite>. Xylanase inhibitors appeared after the emergence of the various subfamilies of chitinases from their common ancestor. In this respect, the xylanase inhibitors are a relatively new invention, and so far no protein has been reported to display both xylanase inhibition and chitinase activities. GH18 XIP-type inhibitors can inhibit xylanases from GH10 and GH11 families <cite>Juge2004</cite>. The inhibition specificity of the GH18 xylanase inhibitors can be explained on the basis of the solved 3-D structure of XIP-I in complex with a GH10 xylanase from ''A. nidulans'' and a GH11 xylanase from ''P. funiculosum'' <cite>Payan2004</cite>. <br />
<br />
<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: Sometimes '''incorrectly''' reported as inverting, this family performs catalysis with '''retention''' of anomeric configuration as first shown on the ''Bacillus ciculans'' enzyme <cite>Armand1994</cite>.<br />
;First catalytic nucleophile identification: This family is one of many that uses neighbouring group participation for catalysis with the N-acetyl carbonyl group acting as the nucleophile; first proposed (I believe) for this family in <cite>AVTA2</cite>.<br />
;First general acid/base residue identification: On the basis of 3-D structure <cite>Perrakis</cite>.<br />
;First 3-D structure: The first two 3-D structures for catalytically active GH18 members were the ''Serratia marcescens'' chitinase A and the plant defence protein hevamine published "back-to-back" in ''Structure'' in 1994 <cite>Perrakis,ATVA1</cite>. In retrospect, however, the non-catalytic "Narbonin" structure was arguably the first GH18 3-D structure, although it is has no enzymatic activity <cite>Hennig1993</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Perrakis pmid=7704527<br />
#ATVA1 pmid=7704528<br />
#AVTA2 pmid=7495789 <br />
#Armand1994 pmid=8168626<br />
#Koshland1953 Koshland, D. (1953) Biol. Rev. 28, 416.<br />
#Armand1997 pmid=9396742<br />
#Housten2002 pmid=12093900<br />
#Tews1996 pmid=8673609<br />
#Daan2001 pmid=11481469<br />
#Macdonald pmid=20209544<br />
#He2010 pmid=20067256<br />
#Davies1998 pmid=9718293<br />
#Daan2003 pmid=12775711<br />
#Henniga1995 pmid=7490746<br />
#Hennig1993 pmid=1628747<br />
#Hennigb1995 pmid=15299319<br />
#TerwisschavanScheltinga1996 pmid=8831791<br />
#Bokma2002 pmid=11846790<br />
#TerwisschavanScheltinga1995 pmid=7495789<br />
#Payan2003 pmid=12617724<br />
#Payan2004 pmid=15181003<br />
#Juge2004 pmid=14871661<br />
#Durand2005 pmid=15794761<br />
<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH018]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_18&diff=5886Glycoside Hydrolase Family 182010-10-12T21:15:39Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]s: ^^^Gideon Davies^^^, ^^^Nathalie Juge^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH18'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known (acid/neighbouring group)<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH18.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
GH18 is unusual in having both catalytically active chitinase (EC 3.2.1.14) and endo-β-N-acetylglucosaminidases (EC 3.2.1.96) but there are also sub-families of non-hydrolytic proteins that function as carbohydrate binding modules / "lectins" or as xylanase inhibitors.<br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
GH18 enzymes belong to a growing group of enzymes (now including GH families [[Glycoside Hydrolase Family 18|18]], [[Glycoside Hydrolase Family 20|20]],[[Glycoside Hydrolase Family 25|25]], [[Glycoside Hydrolase Family 56|56]], [[Glycoside Hydrolase Family 84|84]], and [[Glycoside Hydrolase Family 85|85]]) that perform a double-displacement reaction but instead of the more common enzyme-derived nucleophile they utlize the N-acetamido carbonyl oxygen in what is termed "neighbouring group participation" / "substrate participation" or "anchimeric assistance". Figures showing such a mechanism date back to Koshland's 1953 review <cite>Koshland1953</cite>, indeed they frequent the chemical literature of participating groups long before that, but it is primarily through the work on GH18 <cite>AVTA2</cite> and soon after GH20 <cite>Tews1996,Armand1997</cite> that such a mechanism became well established. In such a mechanism, which occurs with (net) retention of anomeric configuration, the enzyme provides a catalytic acid function to protonate the leaving group to facilitate its departure with the substrate carbonyl oxygen playing the role of nucleophile to generate a bicyclic "oxazoline" intermediate (which subsequently breaks down following the microscopic reverse ''via'' hydrolysis or occasionally transglycosylation). Such a mechanism has a number of facets, one of which is its potential inhibition using thiazolines <cite>Macdonald</cite>.<br />
<br />
<br />
== Catalytic Residues ==<br />
The catalytically active GH18 enzymes use a double displacement reaction mechanism with "neighbouring group participation". Hence there is a catalytic acid residue (glutamate in family GH18, but often also Asp in other families using this mechanism) and in all families apart from GH[[Glycoside Hydrolase Family 85|85]] (where this residue is an amide), a second carboxylate (here Asp) acts to deprotonate the N-acetamido nitrogen during oxazoline formation/breakdown. In family GH18 the two catalytic carboxylates are found in an D-X-G motif whereas in some families the carboxylates may be adjacent such as the DD motif in family GH84 (for example see <cite>He2010</cite>). The physical separation of the two catalytic residues (with the second not in a position to act as a nucleophile itself) has led to confusion in some literature that GH18 and other enzymes (notably GH25) may be inverting enzymes; this is certainly not the case for GH18 and is unlikely to be the case for GH25.<br />
<br />
<br />
== Three-dimensional structures ==<br />
Although these enzymes are frequently multi-modular, the catalytic domains are &alpha; / &beta; barrels <cite>Perrakis,ATVA</cite>.<br />
<br />
Work on the conformational itinerary of catalysis which is extremely similar to other retaining enzymes active on ''gluco''-configured substrates, was provided by the van Aalten group <cite>Daan2001</cite> in 2001 through the trapping of a distorted Michaelis complex in <sup>1,4</sup>B conformation and thus extremely similar to the <sup>1</sup>S<sub>3</sub> skew boats oberserved in GH[[Glycoside Hydrolase Family 5|5]] <cite>Davies1998</cite> for example or the <sup>4</sup>E conformation originally seen for a "neighboring group" enzyme in GH[[Glycoside Hydrolase Family 20|20]] <cite>Tews1996</cite>. More recently, a similar conformation has been observed for the Michaelis complex of another neighboring group enzyme, the GH84 O-GlcNAcase <cite>He2010</cite>. Fungal GH18 enzymes are considered as possible therapeutic targets and a number of programmes are probing this area (for example <cite>Housten2002</cite>).<br />
<br />
One unusual of feature of plant members of the GH18 family is the large number of sequences that encode catalytically-inactive proteins that function as enzyme inhibitors or lectins. Phylogenetic analysis of the plant GH18 family reveals clear distinction between hevamine-type chitinases, putative chitinases and narbonins <cite>Durand2005</cite>. Out of the major subfamilies, only the one that contains hevamine actually contains enzymes of demonstrated activity <cite> TerwisschavanScheltinga1996</cite>. The subfamily of GH18 coding for xylanase inhibitor proteins (XIP) emerged from the hevamine cluster along with concanavalin B. All have nonconservative substitutions of one of the acidic amino acid residues in the catalytic region. In the structure of concanavalin B the catalytic Glu residue is replaced by Gln <cite>Henniga1995</cite>, which mostly account for the lack of chitinase activity reported for this protein. The XIP-type inhibitors all have the third aspartic acid DxxDxDxE mutated into an aromatic residue whereas the catalytic glutamate residue is only conserved in the prototype of cereal xylanase inhibitors, XIP-I (isolated from ''Triticum aetivum'') <cite>Juge2004</cite>. In XIP-I and narbonin, the glutamic acid residues are present in an equivalent position to the catalytic residue in hevamine, but their side chain is fully engaged in salt bridges with neighbouring arginine residues <cite>Hennigb1995Payan2003</cite>, preventing chitinase activity despite the presence of the catalytic residue. Furthermore in both XIP-I and narbonin, the position equivalent to residue Asp in hevamine, which has been proposed to stabilize the positively charged oxazoline reaction intermediate (<cite>TerwisschavanScheltinga1996</cite>), is occupied by a bulky residue<cite>Hennigb1995Payan2003</cite>. The mutation of this Asp residue in alanine in hevamine led to a mutant with approx. 2% residual activity <cite> Bokma2002</cite>. The most striking disruption of the cleft in XIP-I and narbonin is caused by the mutation of subsite -1 Gly which participates in the hydrogen-bonding network with the ligand <cite>ATVA1 TerwisschavanScheltinga1995</cite>, resulting in complete obstruction of subsite -1and preventing access to the catalytic residue <cite>Payan2003</cite>. Xylanase inhibitors appeared after the emergence of the various subfamilies of chitinases from their common ancestor. In this respect, the xylanase inhibitors are a relatively new invention, and so far no protein has been reported to display both xylanase inhibition and chitinase activities. GH18 XIP-type inhibitors can inhibit xylanases from GH10 and GH11 families <cite>Juge2004</cite>. The inhibition specificity of the GH18 xylanase inhibitors can be explained on the basis of the solved 3-D structure of XIP-I in complex with a GH10 xylanase from ''A. nidulans'' and a GH11 xylanase from ''P. funiculosum'' <cite>Payan2004</cite>. <br />
<br />
<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: Sometimes '''incorrectly''' reported as inverting, this family performs catalysis with '''retention''' of anomeric configuration as first shown on the ''Bacillus ciculans'' enzyme <cite>Armand1994</cite>.<br />
;First catalytic nucleophile identification: This family is one of many that uses neighbouring group participation for catalysis with the N-acetyl carbonyl group acting as the nucleophile; first proposed (I believe) for this family in <cite>AVTA2</cite>.<br />
;First general acid/base residue identification: On the basis of 3-D structure <cite>Perrakis</cite>.<br />
;First 3-D structure: The first two 3-D structures for catalytically active GH18 members were the ''Serratia marcescens'' chitinase A and the plant defence protein hevamine published "back-to-back" in ''Structure'' in 1994 <cite>Perrakis,ATVA</cite>. In retrospect, however, the non-catalytic "Narbonin" structure was arguably the first GH18 3-D structure, although it is has no enzymatic activity <cite>Hennig1993</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Perrakis pmid=7704527<br />
#ATVA1 pmid=7704528<br />
#AVTA2 pmid=7495789 <br />
#Armand1994 pmid=8168626<br />
#Koshland1953 Koshland, D. (1953) Biol. Rev. 28, 416.<br />
#Armand1997 pmid=9396742<br />
#Housten2002 pmid=12093900<br />
#Tews1996 pmid=8673609<br />
#Daan2001 pmid=11481469<br />
#Macdonald pmid=20209544<br />
#He2010 pmid=20067256<br />
#Davies1998 pmid=9718293<br />
#Daan2003 pmid=12775711<br />
#Henniga1995 pmid=7490746<br />
#Hennig1993 pmid=1628747<br />
#Hennigb1995 pmid=15299319<br />
#TerwisschavanScheltinga1996 pmid=8831791<br />
#Bokma2002 pmid=11846790<br />
#TerwisschavanScheltinga1995 pmid=7495789<br />
#Payan2003 pmid=12617724<br />
#Payan2004 pmid=15181003<br />
#Juge2004 pmid=14871661<br />
#Durand2005 pmid=15794761<br />
<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH018]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_18&diff=5885Glycoside Hydrolase Family 182010-10-12T21:14:01Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]s: ^^^Gideon Davies^^^, ^^^Nathalie Juge^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH18'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known (acid/neighbouring group)<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH18.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
GH18 is unusual in having both catalytically active chitinase (EC 3.2.1.14) and endo-β-N-acetylglucosaminidases (EC 3.2.1.96) but there are also sub-families of non-hydrolytic proteins that function as carbohydrate binding modules / "lectins" or as xylanase inhibitors.<br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
GH18 enzymes belong to a growing group of enzymes (now including GH families [[Glycoside Hydrolase Family 18|18]], [[Glycoside Hydrolase Family 20|20]],[[Glycoside Hydrolase Family 25|25]], [[Glycoside Hydrolase Family 56|56]], [[Glycoside Hydrolase Family 84|84]], and [[Glycoside Hydrolase Family 85|85]]) that perform a double-displacement reaction but instead of the more common enzyme-derived nucleophile they utlize the N-acetamido carbonyl oxygen in what is termed "neighbouring group participation" / "substrate participation" or "anchimeric assistance". Figures showing such a mechanism date back to Koshland's 1953 review <cite>Koshland1953</cite>, indeed they frequent the chemical literature of participating groups long before that, but it is primarily through the work on GH18 <cite>AVTA2</cite> and soon after GH20 <cite>Tews1996,Armand1997</cite> that such a mechanism became well established. In such a mechanism, which occurs with (net) retention of anomeric configuration, the enzyme provides a catalytic acid function to protonate the leaving group to facilitate its departure with the substrate carbonyl oxygen playing the role of nucleophile to generate a bicyclic "oxazoline" intermediate (which subsequently breaks down following the microscopic reverse ''via'' hydrolysis or occasionally transglycosylation). Such a mechanism has a number of facets, one of which is its potential inhibition using thiazolines <cite>Macdonald</cite>.<br />
<br />
<br />
== Catalytic Residues ==<br />
The catalytically active GH18 enzymes use a double displacement reaction mechanism with "neighbouring group participation". Hence there is a catalytic acid residue (glutamate in family GH18, but often also Asp in other families using this mechanism) and in all families apart from GH[[Glycoside Hydrolase Family 85|85]] (where this residue is an amide), a second carboxylate (here Asp) acts to deprotonate the N-acetamido nitrogen during oxazoline formation/breakdown. In family GH18 the two catalytic carboxylates are found in an D-X-G motif whereas in some families the carboxylates may be adjacent such as the DD motif in family GH84 (for example see <cite>He2010</cite>). The physical separation of the two catalytic residues (with the second not in a position to act as a nucleophile itself) has led to confusion in some literature that GH18 and other enzymes (notably GH25) may be inverting enzymes; this is certainly not the case for GH18 and is unlikely to be the case for GH25.<br />
<br />
<br />
== Three-dimensional structures ==<br />
Although these enzymes are frequently multi-modular, the catalytic domains are &alpha; / &beta; barrels <cite>Perrakis,ATVA</cite>.<br />
<br />
Work on the conformational itinerary of catalysis which is extremely similar to other retaining enzymes active on ''gluco''-configured substrates, was provided by the van Aalten group <cite>Daan2001</cite> in 2001 through the trapping of a distorted Michaelis complex in <sup>1,4</sup>B conformation and thus extremely similar to the <sup>1</sup>S<sub>3</sub> skew boats oberserved in GH[[Glycoside Hydrolase Family 5|5]] <cite>Davies1998</cite> for example or the <sup>4</sup>E conformation originally seen for a "neighboring group" enzyme in GH[[Glycoside Hydrolase Family 20|20]] <cite>Tews1996</cite>. More recently, a similar conformation has been observed for the Michaelis complex of another neighboring group enzyme, the GH84 O-GlcNAcase <cite>He2010</cite>. Fungal GH18 enzymes are considered as possible therapeutic targets and a number of programmes are probing this area (for example <cite>Housten2002</cite>).<br />
<br />
One unusual of feature of plant members of the GH18 family is the large number of sequences that encode catalytically-inactive proteins that function as enzyme inhibitors or lectins. Phylogenetic analysis of the plant GH18 family reveals clear distinction between hevamine-type chitinases, putative chitinases and narbonins <cite>Durand2005</cite>. Out of the major subfamilies, only the one that contains hevamine actually contains enzymes of demonstrated activity <cite> TerwisschavanScheltinga1996</cite>. The subfamily of GH18 coding for xylanase inhibitor proteins (XIP) emerged from the hevamine cluster along with concanavalin B. All have nonconservative substitutions of one of the acidic amino acid residues in the catalytic region. In the structure of concanavalin B the catalytic Glu residue is replaced by Gln <cite>Henniga1995</cite>, which mostly account for the lack of chitinase activity reported for this protein. The XIP-type inhibitors all have the third aspartic acid DxxDxDxE mutated into an aromatic residue whereas the catalytic glutamate residue is only conserved in the prototype of cereal xylanase inhibitors, XIP-I (isolated from ''Triticum aetivum'') <cite>Juge2004</cite>. In XIP-I and narbonin, the glutamic acid residues are present in an equivalent position to the catalytic residue in hevamine, but their side chain is fully engaged in salt bridges with neighbouring arginine residues <cite>Hennigb1995Payan2003</cite>, preventing chitinase activity despite the presence of the catalytic residue. Furthermore in both XIP-I and narbonin, the position equivalent to residue Asp in hevamine, which has been proposed to stabilize the positively charged oxazoline reaction intermediate (<cite>TerwisschavanScheltinga1996</cite>), is occupied by a bulky residue<cite>Hennigb1995Payan2003</cite>. The mutation of this Asp residue in alanine in hevamine led to a mutant with approx. 2% residual activity <cite> Bokma2002</cite>. The most striking disruption of the cleft in XIP-I and narbonin is caused by the mutation of subsite -1 Gly which participates in the hydrogen-bonding network with the ligand <cite>AVTA1 TerwisschavanScheltinga1995</cite>, resulting in complete obstruction of subsite -1and preventing access to the catalytic residue <cite>Payan2003</cite>. Xylanase inhibitors appeared after the emergence of the various subfamilies of chitinases from their common ancestor. In this respect, the xylanase inhibitors are a relatively new invention, and so far no protein has been reported to display both xylanase inhibition and chitinase activities. GH18 XIP-type inhibitors can inhibit xylanases from GH10 and GH11 families <cite>Juge2004</cite>. The inhibition specificity of the GH18 xylanase inhibitors can be explained on the basis of the solved 3-D structure of XIP-I in complex with a GH10 xylanase from ''A. nidulans'' and a GH11 xylanase from ''P. funiculosum'' <cite>Payan2004</cite>. <br />
<br />
<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: Sometimes '''incorrectly''' reported as inverting, this family performs catalysis with '''retention''' of anomeric configuration as first shown on the ''Bacillus ciculans'' enzyme <cite>Armand1994</cite>.<br />
;First catalytic nucleophile identification: This family is one of many that uses neighbouring group participation for catalysis with the N-acetyl carbonyl group acting as the nucleophile; first proposed (I believe) for this family in <cite>AVTA2</cite>.<br />
;First general acid/base residue identification: On the basis of 3-D structure <cite>Perrakis</cite>.<br />
;First 3-D structure: The first two 3-D structures for catalytically active GH18 members were the ''Serratia marcescens'' chitinase A and the plant defence protein hevamine published "back-to-back" in ''Structure'' in 1994 <cite>Perrakis,ATVA</cite>. In retrospect, however, the non-catalytic "Narbonin" structure was arguably the first GH18 3-D structure, although it is has no enzymatic activity <cite>Hennig1993</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Perrakis pmid=7704527<br />
#ATVA1 pmid=7704528<br />
#AVTA2 pmid=7495789 <br />
#Armand1994 pmid=8168626<br />
#Koshland1953 Koshland, D. (1953) Biol. Rev. 28, 416.<br />
#Armand1997 pmid=9396742<br />
#Housten2002 pmid=12093900<br />
#Tews1996 pmid=8673609<br />
#Daan2001 pmid=11481469<br />
#Macdonald pmid=20209544<br />
#He2010 pmid=20067256<br />
#Davies1998 pmid=9718293<br />
#Daan2003 pmid=12775711<br />
#Henniga1995 pmid=7490746<br />
#Hennig1993 pmid=1628747<br />
#Hennigb1995 pmid=15299319<br />
#TerwisschavanScheltinga1996 pmid=8831791<br />
#Bokma2002 pmid=11846790<br />
#TerwisschavanScheltinga1995 pmid=7495789<br />
#Payan2003 pmid=12617724<br />
#Payan2004 pmid=15181003<br />
#Juge2004 pmid=14871661<br />
#Durand2005 pmid=15794761<br />
<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH018]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_18&diff=5884Glycoside Hydrolase Family 182010-10-12T21:10:03Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]s: ^^^Gideon Davies^^^, ^^^Nathalie Juge^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH18'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known (acid/neighbouring group)<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH18.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
GH18 is unusual in having both catalytically active chitinase (EC 3.2.1.14) and endo-β-N-acetylglucosaminidases (EC 3.2.1.96) but there are also sub-families of non-hydrolytic proteins that function as carbohydrate binding modules / "lectins" or as xylanase inhibitors.<br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
GH18 enzymes belong to a growing group of enzymes (now including GH families [[Glycoside Hydrolase Family 18|18]], [[Glycoside Hydrolase Family 20|20]],[[Glycoside Hydrolase Family 25|25]], [[Glycoside Hydrolase Family 56|56]], [[Glycoside Hydrolase Family 84|84]], and [[Glycoside Hydrolase Family 85|85]]) that perform a double-displacement reaction but instead of the more common enzyme-derived nucleophile they utlize the N-acetamido carbonyl oxygen in what is termed "neighbouring group participation" / "substrate participation" or "anchimeric assistance". Figures showing such a mechanism date back to Koshland's 1953 review <cite>Koshland1953</cite>, indeed they frequent the chemical literature of participating groups long before that, but it is primarily through the work on GH18 <cite>AVTA2</cite> and soon after GH20 <cite>Tews1996,Armand1997</cite> that such a mechanism became well established. In such a mechanism, which occurs with (net) retention of anomeric configuration, the enzyme provides a catalytic acid function to protonate the leaving group to facilitate its departure with the substrate carbonyl oxygen playing the role of nucleophile to generate a bicyclic "oxazoline" intermediate (which subsequently breaks down following the microscopic reverse ''via'' hydrolysis or occasionally transglycosylation). Such a mechanism has a number of facets, one of which is its potential inhibition using thiazolines <cite>Macdonald</cite>.<br />
<br />
<br />
== Catalytic Residues ==<br />
The catalytically active GH18 enzymes use a double displacement reaction mechanism with "neighbouring group participation". Hence there is a catalytic acid residue (glutamate in family GH18, but often also Asp in other families using this mechanism) and in all families apart from GH[[Glycoside Hydrolase Family 85|85]] (where this residue is an amide), a second carboxylate (here Asp) acts to deprotonate the N-acetamido nitrogen during oxazoline formation/breakdown. In family GH18 the two catalytic carboxylates are found in an D-X-G motif whereas in some families the carboxylates may be adjacent such as the DD motif in family GH84 (for example see <cite>He2010</cite>). The physical separation of the two catalytic residues (with the second not in a position to act as a nucleophile itself) has led to confusion in some literature that GH18 and other enzymes (notably GH25) may be inverting enzymes; this is certainly not the case for GH18 and is unlikely to be the case for GH25.<br />
<br />
<br />
== Three-dimensional structures ==<br />
Although these enzymes are frequently multi-modular, the catalytic domains are &alpha; / &beta; barrels <cite>Perrakis,ATVA</cite>.<br />
<br />
Work on the conformational itinerary of catalysis which is extremely similar to other retaining enzymes active on ''gluco''-configured substrates, was provided by the van Aalten group <cite>Daan2001</cite> in 2001 through the trapping of a distorted Michaelis complex in <sup>1,4</sup>B conformation and thus extremely similar to the <sup>1</sup>S<sub>3</sub> skew boats oberserved in GH[[Glycoside Hydrolase Family 5|5]] <cite>Davies1998</cite> for example or the <sup>4</sup>E conformation originally seen for a "neighboring group" enzyme in GH[[Glycoside Hydrolase Family 20|20]] <cite>Tews1996</cite>. More recently, a similar conformation has been observed for the Michaelis complex of another neighboring group enzyme, the GH84 O-GlcNAcase <cite>He2010</cite>. Fungal GH18 enzymes are considered as possible therapeutic targets and a number of programmes are probing this area (for example <cite>Housten2002</cite>).<br />
<br />
One unusual of feature of plant members of the GH18 family is the large number of sequences that encode catalytically-inactive proteins that function as enzyme inhibitors or lectins. Phylogenetic analysis of the plant GH18 family reveals clear distinction between hevamine-type chitinases, putative chitinases and narbonins <cite>Durand2005</cite>. Out of the major subfamilies, only the one that contains hevamine actually contains enzymes of demonstrated activity <cite> TerwisschavanScheltinga1996</cite>. The subfamily of GH18 coding for xylanase inhibitor proteins (XIP) emerged from the hevamine cluster along with concanavalin B. All have nonconservative substitutions of one of the acidic amino acid residues in the catalytic region. In the structure of concanavalin B the catalytic Glu residue is replaced by Gln <cite>Henniga1995</cite>, which mostly account for the lack of chitinase activity reported for this protein. The XIP-type inhibitors all have the third aspartic acid DxxDxDxE mutated into an aromatic residue whereas the catalytic glutamate residue is only conserved in the prototype of cereal xylanase inhibitors, XIP-I (isolated from ''Triticum aetivum'') <cite>Juge2004</cite>. In XIP-I and narbonin, the glutamic acid residues are present in an equivalent position to the catalytic residue in hevamine, but their side chain is fully engaged in salt bridges with neighbouring arginine residues <cite>Hennigb1995Payan2003</cite>, preventing chitinase activity despite the presence of the catalytic residue. Furthermore in both XIP-I and narbonin, the position equivalent to residue Asp in hevamine, which has been proposed to stabilize the positively charged oxazoline reaction intermediate (<cite>TerwisschavanScheltinga1996</cite>), is occupied by a bulky residue<cite>Hennigb1995Payan2003</cite>. The mutation of this Asp residue in alanine in hevamine led to a mutant with approx. 2% residual activity <cite> Bokma2002</cite>. The most striking disruption of the cleft in XIP-I and narbonin is caused by the mutation of subsite -1 Gly which participates in the hydrogen-bonding network with the ligand <cite>TerwisschavanScheltinga1994 TerwisschavanScheltinga1995</cite>, resulting in complete obstruction of subsite -1and preventing access to the catalytic residue <cite>Payan2003</cite>. Xylanase inhibitors appeared after the emergence of the various subfamilies of chitinases from their common ancestor. In this respect, the xylanase inhibitors are a relatively new invention, and so far no protein has been reported to display both xylanase inhibition and chitinase activities. GH18 XIP-type inhibitors can inhibit xylanases from GH10 and GH11 families <cite>Juge2004</cite>. The inhibition specificity of the GH18 xylanase inhibitors can be explained on the basis of the solved 3-D structure of XIP-I in complex with a GH10 xylanase from ''A. nidulans'' and a GH11 xylanase from ''P. funiculosum'' <cite>Payan2004</cite>. <br />
<br />
<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: Sometimes '''incorrectly''' reported as inverting, this family performs catalysis with '''retention''' of anomeric configuration as first shown on the ''Bacillus ciculans'' enzyme <cite>Armand1994</cite>.<br />
;First catalytic nucleophile identification: This family is one of many that uses neighbouring group participation for catalysis with the N-acetyl carbonyl group acting as the nucleophile; first proposed (I believe) for this family in <cite>AVTA2</cite>.<br />
;First general acid/base residue identification: On the basis of 3-D structure <cite>Perrakis</cite>.<br />
;First 3-D structure: The first two 3-D structures for catalytically active GH18 members were the ''Serratia marcescens'' chitinase A and the plant defence protein hevamine published "back-to-back" in ''Structure'' in 1994 <cite>Perrakis,ATVA</cite>. In retrospect, however, the non-catalytic "Narbonin" structure was arguably the first GH18 3-D structure, although it is has no enzymatic activity <cite>Hennig1993</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Perrakis pmid=7704527<br />
#ATVA1 pmid=7704528<br />
#AVTA2 pmid=7495789 <br />
#Armand1994 pmid=8168626<br />
#Koshland1953 Koshland, D. (1953) Biol. Rev. 28, 416.<br />
#Armand1997 pmid=9396742<br />
#Housten2002 pmid=12093900<br />
#Tews1996 pmid=8673609<br />
#Daan2001 pmid=11481469<br />
#Macdonald pmid=20209544<br />
#He2010 pmid=20067256<br />
#Davies1998 pmid=9718293<br />
#Daan2003 pmid=12775711<br />
#Henniga1995 pmid=7490746<br />
#Hennig1993 pmid=1628747<br />
#Hennigb1995 pmid=15299319<br />
#TerwisschavanScheltinga1996 pmid=8831791<br />
#Bokma2002 pmid=11846790<br />
#TerwisschavanScheltinga1995 pmid=7495789<br />
#TerwisschavanScheltinga1994 pmid=7704528<br />
#Payan2003 pmid=12617724<br />
#Payan2004 pmid=15181003<br />
#Juge2004 pmid=14871661<br />
#Durand2005 pmid=15794761<br />
<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH018]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_6&diff=5873Glycoside Hydrolase Family 62010-10-11T14:49:38Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: ^^^Kathleen Piens^^^ and ^^^Gideon Davies^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}}<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH6'''<br />
|-<br />
|'''Clan'''<br />
|none<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|acid known, base debated<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH6.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
[[Glycoside hydrolases]] of family 6 cleave &beta;-1,4 glycosidic bonds in cellulose / &beta;-1,4-glucans. Only endoglucanase (EC [{{EClink}}3.2.1.4 3.2.1.4]) and cellobiohydrolase (EC [{{EClink}}3.2.1.91 3.2.1.91]) activity has been reported for both bacterial and eukaryotic members of this family. <br />
<br />
== Kinetics and Mechanism ==<br />
Family 6 enzymes are [[inverting]] enzymes, as first shown by NMR <cite>Knowles1988</cite> on Cellobiohydrolase II (CBH II; Cel6A) from the fungus ''Trichoderma reesei'' (a clonal derivative of ''Hypocrea jecorina'' <cite>Kuhls1996</cite>).<br />
<br />
== Catalytic Residues ==<br />
The first 3-D structure of CBHII provided a strong clue as to the identification of the catalytic acid in the inverting mechanism (Asp 221 in the case of this ''Trichoderma reesei'' Cel6A enzyme. This assigment has withstood the tests of time with strong kinetic support (from kinetics as a function of leaving group ability for a series of enzyme variants) <cite>Damude1995</cite> as well as from all subsequent 3-D analyses of enzyme-ligand complexes (for example <cite>Zou1999 Varrot2005 Varrot2002</cite> ). The identification of the base is, however, far less clear. Simply put this is because there is no clear potential base within hydrogen-bonding distance of a water molecule that could act as the nucleophile in the inversion mechanism. Thus, although there are mutagenesis / kinetic proposals for a base <cite>Damude1995</cite>, the current Zeitgeist is that the attacking water is deprotonated via a string of water molecules in what Sinnott has descibed as a "Grotthuss" mechanism; for which there is solvent kinetic isotope effect support <cite>Koivula2002</cite>. On the basis of structure the residue most likely to act as the base is Asp175 on the ''Trichoderma reesei'' Cel6A although Asp401 may also play a role (see Table 1).<br />
<br />
<br />
----<br />
{| {{Prettytable}} style="text-align:left"<br />
|+ Table 1. Putative catalytic residues of some representatives in GH family 6<br>(with biochemical characterization of wt and mutant enzymes).<br />
! Proposed role<br />
! ''Cf''Cel6A (endo)<br />
! ''Hi''Cel6A (exo)<br />
! ''Hj''Cel6A (exo)<br />
! ''Tf''Cel6A (endo)<br />
! ''Tf''Cel6B (exo)<br />
|-<br />
| Substrate distortion<br />
| Tyr210<br />
| Tyr174<br />
| Tyr169<br />
| Tyr73<br />
| Tyr220<br />
|-<br />
| Increase in pKa acid/Catalytic base<br />
| Asp216<br />
| Asp180<br />
| Asp175<br />
| Asp79<br />
| Asp226<br />
|-<br />
| Proton network<br />
| Gly222?<br />
| Ser186<br />
| Ser181<br />
| Ser85<br />
| Ser232<br />
|-<br />
| Catalytic acid<br />
| Asp252<br />
| Asp226<br />
| Asp221<br />
| Asp117<br />
| Asp274<br />
|-<br />
| Catalytic base/substrate binding<br />
| Asp392<br />
| Asp405<br />
| Asp401<br />
| Asp265<br />
| Asp497<br />
|}<br />
----<br />
<br />
<br />
<br />
== Three-dimensional structures ==<br />
The first crystal structures of cellobiohydrolases and endoglucanases from family [[GH6]] revealed modified &alpha;/&beta; barrel folds which, unlike the classical (&beta;/&alpha;)<sub>8</sub> "TIM" barrel has just seven &beta;-strands forming the central &beta;-barrel. The CBHII structure revealed an active centre (see above) enclosed in a tunnel formed primarily by two surface loops. When, subsequently, the first endoglucanase from GH6 was solved, the active center was observed in a long open groove. The comparison of these two structures thus provided the first insight into how endo or processive activity was modulated, through display of the active centre in a in an open grove, or loop-enclosed tunnel, respectively. In 1995 the UBC group were able to truncate the extended loops of a cellobiohydrolase resulting in an enzyme with more endo-activity <cite>Meinke1995</cite>. To this day the debate continues about the possibilities of loop conformational change in moderating the activity of cellobiohydrolases between exo and endo. Ståhlberg was perhaps the first to explicitly state that ''T. reesei'' "has no true exo-cellulases" <cite>Stberg1993</cite>. It is clear that there is no absolute steric demand for the ''exo'' activity of cellobiohydrolases; the enzymes have a viable "-3" subsite <cite>Varrot1999, Varrot2003</cite>, the loops of the cellobiohydrolases are clearly mobile and show multiple conformations (consistent with occasional opening to support ''endo''-activity, and are also able to act on artificial substrates in which both ends have large appended groups (for example <cite>Armand1997</cite>).<br />
<br />
The nature of how catalysis was achived, and the conformational itinerary of catalysis was first provided by the Uppsala, Grenoble and Gent groups in 1999 <cite>Zou1999</cite> was a trapped Michaelis complex of a thio-oligosaccharide was observed spanning the active centre with the -1 subsite sugar in <sup>2</sup>S<sub>O</sub> conformation which suggestad a pathway around the <sup>2,5</sup>B conformation. Subsequent structural <cite>Varrot2005 Varrot2002</cite> and modelling <cite>Koivula2002</cite> support for these proposals comes from similarly distorted species on other GH6 enzymes and from the observation of a "cellobiosyl isofagomine" in <sup>2,5</sup>B conformation <cite>Varrot2003</cite>.<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: ''Hypocrea jecorina'' cellobiohydrolase Cel6A by NMR <cite>Knowles1988</cite>.<br />
;First general acid/base residue identification: The role of Asp221 as the potential caralytic acid was first proposed on the basis of 3-D structure of the ''Hypocrea jecorina'' cellobiohydrolase CBHII / Cel6A <cite>Rouvinen1990</cite>. Enzyme kinetics of variants, in conjunction with leaving groups requiring provided strong confirmation <cite>Damude1995</cite>. The existance / identification of the base is less clear and current beliefs are that the water is deprotonated via a "solvent wire" through to one of the conserved aspratates near the active centre.<br />
<br />
;First 3-D structure: The catalytic core domain of the ''Trichoderma reesei'' (the organism now known as ''Hypocrea jecorina'') cellobiohydrolase II by the Jones group <cite>Rouvinen1990</cite>. The first endoglucanase in this family was the ''Thermomonospora fusca'' E2 enzyme (catalytic core) solved by the Wilson/Karplus groups<cite>Spezio1993</cite><br />
<br />
== References ==<br />
<biblio><br />
#Knowles1988 Knowles, J.K.C., Lehtovaara, P., Murray, M. and Sinnott, M.L. (1988) Stereochemical course of the action of the cellobioside hydrolases I and II of ''Trichoderma reesei''. J. Chem. Soc., Chem. Commun., 1988, 1401-1402. [http://dx.doi.org/10.1039/C39880001401 DOI: 10.1039/C39880001401]<br />
#Kuhls1996 pmid=8755548<br />
#Rouvinen1990 pmid=2377893<br />
#Spezio1993 pmid=8399160<br />
#Koivula2002 pmid=12188666<br />
#Zou1999 pmid=10508787 <br />
#Varrot2003 pmid=12744312<br />
#Varrot2005 pmid=15824123<br />
#Varrot2002 pmid=12454501<br />
#Varrot1999 pmid=10413461<br />
#Damude1995 pmid=7857933<br />
#Meinke1995 pmid=7876202<br />
#Armand1997 pmid=9006908<br />
#Stberg1993 pmid=8499476<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH006]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_37&diff=5863Glycoside Hydrolase Family 372010-10-08T20:31:09Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: ^^^Tracey Gloster^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH37'''<br />
|-<br />
|'''Clan''' <br />
|GH-G<br />
|-<br />
|'''Mechanism'''<br />
|Inverting<br />
|-<br />
|'''Active site residues'''<br />
|Inferred<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH37.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
GH37 [[glycoside hydrolases]] have been shown, to date, to hydrolyse only the disaccharide trehalose (α-D-glucopyranosyl-(1→1)-α-D-glucopyranoside) into two glucose units (EC 3.2.1.28).<br />
<br />
== Kinetics and Mechanism ==<br />
A trehalase from flesh fly was shown to hydrolyse with inversion of stereochemistry using <sup>18</sup>O labelled water <cite>REF1</cite>. The structural solution of the trehalase from ''Escherichia coli'' also demonstrates the active site catalytic residues are in a position consistent with an [[inverting mechanism]] <cite>REF2</cite>.<br />
<br />
== Catalytic Residues ==<br />
The catalytic residues have not been demonstrated unequivocally, but structural determination of the trehalase from ''Escherichia coli'' in complex with inhibitors in the active site implicate an aspartate residue (Asp312 in ''E. coli'') as the catalytic acid and a glutamate residue (Glu496 in ''E. coli'') as the catalytic base <cite>REF2</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The only structural representative from GH37 to date is the trehalase from ''Escherichia coli'', which was solved using X-ray crystallography <cite>REF2</cite>. The structure revealed a (α/α)<sub>6</sub> barrel fold, similar to other α-toroidal glycosidases such as those in families [[GH94]], [[GH15]] and [[GH65]]. GH37 falls into clan GH-G. Structures have been solved with the inhibitors validoxylamine A, 1-thiatrehazolin and casuarine analogues <cite>REF2,REF3,REF4</cite>.<br />
<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: The inversion of stereochemistry for a trehalase from the flesh fly ''Sarcophaga barbata'' was first demonstrated by Clifford in 1980 <cite>REF1</cite>.<br />
;First catalytic nucleophile identification: Predicted from structure determination <cite>REF2</cite>, but not shown unequivocally. <br />
;First general acid/base residue identification: Predicted from structure determination <cite>REF2</cite>, but not shown unequivocally.<br />
;First 3-D structure: The GH37 trehalase from ''Escherichia coli'' was solved by X-ray crystallography <cite>REF2</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#REF1 pmid=7341233<br />
#REF2 pmid=17455176<br />
#REF3 pmid=19123216<br />
#REF4 pmid=20461849 <br />
<br />
<br />
</biblio><br />
<br />
<br />
[[Category:Glycoside Hydrolase Families|GH037]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_37&diff=5862Glycoside Hydrolase Family 372010-10-08T20:30:28Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Tracey Gloster^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH37'''<br />
|-<br />
|'''Clan''' <br />
|GH-G<br />
|-<br />
|'''Mechanism'''<br />
|Inverting<br />
|-<br />
|'''Active site residues'''<br />
|Inferred<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH37.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
GH37 [[glycoside hydrolases]] have been shown, to date, to hydrolyse only the disaccharide trehalose (α-D-glucopyranosyl-(1→1)-α-D-glucopyranoside) into two glucose units (EC 3.2.1.28).<br />
<br />
== Kinetics and Mechanism ==<br />
A trehalase from flesh fly was shown to hydrolyse with inversion of stereochemistry using <sup>18</sup>O labelled water <cite>REF1</cite>. The structural solution of the trehalase from ''Escherichia coli'' also demonstrates the active site catalytic residues are in a position consistent with an [[inverting mechanism]] <cite>REF2</cite>.<br />
<br />
== Catalytic Residues ==<br />
The catalytic residues have not been demonstrated unequivocally, but structural determination of the trehalase from ''Escherichia coli'' in complex with inhibitors in the active site implicate an aspartate residue (Asp312 in ''E. coli'') as the catalytic acid and a glutamate residue (Glu496 in ''E. coli'') as the catalytic base <cite>REF2</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The only structural representative from GH37 to date is the trehalase from ''Escherichia coli'', which was solved using X-ray crystallography <cite>REF2</cite>. The structure revealed a (α/α)<sub>6</sub> barrel fold, similar to other α-toroidal glycosidases such as those in families [[GH94]], [[GH15]] and [[GH65]]. GH37 falls into clan GH-G. Structures have been solved with the inhibitors validoxylamine A, 1-thiatrehazolin and casuarine analogues <cite>REF2,REF3,REF4</cite>.<br />
<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: The inversion of stereochemistry for a trehalase from the flesh fly ''Sarcophaga barbata'' was first demonstrated by Clifford in 1980 <cite>REF1</cite>.<br />
;First catalytic nucleophile identification: Predicted from structure determination <cite>REF2</cite>, but not shown unequivocally. <br />
;First general acid/base residue identification: Predicted from structure determination <cite>REF2</cite>, but not shown unequivocally.<br />
;First 3-D structure: The GH37 trehalase from ''Escherichia coli'' was solved by X-ray crystallography <cite>REF2</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#REF1 pmid=7341233<br />
#REF2 pmid=17455176<br />
#REF3 pmid=19123216<br />
#REF4 pmid=20461849 <br />
<br />
<br />
</biblio><br />
<br />
<br />
[[Category:Glycoside Hydrolase Families|GH037]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_20&diff=5840Glycoside Hydrolase Family 202010-10-08T16:00:28Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ian Greig^^^<br />
* [[Responsible Curator]]: ^^^David Vocadlo^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH20'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH20.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Content is to be added here.<br />
<br />
This is an example of how to make references to a journal article <cite>Comfort2007</cite>. (See the References section below). Multiple references can go in the same place like this <cite>Comfort2007 He1999</cite>. You can even cite books using just the ISBN <cite>3</cite>. References that are not in PubMed can be typed in by hand <cite>MikesClassic</cite>. <br />
<br />
<br />
== Kinetics and Mechanism ==<br />
History of neighbouring group participation in enzyme-catalyzed REF Lowe and Sinnott and aqueous REF Sinnott and Bruice reactions of glycosides. Use of free energy relationships ships to infer neighbouring group participation. Early japanese work;REF A comparative analysis of the activity of ''Streptomyces plicatus'' ''b''-hexosaminidase (SpHex, GH20) and Vibrio furnisii ''b''-hexosaminidase (ExoII, GH3) towards ''p''-nitrophenyl ''N''-acyl glucosaminides highlights contrasting reactivity trends expected for families of ''b''-glucosaminidase utilizing a mechanism of substrate-assisted catalysis (GH20) and those which do not (GH3): sharp decreases in activity with increasing ''N''-acyl fluorination are observed in the case of the SpHex enzyme whereas negligible changes in activity are observed for ExoII.REF<br />
Loss of activity upon non-reducing end deacatylation <cite>Armand1997</cite>.<br />
<br />
== Catalytic Residues ==<br />
Kinetic and crystallographic analyses of Asp313 mutants of ''Streptomyces plicatus'' ''b''-hexosaminidase show that it plays a critical role in orienting and polarising the substrate's ''N''-acetyl group to act as a nucleophile towards the anomeric centre.<br />
<br />
<br />
== Three-dimensional structures ==<br />
Content is to be added here.<br />
<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: The stereochemistry of hydrolysis of three different hexosaminidases (human placenta, jack bean, and bovine kidney) was shown by the Withers group in 1994 <cite>Lai</cite> and it is (now) assumed that (some of) these are GH20 enzymes. The first stereochemical determination for a fully sequences GH20 was on the ''Serratia marscescens'' enzyme <cite>Armand1997</cite>.<br />
;First catalytic nucleophile identification: This is a neighboring-group participation enzyme with the mechanism suggested both from 3-D structure <cite>Tews1996</cite>, by analogy with GH18 enzymes and through work in which the non-reducing end sugar was de-acetylated resulting in total loss in activity <cite>Armand1997</cite>.<br />
;First general acid/base residue identification: Inferred from the 3-D structure <cite>Tews1996</cite> and by analogy with closely related GH18 chitinases.<br />
;First 3-D structure: The 3-D structure of the ''Serratia marscescens'' chitobiase <cite>Tews1996</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Comfort2007 pmid=17323919<br />
#He1999 pmid=9312086<br />
#3 isbn=978-0-240-52118-3<br />
#MikesClassic Sinnott, M.L. (1990) Catalytic mechanisms of enzymic glycosyl transfer. Chem. Rev. 90, 1171-1202. [http://dx.doi.org/10.1021/cr00105a006 DOI: 10.1021/cr00105a006]<br />
#Armand1997 pmid=9396742<br />
#Tews1996 pmid=8673609<br />
#Lai pmid=7993902<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH020]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_20&diff=5839Glycoside Hydrolase Family 202010-10-08T15:51:28Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ian Greig^^^<br />
* [[Responsible Curator]]: ^^^David Vocadlo^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH20'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH20.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Content is to be added here.<br />
<br />
This is an example of how to make references to a journal article <cite>Comfort2007</cite>. (See the References section below). Multiple references can go in the same place like this <cite>Comfort2007 He1999</cite>. You can even cite books using just the ISBN <cite>3</cite>. References that are not in PubMed can be typed in by hand <cite>MikesClassic</cite>. <br />
<br />
<br />
== Kinetics and Mechanism ==<br />
History of neighbouring group participation in enzyme-catalyzed REF Lowe and Sinnott and aqueous REF Sinnott and Bruice reactions of glycosides. Use of free energy relationships ships to infer neighbouring group participation. Early japanese work;REF A comparative analysis of the activity of ''Streptomyces plicatus'' ''b''-hexosaminidase (SpHex, GH20) and Vibrio furnisii ''b''-hexosaminidase (ExoII, GH3) towards ''p''-nitrophenyl ''N''-acyl glucosaminides highlights contrasting reactivity trends expected for families of ''b''-glucosaminidase utilizing a mechanism of substrate-assisted catalysis (GH20) and those which do not (GH3): sharp decreases in activity with increasing ''N''-acyl fluorination are observed in the case of the SpHex enzyme whereas negligible changes in activity are observed for ExoII.REF<br />
Loss of activity upon non-reducing end deacatylation <cite>Armand1997</cite>.<br />
<br />
== Catalytic Residues ==<br />
Kinetic and crystallographic analyses of Asp313 mutants of ''Streptomyces plicatus'' ''b''-hexosaminidase show that it plays a critical role in orienting and polarising the substrate's ''N''-acetyl group to act as a nucleophile towards the anomeric centre.<br />
<br />
<br />
== Three-dimensional structures ==<br />
Content is to be added here.<br />
<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: The stereochemistry of hydrolysis of three different hexosaminidases (human placenta, jack bean, and bovine kidney)was shown by the Withers group in 1994 <cite>Lai</cite>.<br />
;First catalytic nucleophile identification: This is a neighboring-group participation enzyme with the mechanism suggested both from 3-D structure <cite>Tews1996</cite>, by analogy with GH18 enzymes and through work in which the non-reducing end sugar was de-acetylated resulting in total loss in activity <cite>Armand1997</cite>.<br />
;First general acid/base residue identification: Inferred from the 3-D structure <cite>Tews1996</cite> and by analogy with closely related GH18 chitinases.<br />
;First 3-D structure: The 3-D structure of the ''Serratia marscescens'' chitobiase <cite>Tews1996</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Comfort2007 pmid=17323919<br />
#He1999 pmid=9312086<br />
#3 isbn=978-0-240-52118-3<br />
#MikesClassic Sinnott, M.L. (1990) Catalytic mechanisms of enzymic glycosyl transfer. Chem. Rev. 90, 1171-1202. [http://dx.doi.org/10.1021/cr00105a006 DOI: 10.1021/cr00105a006]<br />
#Armand1997 pmid=9396742<br />
#Tews1996 pmid=8673609<br />
#Lai pmid=7993902<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH020]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_20&diff=5833Glycoside Hydrolase Family 202010-10-07T17:43:14Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ian Greig^^^<br />
* [[Responsible Curator]]: ^^^David Vocadlo^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH20'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH20.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Content is to be added here.<br />
<br />
This is an example of how to make references to a journal article <cite>Comfort2007</cite>. (See the References section below). Multiple references can go in the same place like this <cite>Comfort2007 He1999</cite>. You can even cite books using just the ISBN <cite>3</cite>. References that are not in PubMed can be typed in by hand <cite>MikesClassic</cite>. <br />
<br />
<br />
== Kinetics and Mechanism ==<br />
History of neighbouring group participation in enzyme-catalyzed REF Lowe and Sinnott and aqueous REF Sinnott and Bruice reactions of glycosides. Use of free energy relationships ships to infer neighbouring group participation. Early japanese work;REF Vocadlo and Withers differential analysis. REF<br />
Loss of activity upon non-reducing end deacatylation <cite>Armand1997</cite>.<br />
<br />
== Catalytic Residues ==<br />
Content is to be added here.<br />
<br />
<br />
== Three-dimensional structures ==<br />
Content is to be added here.<br />
<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>Comfort2007</cite>.<br />
;First catalytic nucleophile identification: This is a neighboring-group participation enzyme with the mechanism suggested both from 3-D structure <cite>Tews1996</cite>, by analogy with GH18 enzymes and through work in which the non-reducing end sugar was de-acetylated resulting in total loss in activity <cite>Armand1997</cite>.<br />
;First general acid/base residue identification: Inferred from the 3-D structure <cite>Tews1996</cite> and by analogy with closely related GH18 chitinases.<br />
;First 3-D structure: The 3-D structure of the ''Serratia marscescens'' chitobiase <cite>Tews1996</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Comfort2007 pmid=17323919<br />
#He1999 pmid=9312086<br />
#3 isbn=978-0-240-52118-3<br />
#MikesClassic Sinnott, M.L. (1990) Catalytic mechanisms of enzymic glycosyl transfer. Chem. Rev. 90, 1171-1202. [http://dx.doi.org/10.1021/cr00105a006 DOI: 10.1021/cr00105a006]<br />
#Armand1997 pmid=9396742<br />
#Tews1996 pmid=8673609<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH020]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_20&diff=5832Glycoside Hydrolase Family 202010-10-07T17:40:16Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Ian Greig^^^<br />
* [[Responsible Curator]]: ^^^David Vocadlo^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH20'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH20.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Content is to be added here.<br />
<br />
This is an example of how to make references to a journal article <cite>Comfort2007</cite>. (See the References section below). Multiple references can go in the same place like this <cite>Comfort2007 He1999</cite>. You can even cite books using just the ISBN <cite>3</cite>. References that are not in PubMed can be typed in by hand <cite>MikesClassic</cite>. <br />
<br />
<br />
== Kinetics and Mechanism ==<br />
History of neighbouring group participation in enzyme-catalyzed REF Lowe and Sinnott and aqueous REF Sinnott and Bruice reactions of glycosides. Use of free energy relationships ships to infer neighbouring group participation. Early japanese work;REF Vocadlo and Withers differential analysis. REF<br />
Loss of activity upon non-reducing end deacatylation <cite>Armand1997</cite>.<br />
<br />
== Catalytic Residues ==<br />
Content is to be added here.<br />
<br />
<br />
== Three-dimensional structures ==<br />
Content is to be added here.<br />
<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>Comfort2007</cite>.<br />
;First catalytic nucleophile identification: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>MikesClassic</cite>.<br />
;First general acid/base residue identification: Identified from the 3-D structure <cite>Tews1996</cite> and by analogy with closely related GH18 chitinases.<br />
;First 3-D structure: The 3-D structure of the ''Serratia marscescens'' chitobiase <cite>Tews1996</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Comfort2007 pmid=17323919<br />
#He1999 pmid=9312086<br />
#3 isbn=978-0-240-52118-3<br />
#MikesClassic Sinnott, M.L. (1990) Catalytic mechanisms of enzymic glycosyl transfer. Chem. Rev. 90, 1171-1202. [http://dx.doi.org/10.1021/cr00105a006 DOI: 10.1021/cr00105a006]<br />
#Armand1997 pmid=9396742<br />
#Tews1996 pmid=8673609<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH020]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_5&diff=5831Glycoside Hydrolase Family 52010-10-07T17:14:56Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: ^^^Gideon Davies^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH5'''<br />
|-<br />
|'''Clan''' <br />
|GH-A<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH5.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
GH5 is one of the largest of all CAZy [[glycoside hydrolase]] families. A variety of specificties are annotated to this family notably endoglucanase (cellulase) and endomannanase as well as exoglucanases, exomannanases and β-glucosidase and β-mannosidase. Other activities include 1,6 galactanase, 1,3 mannanase, 1,4 xylanase, endoglycoceramidase, as well as high specificity xyloglucanases. Family GH5 enzymes are found widely distributed across Archae, bacteria and eukaryotes, notably fungi and plants. There are no known human enzymes in GH5. <br />
<br />
== Kinetics and Mechanism ==<br />
Family GH5 enzymes are retaining enzymes, as first shown by NMR <cite>Barras1992</cite> and follow a [[classical Koshland double-displacement mechanism]].<br />
<br />
== Catalytic Residues ==<br />
GH5 enzymes use the [[classical Koshland double-displacement mechanism]] and the two catalytic residues are known to be glutamates found at the C-terminal ends of β-strands 4 (acid/base) and 7 (nucleophile) <cite>Henrissat1996 Jenkins1995</cite>.<br />
<br />
== Three-dimensional structures ==<br />
Three-dimensional structures are available for a very large number of Family GH5 enzymes, the first solved being that of the ''Clostridium thermocellum'' endoglucanase CelC <cite>Alzari1995</cite>. As members of Clan GH-A they have a classical (α/β)<sub>8</sub> TIM barrel fold with the two key active site glutamic acids being approximately 200 residues apart in sequence and located at the C-terminal ends of β-strands 4 (acid/base) and 7 (nucleophile) <cite>Henrissat1996,Jenkins1995</cite>.<br />
<br />
With so many 3D structures in this family, covering many specificities it is clearly hard to pick out notable structural papers. The ''Bacillus agaradhaerens'' Cel5A has been extensively studied, notably in the trapping of enzymatic snapshots along the reaction coordinate <cite>Davies1998</cite> but also as a testbed for glycosidase inhibitor design as crystals often diffract to atomic resolution (for example <cite>Varrot2003</cite>). The reaction coordinate work on the endoglucanases (thus working on ''gluco''-configured substrates) shows that the substrate binds in <sup>1</sup>S<sub>3</sub> conformation with the covalent intermediate in <sup>4</sup>C<sub>1</sub> chair conformation implying catalysis via a <sup>4</sup>H<sub>3</sub> half-chair (near) transition-state. <br />
<br />
By analogy with family GH26 mannnanases <cite>Ducros</cite> and family GH2 &beta;-mannosidases <cite>Tailford</cite> it would seem likely that GH5 mannanases use a different conformational itinerary to their glucosidase relatives, likely via a <sup>1</sup>S<sub>5</sub>-<sup>O</sup>S<sub>2</sub> glycosylation pathway and thus ''via'' a B<sub>2,5</sub> (near) transition-state although direct evidence in this family is limited <cite>Vincent</cite>. An interesting dissection of mannan degrading enzyme systems has been provided by work in the Gilbert group on the diverse GH5 and 26 mannanases in ''Cellvibrio japonicus''(see for example <cite>Hogg,Tailford-2,Cartmell2008</cite>).<br />
<br />
The Rhodococcal endoglycoceramidase II (EGC) in this family has found application in the chemoenzymatic synthesis of ceramide derivatives <cite>Caines2007</cite>. In 2007 the first 3-D structure of a highly specific GH5 xyloglucanase was reported <cite>Gloster2007</cite>; this enzyme makes kinetically productive interactions with both xylose and galactose substituents, as reflected in both a high specific activity on xyloglucan and the kinetics of a series of aryl glycosides.<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: The curator believes this to be the <sup>1</sup>H NMR stereochemical determination for EGZ from ''Erwinia chrysanthemi'' <cite>Barras1992</cite>. GH5 enzymes were also in the comprehensive Gebler study <cite>Gebler1992</cite>.<br />
;First catalytic nucleophile identification: Trapped using the classical Withers 2-fluoro method, here with 2',4'-dinitrophenyl-2-deoxy-2-fluoro-beta-D-cellobioside, reported in Wang and Withers in 1993 <cite>Wang1993</cite>.<br />
<br />
;First general acid/base residue identification: Several mutagenesis papers has alluded to the importance of a conserved glutamate- one that both Dominguez <cite>Dominguez1995</cite> and Ducros <cite>Ducros1995</cite> correctly postulated as the catalytic acid when the 3-D structures were determined. <br />
<br />
;First 3-D structure: The first 3D structures in family GH5 was an endoglucanase (cellulase) from ''Clostridium thermocellum'' reported by the Alzari in 1995 (in a paper which also reported a family GH10 xylanase structure and the similarities between them) <cite>Dominguez1995</cite>. Subsequently, Ducros and colleagues reported the ''Clostridium cellulolyticum'' Cel5A also in 1995 <cite>Ducros1995</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Jenkins1995 pmid=7729513 <br />
#Henrissat1996 pmid=8643635 <br />
#Caines2007 pmid=17329247<br />
#Barras1992 pmid=1563515<br />
#Wang1993 pmid=8100226<br />
#Gebler1992 pmid=1618761 <br />
#Dominguez1995 pmid=7664125<br />
#Ducros1995 pmid=8535787<br />
#Davies1998 pmid=9718293<br />
#Varrot2003 pmid=12812472<br />
#Gloster2007 pmid=17376777<br />
#Ducros pmid=12203498<br />
#Tailford pmid=18408714<br />
#Tailford2 pmid=19441796<br />
#Hogg pmid=12523937<br />
#Vincent pmid=15515081<br />
#Cartmell2008 pmid=18799462 <br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH005]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_5&diff=5830Glycoside Hydrolase Family 52010-10-07T17:13:30Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: ^^^Gideon Davies^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH5'''<br />
|-<br />
|'''Clan''' <br />
|GH-A<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH5.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
GH5 is one of the largest of all CAZy [[glycoside hydrolase]] families. A variety of specificties are annotated to this family notably endoglucanase (cellulase) and endomannanase as well as exoglucanases, exomannanases and β-glucosidase and β-mannosidase. Other activities include 1,6 galactanase, 1,3 mannanase, 1,4 xylanase, endoglycoceramidase, as well as high specificity xyloglucanases. Family GH5 enzymes are found widely distributed across Archae, bacteria and eukaryotes, notably fungi and plants. There are no known human enzymes in GH5. <br />
<br />
== Kinetics and Mechanism ==<br />
Family GH5 enzymes are retaining enzymes, as first shown by NMR <cite>Barras1992</cite> and follow a [[classical Koshland double-displacement mechanism]].<br />
<br />
== Catalytic Residues ==<br />
GH5 enzymes use the [[classical Koshland double-displacement mechanism]] and the two catalytic residues are known to be glutamates found at the C-terminal ends of β-strands 4 (acid/base) and 7 (nucleophile) <cite>Henrissat1996 Jenkins1995</cite>.<br />
<br />
== Three-dimensional structures ==<br />
Three-dimensional structures are available for a very large number of Family GH5 enzymes, the first solved being that of the ''Clostridium thermocellum'' endoglucanase CelC <cite>Alzari1995</cite>. As members of Clan GH-A they have a classical (α/β)<sub>8</sub> TIM barrel fold with the two key active site glutamic acids being approximately 200 residues apart in sequence and located at the C-terminal ends of β-strands 4 (acid/base) and 7 (nucleophile) <cite>Henrissat1996,Jenkins1995</cite>.<br />
<br />
With so many 3D structures in this family, covering many specificities it is clearly hard to pick out notable structural papers. The ''Bacillus agaradhaerens'' Cel5A has been extensively studied, notably in the trapping of enzymatic snapshots along the reaction coordinate <cite>Davies1998</cite> but also as a testbed for glycosidase inhibitor design as crystals often diffract to atomic resolution (for example <cite>Varrot2003</cite>). The reaction coordinate work on the endoglucanases (thus working on ''gluco''-configured substrates) shows that the substrate binds in <sup>1</sup>S<sub>3</sub> conformation with the covalent intermediate in <sup>4</sup>C<sub>1</sub> chair conformation implying catalysis via a <sup>4</sup>H<sub>3</sub> half-chair (near) transition-state. <br />
<br />
By analogy with family GH26 mannnanases <cite>Ducros</cite> and family GH2 &beta;-mannosidases <cite>Tailford</cite> it would seem likely that GH5 mannanases use a different conformational itinerary to their glucosidase relatives, likely via a <sup>1</sup>S<sub>5</sub>-<sup>O</sup>S<sub>2</sub> glycosylation pathway, pergaps via a B<sub>2,5</sub> (near) transition-state although direct evidence in this family is limited <cite>Vincent</cite>. An interesting facet of mannan degrading enzyme systems has been provided by work in the Gilbert group on the diverse GH5 and 26 mannanases in ''Cellvibrio japonicus''(see for example <cite>Hogg,Tailford-2,Cartmell2008</cite>).<br />
<br />
The Rhodococcal endoglycoceramidase II (EGC) in this family has found application in the chemoenzymatic synthesis of ceramide derivatives <cite>Caines2007</cite>. In 2007 the first 3-D structure of a highly specific GH5 xyloglucanase was reported <cite>Gloster2007</cite>; this enzyme makes kinetically productive interactions with both xylose and galactose substituents, as reflected in both a high specific activity on xyloglucan and the kinetics of a series of aryl glycosides.<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: The curator believes this to be the <sup>1</sup>H NMR stereochemical determination for EGZ from ''Erwinia chrysanthemi'' <cite>Barras1992</cite>. GH5 enzymes were also in the comprehensive Gebler study <cite>Gebler1992</cite>.<br />
;First catalytic nucleophile identification: Trapped using the classical Withers 2-fluoro method, here with 2',4'-dinitrophenyl-2-deoxy-2-fluoro-beta-D-cellobioside, reported in Wang and Withers in 1993 <cite>Wang1993</cite>.<br />
<br />
;First general acid/base residue identification: Several mutagenesis papers has alluded to the importance of a conserved glutamate- one that both Dominguez <cite>Dominguez1995</cite> and Ducros <cite>Ducros1995</cite> correctly postulated as the catalytic acid when the 3-D structures were determined. <br />
<br />
;First 3-D structure: The first 3D structures in family GH5 was an endoglucanase (cellulase) from ''Clostridium thermocellum'' reported by the Alzari in 1995 (in a paper which also reported a family GH10 xylanase structure and the similarities between them) <cite>Dominguez1995</cite>. Subsequently, Ducros and colleagues reported the ''Clostridium cellulolyticum'' Cel5A also in 1995 <cite>Ducros1995</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Jenkins1995 pmid=7729513 <br />
#Henrissat1996 pmid=8643635 <br />
#Caines2007 pmid=17329247<br />
#Barras1992 pmid=1563515<br />
#Wang1993 pmid=8100226<br />
#Gebler1992 pmid=1618761 <br />
#Dominguez1995 pmid=7664125<br />
#Ducros1995 pmid=8535787<br />
#Davies1998 pmid=9718293<br />
#Varrot2003 pmid=12812472<br />
#Gloster2007 pmid=17376777<br />
#Ducros pmid=12203498<br />
#Tailford pmid=18408714<br />
#Tailford2 pmid=19441796<br />
#Hogg pmid=12523937<br />
#Vincent pmid=15515081<br />
#Cartmell2008 pmid=18799462 <br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH005]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_5&diff=5829Glycoside Hydrolase Family 52010-10-07T17:12:49Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: ^^^Gideon Davies^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH5'''<br />
|-<br />
|'''Clan''' <br />
|GH-A<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH5.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
GH5 is one of the largest of all CAZy [[glycoside hydrolase]] families. A variety of specificties are annotated to this family notably endoglucanase (cellulase) and endomannanase as well as exoglucanases, exomannanases and β-glucosidase and β-mannosidase. Other activities include 1,6 galactanase, 1,3 mannanase, 1,4 xylanase, endoglycoceramidase, as well as high specificity xyloglucanases. Family GH5 enzymes are found widely distributed across Archae, bacteria and eukaryotes, notably fungi and plants. There are no known human enzymes in GH5. <br />
<br />
== Kinetics and Mechanism ==<br />
Family GH5 enzymes are retaining enzymes, as first shown by NMR <cite>Barras1992</cite> and follow a [[classical Koshland double-displacement mechanism]].<br />
<br />
== Catalytic Residues ==<br />
GH5 enzymes use the [[classical Koshland double-displacement mechanism]] and the two catalytic residues are known to be glutamates found at the C-terminal ends of β-strands 4 (acid/base) and 7 (nucleophile) <cite>Henrissat1996 Jenkins1995</cite>.<br />
<br />
== Three-dimensional structures ==<br />
Three-dimensional structures are available for a very large number of Family GH5 enzymes, the first solved being that of the ''Clostridium thermocellum'' endoglucanase CelC <cite>Alzari1995</cite>. As members of Clan GH-A they have a classical (α/β)<sub>8</sub> TIM barrel fold with the two key active site glutamic acids being approximately 200 residues apart in sequence and located at the C-terminal ends of β-strands 4 (acid/base) and 7 (nucleophile) <cite>Henrissat1996,Jenkins1995</cite>.<br />
<br />
With so many 3D structures in this family, covering many specificities it is clearly hard to pick out notable structural papers. The ''Bacillus agaradhaerens'' Cel5A has been extensively studied, notably in the trapping of enzymatic snapshots along the reaction coordinate <cite>Davies1998</cite> but also as a testbed for glycosidase inhibitor design as crystals often diffract to atomic resolution (for example <cite>Varrot2003</cite>). The reaction coordinate work on the endoglucanases (thus working on ''gluco''-configured substrates) shows that the substrate binds in <sup>1</sup>S<sub>3</sub> conformation with the covalent intermediate in <sup>4</sup>C<sub>1</sub> chair conformation implying catalysis via a <sup>4</sup>H<sub>3</sub> half-chair (near) transition-state. <br />
<br />
By analogy with family GH26 mannnanases <cite>Ducros</cite> and family GH2 &beta;-mannosidases <cite>Tailford</cite> it would seem likely that GH5 mannanases use a different conformational itinerary to their glucosidase relatives, likely via a <sup>1</sup>S<sub>5</sub>-<sup>O</sup>S<sub>2</sub> glycosylation pathway, pergaps via a B<sub>2,5</sub> (near) transition-state although direct evidence in this family is limited <cite>Vincent</cite>. An interesting facet of mannan degrading enzyme systems has been provided by work in the Gilbert group on the diverse GH5 and 26 mannanases in ''Cellvibrio japonicus''(see for example <cite>Hogg,Tailford-2,Cartmell2008</cite>.<br />
<br />
The Rhodococcal endoglycoceramidase II (EGC) in this family has found application in the chemoenzymatic synthesis of ceramide derivatives <cite>Caines2007</cite>. In 2007 the first 3-D structure of a highly specific GH5 xyloglucanase was reported <cite>Gloster2007</cite>; this enzyme makes kinetically productive interactions with both xylose and galactose substituents, as reflected in both a high specific activity on xyloglucan and the kinetics of a series of aryl glycosides.<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: The curator believes this to be the <sup>1</sup>H NMR stereochemical determination for EGZ from ''Erwinia chrysanthemi'' <cite>Barras1992</cite>. GH5 enzymes were also in the comprehensive Gebler study <cite>Gebler1992</cite>.<br />
;First catalytic nucleophile identification: Trapped using the classical Withers 2-fluoro method, here with 2',4'-dinitrophenyl-2-deoxy-2-fluoro-beta-D-cellobioside, reported in Wang and Withers in 1993 <cite>Wang1993</cite>.<br />
<br />
;First general acid/base residue identification: Several mutagenesis papers has alluded to the importance of a conserved glutamate- one that both Dominguez <cite>Dominguez1995</cite> and Ducros <cite>Ducros1995</cite> correctly postulated as the catalytic acid when the 3-D structures were determined. <br />
<br />
;First 3-D structure: The first 3D structures in family GH5 was an endoglucanase (cellulase) from ''Clostridium thermocellum'' reported by the Alzari in 1995 (in a paper which also reported a family GH10 xylanase structure and the similarities between them) <cite>Dominguez1995</cite>. Subsequently, Ducros and colleagues reported the ''Clostridium cellulolyticum'' Cel5A also in 1995 <cite>Ducros1995</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Jenkins1995 pmid=7729513 <br />
#Henrissat1996 pmid=8643635 <br />
#Caines2007 pmid=17329247<br />
#Barras1992 pmid=1563515<br />
#Wang1993 pmid=8100226<br />
#Gebler1992 pmid=1618761 <br />
#Dominguez1995 pmid=7664125<br />
#Ducros1995 pmid=8535787<br />
#Davies1998 pmid=9718293<br />
#Varrot2003 pmid=12812472<br />
#Gloster2007 pmid=17376777<br />
#Ducros pmid=12203498<br />
#Tailford pmid=18408714<br />
#Tailford2 pmid=19441796<br />
#Hogg pmid=12523937<br />
#Vincent pmid=15515081<br />
#Cartmell2008 pmid=18799462 <br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH005]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_5&diff=5828Glycoside Hydrolase Family 52010-10-07T16:14:21Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: ^^^Gideon Davies^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH5'''<br />
|-<br />
|'''Clan''' <br />
|GH-A<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH5.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
GH5 is one of the largest of all CAZy [[glycoside hydrolase]] families. A variety of specificties are annotated to this family notably endoglucanase (cellulase) and endomannanase as well as exoglucanases, exomannanases and β-glucosidase and β-mannosidase. Other activities include 1,6 galactanase, 1,3 mannanase, 1,4 xylanase, endoglycoceramidase, as well as high specificity xyloglucanases. Family GH5 enzymes are found widely distributed across Archae, bacteria and eukaryotes, notably fungi and plants. There are no known human enzymes in GH5. <br />
<br />
== Kinetics and Mechanism ==<br />
Family GH5 enzymes are retaining enzymes, as first shown by NMR <cite>Barras1992</cite> and follow a [[classical Koshland double-displacement mechanism]].<br />
<br />
== Catalytic Residues ==<br />
GH5 enzymes use the [[classical Koshland double-displacement mechanism]] and the two catalytic residues are known to be glutamates found at the C-terminal ends of β-strands 4 (acid/base) and 7 (nucleophile) <cite>Henrissat1996 Jenkins1995</cite>.<br />
<br />
== Three-dimensional structures ==<br />
Three-dimensional structures are available for a very large number of Family GH5 enzymes, the first solved being that of the ''Clostridium thermocellum'' endoglucanase CelC <cite>Alzari1995</cite>. As members of Clan GH-A they have a classical (α/β)<sub>8</sub> TIM barrel fold with the two key active site glutamic acids being approximately 200 residues apart in sequence and located at the C-terminal ends of β-strands 4 (acid/base) and 7 (nucleophile) <cite>Henrissat1996,Jenkins1995</cite>.<br />
<br />
With so many 3D structures in this family, covering many specificities it is clearly hard to pick out notable structural papers. The ''Bacillus agaradhaerens'' Cel5A has been extensively studied, notably in the trapping of enzymatic snapshots along the reaction coordinate <cite>Davies1998</cite> but also as a testbed for glycosidase inhibitor design as crystals often diffract to atomic resolution (for example <cite>Varrot2003</cite>). The reaction coordinate work on the endoglucanases (thus working on ''gluco''-configured substrates) shows that the substrate binds in <sup>1</sup>S<sub>3</sub> conformation with the covalent intermediate in <sup>4</sup>C<sub>1</sub> chair conformation implying catalysis via a <sup>4</sup>H<sub>3</sub> half-chair (near) transition-state. By analogy with family GH26 mannnanases <cite>Ducros</cite> and family GH2 &beta;-mannosidases <cite>Tailford</cite> it would seem likely that GH5 mannanases use a different conformational itinerary to their glucosidase relatives, likely via a <sup>1</sup>S<sub>5</sub>-<sup>O</sup>S<sub>2</sub> glycosylation pathway although direct evidence in this family is limited <cite>Vincent</cite>.<br />
<br />
The Rhodococcal endoglycoceramidase II (EGC) in this family has found application in the chemoenzymatic synthesis of ceramide derivatives <cite>Caines2007</cite>. In 2007 the first 3-D structure of a highly specific GH5 xyloglucanase was reported <cite>Gloster2007</cite>; this enzyme makes kinetically productive interactions with both xylose and galactose substituents, as reflected in both a high specific activity on xyloglucan and the kinetics of a series of aryl glycosides.<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: The curator believes this to be the <sup>1</sup>H NMR stereochemical determination for EGZ from ''Erwinia chrysanthemi'' <cite>Barras1992</cite>. GH5 enzymes were also in the comprehensive Gebler study <cite>Gebler1992</cite>.<br />
;First catalytic nucleophile identification: Trapped using the classical Withers 2-fluoro method, here with 2',4'-dinitrophenyl-2-deoxy-2-fluoro-beta-D-cellobioside, reported in Wang and Withers in 1993 <cite>Wang1993</cite>.<br />
<br />
;First general acid/base residue identification: Several mutagenesis papers has alluded to the importance of a conserved glutamate- one that both Dominguez <cite>Dominguez1995</cite> and Ducros <cite>Ducros1995</cite> correctly postulated as the catalytic acid when the 3-D structures were determined. <br />
<br />
;First 3-D structure: The first 3D structures in family GH5 was an endoglucanase (cellulase) from ''Clostridium thermocellum'' reported by the Alzari in 1995 (in a paper which also reported a family GH10 xylanase structure and the similarities between them) <cite>Dominguez1995</cite>. Subsequently, Ducros and colleagues reported the ''Clostridium cellulolyticum'' Cel5A also in 1995 <cite>Ducros1995</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Jenkins1995 pmid=7729513 <br />
#Henrissat1996 pmid=8643635 <br />
#Caines2007 pmid=17329247<br />
#Barras1992 pmid=1563515<br />
#Wang1993 pmid=8100226<br />
#Gebler1992 pmid=1618761 <br />
#Dominguez1995 pmid=7664125<br />
#Ducros1995 pmid=8535787<br />
#Davies1998 pmid=9718293<br />
#Varrot2003 pmid=12812472<br />
#Gloster2007 pmid=17376777<br />
#Ducros pmid=12203498<br />
#Tailford pmid=18408714<br />
#Vincent pmid=15515081<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH005]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_18&diff=5826Glycoside Hydrolase Family 182010-10-07T11:29:30Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]s: ^^^Gideon Davies^^^, ^^^Nathalie Juge^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH18'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known (acid/neighbouring group)<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH18.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
GH18 is unusual in having both catalytically active chitinase (EC 3.2.1.14) and endo-β-N-acetylglucosaminidases (EC 3.2.1.96) but there are also sub-families of non-hydrolytic proteins that function as carbohydrate binding modules / "lectins" or as xylanase inhibitors.<br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
GH18 enzymes belong to a growing group of enzymes (now including GH families [[Glycoside Hydrolase Family 18|18]], [[Glycoside Hydrolase Family 20|20]],[[Glycoside Hydrolase Family 25|25]], [[Glycoside Hydrolase Family 56|56]], [[Glycoside Hydrolase Family 84|84]], and [[Glycoside Hydrolase Family 85|85]]) that perform a double-displacement reaction but instead of the more common enzyme-derived nucleophile they utlize the N-acetamido carbonyl oxygen in what is termed "neighbouring group participation" / "substrate participation" or "anchimeric assistance". Figures showing such a mechanism date back to Koshland's 1953 review <cite>Koshland1953</cite>, indeed they frequent the chemical literature of participating groups long before that, but it is primarily through the work on GH18 <cite>AVTA2</cite> and soon after GH20 <cite>Tews1996,Armand1997</cite> that such a mechanism became well established. In such a mechanism, which occurs with (net) retention of anomeric configuration, the enzyme provides a catalytic acid function to protonate the leaving group to facilitate its departure with the substrate carbonyl oxygen playing the role of nucleophile to generate a bicyclic "oxazoline" intermediate (which subsequently breaks down following the microscopic reverse ''via'' hydrolysis or occasionally transglycosylation). Such a mechanism has a number of facets, one of which is its potential inhibition using thiazolines <cite>Macdonald</cite>.<br />
<br />
<br />
== Catalytic Residues ==<br />
The catalytically active GH18 enzymes use a double displacement reaction mechanism with "neighbouring group participation". Hence there is a catalytic acid residue (glutamate in family GH18, but often also Asp in other families using this mechanism) and in all families apart from GH[[Glycoside Hydrolase Family 85|85]] (where this residue is an amide), a second carboxylate (here Asp) acts to deprotonate the N-acetamido nitrogen during oxazoline formation/breakdown. In family GH18 the two catalytic carboxylates are found in an D-X-G motif whereas in some families the carboxylates may be adjacent such as the DD motif in family GH84 (for example see <cite>He2010</cite>). The physical separation of the two catalytic residues (with the second not in a position to act as a nucleophile itself) has led to confusion in some literature that GH18 and other enzymes (notably GH25) may be inverting enzymes; this is certainly not the case for GH18 and is unlikely to be the case for GH25.<br />
<br />
<br />
== Three-dimensional structures ==<br />
Although these enzymes are frequently multi-modular, the catalytic domains are &alpha; / &beta; barrels <cite>Perrakis,ATVA</cite>.<br />
<br />
Work on the conformational itinerary of catalysis which is extremely similar to other retaining enzymes active on ''gluco''-configured substrates, was provided by the van Aalten group <cite>Daan2001</cite> in 2001 through the trapping of a distorted Michaelis complex in <sup>1,4</sup>B conformation and thus extremely similar to the <sup>1</sup>S<sub>3</sub> skew boats oberserved in GH[[Glycoside Hydrolase Family 5|5]] <cite>Davies1998</cite> for example or the <sup>4</sup>E conformation originally seen for a "neighboring group" enzyme in GH[[Glycoside Hydrolase Family 20|20]] <cite>Tews1996</cite>. More recently, a similar conformation has been observed for the Michaelis complex of another neighboring group enzyme, the GH84 O-GlcNAcase <cite>He2010</cite>. Fungal GH18 enzymes are considered as possible therapeutic targets and a number of programmes are probing this area (for example <cite>Housten2002</cite>).<br />
<br />
One unusual feauture of GH18 is the large number of sequences that encode catalytically-inactive proteins that function as enzyme inhibitors or lectins. <br />
Some examples, that need some more text include:<br />
Daan Chilectin paper <cite>Daan2003</cite><br />
Hennig Concanavalin B paper <cite>Hennig1995</cite><br />
Narbonin <cite>Hennig1993</cite><br />
<br />
Review of non-catalytic GH18 as enzyme inhibitors <cite>Juge2005</cite>.<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: Sometimes '''incorrectly''' reported as inverting, this family performs catalysis with '''retention''' of anomeric configuration as first shown on the ''Bacillus ciculans'' enzyme <cite>Armand1994</cite>.<br />
;First catalytic nucleophile identification: This family is one of many that uses neighbouring group participation for catalysis with the N-acetyl carbonyl group acting as the nucleophile; first proposed (I believe) for this family in <cite>AVTA2</cite>.<br />
;First general acid/base residue identification: On the basis of 3-D structure <cite>Perrakis</cite>.<br />
;First 3-D structure: The first two 3-D structures for catalytically active GH18 members were the ''Serratia marcescens'' chitinase A and the plant defence protein hevamine published "back-to-back" in ''Structure'' in 1994 <cite>Perrakis,ATVA</cite>. In retrospect, however, the non-catalytic "Narbonin" structure was arguably the first GH18 3-D structure, although it is has no enzymatic activity <cite>Hennig1993</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Perrakis pmid=7704527<br />
#ATVA1 pmid=7704528<br />
#AVTA2 pmid=7495789 <br />
#Armand1994 pmid=8168626<br />
#Koshland1953 Koshland, D. (1953) Biol. Rev. 28, 416.<br />
#Armand1997 pmid=9396742<br />
#Housten2002 pmid=12093900<br />
#Tews1996 pmid=8673609<br />
#Daan2001 pmid=11481469<br />
#Macdonald pmid=20209544<br />
#He2010 pmid=20067256<br />
#Davies1998 pmid=9718293<br />
#Daan2003 pmid=12775711<br />
#Hennig1995 pmid=7490746<br />
#Hennig1993 pmid=1628747<br />
#Juge2005 pmid=15794761<br />
<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH018]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_18&diff=5825Glycoside Hydrolase Family 182010-10-07T11:28:25Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]s: ^^^Gideon Davies^^^, ^^^Nathalie Juge^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH18'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known (acid/neighbouring group)<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH18.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
GH18 is unusual in having both catalytically active chitinase (EC 3.2.1.14) and endo-β-N-acetylglucosaminidases (EC 3.2.1.96) but there are also sub-families of non-hydrolytic proteins that function as carbohydrate binding modules / "lectins" or as xylanase inhibitors.<br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
GH18 enzymes belong to a growing group of enzymes (now including GH families [[Glycoside Hydrolase Family 18|18]], [[Glycoside Hydrolase Family 20|20]],[[Glycoside Hydrolase Family 25|25]], [[Glycoside Hydrolase Family 56|56]], [[Glycoside Hydrolase Family 84|84]], and [[Glycoside Hydrolase Family 85|85]]) that perform a double-displacement reaction but instead of the more common enzyme-derived nucleophile they utlize the N-acetamido carbonyl oxygen in what is termed "neighbouring group participation" / "substrate participation" or "anchimeric assistance". Figures showing such a mechanism date back to Koshland's 1953 review <cite>Koshland1953</cite>, indeed they frequent the chemical literature of participating groups long before that, but it is primarily through the work on GH18 <cite>AVTA2</cite> and soon after GH20 <cite>Tews1996,Armand1997</cite> that such a mechanism became well established. In such a mechanism, which occurs with (net) retention of anomeric configuration, the enzyme provides a catalytic acid function to protonate the leaving group to facilitate its departure with the substrate carbonyl oxygen playing the role of nucleophile to generate a bicyclic "oxazoline" intermediate (which subsequently breaks down following the microscopic reverse ''via'' hydrolysis or occasionally transglycosylation). Such a mechanism has a number of facets, one of which is its potential inhibition using thiazolines <cite>Macdonald</cite>.<br />
<br />
<br />
== Catalytic Residues ==<br />
The catalytically active GH18 enzymes use a double displacement reaction mechanism with "neighbouring group participation". Hence there is a catalytic acid residue (glutamate in family GH18, but often also Asp in other families using this mechanism) and in all families apart from GH[[Glycoside Hydrolase Family 85|85]] (where this residue is an amide), a second carboxylate (here Asp) acts to deprotonate the N-acetamido nitrogen during oxazoline formation/breakdown. In family GH18 the two catalytic carboxylates are found in an D-X-G motif whereas in some families the carboxylates may be adjacent such as the DD motif in family GH84 (for example see <cite>He2010</cite>). The physical separation of the two catalytic residues (with the second not in a position to act as a nucleophile itself) has led to confusion in some literature that GH18 and other enzymes (notably GH25) may be inverting enzymes; this is certainly not the case for GH18 and is unlikely to be the case for GH25.<br />
<br />
<br />
== Three-dimensional structures ==<br />
Although these enzymes are frequently multi-modular, the catalytic domains are &alpha; / &beta; barrels <cite>Perrakis,ATVA</cite>.<br />
<br />
Work on the conformational itinerary of catalysis which is extremely similar to other retaining enzymes active on ''gluco''-configured substrates, was provided by the van Aalten group <cite>Daan2001</cite> in 2001 through the trapping of a distorted Michaelis complex in <sup>1,4</sup>B conformation and thus extremely similar to the <sup>1</sup>S<sub>3</sub> skew boats oberserved in GH[[Glycoside Hydrolase Family 5|5]] <cite>Davies1998</cite> for example or the <sup>4</sup>E conformation originally seen for a "neighboring group" enzyme in GH[[Glycoside Hydrolase Family 20|20]] cite>Tews1996</cite>. More recently, a similar conformation has been observed for the Michaelis complex of another neighboring group enzymem the GH84 O-GlcNAcase <cite>He2010</cite>. Fungal GH18 enzymes are considered as possible therapeutic targets and a number of programmes are probing this area (for example <cite>Housten2002</cite>).<br />
<br />
One unusual feauture of GH18 is the large number of sequences that encode catalytically-inactive proteins that function as enzyme inhibitors or lectins. <br />
Some examples, that need some more text include:<br />
Daan Chilectin paper <cite>Daan2003</cite><br />
Hennig Concanavalin B paper <cite>Hennig1995</cite><br />
Narbonin <cite>Hennig1993</cite><br />
<br />
Review of non-catalytic GH18 as enzyme inhibitors <cite>Juge2005</cite>.<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: Sometimes '''incorrectly''' reported as inverting, this family performs catalysis with '''retention''' of anomeric configuration as first shown on the ''Bacillus ciculans'' enzyme <cite>Armand1994</cite>.<br />
;First catalytic nucleophile identification: This family is one of many that uses neighbouring group participation for catalysis with the N-acetyl carbonyl group acting as the nucleophile; first proposed (I believe) for this family in <cite>AVTA2</cite>.<br />
;First general acid/base residue identification: On the basis of 3-D structure <cite>Perrakis</cite>.<br />
;First 3-D structure: The first two 3-D structures for catalytically active GH18 members were the ''Serratia marcescens'' chitinase A and the plant defence protein hevamine published "back-to-back" in ''Structure'' in 1994 <cite>Perrakis,ATVA</cite>. In retrospect, however, the non-catalytic "Narbonin" structure was arguably the first GH18 3-D structure, although it is has no enzymatic activity <cite>Hennig1993</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Perrakis pmid=7704527<br />
#ATVA1 pmid=7704528<br />
#AVTA2 pmid=7495789 <br />
#Armand1994 pmid=8168626<br />
#Koshland1953 Koshland, D. (1953) Biol. Rev. 28, 416.<br />
#Armand1997 pmid=9396742<br />
#Housten2002 pmid=12093900<br />
#Tews1996 pmid=8673609<br />
#Daan2001 pmid=11481469<br />
#Macdonald pmid=20209544<br />
#He2010 pmid=20067256<br />
#Davies1998 pmid=9718293<br />
#Daan2003 pmid=12775711<br />
#Hennig1995 pmid=7490746<br />
#Hennig1993 pmid=1628747<br />
#Juge2005 pmid=15794761<br />
<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH018]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_18&diff=5824Glycoside Hydrolase Family 182010-10-07T11:27:06Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]s: ^^^Gideon Davies^^^, ^^^Nathalie Juge^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH18'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known (acid/neighbouring group)<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH18.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
GH18 is unusual in having both catalytically active chitinase (EC 3.2.1.14) and endo-β-N-acetylglucosaminidases (EC 3.2.1.96) but there are also sub-families of non-hydrolytic proteins that function as carbohydrate binding modules / "lectins" or as xylanase inhibitors.<br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
GH18 enzymes belong to a growing group of enzymes (now including GH families [[Glycoside Hydrolase Family 18|18]], [[Glycoside Hydrolase Family 20|20]],[[Glycoside Hydrolase Family 25|25]], [[Glycoside Hydrolase Family 56|56]], [[Glycoside Hydrolase Family 84|84]], and [[Glycoside Hydrolase Family 85|85]]) that perform a double-displacement reaction but instead of the more common enzyme-derived nucleophile they utlize the N-acetamido carbonyl oxygen in what is termed "neighbouring group participation" / "substrate participation" or "anchimeric assistance". Figures showing such a mechanism date back to Koshland's 1953 review <cite>Koshland1953</cite>, indeed they frequent the chemical literature of participating groups long before that, but it is primarily through the work on GH18 <cite>AVTA2</cite> and soon after GH20 <cite>Tews1996,Armand1997</cite> that such a mechanism became well established. In such a mechanism, which occurs with (net) retention of anomeric configuration, the enzyme provides a catalytic acid function to protonate the leaving group to facilitate its departure with the substrate carbonyl oxygen playing the role of nucleophile to generate a bicyclic "oxazoline" intermediate (which subsequently breaks down following the microscopic reverse ''via'' hydrolysis or occasionally transglycosylation). Such a mechanism has a number of facets, one of which is its potential inhibition using thiazolines <cite>Macdonald</cite>.<br />
<br />
<br />
== Catalytic Residues ==<br />
The catalytically active GH18 enzymes use a double displacement reaction mechanism with "neighbouring group participation". Hence there is a catalytic acid residue (glutamate in family GH18, but often also Asp in other families using this mechanism) and in all families apart from GH[[Glycoside Hydrolase Family 85|85]] (where this residue is an amide), a second carboxylate (here Asp) acts to deprotonate the N-acetamido nitrogen during oxazoline formation/breakdown. In family GH18 the two catalytic carboxylates are found in an D-X-G motif whereas in some families the carboxylates may be adjacent such as the DD motif in family GH84 (for example see <cite>He2010</cite>). The physical separation of the two catalytic residues (with the second not in a position to act as a nucleophile itself) has led to confusion in some literature that GH18 and other enzymes (notably GH25) may be inverting enzymes; this is certainly not the case for GH18 and is unlikely to be the case for GH25.<br />
<br />
<br />
== Three-dimensional structures ==<br />
Although these enzymes are frequently multi-modular, the catalytic domains are &alpha; / &beta; barrels <cite>Perrakis,ATVA</cite>.<br />
<br />
Work on the conformational itinerary of catalysis which is extremely similar to other retaining enzymes active on ''gluco''-configured substrates, was provided by the van Aalten group <cite>Daan2001</cite> in 2001 through the trapping of a distorted Michaelis complex in <sup>1,4</sup>B conformation and thus extremely similar to the <sup>1</sup>S<sub>3</sub> skew boats oberserved in GH[[Glycoside Hydrolase Family 5|5]] <cite>Davies1998</cite> for example or the <sup>4</sup>E conformation originally seen for a "neighboring group" enzyme in GH[[Glycoside Hydrolase Family 20|20]] cite>Tews1996</cite>. More recently, a similar conformation has been observed for the Michaelis complex of another neighboring group enzymem the GH84 O-GlcNAcase <cite>He2010</cite>. Fungal GH18 enzymes are considered as possible therapeutic targets and a number of programmes are probing this area (for example <cite>Housten2002</cite>).<br />
<br />
One unusual feauture of GH18 is the large number of sequences that encode catalytically-inactive proteins that function as enzyme inhibitors or lectins. <br />
Some examples, that need some more text include:<br />
Daan Chilectin paper <cite>Daan2003</cite><br />
Hennig Concanavalin B paper <cite>Hennig1995</cite><br />
Narbonin <cite>Hennig1993</cite><br />
<br />
Review of non-catalytic GH18 as enzyme inhibitors <cite>Juge2005</cite>.<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: Sometimes '''incorrectly''' reported as inverting, this family performs catalysis with '''retention''' of anomeric configuration as first shown on the ''Bacillus ciculans'' enzyme <cite>Armand1994</cite>.<br />
;First catalytic nucleophile identification: This family is one of many that uses neighbouring group participation for catalysis with the N-acetyl carbonyl group acting as the nucleophile; first proposed (I believe) for this family in <cite>AVTA2</cite>.<br />
;First general acid/base residue identification: On the basis of 3-D structure <cite>Perrakis</cite>.<br />
;First 3-D structure: The first two 3-D structures for catalytically active GH18 members were the ''Serratia marcescens'' chitinase A and the plant defence protein hevamine published "back-to-back" in ''Structure'' in 1994 <cite>Perrakis,ATVA</cite>. In retrospect, however, the non-catalytic "Narbonin" structure was arguably the first GH18 3-D structure, although it is has no enzymatic activity <cite>Hennig1993</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Perrakis pmid=7704527<br />
#ATVA1 pmid=7704528<br />
#AVTA2 pmid=7495789 <br />
#Armand1994 pmid=8168626<br />
#Koshland1953<br />
#Armand1997 pmid=9396742<br />
#Housten2002 pmid=12093900<br />
#Tews1996 pmid=8673609<br />
#Daan2001 pmid=11481469<br />
#Macdonald pmid=20209544<br />
#He2010 pmid=20067256<br />
#Davies1998 pmid=9718293<br />
#Daan2003 pmid=12775711<br />
#Hennig1995 pmid=7490746<br />
#Hennig1993 pmid=1628747<br />
#Juge2005 pmid=15794761<br />
<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH018]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_45&diff=5818Glycoside Hydrolase Family 452010-10-06T20:19:39Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: ^^^Gideon Davies^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH45'''<br />
|-<br />
|'''Clan''' <br />
|none<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|known (but see discussion)<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH45.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
[[Glycoside hydrolases]] of GH45 are endoglucanases (EC 3.2.1.4); mainly the hydrolysis of soluble &beta; -1,4 glucans. Family 45 enzymes are perhaps best known for their uses in the textile / detergent industries (see for example <cite>Schulein1998</cite>).<br />
<br />
== Kinetics and Mechanism ==<br />
The enzymes, formally known as cellulase family "K" in some historic literature, act with inversion of anomeric configuration to generate the &alpha;-D anomer of the oligosaccaride as product. Based upon the structure of the ''Humicola insolens'' endoglucanase V (now known as Cel45) <cite>Davies1993 Davies1995</cite> it was concluded that Asp121 (in an HxD motif) acted as the [[general acid]] (implied by its hydrogen bonding to the glycosidic oxygen of a ligand in the +1 subsite) and that the most likely [[general base]] is Asp10 (in a YxD motif), appropriately positioned "below" the sugar plane. As with many inverting enzymes the base assignment is less secure than that of the acid.<br />
<br />
== Catalytic Residues ==<br />
"Classical" GH45 enzymes likely use twin carboxylates corresponding to Asp10 and 121 of the ''Humicola insolens'' endoglucanase V <cite>Davies1993 Davies1995</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The 3-D structure of canonical GH45 enzymes is a six-stranded &beta;-barrel to which a seventh strand is appended. The structure differs from classical &beta;-barrels in containing both parallel and anti-parallel &beta;-strands. At the time of the first structure solution the fold had ony previously been observed in "Barwin" <cite>Ludvigsen</cite>; a plant defense protein of unknown function. As is now expected for ''endo''-enzymes, the active centre is located in an open substrate-binding groove. The original native (uncomplexed) structure had an disordered loop above the active centre and this was only seen to become ordered subsequently upon the binding of cello-oligosaccharides <cite>Davies1995</cite>.<br />
<br />
Family GH45 enzymes are structurally related to plant <cite>Yennawar</cite> and bacterial <cite>Kerff</cite> expansins. Indeed they even display some of the catalytic centre motifs such as the catalytic acid. The putative catalytic base is absent in plant and bacterial expansins. There are also a few fungal GH45 members, exemplified by ''Phanerochaete chrysosporium'' Cel45 which also appear to lack the putative base <cite>Igarashi</cite>.<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: As part of an analysis of many families reported in <cite>Schou93</cite>.<br />
;First general acid/base residue identification: Catalytic residue proposals have been made solely on the basis of 3-D structure <cite>Davies1993 Davies1995</cite>.<br />
;First 3-D structure: The ''Humicola insolens'' EGV (now Cel45) by the Davies group <cite>Davies1993</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Davies1993 pmid=8377830<br />
#Davies1995 pmid=8519779<br />
#Schou93 pmid=8223652<br />
#Yennawar pmid=16984999<br />
#Kerff pmid=18971341<br />
#Igarashi pmid=18676702<br />
#Ludvigsen pmid=1390665<br />
#Schulein1998 Schülein M, Kauppinen M, Lange L, Lassen S, Andersen L, Klysner S, and Nielsen, J (1998) ''Characterization of fungal cellulases for fiber modification.'' ACS Symposium Series, 687 (Enzyme Applications in Fiber Processing): 66-74. [http://dx.doi.org/10.1021/bk-1998-0687.ch006 DOI: 10.1021/bk-1998-0687.ch006]<br />
<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH045]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_18&diff=5815Glycoside Hydrolase Family 182010-10-06T18:19:48Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Gideon Davies^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH18'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known (acid/neighbouring group)<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH18.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
GH18 is unusual in having both catalytically active chitinase (EC 3.2.1.14) and endo-β-N-acetylglucosaminidases (EC 3.2.1.96) but there are also sub-families of non-hydrolytic proteins that function as carbohydrate binding modules / "lectins" or as xylanase inhibitors.<br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
GH18 enzymes belong to a growing group of enzymes (now including GH families [[Glycoside Hydrolase Family 18|18]], [[Glycoside Hydrolase Family 20|20]],[[Glycoside Hydrolase Family 25|25]], [[Glycoside Hydrolase Family 56|56]], [[Glycoside Hydrolase Family 84|84]], and [[Glycoside Hydrolase Family 85|85]]) that perform a double-displacement reaction but instead of the more common enzyme-derived nucleophile they utlize the N-acetamido carbonyl oxygen in what is termed "neighbouring group participation" / "substrate participation" or "anchimeric assistance". Figures showing such a mechanism date back to Koshland's 1953 review <cite>Koshland1953</cite>, indeed they frequent the chemical literature of participating groups long before that, but it is primarily through the work on GH18 <cite>AVTA2</cite> and soon after GH20 <cite>Tews1996,Armand1997</cite> that such a mechanism became well established. In such a mechanism, which occurs with (net) retention of anomeric configuration, the enzyme provides a catalytic acid function to protonate the leaving group to facilitate its departure with the substrate carbonyl oxygen playing the role of nucleophile to generate a bicyclic "oxazoline" intermediate (which subsequently breaks down following the microscopic reverse ''via'' hydrolysis or occasionally transglycosylation). Such a mechanism has a number of facets, one of which is its potential inhibition using thiazolines <cite>Macdonald</cite>.<br />
<br />
<br />
== Catalytic Residues ==<br />
The catalytically active GH18 enzymes use a double displacement reaction mechanism with "neighbouring group participation". Hence there is a catalytic acid residue (glutamate in family GH18, but often also Asp in other families using this mechanism) and in all families apart from GH[[Glycoside Hydrolase Family 85|85]] (where this residue is an amide), a second carboxylate (here Asp) acts to deprotonate the N-acetamido nitrogen during oxazoline formation/breakdown. In family GH18 the two catalytic carboxylates are found in an D-X-G motif whereas in some families the carboxylates may be adjacent such as the DD motif in family GH84 (for example see <cite>He2010</cite>). The physical separation of the two catalytic residues (with the second not in a position to act as a nucleophile itself) has led to confusion in some literature that GH18 and other enzymes (notably GH25) may be inverting enzymes; this is certainly not the case for GH18 and is unlikely to be the case for GH25.<br />
<br />
<br />
== Three-dimensional structures ==<br />
Although these enzymes are frequently multi-modular, the catalytic domains are &alpha; / &beta; barrels <cite>Perrakis,ATVA</cite>.<br />
<br />
Work on the conformational itinerary of catalysis which is extremely similar to other retaining enzymes active on ''gluco''-configured substrates, was provided by the van Aalten group <cite>Daan2001</cite> in 2001 through the trapping of a distorted Michaelis complex in <sup>1,4</sup>B conformation and thus extremely similar to the <sup>1</sup>S<sub>3</sub> skew boats oberserved in GH[[Glycoside Hydrolase Family 5|5]] <cite>Davies1998</cite> for example or the <sup>4</sup>E conformation originally seen for a "neighboring group" enzyme in GH[[Glycoside Hydrolase Family 20|20]] cite>Tews1996</cite>. More recetly, a similar conformation has been observed for the Michaelis complex of another neighboring group enzymem the GH84 O-GlcNAcase <cite>He2010</cite>. Fungal GH18 enzymes are considered as possible therapeutic targets and a number of programmes are probing this area (for example <cite>Housten2002</cite>).<br />
<br />
One unusual feauture of GH18 are the large numbers of sequences that encode catalytically-inactive proteins that function as enzyme inhibitors or lectins. '''SOMEONE ELSE WRITE THIS?'''<br />
<br />
Daan Chilectin paper <cite>Daan2003</cite><br />
Hennig Concanavalin B paper <cite>Hennig1995</cite><br />
Narbonin <cite>Hennig1993</cite><br />
<br />
Review of non-catalytic GH18 as enzyme inhibitors <cite>Juge2005</cite>.<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: Sometimes '''incorrectly''' reported as inverting, this family performs catalysis with '''retention''' of anomeric configuration as first shown on the ''Bacillus ciculans'' enzyme <cite>Armand1994</cite>.<br />
;First catalytic nucleophile identification: This family is one of many that uses neighbouring group participation for catalysis with the N-acetyl carbonyl group acting as the nucleophile; first proposed (I believe) for this family in <cite>AVTA2</cite>.<br />
;First general acid/base residue identification: On the basis of 3-D structure <cite>Perrakis</cite>.<br />
;First 3-D structure: The first two 3-D structures for catalytically active GH18 members were the ''Serratia marcescens'' chitinase A and the plant defence protein hevamine published "back-to-back" in ''Structure'' in 1994 <cite>Perrakis,ATVA</cite>. In retrospect, however, the non-catalytic "Narbonin" structure was arguably the first GH18 3-D structure, although it is has no enzymatic activity <cite>Hennig1993</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Perrakis pmid=7704527<br />
#ATVA1 pmid=7704528<br />
#AVTA2 pmid=7495789 <br />
#Armand1994 pmid=8168626<br />
#Koshland1953<br />
#Armand1997 pmid=9396742<br />
#Housten2002 pmid=12093900<br />
#Tews1996 pmid=8673609<br />
#Daan2001 pmid=11481469<br />
#Macdonald pmid=20209544<br />
#He2010 pmid=20067256<br />
#Davies1998 pmid=9718293<br />
#Daan2003 pmid=12775711<br />
#Hennig1995 pmid=7490746<br />
#Hennig1993 pmid=1628747<br />
#Juge2005 pmid=15794761<br />
<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH018]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_18&diff=5814Glycoside Hydrolase Family 182010-10-06T18:18:51Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Gideon Davies^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH18'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known (acid/neighbouring group)<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH18.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
GH18 is unusual in having both catalytically active chitinase (EC 3.2.1.14) and endo-β-N-acetylglucosaminidases (EC 3.2.1.96) but there are also sub-families of non-hydrolytic proteins that function as carbohydrate binding modules / "lectins" or as xylanase inhibitors.<br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
GH18 enzymes belong to a growing group of enzymes (now including GH families [[Glycoside Hydrolase Family 18|18]], [[Glycoside Hydrolase Family 20|20]],[[Glycoside Hydrolase Family 25|25]], [[Glycoside Hydrolase Family 56|56]], [[Glycoside Hydrolase Family 84|84]], and [[Glycoside Hydrolase Family 85|85]]) that perform a double-displacement reaction but instead of the more common enzyme-derived nucleophile they utlize the N-acetamido carbonyl oxygen in what is termed "neighbouring group participation" / "substrate participation" or "anchimeric assistance". Figures showing such a mechanism date back to Koshland's 1953 review <cite>Koshland1953</cite>, indeed they frequent the chemical literature of participating groups long before that, but it is primarily through the work on GH18 <cite>AVTA2</cite> and soon after GH20 <cite>Tews1996,Armand1997</cite> that such a mechanism became well established. In such a mechanism, which occurs with (net) retention of anomeric configuration, the enzyme provides a catalytic acid function to protonate the leaving group to facilitate its departure with the substrate carbonyl oxygen playing the role of nucleophile to generate a bicyclic "oxazoline" intermediate (which subsequently breaks down following the microscopic reverse ''via'' hydrolysis or occasionally transglycosylation). Such a mechanism has a number of facets, one of which is its potential inhibition using thiazolines <cite>Macdonald</cite>.<br />
<br />
<br />
== Catalytic Residues ==<br />
The catalytically active GH18 enzymes use a double displacement reaction mechanism with "neighbouring group participation". Hence there is a catalytic acid residue (glutamate in family GH18, but often also Asp in other families using this mechanism) and in all families apart from GH[[Glycoside Hydrolase Family 85|85]] (where this residue is an amide), a second carboxylate (here Asp) acts to deprotonate the N-acetamido nitrogen during oxazoline formation/breakdown. In family GH18 the two catalytic carboxylates are found in an D-X-G motif whereas in some families the carboxylates may be adjacent such as the DD motif in family GH84 (for example see <cite>He2010</cite>). The physical separation of the two catalytic residues (with the second not in a position to act as a nucleophile itself) has led to confusion in some literature that GH18 and other enzymes (notably GH25) may be inverting enzymes; this is certainly not the case for GH18 and is unlikely to be the case for GH25.<br />
<br />
<br />
== Three-dimensional structures ==<br />
Although these enzymes are frequently multi-modular, the catalytic domains are &alpha; / &beta; barrels <cite>Perrakis,ATVA</cite>.<br />
<br />
Work on the conformational itinerary of catalysis which is extremely similar to other retaining enzymes active on ''gluco''-configured substrates, was provided by the van Aalten group <cite>Daan2001</cite> in 2001 through the trapping of a distorted Michaelis complex in <sup>1,4</sup>B conformation and thus extremely similar to the <sup>1</sup>S<sub>3</sub> skew boats oberserved in GH[[Glycoside Hydrolase Family 5|5]] <cite>Davies1998</cite> for example or the <sup>4</sup>E conformation originally seen for a "neighboring group" enzyme in GH[[Glycoside Hydrolase Family 20|20]] cite>Tews1996</cite>. More recetly, a similar conformation has been observed for the Michaelis complex of another neighboring group enzymem the GH84 O-GlcNAcase <cite>He2010</cite>. Fungal GH18 enzymes are considered as possible therapeutic targets and a number of programmes are probing this area (for example <cite>Housten2002</cite>).<br />
<br />
One unusual feauture of GH18 are the latge numbers of sequences that encode catalytically-inactive proteins that function as enzyme inhibitors or lectins. '''SOMEONE ELSE WRITE THIS?'''<br />
<br />
Daan Chilectin paper <cite>Daan2003</cite><br />
Hennig Concanavalin B paper <cite>Hennig1995</cite><br />
Narbonin <cite>Hennig1993</cite><br />
<br />
Review of non-catalytic GH18 as enzyme inhibitors <cite>Juge2005</cite>.<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: Sometimes '''incorrectly''' reported as inverting, this family performs catalysis with '''retention''' of anomeric configuration as first shown on the ''Bacillus ciculans'' enzyme <cite>Armand1994</cite>.<br />
;First catalytic nucleophile identification: This family is one of many that uses neighbouring group participation for catalysis with the N-acetyl carbonyl group acting as the nucleophile; first proposed (I believe) for this family in <cite>AVTA2</cite>.<br />
;First general acid/base residue identification: On the basis of 3-D structure <cite>Perrakis</cite>.<br />
;First 3-D structure: The first two 3-D structures for catalytically active GH18 members were the ''Serratia marcescens'' chitinase A and the plant defence protein hevamine published "back-to-back" in ''Structure'' in 1994 <cite>Perrakis,ATVA</cite>. In retrospect, however, the non-catalytic "Narbonin" structure was arguably the first GH18 3-D structure, althoigh it is has no enzymatic activity <cite>Hennig1993</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Perrakis pmid=7704527<br />
#ATVA1 pmid=7704528<br />
#AVTA2 pmid=7495789 <br />
#Armand1994 pmid=8168626<br />
#Koshland1953<br />
#Armand1997 pmid=9396742<br />
#Housten2002 pmid=12093900<br />
#Tews1996 pmid=8673609<br />
#Daan2001 pmid=11481469<br />
#Macdonald pmid=20209544<br />
#He2010 pmid=20067256<br />
#Davies1998 pmid=9718293<br />
#Daan2003 pmid=12775711<br />
#Hennig1995 pmid=7490746<br />
#Hennig1993 pmid=1628747<br />
#Juge2005 pmid=15794761<br />
<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH018]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_18&diff=5813Glycoside Hydrolase Family 182010-10-06T18:16:18Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Gideon Davies^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH18'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known (acid/neighbouring group)<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH18.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
GH18 is unusual in having both catalytically active chitinase (EC 3.2.1.14) and endo-β-N-acetylglucosaminidases (EC 3.2.1.96) but there are also sub-families of non-hydrolytic proteins that function as carbohydrate binding modules / "lectins" or as xylanase inhibitors.<br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
GH18 enzymes belong to a growing group of enzymes (now including GH families [[Glycoside Hydrolase Family 18|18]], [[Glycoside Hydrolase Family 20|20]],[[Glycoside Hydrolase Family 25|25]], [[Glycoside Hydrolase Family 56|56]], [[Glycoside Hydrolase Family 84|84]], and [[Glycoside Hydrolase Family 85|85]]) that perform a double-displacement reaction but instead of the more common enzyme-derived nucleophile they utlize the N-acetamido carbonyl oxygen in what is termed "neighbouring group participation" / "substrate participation" or "anchimeric assistance". Figures showing such a mechanism date back to Koshland's 1953 review <cite>Koshland1953</cite>, indeed they frequent the chemical literature of participating groups long before that, but it is primarily through the work on GH18 <cite>AVTA2</cite> and soon after GH20 <cite>Tews1996,Armand1997</cite> that such a mechanism became well established. In such a mechanism, which occurs with (net) retention of anomeric configuration, the enzyme provides a catalytic acid function to protonate the leaving group to facilitate its departure with the substrate carbonyl oxygen playing the role of nucleophile to generate a bicyclic "oxazoline" intermediate (which subsequently breaks down following the microscopic reverse ''via'' hydrolysis or occasionally transglycosylation). Such a mechanism has a number of facets, one of which is its potential inhibition using thiazolines <cite>Macdonald</cite>.<br />
<br />
<br />
== Catalytic Residues ==<br />
The catalytically active GH18 enzymes use a double displacement reaction mechanism with "neighbouring group participation". Hence there is a catalytic acid residue (glutamate in family GH18, but often also Asp in other families using this mechanism) and in all families apart from GH[[Glycoside Hydrolase Family 85|85]] (where this residue is an amide), a second carboxylate (here Asp) acts to deprotonate the N-acetamido nitrogen during oxazoline formation/breakdown. In family GH18 the two catalytic carboxylates are found in an D-X-G motif whereas in some families the carboxylates may be adjacent such as the DD motif in family GH84 (for example see <cite>He2010</cite>). The physical separation of the two catalytic residues (with the second not in a position to act as a nucleophile itself) has led to confusion in some literature that GH18 and other enzymes (notably GH25) may be inverting enzymes; this is certainly not the case for GH18 and is unlikely to be the case for GH25.<br />
<br />
<br />
== Three-dimensional structures ==<br />
Although these enzymes are frequently multi-modular, the catalytic domains are &alpha; / &beta; barrels <cite>Perrakis,ATVA</cite>.<br />
<br />
Work on the conformational itinerary of catalysis which is extremely similar to other retaining enzymes active on ''gluco''-configured substrates, was provided by the van Aalten group <cite>Daan2001</cite> in 2001 through the trapping of a distorted Michaelis complex in <sup>1,4</sup>B conformation and thus extremely similar to the <sup>1</sup>S<sub>3</sub> skew boats oberserved in GH[[Glycoside Hydrolase Family 5|5]] <cite>Davies1998</cite> for example or the <sup>4</sup>E conformation originally seen for a "neighboring group" enzyme in GH[[Glycoside Hydrolase Family 20|20]] cite>Tews1996</cite>. More recetly, a similar conformation has been observed for the Michaelis complex of another neighboring group enzymem the GH84 O-GlcNAcase <cite>He2010</cite>. Fungal GH18 enzymes are considered as possible therapeutic targets and a number of programmes are probing this area (for example <cite>Housten2002</cite>).<br />
<br />
One unusual feauture of GH18 are the latge numbers of sequences that encode catalytically-inactive proteins that function as enzyme inhibitors or lectins. '''SOMEONE ELSE WRITE THIS?'''<br />
<br />
Daan Chilectin paper <cite>Daan2003</cite><br />
Hennig Concanavaline B paper <cite>Hennig1995</cite><br />
Narbonin <cite>Hennig1993</cite><br />
<br />
Review of non-catalytic GH18 as enzyme inhibitors <cite>Juge2005</cite>.<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: Sometimes '''incorrectly''' reported as inverting, this family performs catalysis with '''retention''' of anomeric configuration as first shown on the ''Bacillus ciculans'' enzyme <cite>Armand1994</cite>.<br />
;First catalytic nucleophile identification: This family is one of many that uses neighbouring group participation for catalysis with the N-acetyl carbonyl group acting as the nucleophile; first proposed (I believe) for this family in <cite>AVTA2</cite>.<br />
;First general acid/base residue identification: On the basis of 3-D structure <cite>Perrakis</cite>.<br />
;First 3-D structure: The first two 3-D structures for catalytically active GH18 members were the ''Serratia marcescens'' chitinase A and the plant defence protein hevamine published "back-to-back" in ''Structure'' in 1994 <cite>Perrakis,ATVA</cite>. In retrospect, however, the non-catalytic "Narbonin" structure was arguably the first GH18 3-D structure, althoigh it is has no enzymatic activity <cite>Hennig1993</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Perrakis pmid=7704527<br />
#ATVA1 pmid=7704528<br />
#AVTA2 pmid=7495789 <br />
#Armand1994 pmid=8168626<br />
#Koshland1953<br />
#Armand1997 pmid=9396742<br />
#Housten2002 pmid=12093900<br />
#Tews1996 pmid=8673609<br />
#Daan2001 pmid=11481469<br />
#Macdonald pmid=20209544<br />
#He2010 pmid=20067256<br />
#Davies1998 pmid=9718293<br />
#Daan2003 pmid=12775711<br />
#Hennig1995 pmid=7490746<br />
#Hennig1993 pmid= 1628747<br />
#Juge2005 pmid=15794761<br />
<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH018]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_18&diff=5812Glycoside Hydrolase Family 182010-10-06T18:13:39Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Gideon Davies^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH18'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known (acid/neighbouring group)<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH18.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
GH18 is unusual in having both catalytically active chitinase (EC 3.2.1.14) and endo-β-N-acetylglucosaminidases (EC 3.2.1.96) but there are also sub-families of non-hydrolytic proteins that function as carbohydrate binding modules / "lectins" or as xylanase inhibitors.<br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
GH18 enzymes belong to a growing group of enzymes (now including GH families [[Glycoside Hydrolase Family 18|18]], [[Glycoside Hydrolase Family 20|20]],[[Glycoside Hydrolase Family 25|25]], [[Glycoside Hydrolase Family 56|56]], [[Glycoside Hydrolase Family 84|84]], and [[Glycoside Hydrolase Family 85|85]]) that perform a double-displacement reaction but instead of the more common enzyme-derived nucleophile they utlize the N-acetamido carbonyl oxygen in what is termed "neighbouring group participation" / "substrate participation" or "anchimeric assistance". Figures showing such a mechanism date back to Koshland's 1953 review <cite>Koshland1953</cite>, indeed they frequent the chemical literature of participating groups long before that, but it is primarily through the work on GH18 <cite>AVTA2</cite> and soon after GH20 <cite>Tews1996,Armand1997</cite> that such a mechanism became well established. In such a mechanism, which occurs with (net) retention of anomeric configuration, the enzyme provides a catalytic acid function to protonate the leaving group to facilitate its departure with the substrate carbonyl oxygen playing the role of nucleophile to generate a bicyclic "oxazoline" intermediate (which subsequently breaks down following the microscopic reverse ''via'' hydrolysis or occasionally transglycosylation). Such a mechanism has a number of facets, one of which is its potential inhibition using thiazolines <cite>Macdonald</cite>.<br />
<br />
<br />
== Catalytic Residues ==<br />
The catalytically active GH18 enzymes use a double displacement reaction mechanism with "neighbouring group participation". Hence there is a catalytic acid residue (glutamate in family GH18, but often also Asp in other families using this mechanism) and in all families apart from GH[[Glycoside Hydrolase Family 85|85]] (where this residue is an amide), a second carboxylate (here Asp) acts to deprotonate the N-acetamido nitrogen during oxazoline formation/breakdown. In family GH18 the two catalytic carboxylates are found in an D-X-G motif whereas in some families the carboxylates may be adjacent such as the DD motif in family GH84 (for example see <cite>He2010</cite>). The physical separation of the two catalytic residues (with the second not in a position to act as a nucleophile itself) has led to confusion in some literature that GH18 and other enzymes (notably GH25) may be inverting enzymes; this is certainly not the case for GH18 and is unlikely to be the case for GH25.<br />
<br />
<br />
== Three-dimensional structures ==<br />
Although these enzymes are frequently multi-modular, the catalytic domains are &alpha; / &beta; barrels <cite>Perrakis,ATVA</cite>.<br />
<br />
Work on the conformational itinerary of catalysis which is extremely similar to other retaining enzymes active on ''gluco''-configured substrates, was provided by the van Aalten group <cite>Daan2001</cite> in 2001 through the trapping of a distorted Michaelis complex in <sup>1,4</sup>B conformation and thus extremely similar to the <sup>1</sup>S<sub>3</sub> skew boats oberserved in GH[[Glycoside Hydrolase Family 5|5]] <cite>Davies1998</cite> for example or the <sup>4</sup>E conformation originally seen for a "neighboring group" enzyme in GH[[Glycoside Hydrolase Family 20|20]] cite>Tews1996</cite>. More recetly, a similar conformation has been observed for the Michaelis complex of another neighboring group enzymem the GH84 O-GlcNAcase <cite>He2010</cite>. Fungal GH18 enzymes are considered as possible therapeutic targets and a number of programmes are probing this area (for example <cite>Housten2002</cite>).<br />
<br />
One unusual feauture of GH18 are the latge numbers of sequences that encode catalytically-inactive proteins that function as enzyme inhibitors or lectins. '''SOMEONE ELSE WRITE THIS?'''<br />
<br />
Daan Chilectin paper <cite>Daan2003</cite><br />
Hennig Concanavaline B paper <cite>Hennig1995</cite><br />
Narbonin <cite>Hennig1993</cite><br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: Sometimes '''incorrectly''' reported as inverting, this family performs catalysis with '''retention''' of anomeric configuration as first shown on the ''Bacillus ciculans'' enzyme <cite>Armand1994</cite>.<br />
;First catalytic nucleophile identification: This family is one of many that uses neighbouring group participation for catalysis with the N-acetyl carbonyl group acting as the nucleophile; first proposed (I believe) for this family in <cite>AVTA2</cite>.<br />
;First general acid/base residue identification: On the basis of 3-D structure <cite>Perrakis</cite>.<br />
;First 3-D structure: The first two 3-D structures for catalytically active GH18 members were the ''Serratia marcescens'' chitinase A and the plant defence protein hevamine published "back-to-back" in ''Structure'' in 1994 <cite>Perrakis,ATVA</cite>. In retrospect, however, the non-catalytic "Narbonin" structure was arguably the first GH18 3-D structure, althoigh it is has no enzymatic activity <cite>Hennig1993</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Perrakis pmid=7704527<br />
#ATVA1 pmid=7704528<br />
#AVTA2 pmid=7495789 <br />
#Armand1994 pmid=8168626<br />
#Koshland1953<br />
#Armand1997 pmid=9396742<br />
#Housten2002 pmid=12093900<br />
#Tews1996 pmid=8673609<br />
#Daan2001 pmid=11481469<br />
#Macdonald pmid=20209544<br />
#He2010 pmid=20067256<br />
#Davies1998 pmid=9718293<br />
#Daan2003 pmid=12775711<br />
#Hennig1995 pmid=7490746<br />
#Hennig1993 pmid= 1628747<br />
<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH018]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_5&diff=5811Glycoside Hydrolase Family 52010-10-06T16:07:08Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: ^^^Gideon Davies^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH5'''<br />
|-<br />
|'''Clan''' <br />
|GH-A<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH5.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
GH5 is one of the largest of all CAZy [[glycoside hydrolase]] families. A variety of specificties are annotated to this family notably endoglucanase (cellulase) and endomannanase as well as exoglucanases, exomannanases and β-glucosidase and β-mannosidase. Other activities include 1,6 galactanase, 1,3 mannanase, 1,4 xylanase, endoglycoceramidase, as well as high specificity xyloglucanases. Family GH5 enzymes are found widely distributed across Archae, bacteria and eukaryotes, notably fungi and plants. There are no known human enzymes in GH5. <br />
<br />
<br />
== Kinetics and Mechanism ==<br />
Family GH5 enzymes are retaining enzymes, as first shown by NMR <cite>Barras1992</cite> and follow a [[classical Koshland double-displacement mechanism]].<br />
<br />
== Catalytic Residues ==<br />
GH5 enzymes use the [[classical Koshland double-displacement mechanism]] and the two catalytic residues are known to be glutamates found at the C-terminal ends of β-strands 4 (acid/base) and 7 (nucleophile) <cite>Henrissat1996,Jenkins1995</cite>.<br />
<br />
<br />
== Three-dimensional structures ==<br />
Three-dimensional structures are available for a very large number of Family GH5 enzymes, the first solved being that of the ''Clostridium thermocellum'' endoglucanase CelC <cite>Alzari1995</cite>. As members of Clan GH-A they have a classical (α/β)<sub>8</sub> TIM barrel fold with the two key active site glutamic acids being approximately 200 residues apart in sequence and located at the C-terminal ends of β-strands 4 (acid/base) and 7 (nucleophile) <cite>Henrissat1996,Jenkins1995</cite>.<br />
<br />
With so many 3D structures in this family, covering many specificities it is clearly hard to pick out notable structural papers. The ''Bacillus agaradhaerens'' Cel5A has been extensively studied, notably in the trapping of enzymatic snapshots along the reaction coordinate <cite>Davies1998</cite> but also as a testbed for glycosidase inhibitor design as crystals often diffract to atomic resolution (for example <cite>Varrot2003</cite>). The reaction coordinate work on the endoglucanases (thus working on ''gluco''-configured substrates) shows that the substrate binds in <sup>1</sup>S<sub>3</sub> conformation with the covalent intermediate in <sup>4</sup>C<sub>1</sub> chair conformation implying catalysis via a <sup>4</sup>H<sub>3</sub> half-chair (near) transition-state. Mannanases from this family likely use a different itinerary more akin to that used by family GH26 mannnanases <cite>Ducros</cite> and family GH2 &beta;-mannosidases <cite>Tailford</cite>.<br />
<br />
The Rhodococcal endoglycoceramidase II (EGC) in this family has found application in the chemoenzymatic synthesis of ceramide derivatives <cite>Caines2007</cite>. In 2007 the first 3-D structure of a highly specific GH5 xyloglucanase was reported <cite>Gloster2007</cite>; this enzyme makes kinetically productive interactions with both xylose and galactose substituents, as reflected in both a high specific activity on xyloglucan and the kinetics of a series of aryl glycosides.<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: The curator believes this to be the <sup>1</sup>H NMR stereochemical determination for EGZ from ''Erwinia chrysanthemi'' <cite>Barras1992</cite>. GH5 enzymes were also in the comprehensive Gebler study <cite>Gebler1992</cite>.<br />
;First catalytic nucleophile identification: Trapped using the classical Withers 2-fluoro method, here with 2',4'-dinitrophenyl-2-deoxy-2-fluoro-beta-D-cellobioside, reported in Wang and Withers in 1993 <cite>Wang1993</cite>.<br />
<br />
;First general acid/base residue identification: Several mutagenesis papers has alluded to the importance of a conserved glutamate- one that both Dominguez <cite>Dominguez1995</cite> and Ducros <cite>Ducros1995</cite> correctly postulated as the catalytic acid when the 3-D structures were determined. <br />
<br />
;First 3-D structure: The first 3D structures in family GH5 was an endoglucanase (cellulase) from ''Clostridium thermocellum'' reported by the Alzari in 1995 (in a paper which also reported a family GH10 xylanase structure and the similarities between them) <cite>Dominguez1995</cite>. Subsequently, Ducros and colleagues reported the ''Clostridium cellulolyticum'' Cel5A also in 1995 <cite>Ducros1995</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Jenkins1995 pmid=7729513 <br />
#Henrissat1996 pmid=8643635 <br />
#Caines2007 pmid=17329247<br />
#Barras1992 pmid=1563515<br />
#Wang1993 pmid=8100226<br />
#Gebler1992 pmid=1618761 <br />
#Dominguez1995 pmid=7664125<br />
#Ducros1995 pmid=8535787<br />
#Davies1998 pmid=9718293<br />
#Varrot2003 pmid=12812472<br />
#Gloster2007 pmid=17376777<br />
#Ducros pmid=12203498<br />
#Tailford pmid=18408714<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH005]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_18&diff=5810Glycoside Hydrolase Family 182010-10-06T16:01:45Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Gideon Davies^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH18'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known (acid/neighbouring group)<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH18.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
GH18 is unusual in having both catalytically active chitinase (EC 3.2.1.14) and endo-β-N-acetylglucosaminidases (EC 3.2.1.96) but there are also sub-families of non-hydrolytic proteins that function as carbohydrate binding modules / "lectins" or as xylanase inhibitors.<br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
GH18 enzymes belong to a growing group of enzymes (now including GH families [[Glycoside Hydrolase Family 18|18]], [[Glycoside Hydrolase Family 20|20]],[[Glycoside Hydrolase Family 25|25]], [[Glycoside Hydrolase Family 56|56]], [[Glycoside Hydrolase Family 84|84]], and [[Glycoside Hydrolase Family 85|85]]) that perform a double-displacement reaction but instead of the more common enzyme-derived nucleophile they utlize the N-acetamido carbonyl oxygen in what is termed "neighbouring group participation" / "substrate participation" or "anchimeric assistance". Figures showing such a mechanism date back to Koshland's 1953 review <cite>Koshland1953</cite>, indeed they frequent the chemical literature of participating groups long before that, but it is primarily through the work on GH18 <cite>AVTA2</cite> and soon after GH20 <cite>Tews1996,Armand1997</cite> that such a mechanism became well established. In such a mechanism, which occurs with (net) retention of anomeric configuration, the enzyme provides a catalytic acid function to protonate the leaving group to facilitate its departure with the substrate carbonyl oxygen playing the role of nucleophile to generate a bicyclic "oxazoline" intermediate (which subsequently breaks down following the microscopic reverse ''via'' hydrolysis or occasionally transglycosylation). Such a mechanism has a number of facets, one of which is its potential inhibition using thiazolines <cite>Macdonald</cite>.<br />
<br />
<br />
== Catalytic Residues ==<br />
The catalytically active GH18 enzymes use a double displacement reaction mechanism with "neighbouring group participation". Hence there is a catalytic acid residue (glutamate in family GH18, but often also Asp in other families using this mechanism) and in all families apart from GH[[Glycoside Hydrolase Family 85|85]] (where this residue is an amide), a second carboxylate (here Asp) acts to deprotonate the N-acetamido nitrogen during oxazoline formation/breakdown. In family GH18 the two catalytic carboxylates are found in an D-X-G motif whereas in some families the carboxylates may be adjacent such as the DD motif in family GH84 (for example see <cite>He2010</cite>). The physical separation of the two catalytic residues (with the second not in a position to act as a nucleophile itself) has led to confusion in some literature that GH18 and other enzymes (notably GH25) may be inverting enzymes; this is certainly not the case for GH18 and is unlikely to be the case for GH25.<br />
<br />
<br />
== Three-dimensional structures ==<br />
Although these enzymes are frequently multi-modular, the catalytic domains are &alpha; / &beta; barrels <cite>Perrakis,ATVA</cite>.<br />
<br />
Work on the conformational itinerary of catalysis which is extremely similar to other retaining enzymes active on ''gluco''-configured substrates, was provided by the van Aalten group <cite>Daan2001</cite> in 2001 through the trapping of a distorted Michaelis complex in <sup>1,4</sup>B conformation and thus extremely similar to the <sup>1</sup>S<sub>3</sub> skew boats oberserved in GH[[Glycoside Hydrolase Family 5|5]] <cite>Davies1998</cite> for example or the <sup>4</sup>E conformation originally seen for a "neighboring group" enzyme in GH[[Glycoside Hydrolase Family 20|20]] cite>Tews1996</cite>. More recetly, a similar conformation has been observed for the Michaelis complex of another neighboring group enzymem the GH84 O-GlcNAcase <cite>He2010</cite>. Fungal GH18 enzymes are considered as possible therapeutic targets and a number of programmes are probing this area (for example <cite>Housten2002</cite>).<br />
<br />
One unusual feauture of GH18 are the latge numbers of sequences that encode catalytically-inactive proteins that function as enzyme inhibitors or lectins. '''SOMEONE ELSE WRITE THIS?'''<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: Sometimes '''incorrectly''' reported as inverting, this family performs catalysis with '''retention''' of anomeric configuration as first shown on the ''Bacillus ciculans'' enzyme <cite>Armand1994</cite>.<br />
;First catalytic nucleophile identification: This family is one of many that uses neighbouring group participation for catalysis with the N-acetyl carbonyl group acting as the nucleophile; first proposed (I believe) for this family in <cite>AVTA2</cite>.<br />
;First general acid/base residue identification: On the basis of 3-D structure <cite>Perrakis</cite>.<br />
;First 3-D structure: The first two 3-D structures for GH18 members were the ''Serratia marcescens'' chitinase A and the plant defence protein hevamine published "back-to-back" in ''Structure'' in 1994 <cite>Perrakis,ATVA</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Perrakis pmid=7704527<br />
#ATVA1 pmid=7704528<br />
#AVTA2 pmid=7495789 <br />
#Armand1994 pmid=8168626<br />
#Koshland1953<br />
#Armand1997 pmid=9396742<br />
#Housten2002 pmid=12093900<br />
#Tews1996 pmid=8673609<br />
#Daan2001 pmid=11481469<br />
#Macdonald pmid=20209544<br />
#He2010 pmid=20067256<br />
#Davies1998 pmid=9718293<br />
<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH018]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_18&diff=5809Glycoside Hydrolase Family 182010-10-06T15:59:16Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Gideon Davies^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH18'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known (acid/neighbouring group)<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH18.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
GH18 is unusual in having both catalytically active chitinase (EC 3.2.1.14) and endo-β-N-acetylglucosaminidases (EC 3.2.1.96) but there are also sub-families of non-hydrolytic proteins that function as carbohydrate binding modules / "lectins" or as xylanase inhibitors.<br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
GH18 enzymes belong to a growing group of enzymes (now including GH families [[Glycoside Hydrolase Family 18|18]], [[Glycoside Hydrolase Family 20|20]],[[Glycoside Hydrolase Family 25|25]], [[Glycoside Hydrolase Family 56|56]], [[Glycoside Hydrolase Family 84|84]], and [[Glycoside Hydrolase Family 85|85]]) that perform a double-displacement reaction but instead of the more common enzyme-derived nucleophile they utlize the N-acetamido carbonyl oxygen in what is termed "neighbouring group participation" / "substrate participation" or "anchimeric assistance". Figures showing such a mechanism date back to Koshland's 1953 review <cite>Koshland1953</cite>, indeed they frequent the chemical literature of participating groups long before that, but it is primarily through the work on GH18 <cite>AVTA2</cite> and soon after GH20 <cite>Tews1996,Armand1997</cite> that such a mechanism became well established. In such a mechanism, which occurs with (net) retention of anomeric configuration, the enzyme provides a catalytic acid function to protonate the leaving group to facilitate its departure with the substrate carbonyl oxygen playing the role of nucleophile to generate a bicyclic "oxazoline" intermediate (which subsequently breaks down following the microscopic reverse ''via'' hydrolysis or occasionally transglycosylation). Such a mechanism has a number of facets, one of which is its potential inhibition using thiazolines <cite>Macdonald</cite>.<br />
<br />
<br />
== Catalytic Residues ==<br />
The catalytically active GH18 enzymes use a double displacement reaction mechanism with "neighbouring group participation". Hence there is a catalytic acid residue (glutamate in family GH18, but often also Asp in other families using this mechanism) and in all families apart from GH[[Glycoside Hydrolase Family 85|85]] (where this residue is an amide), a second carboxylate (here Asp) acts to deprotonate the N-acetamido nitrogen during oxazoline formation/breakdown. In family GH18 the two catalytic carboxylates are found in an D-X-G motif whereas in some families the carboxylates may be adjacent such as the DD motif in family GH84 (for example see <cite>He2010</cite>). The physical separation of the two catalytic residues (with the second not in a position to act as a nucleophile itself) has led to confusion in some literature that GH18 and other enzymes (notably GH25) may be inverting enzymes; this is certainly not the case for GH18 and is unlikely to be the case for GH25.<br />
<br />
<br />
== Three-dimensional structures ==<br />
Although these enzymes are frequently multi-modular, the catalytic domains are &alpha; / &beta; barrels <cite>Perrakis,ATVA</cite>.<br />
<br />
Work on the conformational itinerary of catalysis which is extremely similar to other retaining enzymes active on ''gluco''-configured substrates, was provided by the van Aalten group <cite>Daan2001</cite> in 2001 through the trapping of a distorted Michaelis complex in <sup>1,4</sup>B conformation and thus extremely similar to the <sup>1</sup>S<sub>3</sub> skew boats oberserved in GH[[Glycoside Hydrolase Family 5|5]] <cite>Davies1998</cite> for example or the <sup>4</sup>E conformation originally seen for a "neighboring group" enzyme in GH[[Glycoside Hydrolase Family 20|20]] and the approximate <sup>1,4</sup>B conformation recently observed in the GH84 O-GlcNAcase<cite>He2010</cite>. Fungal GH18 enzymes are considered as possible therapeutic targets and a number of programmes are probing this area (for example <cite>Housten2002</cite>).<br />
<br />
One unusual feauture of GH18 are the latge numbers of sequences that encode catalytically-inactive proteins that function as enzyme inhibitors or lectins. '''SOMEONE ELSE WRITE THIS?'''<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: Sometimes '''incorrectly''' reported as inverting, this family performs catalysis with '''retention''' of anomeric configuration as first shown on the ''Bacillus ciculans'' enzyme <cite>Armand1994</cite>.<br />
;First catalytic nucleophile identification: This family is one of many that uses neighbouring group participation for catalysis with the N-acetyl carbonyl group acting as the nucleophile; first proposed (I believe) for this family in <cite>AVTA2</cite>.<br />
;First general acid/base residue identification: On the basis of 3-D structure <cite>Perrakis</cite>.<br />
;First 3-D structure: The first two 3-D structures for GH18 members were the ''Serratia marcescens'' chitinase A and the plant defence protein hevamine published "back-to-back" in ''Structure'' in 1994 <cite>Perrakis,ATVA</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Perrakis pmid=7704527<br />
#ATVA1 pmid=7704528<br />
#AVTA2 pmid=7495789 <br />
#Armand1994 pmid=8168626<br />
#Koshland1953<br />
#Armand1997 pmid=9396742<br />
#Housten2002 pmid=12093900<br />
#Tews1996 pmid=8673609<br />
#Daan2001 pmid=11481469<br />
#Macdonald pmid=20209544<br />
#He2010 pmid=20067256<br />
#Davies1998 pmid=9718293<br />
<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH018]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_18&diff=5808Glycoside Hydrolase Family 182010-10-06T15:58:33Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Gideon Davies^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH18'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known (acid/neighbouring group)<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH18.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
GH18 is unusual in having both catalytically active chitinase (EC 3.2.1.14) and endo-β-N-acetylglucosaminidases (EC 3.2.1.96) but there are also sub-families of non-hydrolytic proteins that function as carbohydrate binding modules / "lectins" or as xylanase inhibitors.<br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
GH18 enzymes belong to a growing group of enzymes (now including GH families [[Glycoside Hydrolase Family 18|18]], [[Glycoside Hydrolase Family 20|20]],[[Glycoside Hydrolase Family 25|25]], [[Glycoside Hydrolase Family 56|56]], [[Glycoside Hydrolase Family 84|84]], and [[Glycoside Hydrolase Family 85|85]]) that perform a double-displacement reaction but instead of the more common enzyme-derived nucleophile they utlize the N-acetamido carbonyl oxygen in what is termed "neighbouring group participation" / "substrate participation" or "anchimeric assistance". Figures showing such a mechanism date back to Koshland's 1953 review <cite>Koshland1953</cite>, indeed they frequent the chemical literature of participating groups long before that, but it is primarily through the work on GH18 <cite>AVTA2</cite> and soon after GH20 <cite>Tews1996,Armand1997</cite> that such a mechanism became well established. In such a mechanism, which occurs with (net) retention of anomeric configuration, the enzyme provides a catalytic acid function to protonate the leaving group to facilitate its departure with the substrate carbonyl oxygen playing the role of nucleophile to generate a bicyclic "oxazoline" intermediate (which subsequently breaks down following the microscopic reverse ''via'' hydrolysis or occasionally transglycosylation). Such a mechanism has a number of facets, one of which is its potential inhibition using thiazolines <cite>Macdonald</cite>.<br />
<br />
<br />
== Catalytic Residues ==<br />
The catalytically active GH18 enzymes use a double displacement reaction mechanism with "neighbouring group participation". Hence there is a catalytic acid residue (glutamate in family GH18, but often also Asp in other families using this mechanism) and in all families apart from GH[[Glycoside Hydrolase Family 85|85]] (where this residue is an amide), a second carboxylate (here Asp) acts to deprotonate the N-acetamido nitrogen during oxazoline formation/breakdown. In family GH18 the two catalytic carboxylates are found in an D-X-G motif whereas in some families the carboxylates may be adjacent such as the DD motif in family GH84 (for example see <cite>He2010</cite>). The physical separation of the two catalytic residues (with the second not in a position to act as a nucleophile itself) has led to confusion in some literature that GH18 and other enzymes (notably GH25) may be inverting enzymes; this is certainly not the case for GH18 and is unlikely to be the case for GH25.<br />
<br />
<br />
== Three-dimensional structures ==<br />
Although these enzymes are frequently multi-modular, the catalytic domains are &alpha; / &beta; barrels <cite>Perrakis,ATVA</cite>.<br />
<br />
Work on the conformational itinerary of catalysis which is extremely similar to other retaining enzymes active on ''gluco''-configured substrates, was provided by the van Aalten group <cite>Daan2001</cite> in 2001 through the trapping of a distorted Michaelis complex in <sup>1,4</sup>B conformation and thus extremely similar to the <sup>1</sup>S<sub>3</sub> skew boats oberserved in GH[[Glycoside Hydrolase Family 5|5]] <cite>Davies1998</cite> for example or the <sup>4</sup>E conformation originally seen for a "neighboring group" enzyme in GH[[Glycoside Hydrolase Family 20|20]] and the approximate <sup>1,4</sup>B conformation recently observed in the GH84 O-GlcNAcase<cite>He2010</cite>. Fungal GH18 enzymes are considered as possible therapeutic targets and a number of programmes are probing this area (for example <cite>Housten2002</cite>.<br />
<br />
One unusual feauture of GH18 are the latge numbers of sequences that encode catalytically-inactive proteins that function as enzyme inhibitors or lectins. '''SOMEONE ELSE WRITE THIS?'''<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: Sometimes '''incorrectly''' reported as inverting, this family performs catalysis with '''retention''' of anomeric configuration as first shown on the ''Bacillus ciculans'' enzyme <cite>Armand1994</cite>.<br />
;First catalytic nucleophile identification: This family is one of many that uses neighbouring group participation for catalysis with the N-acetyl carbonyl group acting as the nucleophile; first proposed (I believe) for this family in <cite>AVTA2</cite>.<br />
;First general acid/base residue identification: On the basis of 3-D structure <cite>Perrakis</cite>.<br />
;First 3-D structure: The first two 3-D structures for GH18 members were the ''Serratia marcescens'' chitinase A and the plant defence protein hevamine published "back-to-back" in ''Structure'' in 1994 <cite>Perrakis,ATVA</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Perrakis pmid=7704527<br />
#ATVA1 pmid=7704528<br />
#AVTA2 pmid=7495789 <br />
#Armand1994 pmid=8168626<br />
#Koshland1953<br />
#Armand1997 pmid=9396742<br />
#Housten2002 pmid=12093900<br />
#Tews1996 pmid=8673609<br />
#Daan2001 pmid=11481469<br />
#Macdonald pmid=20209544<br />
#He2010 pmid=20067256<br />
#Davies1998 pmid=9718293<br />
<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH018]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_18&diff=5807Glycoside Hydrolase Family 182010-10-06T15:53:40Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Gideon Davies^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH18'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known (acid/neighbouring group)<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH18.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
GH18 is unusual in having both catalytically active chitinase (EC 3.2.1.14) and endo-β-N-acetylglucosaminidases (EC 3.2.1.96) but there are also sub-families of non-hydrolytic proteins that function as carbohydrate binding modules / "lectins" or as xylanase inhibitors.<br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
GH18 enzymes belong to a growing group of enzymes (now including GH families [[Glycoside Hydrolase Family 18|18]], [[Glycoside Hydrolase Family 20|20]],[[Glycoside Hydrolase Family 25|25]], [[Glycoside Hydrolase Family 56|56]], [[Glycoside Hydrolase Family 84|84]], and [[Glycoside Hydrolase Family 85|85]]) that perform a double-displacement reaction but instead of the more common enzyme-derived nucleophile they utlize the N-acetamido carbonyl oxygen in what is termed "neighbouring group participation" / "substrate participation" or "anchimeric assistance". Figures showing such a mechanism date back to Koshland's 1953 review <cite>Koshland1953</cite>, indeed they frequent the chemical literature of participating groups long before that, but it is primarily through the work on GH18 <cite>AVTA2</cite> and soon after GH20 <cite>Tews1996,Armand1997</cite> that such a mechanism became well established. In such a mechanism, which occurs with (net) retention of anomeric configuration, the enzyme provides a catalytic acid function to protonate the leaving group to facilitate its departure with the substrate carbonyl oxygen playing the role of nucleophile to generate a bicyclic "oxazoline" intermediate (which subsequently breaks down following the microscopic reverse ''via'' hydrolysis or occasionally transglycosylation). Such a mechanism has a number of facets, one of which is its potential inhibition using thiazolines <cite>Macdonald</cite>.<br />
<br />
<br />
== Catalytic Residues ==<br />
The catalytically active GH18 enzymes use a double displacement reaction mechanism with "neighbouring group participation". Hence there is a catalytic acid residue (glutamate in family GH18, but often also Asp in other families using this mechanism) and in all families apart from GH[[Glycoside Hydrolase Family 85|85]] (where this residue is an amide), a second carboxylate (here Asp) acts to deprotonate the N-acetamido nitrogen during oxazoline formation/breakdown. In family GH18 the two catalytic carboxylates are found in an D-X-G motif whereas in some families the carboxylates may be adjacent such as the DD motif in family GH84 (for example see <cite>He2010</cite>).<br />
<br />
<br />
== Three-dimensional structures ==<br />
Although these enzymes are frequently multi-modular, the catalytic domains are &alpha; / &beta; barrels <cite>Perrakis,ATVA</cite>.<br />
<br />
Work on the conformational itinerary of catalysis which is extremely similar to other retaining enzymes active on ''gluco''-configured substrates, was provided by the van Aalten group <cite>Daan2001</cite> in 2001 through the trapping of a distorted Michaelis complex in <sup>1,4</sup>B conformation and thus extremely similar to the <sup>1</sup>S<sub>3</sub> skew boats oberserved in GH[[Glycoside Hydrolase Family 5|5]] <cite>Davies1998</cite> for example or the <sup>4</sup>E conformation originally seen for a "neighboring group" enzyme in GH[[Glycoside Hydrolase Family 20|20]] and the approximate <sup>1,4</sup>B conformation recently observed in the GH84 O-GlcNAcase<cite>He2010</cite>. Fungal GH18 enzymes are considered as possible therapeutic targets and a number of programmes are probing this area (for example <cite>Housten2002</cite>.<br />
<br />
One unusual feauture of GH18 are the latge numbers of sequences that encode catalytically-inactive proteins that function as enzyme inhibitors or lectins. '''SOMEONE ELSE WRITE THIS?'''<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: Sometimes '''incorrectly''' reported as inverting, this family performs catalysis with '''retention''' of anomeric configuration as first shown on the ''Bacillus ciculans'' enzyme <cite>Armand1994</cite>.<br />
;First catalytic nucleophile identification: This family is one of many that uses neighbouring group participation for catalysis with the N-acetyl carbonyl group acting as the nucleophile; first proposed (I believe) for this family in <cite>AVTA2</cite>.<br />
;First general acid/base residue identification: On the basis of 3-D structure <cite>Perrakis</cite>.<br />
;First 3-D structure: The first two 3-D structures for GH18 members were the ''Serratia marcescens'' chitinase A and the plant defence protein hevamine published "back-to-back" in ''Structure'' in 1994 <cite>Perrakis,ATVA</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Perrakis pmid=7704527<br />
#ATVA1 pmid=7704528<br />
#AVTA2 pmid=7495789 <br />
#Armand1994 pmid=8168626<br />
#Koshland1953<br />
#Armand1997 pmid=9396742<br />
#Housten2002 pmid=12093900<br />
#Tews1996 pmid=8673609<br />
#Daan2001 pmid=11481469<br />
#Macdonald pmid=20209544<br />
#He2010 pmid=20067256<br />
#Davies1998 pmid=9718293<br />
<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH018]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_18&diff=5806Glycoside Hydrolase Family 182010-10-06T15:52:08Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Gideon Davies^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH18'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known (acid/neighbouring group)<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH18.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
GH18 is unusual in having both catalytically active chitinase (EC 3.2.1.14) and endo-β-N-acetylglucosaminidases (EC 3.2.1.96) but there are also sub-families of non-hydrolytic proteins that function as carbohydrate binding modules / "lectins" or as xylanase inhibitors.<br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
GH18 enzymes belong to a growing group of enzymes (now including GH families [[Glycoside Hydrolase Family 18|18]], [[Glycoside Hydrolase Family 20|20]],[[Glycoside Hydrolase Family 25|25]], [[Glycoside Hydrolase Family 56|56]], [[Glycoside Hydrolase Family 84|84]], and [[Glycoside Hydrolase Family 85|85]]) that perform a double-displacement reaction but instead of the more common enzyme-derived nucleophile they utlize the N-acetamido carbonyl oxygen in what is termed "neighbouring group participation" / "substrate participation" or "anchimeric assistance". Figures showing such a mechanism date back to Koshland's 1953 review <cite>Koshland1953</cite>, indeed they frequent the chemical literature of participating groups long before that, but it is primarily through the work on GH18 <cite>AVTA2</cite> and soon after GH20 <cite>Tews1996,Armand1997</cite> that such a mechanism became well established. In such a mechanism, which occurs with (net) retention of anomeric configuration, the enzyme provides a catalytic acid function to protonate the leaving group to facilitate its departure with the substrate carbonyl oxygen playing the role of nucleophile to generate a bicyclic "oxazoline" intermediate (which subsequently breaks down following the microscopic reverse ''via'' hydrolysis or occasionally transglycosylation). Such a mechanism has a number of facets, one of which is its potential inhibition using thiazolines <cite>Macdonald</cite>.<br />
<br />
<br />
== Catalytic Residues ==<br />
The catalytically active GH18 enzymes use a double displacement reaction mechanism with "neighbouring group participation". Hence there is a catalytic acid residue (glutamate in family GH18, but often also Asp in other families using this mechanism) and in all families apart from GH[[Glycoside Hydrolase Family 85|85]] (where this residue is an amide), a second carboxylate (here Asp) acts to deprotonate the N-acetamido nitrogen during oxazoline formation/breakdown. In family GH18 the two catalytic carboxylates are found in an D-X-G motif whereas in some families the carboxylates may be adjacent such as the DD motif in family GH84 (for example see <cite>He2010</cite>).<br />
<br />
<br />
== Three-dimensional structures ==<br />
Although these enzymes are frequently multi-modular, the catalytic domains are &alpha; / &beta; barrels <cite>Perrakis,ATVA</cite>.<br />
<br />
Work on the conformational itinerary of catalysis which is extremely similar to other retaining enzymes active on ''gluco''-configured substrates, was provided by the van Aalten group <cite>Daan2001</cite> in 2001 through the trapoping of a distorted Michaleis complex in <sup>1,4</sup>B conformation and thus extremely similar to the <sup>1</sup>S<sub>3</sub> skew boats oberserved in GH[[Glycoside Hydrolase Family 5|5]] for example or the <sup>4</sup>E conformation originally seen for a "neighboring group" enzyme in GH[[Glycoside Hydrolase Family 20|20]] and the approximate <sup>1,4</sup>B conformation recently observed in the GH84 O-GlcNAcase<cite>He2010</cite>. Fungal GH18 enzymes are considered as possible therapeutic targets and a number of programmes are probing this area (for example <cite>Housten2002</cite>.<br />
<br />
One unusual feauture of GH18 are the latge numbers of sequences that encode catalytically-inactive proteins that function as enzyme inhibitors or lectins. '''SOMEONE ELSE WRITE THIS?'''<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: Sometimes '''incorrectly''' reported as inverting, this family performs catalysis with '''retention''' of anomeric configuration as first shown on the ''Bacillus ciculans'' enzyme <cite>Armand1994</cite>.<br />
;First catalytic nucleophile identification: This family is one of many that uses neighbouring group participation for catalysis with the N-acetyl carbonyl group acting as the nucleophile; first proposed (I believe) for this family in <cite>AVTA2</cite>.<br />
;First general acid/base residue identification: On the basis of 3-D structure <cite>Perrakis</cite>.<br />
;First 3-D structure: The first two 3-D structures for GH18 members were the ''Serratia marcescens'' chitinase A and the plant defence protein hevamine published "back-to-back" in ''Structure'' in 1994 <cite>Perrakis,ATVA</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Perrakis pmid=7704527<br />
#ATVA1 pmid=7704528<br />
#AVTA2 pmid=7495789 <br />
#Armand1994 pmid=8168626<br />
#Koshland1953<br />
#Armand1997 pmid=9396742<br />
#Housten2002 pmid=12093900<br />
#Tews1996 pmid=8673609<br />
#Daan2001 pmid=11481469<br />
#Macdonald pmid=20209544<br />
#He2010 pmid=20067256<br />
<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH018]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_18&diff=5805Glycoside Hydrolase Family 182010-10-06T15:51:01Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Gideon Davies^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH18'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known (acid/neighbouring group)<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH18.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
GH18 is unusual in having both catalytically active chitinase (EC 3.2.1.14) and endo-β-N-acetylglucosaminidases (EC 3.2.1.96) but there are also sub-families of non-hydrolytic proteins that function as carbohydrate binding modules / "lectins" or as xylanase inhibitors.<br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
GH18 enzymes belong to a growing group of enzymes (now including GH families [[Glycoside Hydrolase Family 18|18]], [[Glycoside Hydrolase Family 20|20]],[[Glycoside Hydrolase Family 25|25]], [[Glycoside Hydrolase Family 56|56]], [[Glycoside Hydrolase Family 84|84]], and [[Glycoside Hydrolase Family 85|85]]) that perform a double-displacement reaction but instead of the more common enzyme-derived nucleophile they utlize the N-acetamido carbonyl oxygen in what is termed "neighbouring group participation" / "substrate participation" or "anchimeric assistance". Figures showing such a mechanism date back to Koshland's 1953 review <cite>Koshland1953</cite>, indeed they frequent the chemical literature of participating groups long before that, but it is primarily through the work on GH18 <cite>AVTA2</cite> and soon after GH20 <cite>Tews1996,Armand1997</cite> that such a mechanism became well established. In such a mechanism, which occurs with (net) retention of anomeric configuration, the enzyme provides a catalytic acid function to protonate the leaving group to facilitate its departure with the substrate carbonyl oxygen playing the role of nucleophile to generate a bicyclic "oxazoline" intermediate (which subsequently breaks down following the microscopic reverse ''via'' hydrolysis or occasionally transglycosylation). Such a mechanism has a number of facets, one of which is its potential inhibition using thiazolines <cite>Macdonald</cite>.<br />
<br />
<br />
== Catalytic Residues ==<br />
The catalytically active GH18 enzymes use a double displacement reaction mechanism with "neighbouring group participation". Hence there is a catalytic acid residue (glutamate in family GH18, but often also Asp in other families using this mechanism) and in all families apart from GH[[Glycoside Hydrolase Family 85|85]] (where this residue is an amide), a second carboxylate (here Asp) acts to deprotonate the N-acetamido nitrogen during oxazoline formation/breakdown. In family GH18 the two catalytic carboxylates are found in an D-X-G motif whereas in some families the carboxylates may be adjacent such as the DD motif in family GH84 (for example see <cite>He2010</cite>).<br />
<br />
<br />
== Three-dimensional structures ==<br />
Although these enzymes are frequently multi-modular, the catalytic domains are &alpha; / &beta; barrels <cite>Perrakis,ATVA</cite>.<br />
<br />
Work on the conformational itinerary of catalysis which is extremely similar to other retaining enzymes active on ''gluco''-configured substrates, was provided by the van Aalten group <cite>Daan2001</cite> in 2001 through the trapoping of a distorted Michaleis complex in <sup>1,4</sup>B conformation and thus extremely similar to the <sup>1</sup>S<sub>3</sub> skew boats oberserved in GH[[Glycoside Hydrolase Family 5|5]] for example or the <sup>4</sup>E conformation originally seen for a "neighboring group" enzyme in GH[[Glycoside Hydrolase Family 20|20]] and the approximate <sup>1,4</sup>B conformation recently observed in the GH84 O-GlcNAcase<cite>He2010</cite>. Fungal GH18 enzymes are considered as possible therapeutic targets and a number of programmes are probing this area (for example <cite>Housten2002</cite>.<br />
<br />
One unusual feauture of GH18 are the latge numbers of sequences that encode catalytically-inactive proteins that function as enzyme inhibitors or lectins. '''SOMEONE ELSE WRITE THIS?'''<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: Sometimes '''incorrectly''' reported as inverting, this family performs catalysis with '''retention''' of anomeric configuration as first shown on the ''Bacillus ciculans'' enzyme <cite>Armand1994</cite>.<br />
;First catalytic nucleophile identification: This family is one of many that uses neighbouring group participation for catalysis with the N-acetyl carbonyl group acting as the nucleophile; first proposed (I believe) for this family in <cite>AVTA2</cite>.<br />
;First general acid/base residue identification: On the basis of 3-D structure <cite>Perrakis</cite>.<br />
;First 3-D structure: The first two 3-D structures for GH18 members were the ''Serratia marcescens'' chitinase A and the plant defence protein hevamine published "back-to-back" in ''Structure'' in 1994 <cite>Perrakis,ATVA</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Perrakis pmid=7704527<br />
#ATVA1 pmid=7704528<br />
#AVTA2 pmid=7495789 <br />
#Armand1994 pmid=8168626<br />
#Koshland1953<br />
#Armand1997 pmid=9396742<br />
#Housten2002 pmid=12093900<br />
#Tews1996 pmid=8673609<br />
#Daan2001 pmid=11481469<br />
#Macdonald pmid=20209544<br />
#He2010 pmid=20067256<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH018]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_18&diff=5804Glycoside Hydrolase Family 182010-10-06T15:49:38Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Gideon Davies^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH18'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known (acid/neighbouring group)<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH18.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
GH18 is unusual in having both catalytically active chitinase (EC 3.2.1.14) and endo-β-N-acetylglucosaminidases (EC 3.2.1.96) but there are also sub-families of non-hydrolytic proteins that function as carbohydrate binding modules / "lectins" or as xylanase inhibitors.<br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
GH18 enzymes belong to a growing group of enzymes (now including [[Glycoside Hydrolase Family 18|18]], [[Glycoside Hydrolase Family 20|20]],[[Glycoside Hydrolase Family 25|25]], [[Glycoside Hydrolase Family 56|56]], [[Glycoside Hydrolase Family 84|84]], and [[Glycoside Hydrolase Family 85|85]]) that perform a double-displacement reaction but instead of the more common enzyme-derived nucleophile they utlize the N-acetamido carbonyl oxygen in what is termed "neighbouring group participation" / "substrate participation" or "anchimeric assistance". Figures showing such a mechanism date back to Koshland's 1953 review <cite>Koshland1953</cite>, indeed they frequent the chemical literature of participating groups long before that, but it is primarily through the work on GH18 <cite>AVTA2</cite> and soon after GH20 <cite>Tews1996,Armand1997</cite> that such a mechanism became well established. In such a mechanism, which occurs with (net) retention of anomeric configuration, the enzyme provides a catalytic acid function to protonate the leaving group to facilitate its departure with the substrate carbonyl oxygen playing the role of nucleophile to generate a bicyclic "oxazoline" intermediate (which subsequently breaks down following the microscopic reverse ''via'' hydrolysis or occasionally transglycosylation). Such a mechanism has a number of facets, one of which is its potential inhibition using thiazolines <cite>Macdonald</cite>.<br />
<br />
<br />
== Catalytic Residues ==<br />
The catalytically active GH18 enzymes use a double displacement reaction mechanism with "neighbouring group participation". Hence there is a catalytic acid residue (glutamate in family GH18, but often also Asp in other families using this mechanism) and in all families apart from [[Glycoside Hydrolase Family 85|85]] (where this residue is an amide), a second carboxylate (here Asp) acts to deprotonate the N-acetamido nitrogen during oxazoline formation/breakdown. In family GH18 the two catalytic carboxylates are found in an D-X-G motif whereas in some families the carboxylates may be adjacent such as the DD motif in family GH84 (for example see <cite>He2010</cite>).<br />
<br />
<br />
== Three-dimensional structures ==<br />
Although these enzymes are frequently multi-modular, the catalytic domains are &alpha; / &beta; barrels <cite>Perrakis,ATVA</cite>.<br />
<br />
Work on the conformational itinerary of catalysis which is extremely similar to other retaining enzymes active on ''gluco''-configured substrates, was provided by the van Aalten group <cite>Daan2001</cite> in 2001 through the trapoping of a distorted Michaleis complex in <sup>1,4</sup>B conformation and thus extremely similar to the <sup>1</sup>S<sub>3</sub> skew boats oberserved in [[Glycoside Hydrolase Family 5|5]] for example or the <sup>4</sup>E conformation originally seen for a "neighboring group" enzyme in [[Glycoside Hydrolase Family 20|20]] and the approximate <sup>1,4</sup>B conformation recently observed in the GH84 O-GlcNAcase<cite>He2010</cite>. Fungal GH18 enzymes are considered as possible therapeutic targets and a number of programmes are probing this area (for example <cite>Housten2002</cite>.<br />
<br />
One unusual feauture of GH18 are the latge numbers of sequences that encode catalytically-inactive proteins that function as enzyme inhibitors or lectins. '''SOMEONE ELSE WRITE THIS?'''<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: Sometimes '''incorrectly''' reported as inverting, this family performs catalysis with '''retention''' of anomeric configuration as first shown on the ''Bacillus ciculans'' enzyme <cite>Armand1994</cite>.<br />
;First catalytic nucleophile identification: This family is one of many that uses neighbouring group participation for catalysis with the N-acetyl carbonyl group acting as the nucleophile; first proposed (I believe) for this family in <cite>AVTA2</cite>.<br />
;First general acid/base residue identification: On the basis of 3-D structure <cite>Perrakis</cite>.<br />
;First 3-D structure: The first two 3-D structures for GH18 members were the ''Serratia marcescens'' chitinase A and the plant defence protein hevamine published "back-to-back" in ''Structure'' in 1994 <cite>Perrakis,ATVA</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Perrakis pmid=7704527<br />
#ATVA1 pmid=7704528<br />
#AVTA2 pmid=7495789 <br />
#Armand1994 pmid=8168626<br />
#Koshland1953<br />
#Armand1997 pmid=9396742<br />
#Housten2002 pmid=12093900<br />
#Tews1996 pmid=8673609<br />
#Daan2001 pmid=11481469<br />
#Macdonald pmid=20209544<br />
#He2010 pmid=20067256<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH018]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_18&diff=5803Glycoside Hydrolase Family 182010-10-06T15:44:36Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Gideon Davies^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH18'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known (acid/neighbouring group)<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH18.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
GH18 is unusual in having both catalytically active chitinase (EC 3.2.1.14) and endo-β-N-acetylglucosaminidases (EC 3.2.1.96) but there are also sub-families of non-hydrolytic proteins that function as carbohydrate binding modules / "lectins" or as xylanase inhibitors.<br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
GH18 enzymes belong to a growing group of enzymes (now including [[Glycoside Hydrolase Family 18|18]], [[Glycoside Hydrolase Family 20|20]],[[Glycoside Hydrolase Family 25|25]], [[Glycoside Hydrolase Family 56|56]], [[Glycoside Hydrolase Family 84|84]], and [[Glycoside Hydrolase Family 85|85]]) that perform a double-displacement reaction but instead of the more common enzyme-derived nucleophile they utlize the N-acetamido carbonyl oxygen in what is termed "neighbouring group participation" / "substrate participation" or "anchimeric assistance". Figures showing such a mechanism date back to Koshland's 1953 review <cite>Koshland1953</cite>, indeed they frequent the chemical literature of participating groups long before that, but it is primarily through the work on GH18 <cite>AVTA2</cite> and soon after GH20 <cite>Tews1996,Armand1997</cite> that such a mechanism became well established. In such a mechanism, which occurs with (net) retention of anomeric configuration, the enzyme provides a catalytic acid function to protonate the leaving group to facilitate its departure with the substrate carbonyl oxygen playing the role of nucleophile to generate a bicyclic "oxazoline" intermediate (which subsequently breaks down following the microscopic reverse ''via'' hydrolysis or occasionally transglycosylation). Such a mechanism has a number of facets, one of which is its potential inhibition using thiazolines <cite>Macdonald</cite>.<br />
<br />
<br />
== Catalytic Residues ==<br />
The catalytically active GH18 enzymes use a double displacement reaction mechanism with "neighbouring group participation". Hence there is a catalytic acid residue (glutamate in family GH18, but often also Asp in other families using this mechanism) and in all families apart from [[Glycoside Hydrolase Family 85|85]] (where this residue is an amide), a second carboxylate (here Asp) acts to deprotonate the N-acetamido nitrogen during oxazoline formation/breakdown. In family GH18 the two catalytic carboxylates are found in an D-X-G motif whereas in some families the carboxylates may be adjacent such as the DD motif in family GH84 (for example see <cite>He2010</cite>).<br />
<br />
<br />
== Three-dimensional structures ==<br />
Although these enzymes are frequently multi-modular, the catalytic domains are @alpha; / &beta; barrels <cite>Perrakis,ATVA</cite>.<br />
<br />
Work on the conformational itinerary of catalysis which is extremely similar to other retaining enzymes active on ''gluco''-configured substrates, was provided by the van Aalten group <cite>Daan2001</cite> in 2001 through the trapoping of a distorted Michaleis complex in 1,4B conformation and thus extremely similar to the 1S3 skew boats oberserved in [[Glycoside Hydrolase Family 5|5]] for example or the 4E conformation originally seen for a neighboring group enzyme in [[Glycoside Hydrolase Family 20|20]].<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: Sometimes '''incorrectly''' reported as inverting, this family performs catalysis with '''retention''' of anomeric configuration as first shown on the ''Bacillus ciculans'' enzyme <cite>Armand1994</cite>.<br />
;First catalytic nucleophile identification: This family is one of many that uses neighbouring group participation for catalysis with the N-acetyl carbonyl group acting as the nucleophile; first proposed (I believe) for this family in <cite>AVTA2</cite>.<br />
;First general acid/base residue identification: On the basis of 3-D structure <cite>Perrakis</cite>.<br />
;First 3-D structure: The first two 3-D structures for GH18 members were the ''Serratia marcescens'' chitinase A and the plant defence protein hevamine published "back-to-back" in ''Structure'' in 1994 <cite>Perrakis,ATVA</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Perrakis pmid=7704527<br />
#ATVA1 pmid=7704528<br />
#AVTA2 pmid=7495789 <br />
#Armand1994 pmid=8168626<br />
#Koshland1953<br />
#Armand1997 pmid=9396742<br />
#Housten2002 pmid=12093900<br />
#Tews1996 pmid=8673609<br />
#Daan2001 pmid=11481469<br />
#Macdonald pmid=20209544<br />
#He2010 pmid=20067256<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH018]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_18&diff=5802Glycoside Hydrolase Family 182010-10-06T15:37:23Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Gideon Davies^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH18'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known (acid/neighbouring group)<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH18.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
GH18 is unusual in having both catalytically active chitinase (EC 3.2.1.14) and endo-β-N-acetylglucosaminidases (EC 3.2.1.96) but there are also sub-families of non-hydrolytic proteins that function as carbohydrate binding modules / "lectins" or as xylanase inhibitors.<br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
GH18 enzymes belong to a growing group of enzymes (now including [[Glycoside Hydrolase Family 18|18]], [[Glycoside Hydrolase Family 20|20]],[[Glycoside Hydrolase Family 25|25]], [[Glycoside Hydrolase Family 56|56]], [[Glycoside Hydrolase Family 84|84]], and [[Glycoside Hydrolase Family 85|85]]) that perform a double-displacement reaction but instead of the more common enzyme-derived nucleophile they utlize the N-acetamido carbonyl oxygen in what is termed "neighbouring group participation" / "substrate participation" or "anchimeric assistance". Figures showing such a mechanism date back to Koshland's 1953 review, indeed they frequent the chemical literature of participating groups long before that, but it is primarily through the work on GH18 <cite>AVTA2</cite> and simultaneously GH20 <cite>Tews1996,Armand1997</cite> that such a mechanism became well established. In such a mechanism, which occurs with (net) retention of anomeric configuration, the enzyme provides a catalytic acid function to protonate the leaving group to facilitate its departure with the substrate carbonyl oxygen playing the role of nucleophile to generate a bicyclic "oxazoline" intermediate (which subsequently breaks down following the microscopic reverse ''via'' hydrolysis or occasionally transglycosylation). Such a mechanism has a number of facets one of which is its potential inhibition using thiazolines <cite>Macdonald</cite>.<br />
<br />
<br />
== Catalytic Residues ==<br />
The catalytically active GH18 enzymes use a double displacement reaction mechanism with "neighbouring group participation". Hence there is a catalytic acid residue (glutamate in family GH18, but often also Asp in other families using this mechanism) and in all familyes apart from [[Glycoside Hydrolase Family 85|85]] (where this residue is an amide), a second carboxylate (here Asp) acts to deprotonate the N-acetamido nitrogen during oxazoline formation/breakdown. In family Gh18 the two catalytic carboxylates are found in an D-X-G motif whereas in some families the carboxylates may be adjacent such as the DD motif in family GH84 (for example see <cite>He2010</cite>.<br />
<br />
<br />
== Three-dimensional structures ==<br />
Content is to be added here.<br />
<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: Sometimes '''incorrectly''' reported as inverting, this family performs catalysis with '''retention''' of anomeric configuration as first shown on the ''Bacillus ciculans'' enzyme <cite>Armand1994</cite>.<br />
;First catalytic nucleophile identification: This family is one of many that uses neighbouring group participation for catalysis with the N-acetyl carbonyl group acting as the nucleophile; first proposed (I believe) for this family in <cite>AVTA2</cite>.<br />
;First general acid/base residue identification: On the basis of 3-D structure <cite>Perrakis</cite>.<br />
;First 3-D structure: The first two 3-D structures for GH18 members were the ''Serratia marcescens'' chitinase A and the plant defence protein hevamine published "back-to-back" in ''Structure'' in 1994 <cite>Perrakis,ATVA</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Perrakis pmid=7704527<br />
#ATVA1 pmid=7704528<br />
#AVTA2 pmid=7495789 <br />
#Armand1994 pmid=8168626<br />
#Koshland1953<br />
#Armand1997 pmid=9396742<br />
#Housten2002 pmid=12093900<br />
#Tews1996 pmid=8673609<br />
#Daan2001 pmid=11481469<br />
#Macdonald pmid=20209544<br />
#He2010 pmid=20067256<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH018]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_18&diff=5801Glycoside Hydrolase Family 182010-10-06T15:29:03Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Gideon Davies^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH18'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known (acid/neighbouring group)<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH18.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
GH18 is unusual in having both catalytically active chitinase (EC 3.2.1.14) and endo-β-N-acetylglucosaminidases (EC 3.2.1.96) but there are also sub-families of non-hydrolytic proteins that function as carbohydrate binding modules / "lectins" or as xylanase inhibitors.<br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
GH18 enzymes belong to a growing group of enzymes (now including [[Glycoside Hydrolase Family 18|18]], [[Glycoside Hydrolase Family 20|20]],[[Glycoside Hydrolase Family 25|25]], [[Glycoside Hydrolase Family 56|56]], [[Glycoside Hydrolase Family 84|84]], and [[Glycoside Hydrolase Family 85|85]]) that perform a double-displacement reaction but instead of the more common enzyme-derived nucleophile they utlize the N-acetamido carbonyl oxygen in what is termed "neighbouring group participation" / "substrate participation" or "anchimeric assistance". Figures showing such a mechanism date back to Koshland's 1953 review, indeed they frequent the chemical literature of participating groups long before that, but it is primarily through the work on GH18 and simultaneously GH20 that such a mechanism became well established. In such a mechanism, which occurs with (net) retention of anomeric configuration, the enzyme provides a catalytic acid function to protonate the leaving group to facilitate its departure with the substrate carbonyl oxygen playing the role of nucleophile to generate a bicyclic "oxazoline" intermediate (which subsequently breaks down following the microscopic reverse ''via'' hydrolysis or occasionally transglycosylation).<br />
<br />
<br />
== Catalytic Residues ==<br />
The catalytically active GH18 enzymes use a double displacement reaction mechanism with "neighbouring group participation". <br />
<br />
<br />
== Three-dimensional structures ==<br />
Content is to be added here.<br />
<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: Sometimes '''incorrectly''' reported as inverting, this family performs catalysis with '''retention''' of anomeric configuration as first shown on the ''Bacillus ciculans'' enzyme <cite>Armand1994</cite>.<br />
;First catalytic nucleophile identification: This family is one of many that uses neighbouring group participation for catalysis with the N-acetyl carbonyl group acting as the nucleophile; first proposed (I believe) for this family in <cite>AVTA2</cite>.<br />
;First general acid/base residue identification: On the basis of 3-D structure <cite>Perrakis</cite>.<br />
;First 3-D structure: The first two 3-D structures for GH18 members were the ''Serratia marcescens'' chitinase A and the plant defence protein hevamine published "back-to-back" in ''Structure'' in 1994 <cite>Perrakis,ATVA</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Perrakis pmid=7704527<br />
#ATVA1 pmid=7704528<br />
#AVTA2 pmid=7495789 <br />
#Armand1994 pmid=8168626<br />
#Koshland1953<br />
#Armand1997 pmid=9396742<br />
#Housten2002 pmid=12093900<br />
#Tews1996 pmid=8673609<br />
#Daan2001 pmid=11481469<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH018]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_18&diff=5800Glycoside Hydrolase Family 182010-10-06T15:23:15Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Gideon Davies^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH18'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known (acid/neighbouring group)<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH18.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
GH18 is unusual in having both catalytically active chitinase (EC 3.2.1.14) and endo-β-N-acetylglucosaminidases (EC 3.2.1.96) but there are also sub-families of non-hydrolytic proteins that function as carbohydrate binding modules / "lectins" or as xylanase inhibitors.<br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
GH18 enzymes belong to a growing group of enzymes (now including GH18, 20, 25, 56, 84 and 85) that perform a double-displacement reaction but instead of the more common enzyme-derived nucleophile they utlize the N-acetamido carbonyl oxygen in what is termed "neighbouring group participation" / "substrate participation" or "anchimeric assistance". Figures showing such a mechanism date back to Koshland's 1953 review, indeed they frequent the chemical literature of participating groups long before that, but it is primarily through the work on GH18 and simultaneously GH20 that such a mechanism became well established. In such a mechanism, which occurs with (net) retention of anomeric configuration, the enzyme provides a catalytic acid function to protonate the leaving group to facilitate its departure with the substrate carbonyl oxygen playing the role of nucleophile to generate a bicyclic "oxazoline" intermediate (which subsequently breaks down following the microscopic reverse ''via'' hydrolysis or occasionally transglycosylation).<br />
<br />
<br />
== Catalytic Residues ==<br />
The catalytically active GH18 enzymes use a double displacement reaction mechanism with "neighbouring group participation". <br />
<br />
<br />
== Three-dimensional structures ==<br />
Content is to be added here.<br />
<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: Sometimes '''incorrectly''' reported as inverting, this family performs catalysis with '''retention''' of anomeric configuration as first shown on the ''Bacillus ciculans'' enzyme <cite>Armand1994</cite>.<br />
;First catalytic nucleophile identification: This family is one of many that uses neighbouring group participation for catalysis with the N-acetyl carbonyl group acting as the nucleophile; first proposed (I believe) for this family in <cite>AVTA2</cite>.<br />
;First general acid/base residue identification: On the basis of 3-D structure <cite>Perrakis</cite>.<br />
;First 3-D structure: The first two 3-D structures for GH18 members were the ''Serratia marcescens'' chitinase A and the plant defence protein hevamine published "back-to-back" in ''Structure'' in 1994 <cite>Perrakis,ATVA</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Perrakis pmid=7704527<br />
#ATVA1 pmid=7704528<br />
#AVTA2 pmid=7495789 <br />
#Armand1994 pmid=8168626<br />
#Koshland1953<br />
#Armand<br />
#<br />
#Tews2006<br />
#Daan<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH018]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_5&diff=5799Glycoside Hydrolase Family 52010-10-06T14:55:46Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: ^^^Gideon Davies^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH5'''<br />
|-<br />
|'''Clan''' <br />
|GH-A<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH5.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
GH5 is one of the largest of all CAZy [[glycoside hydrolase]] families. A variety of specificties are annotated to this family notably endoglucanase (cellulase) and endomannanase as well as exoglucanases, exomannanases and β-glucosidase and β-mannosidase. Other activities include 1,6 galactanase, 1,3 mannanase, 1,4 xylanase, endoglycoceramidase, as well as high specificity xyloglucanases. Family GH5 enzymes are found widely distributed across Archae, bacteria and eukaryotes, notably fungi and plants. There are no known human enzymes in GH5. <br />
<br />
<br />
== Kinetics and Mechanism ==<br />
Family GH5 enzymes are retaining enzymes, as first shown by NMR <cite>Barras1992</cite> and follow a [[classical Koshland double-displacement mechanism]].<br />
<br />
== Catalytic Residues ==<br />
GH5 enzymes use the [[classical Koshland double-displacement mechanism]] and the two catalytic residues are known to be glutamates found at the C-terminal ends of β-strands 4 (acid/base) and 7 (nucleophile) <cite>Henrissat1996,Jenkins1995</cite>.<br />
<br />
<br />
== Three-dimensional structures ==<br />
Three-dimensional structures are available for a very large number of Family GH5 enzymes, the first solved being that of the ''Clostridium thermocellum'' endoglucanase CelC <cite>Alzari1995</cite>. As members of Clan GH-A they have a classical (α/β)<sub>8</sub> TIM barrel fold with the two key active site glutamic acids being approximately 200 residues apart in sequence and located at the C-terminal ends of β-strands 4 (acid/base) and 7 (nucleophile) <cite>Henrissat1996,Jenkins1995</cite>.<br />
<br />
With so many 3D structures in this family, covering many specificities it is clearly hard to pick out notable structural papers. The ''Bacillus agaradhaerens'' Cel5A has been extensively studied, notably in the trapping of enzymatic snapshots along the reaction coordinate <cite>Davies1998</cite> but also as a testbed for glycosidase inhibitor design as crystals often diffract to atomic resolution (for example <cite>Varrot2003</cite>). The reaction coordinate work on the endoglucanases (thus working on ''gluco''-configured substrates) shows that the substrate binds in <sup>1</sup>S<sub>3</sub> conformation with the covalent intermediate in <sup>4</sup>C<sub>1</sub> chair conformation implying catalysis via a <sup>4</sup>H<sub>3</sub> half-chair (near) transition-state. mannanases from this family likely use a different itinerary more akin to that used by damily GH26 mannnanases <cite>Ducros</cite> and family GH2 &beta;-mannosidases <cite>Tailford</cite>.<br />
<br />
The Rhodococcal endoglycoceramidase II (EGC) in this family has found application in the chemoenzymatic synthesis of ceramide derivatives <cite>Caines2007</cite>. In 2007 the first 3-D structure of a highly specific GH5 xyloglucanase was reported <cite>Gloster2007</cite>; this enzyme makes kinetically productive interactions with both xylose and galactose substituents, as reflected in both a high specific activity on xyloglucan and the kinetics of a series of aryl glycosides.<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: The curator believes this to be the <sup>1</sup>H NMR stereochemical determination for EGZ from ''Erwinia chrysanthemi'' <cite>Barras1992</cite>. GH5 enzymes were also in the comprehensive Gebler study <cite>Gebler1992</cite>.<br />
;First catalytic nucleophile identification: Trapped using the classical Withers 2-fluoro method, here with 2',4'-dinitrophenyl-2-deoxy-2-fluoro-beta-D-cellobioside, reported in Wang and Withers in 1993 <cite>Wang1993</cite>.<br />
<br />
;First general acid/base residue identification: Several mutagenesis papers has alluded to the importance of a conserved glutamate- one that both Dominguez <cite>Dominguez1995</cite> and Ducros <cite>Ducros1995</cite> correctly postulated as the catalytic acid when the 3-D structures were determined. <br />
<br />
;First 3-D structure: The first 3D structures in family GH5 was an endoglucanase (cellulase) from ''Clostridium thermocellum'' reported by the Alzari in 1995 (in a paper which also reported a family GH10 xylanase structure and the similarities between them) <cite>Dominguez1995</cite>. Subsequently, Ducros and colleagues reported the ''Clostridium cellulolyticum'' Cel5A also in 1995 <cite>Ducros1995</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Jenkins1995 pmid=7729513 <br />
#Henrissat1996 pmid=8643635 <br />
#Caines2007 pmid=17329247<br />
#Barras1992 pmid=1563515<br />
#Wang1993 pmid=8100226<br />
#Gebler1992 pmid=1618761 <br />
#Dominguez1995 pmid=7664125<br />
#Ducros1995 pmid=8535787<br />
#Davies1998 pmid=9718293<br />
#Varrot2003 pmid=12812472<br />
#Gloster2007 pmid=17376777<br />
#Ducros pmid=12203498<br />
#Tailford pmid=18408714<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH005]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_5&diff=5798Glycoside Hydrolase Family 52010-10-06T14:55:09Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: ^^^Gideon Davies^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH5'''<br />
|-<br />
|'''Clan''' <br />
|GH-A<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH5.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
GH5 is one of the largest of all CAZy [[glycoside hydrolase]] families. A variety of specificties are annotated to this family notably endoglucanase (cellulase) and endomannanase as well as exoglucanases, exomannanases and β-glucosidase and β-mannosidase. Other activities include 1,6 galactanase, 1,3 mannanase, 1,4 xylanase, endoglycoceramidase, as well as high specificity xyloglucanases. Family GH5 enzymes are found widely distributed across Archae, bacteria and eukaryotes, notably fungi and plants. There are no known human enzymes in GH5. <br />
<br />
<br />
== Kinetics and Mechanism ==<br />
Family GH5 enzymes are retaining enzymes, as first shown by NMR <cite>Barras1992</cite> and follow a [[classical Koshland double-displacement mechanism]].<br />
<br />
== Catalytic Residues ==<br />
GH5 enzymes use the [[classical Koshland double-displacement mechanism]] and the two catalytic residues are known to be glutamates found at the C-terminal ends of β-strands 4 (acid/base) and 7 (nucleophile) <cite>Henrissat1996,Jenkins1995</cite>.<br />
<br />
<br />
== Three-dimensional structures ==<br />
Three-dimensional structures are available for a very large number of Family GH5 enzymes, the first solved being that of the ''Clostridium thermocellum'' endoglucanase CelC <cite>Alzari1995</cite>. As members of Clan GH-A they have a classical (α/β)<sub>8</sub> TIM barrel fold with the two key active site glutamic acids being approximately 200 residues apart in sequence and located at the C-terminal ends of β-strands 4 (acid/base) and 7 (nucleophile) <cite>Henrissat1996,Jenkins1995</cite>.<br />
<br />
With so many 3D structures in this family, covering many specificities it is clearly hard to pick out notable structural papers. The ''Bacillus agaradhaerens'' Cel5A has been extensively studied, notably in the trapping of enzymatic snapshots along the reaction coordinate <cite>Davies1998</cite> but also as a testbed for glycosidase inhibitor design as crystals often diffract to atomic resolution (for example <cite>Varrot2003</cite>). The reaction coordinate work on the endoglucanases (thus working on ''gluco''-configured substrates) shows that the substrate binds in <sup>1</sup>S<sub>3</sub> conformation with tehe covalent intermediate in <sup>4</sup>C<sub>1</sub> chair conformation implying catalysis via a <sup>4</sup>H<sub>3</sub> half-chair (near) transition-state. mannanases from this family likely use a different itinerary more akin to that used by damily GH26 mannnases <cite>Ducros</cite> and family GH2 &beta;-mannosidases <cite>Tailford</cite>.<br />
<br />
The Rhodococcal endoglycoceramidase II (EGC) in this family has found application in the chemoenzymatic synthesis of ceramide derivatives <cite>Caines2007</cite>. In 2007 the first 3-D structure of a highly specific GH5 xyloglucanase was reported <cite>Gloster2007</cite>; this enzyme makes kinetically productive interactions with both xylose and galactose substituents, as reflected in both a high specific activity on xyloglucan and the kinetics of a series of aryl glycosides.<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: The curator believes this to be the <sup>1</sup>H NMR stereochemical determination for EGZ from ''Erwinia chrysanthemi'' <cite>Barras1992</cite>. GH5 enzymes were also in the comprehensive Gebler study <cite>Gebler1992</cite>.<br />
;First catalytic nucleophile identification: Trapped using the classical Withers 2-fluoro method, here with 2',4'-dinitrophenyl-2-deoxy-2-fluoro-beta-D-cellobioside, reported in Wang and Withers in 1993 <cite>Wang1993</cite>.<br />
<br />
;First general acid/base residue identification: Several mutagenesis papers has alluded to the importance of a conserved glutamate- one that both Dominguez <cite>Dominguez1995</cite> and Ducros <cite>Ducros1995</cite> correctly postulated as the catalytic acid when the 3-D structures were determined. <br />
<br />
;First 3-D structure: The first 3D structures in family GH5 was an endoglucanase (cellulase) from ''Clostridium thermocellum'' reported by the Alzari in 1995 (in a paper which also reported a family GH10 xylanase structure and the similarities between them) <cite>Dominguez1995</cite>. Subsequently, Ducros and colleagues reported the ''Clostridium cellulolyticum'' Cel5A also in 1995 <cite>Ducros1995</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Jenkins1995 pmid=7729513 <br />
#Henrissat1996 pmid=8643635 <br />
#Caines2007 pmid=17329247<br />
#Barras1992 pmid=1563515<br />
#Wang1993 pmid=8100226<br />
#Gebler1992 pmid=1618761 <br />
#Dominguez1995 pmid=7664125<br />
#Ducros1995 pmid=8535787<br />
#Davies1998 pmid=9718293<br />
#Varrot2003 pmid=12812472<br />
#Gloster2007 pmid=17376777<br />
#Ducros pmid=12203498<br />
#Tailford pmid=18408714<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH005]]</div>Gideon Davieshttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_5&diff=5797Glycoside Hydrolase Family 52010-10-06T14:54:24Z<p>Gideon Davies: </p>
<hr />
<div><!-- CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{CuratorApproved}}<br />
* [[Author]]: ^^^Gideon Davies^^^<br />
* [[Responsible Curator]]: ^^^Gideon Davies^^^<br />
----<br />
<br />
<!-- The data in the table below should be updated by the Author/Curator according to current information on the family --><br />
<div style="float:right"><br />
{| {{Prettytable}} <br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH5'''<br />
|-<br />
|'''Clan''' <br />
|GH-A<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH5.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
GH5 is one of the largest of all CAZy [[glycoside hydrolase]] families. A variety of specificties are annotated to this family notably endoglucanase (cellulase) and endomannanase as well as exoglucanases, exomannanases and β-glucosidase and β-mannosidase. Other activities include 1,6 galactanase, 1,3 mannanase, 1,4 xylanase, endoglycoceramidase, as well as high specificity xyloglucanases. Family GH5 enzymes are found widely distributed across Archae, bacteria and eukaryotes, notably fungi and plants. There are no known human enzymes in GH5. <br />
<br />
<br />
== Kinetics and Mechanism ==<br />
Family GH5 enzymes are retaining enzymes, as first shown by NMR <cite>Barras1992</cite> and follow a [[classical Koshland double-displacement mechanism]].<br />
<br />
== Catalytic Residues ==<br />
GH5 enzymes use the [[classical Koshland double-displacement mechanism]] and the two catalytic residues are known to be glutamates found at the C-terminal ends of β-strands 4 (acid/base) and 7 (nucleophile) <cite>Henrissat1996</cite><cite>Jenkins1995</cite>.<br />
<br />
<br />
== Three-dimensional structures ==<br />
Three-dimensional structures are available for a very large number of Family GH5 enzymes, the first solved being that of the ''Clostridium thermocellum'' endoglucanase CelC <cite>Alzari1995</cite>. As members of Clan GH-A they have a classical (α/β)<sub>8</sub> TIM barrel fold with the two key active site glutamic acids being approximately 200 residues apart in sequence and located at the C-terminal ends of β-strands 4 (acid/base) and 7 (nucleophile) <cite>Henrissat1996,Jenkins1995</cite>.<br />
<br />
With so many 3D structures in this family, covering many specificities it is clearly hard to pick out notable structural papers. The ''Bacillus agaradhaerens'' Cel5A has been extensively studied, notably in the trapping of enzymatic snapshots along the reaction coordinate <cite>Davies1998</cite> but also as a testbed for glycosidase inhibitor design as crystals often diffract to atomic resolution (for example <cite>Varrot2003</cite>). The reaction coordinate work on the endoglucanases (thus working on ''gluco''-configured substrates) shows that the substrate binds in <sup>1</sup>S<sub>3</sub> conformation with tehe covalent intermediate in <sup>4</sup>C<sub>1</sub> chair conformation implying catalysis via a <sup>4</sup>H<sub>3</sub> half-chair (near) transition-state. mannanases from this family likely use a different itinerary more akin to that used by damily GH26 mannnases <cite>Ducros</cite> and family GH2 &beta;-mannosidases <cite>Tailford</cite>.<br />
<br />
The Rhodococcal endoglycoceramidase II (EGC) in this family has found application in the chemoenzymatic synthesis of ceramide derivatives <cite>Caines2007</cite>. In 2007 the first 3-D structure of a highly specific GH5 xyloglucanase was reported <cite>Gloster2007</cite>; this enzyme makes kinetically productive interactions with both xylose and galactose substituents, as reflected in both a high specific activity on xyloglucan and the kinetics of a series of aryl glycosides.<br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination: The curator believes this to be the <sup>1</sup>H NMR stereochemical determination for EGZ from ''Erwinia chrysanthemi'' <cite>Barras1992</cite>. GH5 enzymes were also in the comprehensive Gebler study <cite>Gebler1992</cite>.<br />
;First catalytic nucleophile identification: Trapped using the classical Withers 2-fluoro method, here with 2',4'-dinitrophenyl-2-deoxy-2-fluoro-beta-D-cellobioside, reported in Wang and Withers in 1993 <cite>Wang1993</cite>.<br />
<br />
;First general acid/base residue identification: Several mutagenesis papers has alluded to the importance of a conserved glutamate- one that both Dominguez <cite>Dominguez1995</cite> and Ducros <cite>Ducros1995</cite> correctly postulated as the catalytic acid when the 3-D structures were determined. <br />
<br />
;First 3-D structure: The first 3D structures in family GH5 was an endoglucanase (cellulase) from ''Clostridium thermocellum'' reported by the Alzari in 1995 (in a paper which also reported a family GH10 xylanase structure and the similarities between them) <cite>Dominguez1995</cite>. Subsequently, Ducros and colleagues reported the ''Clostridium cellulolyticum'' Cel5A also in 1995 <cite>Ducros1995</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Jenkins1995 pmid=7729513 <br />
#Henrissat1996 pmid=8643635 <br />
#Caines2007 pmid=17329247<br />
#Barras1992 pmid=1563515<br />
#Wang1993 pmid=8100226<br />
#Gebler1992 pmid=1618761 <br />
#Dominguez1995 pmid=7664125<br />
#Ducros1995 pmid=8535787<br />
#Davies1998 pmid=9718293<br />
#Varrot2003 pmid=12812472<br />
#Gloster2007 pmid=17376777<br />
#Ducros pmid=12203498<br />
#Tailford pmid=18408714<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH005]]</div>Gideon Davies