https://www.cazypedia.org/api.php?action=feedcontributions&user=Alan+Cartmell&feedformat=atomCAZypedia - User contributions [en-ca]2024-03-29T01:20:24ZUser contributionsMediaWiki 1.35.10https://www.cazypedia.org/index.php?title=User:Alan_Cartmell&diff=17254User:Alan Cartmell2023-05-16T09:06:46Z<p>Alan Cartmell: </p>
<hr />
<div>[[Image:AlanCartmell.png|thumb|200px|right]]<br />
Alan Cartmell did his B.Sc. in Biochemistry at Newcastle University and then completed both an M.Res and Ph.D under the supervision of Professor [[User:Harry Gilbert|Harry Gilbert]]. The work during his doctoral studies focused on structure/function studies of novel glycoside hydrolases from [[GH26]], [[GH43]] and [[GH124]] families. He then undertook a two year postdoctoral fellowship at the La Jolla institute for Allergy and Immunology in the laboratory of Professor Dirk Zajonc. The position was funded by a juvenile diabetes research foundation junior postdoctoral fellowship and focused on the class I tyrosine phosphatase PTPN22 involved in type 1 diabetes. He then had a temporary position in the laboratory of Professor [[User:Spencer Williams|Spencer Williams]] focusing on elucidating the mechanism of action of [[GH76]] enzymes. After this short spell with Professor [[User:Spencer Williams|Spencer Williams]] he returned to Professor [[User:Harry Gilbert|Harry Gilbert]]'s laboratory where he worked on elucidating how members of the human gut microbiota (HGM) catabolised plant glycans (Pectins and Arabinogalactans) from the human diet. He is currently a Lecturer at the University of Liverpool with a recent focus on exploring how sulfated glycans, such as glycosaminoglycans and sulfomucin, are metabolised by the HGM and the host itself.<br />
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<!-- Do not remove this Category tag --><br />
[[Category:Contributors|Cartmell,Alan]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_42&diff=16824Polysaccharide Lyase Family 422022-03-20T16:48:45Z<p>Alan Cartmell: </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]]s: [[User:Alan Cartmell|Alan Cartmell]] and [[User:Harry Gilbert|Harry Gilbert]]<br />
* [[Responsible Curator]]: [[User:Alan Cartmell|Alan Cartmell]]<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 />
<br />
{| {{Prettytable}}<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''Polysaccharide Lyase Family PL42'''<br />
|-<br />
| '''Clan'''<br />
| None <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}}PL42.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
== Substrate specificities ==<br />
Three members of this family (BT3686, BACOVA_0349 and HMPREF9455_02360) have been shown to be exo-α-L-rhamnosidases, targeting rhamnose linked α-1,4 to glucuronic acid (Rha-GlcA) in the complex arabinogalactan protein (AGP) from gum arabic (AGP-GA) <cite>Munoz-Munoz2017</cite>. A fungal member of this family (FoRham1 from ''Fusarium oxysporum 12S'') was shown to cleave the Rha-GlcA linkage in AGP-GA harnessing anti-β-elimination chemistry generating L-rhamnose and C4-C5 unsaturated D-glucuronic acid at the new non-reducing end <cite>Kondo2021</cite>. Three PL42 enzymes were shown to cleave the Rha-GlcA linkage in the highly sulfated AGP from red wine (AGP-Wi) through a β-elimination or exo-lyase mechanism <cite>Munoz-Munoz2021</cite>. Although these three enzymes did not display lyase activity against AGP-GA, one of the CAZymes, BT3686, cleaved the glycan through a glycoside hydrolase mechanism. Thus, BT3686 contains two distinct active sites that cleave glycosidic linkages through a hydrolase and lyase mechanism, respectively. The PL42 family was originally assigned to glycoside hydrolase family GH145. It is evident, however, that the catalytic histidine (see below) in the glycoside hydrolase active site is not highly conserved indicating that many of the enzymes in this family will not catalyse a hydrolytic reaction. In contrast, there is an extremely high degree of sequence conservation in the lyase active site, including invariant catalytic residues. Thus, β-elimination is likely to be the dominant activity displayed by enzymes in this family. GH145 was therefore reassigned to a polysaccharide lyase family; PL42. <br />
<br />
== Kinetics and Mechanism ==<br />
The β-elimination catalyzed by PL42 enzymes results in the formation of a C4-C5 unsaturated sugar residue at the new non-reducing end. The first step is the neutralization of the acid group in the +1 subsite by a conserved arginine. A histidine abstracts the labile proton at C5. The same histidine is also believed to act as the catalytic acid, protonating the leaving group (L-Rha) resulting in glycosidic bond cleavage <cite>Kondo2021</cite>.<br />
<br />
With respect to the glycoside hydrolase activity displayed by some PL42 enzymes, the catalytic mechanism was explored using BT3686 from ''Bacteroides thetaiotamicron'' and AGP-GA as the substrate. NMR analysis of the reaction revealed the family operates via a retaining mechanism <cite>Munoz-Munoz2017</cite>. Rather than using a standard double displacement mechanism the enzyme is speculatively predicted to perform catalysis via an epoxide intermediate, similar to GH99 enzymes <cite>Thompson2012 Fernandes2018</cite>. BT3686 is proposed to perform catalysis via a substrate assisted mechanism, requiring the carboxyl group of the glucuronic acid and a single catalytic histidine; both acting as an acid/base. This histidine is predicted to deprotonate the O2 of rhamnose, allowing O2 to attack C1 and form an epoxide. Simultaneously the carboxyl group of the glucuronic acid may deprotonate a water molecule generating a hydroxyl group to attach the C1 of rhamnose and allowing protonation of its own O4 thus, leading to glycosidic bond cleavage <cite>Munoz-Munoz2017</cite>. Further work is needed to confirm the mechanism by which some PL42 enzymes operate through a glycoside hydrolase mechanism.<br />
== Catalytic Residues ==<br />
With respect to the lyase mechanism, of which FoRham1 is the exemplar, X-ray crystallography of enzyme-substrate complexes and mutagenesis studies showed that Arg166 neutralizes the acid group of the substrate and His85 is proposed to act as the catalytic acid-base <cite>Kondo2021</cite>.<br />
<br />
With respect to glycoside hydrolase activity, using BT3686 as the exemplar, a single catalytic histidine, His48, was shown to be critical for activity <cite>Munoz-Munoz2017</cite>. This was the only residue that, when mutated (to Gln, Ala and Gly), caused complete loss of activity. The histidine is thought to act as the catalytic acid/base. Several homologues of BT3686 with >80% sequence identity to the ''B. thetaiotaomicron'' enzyme displayed no rhamnosidase activity. These enzymes have a Gln at the equivalent position to His48 in BT3686. Replacing Gln48 with a histidine in the related enzymes BACINT_00347 and BACCELL_00856, from ''Bacteroides intestinalis'' and ''Bacteroides cellulosilyticus'', respectively, introduced rhamnosidase activity <cite>Munoz-Munoz2017</cite>. No second catalytic residue could be identified and it was tentatively proposed that the glucurnonic acid participates as a second acid/base residue, protonating its own O4 and activating a water molecule (see above).<br />
<br />
== Three-dimensional structures ==<br />
PL42 enzymes comprise a single catalytic domain displaying a seven bladed β-propeller fold. Each blade is composed of four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein, which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. The glycoside hydrolase active site is located on the posterior surface, while the anterior surface houses the β-elimination or lyase catalytic apparatus. PL42 is distantly related to PL25 and PL24, in which the anterior surface houses the catalytic apparatus <cite>Ulaganathan2017 Ulaganathan2018 </cite>.<br />
<br />
== Family Firsts ==<br />
=== Polysaccharide lyase activity ===<br />
;First demonstration of lyase activity: FoRham1 from ''Fusarium oxysporum 12S''. Activity shown against AGP-GA derived oligosaccharides by UV absorbance spectroscopy and HPAEC <cite>Kondo2021</cite>.<br />
;First catalytic base/acid identification: FoRham1 His85 was suggested as the catalytic acid/base based upon the crystal structure of the enzyme-substrate complex, residue conservation, mutagenesis and activity analysis (H311A was inactive) <cite>Kondo2021</cite>.<br />
;First charge neutralizer identification: FoRham1 Arg166 was suggested as the charge neutralizer based on the crystal structure (the proximity of the carboxylate group of glucuronic acid at the +1 subsite to the arginine) its conservation, mutagenesis and activity analysis (R166A was inactive).;First 3-D structure: FoRham1 from ''Fusarium oxysporum'' 12S <cite>Kondo2021</cite>.<br />
<br />
=== Glycoside hydrolase activity ===<br />
;First stereochemistry determination: Determined for the ''Bacteroides thetaiotaomicron'' enzyme BT3686 <cite>Munoz-Munoz2017</cite>.<br />
;First catalytic acid/base residue identification: Predicted to be a histidine <cite>Munoz-Munoz2017</cite>.<br />
;Second general acid/base residue identification: Predicted to be provided by the substrate <cite>Munoz-Munoz2017</cite>.<br />
;First 3-D structure: BT3686, BACINT_00347 and BACCELL_00856 from ''Bacteroides thetaiotaomicron'', ''Bacteroides intestinalis'' and ''Bacteroides cellulosilyticus'', respectively, were the first PL42 enzymes to have their structures solved <cite>Munoz-Munoz2017</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Munoz-Munoz2017 pmid=28396425<br />
#Kondo2021 pmid=34303708<br />
#Munoz-Munoz2021 pmid=34340552<br />
#Thompson2012 pmid=22219371<br />
#Fernandes2018 pmid=29508463<br />
#Ulaganathan2017 pmid=28290654<br />
#Ulaganathan2018 pmid=29382716<br />
</biblio><br />
<br />
<br />
[[Category:Polysaccharide Lyase Families|PL045]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=User:Alan_Cartmell&diff=16200User:Alan Cartmell2021-03-29T19:27:27Z<p>Alan Cartmell: </p>
<hr />
<div>[[Image:AlanCartmell.png|thumb|200px|right]]<br />
Alan Cartmell did his B.Sc. in Biochemistry at Newcastle University and then completed both an M.Res and Ph.D under the supervision of Professor ^^^Harry Gilbert^^^. The work during his doctoral studies focused on structure/function studies of novel glycoside hydrolases from [[GH26]], [[GH43]] and [[GH124]] families. He then undertook a two year postdoctoral fellowship at the La Jolla institute for Allergy and Immunology in the laboratory of Professor Dirk Zajonc. The position was funded by a juvenile diabetes research foundation junior postdoctoral fellowship and focussed on the class I tyrosine phosphatase PTPN22 involved in type 1 diabetes. He then had a temporary 3 month position in the laboratory of Professor ^^^Spencer Williams^^^ focusing on elucidating the mechanism of action of [[GH76]] enzymes. After this short spell with Professor ^^^Spencer Williams^^^ he returned to Professor ^^^Harry Gilbert^^^'s laboratory where he worked on elucidating how members of the human gut microbiota (HGM) catabolised plant glycans (Pectins and Arabinogalactans) from the human diet. He is currently a Tenure-Track Fellow at the University of Liverpool with a recent focus on exploring how sulfated glycans, such as glycosaminoglycans and sulfomucin, are metabolised by the HGM and the host itself.<br />
<br />
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<!-- Do not remove this Category tag --><br />
[[Category:Contributors|Cartmell,Alan]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_137&diff=14848Glycoside Hydrolase Family 1372020-05-12T08:25:04Z<p>Alan Cartmell: </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]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Alan Cartmell^^^<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 GH137'''<br />
|-<br />
|'''Clan''' <br />
|None<br />
|-<br />
|'''Mechanism'''<br />
|Unknown<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH137.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
The only activity identified to date is β-L-arabinofuranosidase activity displayed by the enzyme BT0996. This enzyme removes β linked L-arabinose from the terminus of side chain B in the complex glycan rhamnogalacturonan ii (RGII) <cite>Ndeh2017</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
BT0996 was active both on intact RGII and on Chain B released from RGII <cite>Ndeh2017</cite>. A thorough mutagenic strategy was performed on BT0996 and identified two glutamates to be essential for activity, Glu159 and Glu240 (see below) <cite>Ndeh2017</cite>. The mechanism for arabinofuranosidedases are challenging to elucidate due to rapid tautomerisation of free arbinofuranose in solution to α and β anomers of both arabinopyranose (major confomer) and arabinofuranose. <br />
<br />
== Catalytic Residues ==<br />
The catalytic residues were shown to be a pair of glutamates. The catalytic residue assignment was made based on both structural, substrate and product complexes, and mutagenic information. Glu159 and Glu240 were mutated to Ala and Gln. E159Q and E240A and E240Q were completely inactive, whilst E159A was only 26 fold less active. Despite the activity of E159A, these were the only residues that ablated activity. They sit around 6 Angstroms apart. Typically retaining enzymes are expected to have their catalytic residues ~5.5 Angstroms apart, whilst in inverting enzymes they are expected to be ~10 Angstroms apart <cite>Davies1995</cite>. Glu159 sits beneath the alpha face of the -1 β-linked arabinose, 3.2 Angstroms from the anomeric carbon, placing it in a an ideal position to act as a catalytic nucleophile. Glu240 resides 5 Angstroms from the glycosidic oxygen which somewhat far to act as catalytic acid/base in a retaining mechanism. Alternatively, one could also speculate that at a distance of 4.6 Angstroms from the anomeric carbon Glu240 could potentially act as a catalytic base in an inverting mechanism, with Glu159 acting as the catalytic acid being at a distance of 3.7 Angstroms from the glycosidic oxygen <cite>Ndeh2017</cite>. <br />
<br />
== Three-dimensional structures ==<br />
The structure of BT0996 comprises a single domain which is a five bladed β-propeller fold. Each blade is composed of three to four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. It should be noted that BT0996 is appended to a GH2 from clan GH-A. This GH2 targets β-D-GlcA linkage in Chain A of RGII <cite>Ndeh2017</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Not Known.<br />
;First catalytic nucleophile/base identification: Inferred to be Glu159 in BT0996 <cite>Ndeh2017</cite>.<br />
;First general acid/base residue identification: Inferred to be Glu240 in BT0996 <cite>Ndeh2017</cite>.<br />
;First 3-D structure: The first structure determination for GH137 was of BT0996 from the organism ''Bacteroides thetaiotaomicon'' <cite>Ndeh2017</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Ndeh2017 pmid=28329766<br />
#Davies1995 pmid=8535779<br />
<br />
</biblio><br />
[[Category:Glycoside Hydrolase Families|GH137]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_137&diff=14847Glycoside Hydrolase Family 1372020-05-12T08:23:44Z<p>Alan Cartmell: </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]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Alan Cartmell^^^<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 GH137'''<br />
|-<br />
|'''Clan''' <br />
|None<br />
|-<br />
|'''Mechanism'''<br />
|Unknown<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH137.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
The only activity identified to date is β-L-arabinofuranosidase activity displayed by the enzyme BT0996. This enzyme removes β linked L-arabinose from the terminus of side chain B in the complex glycan rhamnogalacturonan ii (RGII) <cite>Ndeh2017</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
BT0996 was active both on intact RGII and on Chain B released from RGII <cite>Ndeh2017</cite>. A thorough mutagenic strategy was performed on BT0996 and identified two glutamates to be essential for activity, Glu159 and Glu240 (see below) <cite>Ndeh2017</cite>. The mechanism for arabinofuranosidedases are challenging to elucidate due to rapid tautomerisation of free arbinofuranose in solution to α and β anomers of both arabinopyranose (major confomer) and arabinofuranose. <br />
<br />
== Catalytic Residues ==<br />
The catalytic residues were shown to be a pair of glutamates. The catalytic residue assignment was made based on both structural, substrate and product complexes, and mutagenic information. Glu159 and Glu240 were mutated to Ala and Gln. E159Q and E240A and E240Q were completely inactive, whilst E159A was only 26 fold less active. Despite the activity of E159A, these were the only residues that ablated activity. They sit around 6 Angstroms apart. Typically retaining enzymes are expected to have their catalytic residues ~5.5 Angstroms apart, whilst in inverting enzymes they are expected to be ~10 Angstroms apart <cite>Davies1995</cite>. Glu159 sits beneath the alpha face of the -1 β-linked arabinose, 3.2 Angstroms from the anomeric carbon, placing it in a an ideal position to act as a catalytic nucleophile. Glu240 resides 5 Angstroms from the glycosidic oxygen which somewhat far to act as catalytic acid/base in a retaining mechanism. Alternatively, one could also speculate that at a distance of 4.6 Angstroms from the anomeric carbon Glu240 could potentially act as a catalytic base in an inverting mechanism, with Glu159 acting as the catalytic acid being at a distance of 3.7 Angstroms from the glycosidic oxygen <cite>Ndeh2017</cite>. <br />
<br />
== Three-dimensional structures ==<br />
The structure of BT0996 comprises a single domain which is a five bladed β-propeller fold. Each blade is composed of three to four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. It should be noted that BT0996 is appended to a GH2 from clan GHA. This GH2 targets β-D-GlcA linkage in Chain A of RGII <cite>Ndeh2017</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Not Known.<br />
;First catalytic nucleophile/base identification: Inferred to be Glu159 in BT0996 <cite>Ndeh2017</cite>.<br />
;First general acid/base residue identification: Inferred to be Glu240 in BT0996 <cite>Ndeh2017</cite>.<br />
;First 3-D structure: The first structure determination for GH137 was of BT0996 from the organism ''Bacteroides thetaiotaomicon'' <cite>Ndeh2017</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Ndeh2017 pmid=28329766<br />
#Davies1995 pmid=8535779<br />
<br />
</biblio><br />
[[Category:Glycoside Hydrolase Families|GH137]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_145&diff=14846Glycoside Hydrolase Family 1452020-05-12T08:22:16Z<p>Alan Cartmell: </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]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Alan Cartmell^^^<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 />
<br />
{| {{Prettytable}}<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH145'''<br />
|-<br />
| '''Clan'''<br />
| None <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}}GH145.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
== Substrate specificities ==<br />
Two members of this family have been shown to be an exo-α-L-rhamnosidases, targeting rhamnose linked α-1,4 to glucuronic acid in the complex arabinogalactan protein gum arabic <cite>Munoz-Munoz2017 Cartmell2019</cite>. <br />
<br />
== Kinetics and Mechanism ==<br />
NMR, using the arabinogalactan protein (AGP) gum arabic as the substrate, revealed the family operates via a retaining mechanism <cite>Munoz-Munoz2017</cite>. Rather than using a standard double displacement mechanism the enzyme is speculatively predicted to perform catalysis via an epoxide intermediate, similar to GH99 enzymes <cite>Thompson2012 Fernandes2018</cite>. GH145, however, is proposed to perform catalysis via a substrate assisted mechanism, requiring the carboxyl group of the glucuronic acid and a single catalytic histidine; both acting as an acid/base. This histidine is predicted to deprotonate the O2 of rhamnose, allowing O2 to attack C1 and form an epoxide. Simultaneously the carboxyl group of the glucuronic acid may deprotonate a water molecule generating a hydroxyl group to attach the C1 of rhamnose and allowing protonation of its own O4 thus, leading to glycosidic bond cleavage <cite>Munoz-Munoz2017</cite>. Further work is needed to confirm the mechanism by which GH145 operates. <br />
<br />
== Catalytic Residues ==<br />
A single catalytic histidine, His48 in BT3686, has been shown to be critical for activity. This was the only residue mutated (to Gln, Ala and Gly) that caused loss of activity and is thought to act as an acid/base. Several homologues of BT3686 exist, which although >80 % identical are inactive due to having Gln at the equivalent position to His48 in BT3686. The introduction of a histidine at into related enzymes BACINT_00347 and BACCELL_00856, from ''bacteroides intestinalis'' and ''bacteroides cellulosilyticus'', generating the mutants Q48H in both proteins, is sufficient to introduce rhamnosidase activity into these, otherwise inactive, enzymes <cite>Munoz-Munoz2017</cite>. No second catalytic residue to could be identified and it was tentatively proposed that the glucurnonic acid participates as a second acid/base residue, portonating its own O4 and activating a water molecule. <br />
<br />
== Three-dimensional structures ==<br />
GH145 comprise a single domain which is a seven bladed β-propeller fold. Each blade is composed of four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. The active site of these α-L-rhamnosidases is located on the opposite side, termed the posterior surface, of CAZymes with similar β-propeller folds. The "normal" side, termed the anterior surface, of the β-propeller bears the highest residue conservation and may well have another function. GH145 is distantly related to [[PL25]] which utilise the anterior surface suggesting that the this surface in GH145 may have another activity <cite>Munoz-Munoz2017 Ulaganathan2017</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Determined for the ''bacteroides thetaiotaomicron'' enzyme BT3686 <cite>Munoz-Munoz2017</cite>.<br />
;First catalytic acid/base residue identification: Predicted to be a histidine <cite>Munoz-Munoz2017</cite>.<br />
;Second general acid/base residue identification: Predicted to be provided by the substrate <cite>Munoz-Munoz2017</cite>.<br />
;First 3-D structure: BT3686, BACINT_00347 and BACCELL_00856 were the first enzymes to have their structures solved from the organisms ''bacteroides thetaiotaomicron'', ''bacteroides intestinalis'' and ''bacteroides cellulosilyticus'', respectively. <cite>Munoz-Munoz2017</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Munoz-Munoz2017 pmid=28396425<br />
#Cartmell2019 pmid=31541200<br />
#Thompson2012 pmid=22219371<br />
#Fernandes2018 pmid=29508463<br />
#Ulaganathan2017 pmid=28290654<br />
</biblio><br />
<br />
<br />
[[Category:Glycoside Hydrolase Families|GH145]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_145&diff=14845Glycoside Hydrolase Family 1452020-05-12T08:20:24Z<p>Alan Cartmell: </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]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Alan Cartmell^^^<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 />
<br />
{| {{Prettytable}}<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH145'''<br />
|-<br />
| '''Clan'''<br />
| None <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}}GH145.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
== Substrate specificities ==<br />
Two members of this family have been shown to be an exo-α-L-rhamnosidases, targeting rhamnose linked α-1,4 to glucuronic acid in the complex arabinogalactan protein gum arabic <cite>Munoz-Munoz2017 Cartmell2019</cite>. <br />
<br />
== Kinetics and Mechanism ==<br />
NMR, using the arabinogalactan protein (AGP) gum arabic as the substrate, revealed the family operates via a retaining mechanism <cite>Munoz-Munoz2017</cite>. Rather than using a standard double displacement mechanism the enzyme is speculatively predicted to perform catalysis via an epoxide intermediate, similar to GH99 enzymes <cite>Thompson2012 Fernandes2018</cite>. GH145, however, is proposed to perform catalysis via a substrate assisted mechanism, requiring the carboxyl group of the glucuronic acid and a single catalytic histidine; both acting as an acid/base. This histidine is predicted to deprotonate the O2 of rhamnose, allowing O2 to attack C1 and form an epoxide. Simultaneously the carboxyl group of the glucuronic acid may deprotonate a water molecule generating a hydroxyl group to attach the C1 of rhamnose and allowing protonation of its own O4 thus, leading to glycosidic bond cleavage <cite>Munoz-Munoz2017</cite>. Further work is needed to confirm the mechanism by which GH145 operates. <br />
<br />
== Catalytic Residues ==<br />
A single catalytic histidine, His48 in BT3686, has been shown to be critical for activity. This was the only residue mutated (to Gln, Ala and Gly) that caused loss of activity and is thought to act as an acid/base. Several homologues of BT3686 exist, which although >80 % identical are inactive due to having Gln at the equivalent position to His48 in BT3686. The introduction of a histidine at into related enzymes BACINT_00347 and BACCELL_00856, from bacteroides intestinalis'' and ''bacteroides cellulosilyticus, generating the mutants Q48H in both proteins, is sufficient to introduce rhamnosidase activity into these enzymes <cite>Munoz-Munoz2017</cite>. No second catalytic residue to could be identified and it was tentatively proposed that the glucurnonic acid participates as a second acid/base residue, portonating its own O4 and activating a water molecule. <br />
<br />
== Three-dimensional structures ==<br />
GH145 comprise a single domain which is a seven bladed β-propeller fold. Each blade is composed of four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. The active site of these α-L-rhamnosidases is located on the opposite side, termed the posterior surface, of CAZymes with similar β-propeller folds. The "normal" side, termed the anterior surface, of the β-propeller bears the highest residue conservation and may well have another function. GH145 is distantly related to [[PL25]] which utilise the anterior surface suggesting that the this surface in GH145 may have another activity <cite>Munoz-Munoz2017 Ulaganathan2017</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Determined for the ''bacteroides thetaiotaomicron'' enzyme BT3686 <cite>Munoz-Munoz2017</cite>.<br />
;First catalytic acid/base residue identification: Predicted to be a histidine <cite>Munoz-Munoz2017</cite>.<br />
;Second general acid/base residue identification: Predicted to be provided by the substrate <cite>Munoz-Munoz2017</cite>.<br />
;First 3-D structure: BT3686, BACINT_00347 and BACCELL_00856 were the first enzymes to have their structures solved from the organisms ''bacteroides thetaiotaomicron'', ''bacteroides intestinalis'' and ''bacteroides cellulosilyticus'', respectively. <cite>Munoz-Munoz2017</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Munoz-Munoz2017 pmid=28396425<br />
#Cartmell2019 pmid=31541200<br />
#Thompson2012 pmid=22219371<br />
#Fernandes2018 pmid=29508463<br />
#Ulaganathan2017 pmid=28290654<br />
</biblio><br />
<br />
<br />
[[Category:Glycoside Hydrolase Families|GH145]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_137&diff=14844Glycoside Hydrolase Family 1372020-05-12T08:02:56Z<p>Alan Cartmell: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<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 GH137'''<br />
|-<br />
|'''Clan''' <br />
|None<br />
|-<br />
|'''Mechanism'''<br />
|Unknown<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH137.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
The only activity identified to date is β-L-arabinofuranosidase activity displayed by the enzyme BT0996. This enzyme removes β linked L-arabinose from the terminus of side chain B in the complex glycan rhamnogalacturonan ii (RGII) <cite>Ndeh2017</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
BT0996 was active both on intact RGII and on Chain B released from RGII <cite>Ndeh2017</cite>. A thorough mutagenic strategy was performed on BT0996 and identified two glutamates to be essential for activity, Glu159 and Glu240 (see below) <cite>Ndeh2017</cite>. The mechanism for arabinofuranosidedases are challenging to elucidate due to rapid tautomerisation of free arbinofuranose in solution to α and β anomers of both arabinopyranose (major confomer) and arabinofuranose. <br />
<br />
== Catalytic Residues ==<br />
The catalytic residues were shown to be a pair of glutamates. The catalytic residue assignment was made based on both structural, substrate and product complexes, and mutagenic information. Glu159 and Glu240 were mutated to Ala and Gln. E159Q and E240A and E240Q were completely inactive, whilst E159A was only 26 fold less active. Despite the activity of E159A, these were the only residues that ablated activity. They sit around 6 Angstroms apart. Typically retaining enzymes are expected to have their catalytic residues ~5.5 Angstroms apart, whilst in inverting enzymes they are expected to be ~10 Angstroms apart <cite>Davies1995</cite>. Glu159 sits beneath the alpha face of the -1 β-linked arabinose, 3.2 Angstroms from the anomeric carbon, placing it in a an ideal position to act as a catalytic nucleophile. Glu240 resides 5 Angstroms from the glycosidic oxygen which somewhat far to act as catalytic acid/base in a retaining mechanism. Alternatively, one could also speculate that at a distance of 4.6 Angstroms from the anomeric carbon Glu240 could potentially act as a catalytic base in an inverting mechanism, with Glu159 acting as the catalytic acid being at a distance of 3.7 Angstroms from the glycosidic oxygen <cite>Ndeh2017</cite>. <br />
<br />
== Three-dimensional structures ==<br />
The structure of BT0996 comprises a single domain which is a five bladed β-propeller fold. Each blade is composed of three to four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. It should be noted that BT0996 is appended to a GH2 from clan GHA. This GH2 targets β-D-GlcA linkage in Chain A of RGII <cite>Ndeh2017</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Not Known.<br />
;First catalytic nucleophile/base identification: Inferred to be Glu159 in BT0996 <cite>Ndeh2017</cite>.<br />
;First general acid/base residue identification: Inferred to be Glu240 in BT0996 <cite>Ndeh2017</cite>.<br />
;First 3-D structure: The first structure determination for GH137 was of BT0996 from the organism ''Bacteroides thetaiotaomicon'' <cite>Ndeh2017</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Ndeh2017 pmid=28329766<br />
#Davies1995 pmid=8535779<br />
<br />
</biblio><br />
[[Category:Glycoside Hydrolase Families|GH137]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=User:Alan_Cartmell&diff=14843User:Alan Cartmell2020-05-12T08:00:11Z<p>Alan Cartmell: </p>
<hr />
<div>[[Image:AlanCartmell.png|thumb|200px|right]]<br />
Alan Cartmell did his B.Sc. in Biochemistry at Newcastle University and then completed both an M.Res and Ph.D under the supervision of Professor ^^^Harry Gilbert^^^. The work during his doctoral studies focused on structure/function studies of novel glycoside hydrolases from [[GH26]], [[GH43]] and [[GH124]] families. He then undertook a two year postdoctoral fellowship at the La Jolla institute for Allergy and Immunology in the laboratory of Professor Dirk Zajonc. The position was funded by a juvenile diabetes research foundation junior postdoctoral fellowship and focussed on the class I tyrosine phosphatase PTPN22 involved in type 1 diabetes. He then had a temporary 3 month position in the laboratory of Professor ^^^Spencer Williams^^^ focusing on elucidating the mechanism of action of [[GH76]] enzymes. After this short spell with Professor ^^^Spencer Williams^^^ he returned to Professor ^^^Harry Gilbert^^^'s laboratory where he worked on elucidating how members of the human gut microbiota (HGM) catabolised plant glycans (Pectins and Arabinogalactans) from the human diet. I am currently a Tenure-Track Fellow at the University of Liverpool with a recent focus on exploring how sulfated glycans, such as glycosaminoglycans and sulfomucin, are metabolised by the HGM and the host itself.<br />
<br />
----<br />
<br />
<!-- Do not remove this Category tag --><br />
[[Category:Contributors|Cartmell,Alan]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=User:Alan_Cartmell&diff=14842User:Alan Cartmell2020-05-12T07:59:47Z<p>Alan Cartmell: </p>
<hr />
<div>[[Image:AlanCartmell.png|thumb|200px|right]]<br />
Alan Cartmell did his B.Sc. in Biochemistry at Newcastle University and then completed both an M.Res and Ph.D under the supervision of Professor ^^^Harry Gilbert^^^. The work during his doctoral studies focused on structure/function studies of novel glycoside hydrolases from [[GH26]], [[GH43]] and [[GH124]] families. He then undertook a two year postdoctoral fellowship at the La Jolla institute for Allergy and Immunology in the laboratory of Professor Dirk Zajonc. The position was funded by a juvenile diabetes research foundation junior postdoctoral fellowship and focussed on the class I tyrosine phosphatase PTPN22 involved in type 1 diabetes. He then had a temporary 3 month position in the laboratory of Professor ^^^Spencer Williams^^^ focusing on elucidating the mechanism of action of [[GH76]] enzymes. After this short spell with Professor ^^^Spencer Williams^^^ he returned to Professor ^^^Harry Gilbert^^^'s laboratory where he worked on elucidating how members of the human gut microbiota (HGM) catabolised plant glycans (Pectins and Arabinogalactans) from the human diet. I am currently a Tenure-Track Fellow at the University of Liverpool with a recent focus on exploring how sulfated glycans, such as glycosaminoglycans and sulfomucin, are metabolised by the HGM and the host itself.<br />
<br />
----<br />
<br />
<biblio><br />
</biblio><br />
<br />
<!-- Do not remove this Category tag --><br />
[[Category:Contributors|Cartmell,Alan]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=User:Alan_Cartmell&diff=14841User:Alan Cartmell2020-05-12T07:59:19Z<p>Alan Cartmell: </p>
<hr />
<div>[[Image:AlanCartmell.png|thumb|200px|right]]<br />
Alan Cartmell did his B.Sc. in Biochemistry at Newcastle University and then completed both an M.Res and Ph.D under the supervision of Professor ^^^Harry Gilbert^^^. The work during his doctoral studies focused on structure/function studies of novel glycoside hydrolases from [[GH26]], [[GH43]] and [[GH124]] families. He then undertook a two year postdoctoral fellowship at the La Jolla institute for Allergy and Immunology in the laboratory of Professor Dirk Zajonc. The position was funded by a juvenile diabetes research foundation junior postdoctoral fellowship and focussed on the class I tyrosine phosphatase PTPN22 involved in type 1 diabetes. He then had a temporary 3 month position in the laboratory of Professor ^^^Spencer Williams^^^ focusing on elucidating the mechanism of action of [[GH76]] enzymes. After this short spell with Professor ^^^Spencer Williams^^^ he returned to Professor ^^^Harry Gilbert^^^'s laboratory where he worked on elucidating how members of the human gut microbiota (HGM) catabolised plant glycans (Pectins and Arabinogalactans) from the human diet. I am currently a Tenure-Track Fellow at the University of Liverpool with a recent focus on exploring how sulfated glycans, such as glycosaminoglycans and sulfomucin, are metabolised by the HGM and the host itself.<br />
<br />
----<br />
<br />
<biblio><br />
<br />
<br />
</biblio><br />
<br />
<!-- Do not remove this Category tag --><br />
[[Category:Contributors|Cartmell,Alan]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=File:AlanCartmell.png&diff=14840File:AlanCartmell.png2020-05-12T07:58:18Z<p>Alan Cartmell: </p>
<hr />
<div></div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_137&diff=14838Glycoside Hydrolase Family 1372020-05-11T20:32:43Z<p>Alan Cartmell: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<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 GH137'''<br />
|-<br />
|'''Clan''' <br />
|None<br />
|-<br />
|'''Mechanism'''<br />
|Unknown<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH137.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
The only activity identified to date is β-L-arabinofuranosidase activity displayed by the enzyme BT0996. This enzyme removes β linked L-arabinose from the terminus of side chain B in the complex glycan rhamnogalacturonan ii (RGII) <cite>Ndeh2017</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
BT0996 was active both on intact RGII and on Chain B released from RGII <cite>Ndeh2017</cite>. A thorough mutagenic strategy was performed on BT0996 and identified two glutamates to be essential for activity, Glu159 and Glu240 (see below) <cite>Ndeh2017</cite>. The mechanism for arabinofuranosidedases are challenging to elucidate due to rapid tautomerisation of free arbinofuranose in solution to α and β anomers of both arabinopyranose (major confomer) and arabinofuranose. <br />
<br />
== Catalytic Residues ==<br />
The catalytic residues were shown to be a pair of glutamates. They sit around 6 Angstroms apart. Typically retaining enzymes are expected to have their catalytic residues ~5.5 Angstroms apart, whilst in inverting enzymes they are expected to be ~10 Angstroms apart <cite>Davies1995</cite>. Glu159 sits beneath the alpha face of the -1 β-linked arabinose, 3.2 Angstroms from the anomeric carbon, placing it in a an ideal position to act as a catalytic nucleophile. Glu240 resides 5 Angstroms from the glycosidic oxygen which somewhat far to act as catalytic acid/base in a retaining mechanism. Alternatively, one could also speculate that at a distance of 4.6 Angstroms from the anomeric carbon Glu240 could potentially act as a catalytic base in an inverting mechanism, with Glu159 acting as the catalytic acid being at a distance of 3.7 Angstroms from the glycosidic oxygen <cite>Ndeh2017</cite>. <br />
<br />
== Three-dimensional structures ==<br />
The structure of BT0996 comprises a single domain which is a five bladed β-propeller fold. Each blade is composed of three to four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. It should be noted that BT0996 is appended to a GH2 from clan GHA. This GH2 targets β-D-GlcA linkage in Chain A of RGII <cite>Ndeh2017</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Not Known.<br />
;First catalytic nucleophile/base identification: Inferred to be Glu159 in BT0996 <cite>Ndeh2017</cite>.<br />
;First general acid/base residue identification: Inferred to be Glu240 in BT0996 <cite>Ndeh2017</cite>.<br />
;First 3-D structure: The first structure determination for GH137 was of BT0996 from the organism ''Bacteroides thetaiotaomicon'' <cite>Ndeh2017</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Ndeh2017 pmid=28329766<br />
#Davies1995 pmid=8535779<br />
<br />
</biblio><br />
[[Category:Glycoside Hydrolase Families|GH137]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_137&diff=14837Glycoside Hydrolase Family 1372020-05-11T20:32:02Z<p>Alan Cartmell: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<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 GH137'''<br />
|-<br />
|'''Clan''' <br />
|None<br />
|-<br />
|'''Mechanism'''<br />
|Unknown<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH137.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
The only activity identified to date is β-L-arabinofuranosidase activity displayed by the enzyme BT0996. This enzyme removes β linked L-arabinose from the terminus of side chain B in the complex glycan rhamnogalacturonan ii (RGII) <cite>Ndeh2017</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
BT0996 was active both on intact RGII and on Chain B released from RGII. A thorough mutagenic strategy was performed on BT0996 and identified two glutamates to be essential for activity, Glu159 and Glu240 (see below). The mechanism for arabinofuranosidedases are challenging to elucidate due to rapid tautomerisation of free arbinofuranose in solution to α and β anomers of both arabinopyranose (major confomer) and arabinofuranose. <br />
<br />
== Catalytic Residues ==<br />
The catalytic residues were shown to be a pair of glutamates. They sit around 6 Angstroms apart. Typically retaining enzymes are expected to have their catalytic residues ~5.5 Angstroms apart, whilst in inverting enzymes they are expected to be ~10 Angstroms apart <cite>Davies1995</cite>. Glu159 sits beneath the alpha face of the -1 β-linked arabinose, 3.2 Angstroms from the anomeric carbon, placing it in a an ideal position to act as a catalytic nucleophile. Glu240 resides 5 Angstroms from the glycosidic oxygen which somewhat far to act as catalytic acid/base in a retaining mechanism. Alternatively, one could also speculate that at a distance of 4.6 Angstroms from the anomeric carbon Glu240 could potentially act as a catalytic base in an inverting mechanism, with Glu159 acting as the catalytic acid being at a distance of 3.7 Angstroms from the glycosidic oxygen <cite>Ndeh2017</cite>. <br />
<br />
== Three-dimensional structures ==<br />
The structure of BT0996 comprises a single domain which is a five bladed β-propeller fold. Each blade is composed of three to four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. It should be noted that BT0996 is appended to a GH2 from clan GHA. This GH2 targets β-D-GlcA linkage in Chain A of RGII <cite>Ndeh2017</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Not Known.<br />
;First catalytic nucleophile/base identification: Inferred to be Glu159 in BT0996 <cite>Ndeh2017</cite>.<br />
;First general acid/base residue identification: Inferred to be Glu240 in BT0996 <cite>Ndeh2017</cite>.<br />
;First 3-D structure: The first structure determination for GH137 was of BT0996 from the organism ''Bacteroides thetaiotaomicon'' <cite>Ndeh2017</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Ndeh2017 pmid=28329766<br />
#Davies1995 pmid=8535779<br />
<br />
</biblio><br />
[[Category:Glycoside Hydrolase Families|GH137]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=User:Alan_Cartmell&diff=14836User:Alan Cartmell2020-05-11T19:58:39Z<p>Alan Cartmell: </p>
<hr />
<div>[[Image:AlanCartmell.png|thumb|200px|right]]<br />
Alan Cartmell did his B.Sc. in Biochemistry at Newcastle University and then completed both an M.Res and Ph.D under the supervision of Professor ^^^Harry Gilbert^^^. The work during his doctoral studies focused on structure/function studies of novel glycoside hydrolases from [[GH26]], [[GH43]] and [[GH124]] families. He then undertook a two year postdoctoral fellowship at the La Jolla institute for Allergy and Immunology in the laboratory of Professor Dirk Zajonc. The position was funded by a juvenile diabetes research foundation junior postdoctoral fellowship and focussed on the class I tyrosine phosphatase PTPN22 involved in type 1 diabetes. He then had a temporary 3 month position in the laboratory of Professor ^^^Spencer Williams^^^ focusing on elucidating the mechanism of action of GH76 enzymes. After this short spell with Professor ^^^Spencer Williams^^^ he returned to Professor ^^^Harry Gilbert^^^'s laboratory where he worked on elucidating how members of the human gut microbiota (HGM) catabolised plant glycans (Pectins and Arabinogalactans) from the human diet. I am currently a Tenure-Track Fellow at the University of Liverpool with a recent focus on exploring how sulfated glycans, such as glycosaminoglycans and sulfomucin, are metabolised by the HGM and the host itself.<br />
<br />
----<br />
<br />
<biblio><br />
#Gilbert2008 pmid=18430603<br />
<br />
</biblio><br />
<br />
<!-- Do not remove this Category tag --><br />
[[Category:Contributors|Cartmell,Alan]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=User:Alan_Cartmell&diff=14835User:Alan Cartmell2020-05-11T19:45:50Z<p>Alan Cartmell: </p>
<hr />
<div>[[Image:AlanCartmell.png|200px|right]]<br />
Alan Cartmell did his B.Sc. in Biochemistry at Newcastle University and then completed both an M.Res and Ph.D under the supervision of Professor ^^^Harry Gilbert^^^. The work during his doctoral studies focused on structure/function studies of novel glycoside hydrolases from [[GH26]], [[GH43]] and [[GH124]] families. He then undertook a two year postdoctoral fellowship at the La Jolla institute for Allergy and Immunology in the laboratory of Professor Dirk Zajonc. The position was funded by a juvenile diabetes research foundation junior postdoctoral fellowship and focussed on the class I tyrosine phosphatase PTPN22 involved in type 1 diabetes. He then had a temporary 3 month position in the laboratory of Professor ^^^Spencer Williams^^^ focusing on elucidating the mechanism of action of GH76 enzymes. After this short spell with Professor ^^^Spencer Williams^^^ he returned to Professor ^^^Harry Gilbert^^^'s laboratory where he worked on elucidating how members of the human gut microbiota (HGM) catabolised plant glycans (Pectins and Arabinogalactans) from the human diet. I am currently a Tenure-Track Fellow at the University of Liverpool with a recent focus on exploring how sulfated glycans, such as glycosaminoglycans and sulfomucin, are metabolised by the HGM and the host itself.<br />
<br />
----<br />
<br />
<biblio><br />
#Gilbert2008 pmid=18430603<br />
<br />
</biblio><br />
<br />
<!-- Do not remove this Category tag --><br />
[[Category:Contributors|Cartmell,Alan]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_137&diff=14834Glycoside Hydrolase Family 1372020-05-11T19:26:33Z<p>Alan Cartmell: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<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 GH137'''<br />
|-<br />
|'''Clan''' <br />
|None<br />
|-<br />
|'''Mechanism'''<br />
|Unknown<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH137.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
The only activity identified to date is β-L-arabinofuranosidase activity displayed by the enzyme BT0996. This enzyme removes β linked L-arabinose from the terminus of side chain B in the complex glycan rhamnogalacturonan ii (RGII) <cite>Ndeh2017</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Unknown <br />
<br />
== Catalytic Residues ==<br />
The catalytic residues were shown to be a pair of glutamates. They sit around 6 Angstroms apart. Typically retaining enzymes are expected to have their catalytic residues ~5.5 Angstroms apart, whilst in inverting enzymes they are expected to be ~10 Angstroms apart <cite>Davies1995</cite>. Glu159 sits beneath the alpha face of the -1 β-linked arabinose, 3.2 Angstroms from the anomeric carbon, placing it in a an ideal position to act as a catalytic nucleophile. Glu240 resides 5 Angstroms from the glycosidic oxygen which somewhat far to act as catalytic acid/base in a retaining mechanism. Alternatively, one could also speculate that at a distance of 4.6 Angstroms from the anomeric carbon Glu240 could potentially act as a catalytic base in an inverting mechanism, with Glu159 acting as the catalytic acid being at a distance of 3.7 Angstroms from the glycosidic oxygen <cite>Ndeh2017</cite>. <br />
<br />
== Three-dimensional structures ==<br />
The structure of BT0996 comprises a single domain which is a five bladed β-propeller fold. Each blade is composed of three to four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. It should be noted that BT0996 is appended to a GH2 from clan GHA. This GH2 targets β-D-GlcA linkage in Chain A of RGII <cite>Ndeh2017</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Not Known.<br />
;First catalytic nucleophile/base identification: Inferred to be Glu159 in BT0996 <cite>Ndeh2017</cite>.<br />
;First general acid/base residue identification: Inferred to be Glu240 in BT0996 <cite>Ndeh2017</cite>.<br />
;First 3-D structure: The first structure determination for GH137 was of BT0996 from the organism ''Bacteroides thetaiotaomicon'' <cite>Ndeh2017</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Ndeh2017 pmid=28329766<br />
#Davies1995 pmid=8535779<br />
<br />
</biblio><br />
[[Category:Glycoside Hydrolase Families|GH137]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_140&diff=14833Glycoside Hydrolase Family 1402020-05-11T19:18:39Z<p>Alan Cartmell: </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]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Alan Cartmell^^^<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 GH140'''<br />
|-<br />
|'''Clan''' <br />
|None<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}}GH140.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Thus far only one member of the family has been characterised, BT1012 from bacteroides thetaiotaomicron. BT1012 displays endo-apiosidase activity targeting α1,2 linked apiose at the base of the sidechains A and B in the complex glycan rhamnogalacturonan ii (RGII) <cite>Ndeh2017</cite>. Cleavage of the RGII backbone must occur before BT1012 can act <cite>Ndeh2017</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH140 likely uses a, retaining, double displacement mechanism. This is strongly supported by methanolysis experiments where BT1012 was incubated with trisaccharide L-rhamnose-β1,3-D-apiose-α1,2-D-galacturonic acid-O-methyl in the presence of 10 % methanol. This experiment performed with BT1012 generated the product L-rhamnose-β1,3-D-apiose-O-methyl suggesting a retaining mechanism <cite>Ndeh2017</cite>. Glycoside hydrolases that utilise a retaining mechanism, but not those that use an inverting mechanism, can utilise methanol as an external nucleophile and thus generate a methylated product. <br />
<br />
== Catalytic Residues ==<br />
The catalytic residues are an aspartate and glutamate located on the top of β-strands 4 and 7, respectively <cite>Ndeh2017</cite>. This could mean GH140 is a distant relative of Clan GH-A enzymes, however in with GH-A the catalytic residue atop of β-strands 4 and 7 are both glutamates. In the absence of a ligand bound complex or more detailed biochemical analysis <cite>Shallom2002</cite> (preferably both) it is not possible to say which of the catalytic residues is the nucleophile or acid/base.<br />
<br />
== Three-dimensional structures ==<br />
GH140 adopts a (β/α)<sub>8</sub> , TIM barrel, where a central barrel of eight β strands are encircled by eight α helices <cite>Ndeh2017</cite>. BT1012, the only GH140 structure available, also has a Ig like domain that stacks against the TIM barrel likely providing structural stability, similar to the role of Ig like domains in [[GH43]] enzymes <cite>McKee2012 Cartmell2011</cite>. <br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Methanolysis experiments suggest a retaining mechanism <cite>Ndeh2017</cite>.<br />
;First catalytic nucleophile identification: Not known.<br />
;First general acid/base residue identification: Not Known.<br />
;First 3-D structure: BT1012 from ''Bacteroides thetaiotaomicron'' <cite>Ndeh2017</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Ndeh2017 pmid=28329766<br />
#Shallom2002 pmid=12221104<br />
#McKee2012 pmid=22492980<br />
#Cartmell2011 pmid=21339299<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH140]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_145&diff=14832Glycoside Hydrolase Family 1452020-05-11T19:18:21Z<p>Alan Cartmell: </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]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Alan Cartmell^^^<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 />
<br />
{| {{Prettytable}}<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH145'''<br />
|-<br />
| '''Clan'''<br />
| None <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}}GH145.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
== Substrate specificities ==<br />
Two members of this family have been shown to be an exo-α-L-rhamnosidases, targeting rhamnose linked α-1,4 to glucuronic acid in the complex arabinogalactan protein gum arabic <cite>Munoz-Munoz2017 Cartmell2019</cite>. <br />
<br />
== Kinetics and Mechanism ==<br />
NMR, using the arabinogalactan protein (AGP) gum arabic as the substrate, revealed the family operates via a retaining mechanism <cite>Munoz-Munoz2017</cite>. Rather than using a standard double displacement mechanism the enzyme is speculatively predicted to perform catalysis via an epoxide intermediate, similar to GH99 enzymes <cite>Thompson2012 Fernandes2018</cite>. GH145, however, is proposed to perform catalysis via a substrate assisted mechanism, requiring the carboxyl group of the glucuronic acid and a single catalytic histidine; both acting as an acid/base. This histidine is predicted to deprotonate the O2 of rhamnose, allowing O2 to attack C1 and form an epoxide. Simultaneously the carboxyl group of the glucuronic acid may deprotonate a water molecule generating a hydroxyl group to attach the C1 of rhamnose and allowing protonation of its own O4 thus, leading to glycosidic bond cleavage <cite>Munoz-Munoz2017</cite>. Further work is needed to confirm the mechanism by which GH145 operates. <br />
<br />
== Catalytic Residues ==<br />
A single catalytic histidine has been shown to be critical for activity. The introduction of the catalytic histidine into related enzymes, which lack the histidine and rhamnosidase activity, is sufficient to introduce rhamnosidase activity into these enzymes <cite>Munoz-Munoz2017</cite>.<br />
<br />
== Three-dimensional structures ==<br />
GH145 comprise a single domain which is a seven bladed β-propeller fold. Each blade is composed of four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. The active site of these α-L-rhamnosidases is located on the opposite side, termed the posterior surface, of CAZymes with similar β-propeller folds. The "normal" side, termed the anterior surface, of the β-propeller bears the highest residue conservation and may well have another function. GH145 is distantly related to [[PL25]] which utilise the anterior surface suggesting that the this surface in GH145 may have another activity <cite>Munoz-Munoz2017 Ulaganathan2017</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Determined for the ''bacteroides thetaiotaomicron'' enzyme BT3686 <cite>Munoz-Munoz2017</cite>.<br />
;First catalytic acid/base residue identification: Predicted to be a histidine <cite>Munoz-Munoz2017</cite>.<br />
;Second general acid/base residue identification: Predicted to be provided by the substrate <cite>Munoz-Munoz2017</cite>.<br />
;First 3-D structure: BT3686, BACINT_00347 and BACCELL_00856 were the first enzymes to have their structures solved from the organisms ''bacteroides thetaiotaomicron'', ''bacteroides intestinalis'' and ''bacteroides cellulosilyticus'', respectively. <cite>Munoz-Munoz2017</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Munoz-Munoz2017 pmid=28396425<br />
#Cartmell2019 pmid=31541200<br />
#Thompson2012 pmid=22219371<br />
#Fernandes2018 pmid=29508463<br />
#Ulaganathan2017 pmid=28290654<br />
</biblio><br />
<br />
<br />
[[Category:Glycoside Hydrolase Families|GH145]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_140&diff=14831Glycoside Hydrolase Family 1402020-05-11T19:17:16Z<p>Alan Cartmell: </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]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Alan Cartmell^^^<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 GH140'''<br />
|-<br />
|'''Clan''' <br />
|No clan assigned<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}}GH140.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Thus far only one member of the family has been characterised, BT1012 from bacteroides thetaiotaomicron. BT1012 displays endo-apiosidase activity targeting α1,2 linked apiose at the base of the sidechains A and B in the complex glycan rhamnogalacturonan ii (RGII) <cite>Ndeh2017</cite>. Cleavage of the RGII backbone must occur before BT1012 can act <cite>Ndeh2017</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH140 likely uses a, retaining, double displacement mechanism. This is strongly supported by methanolysis experiments where BT1012 was incubated with trisaccharide L-rhamnose-β1,3-D-apiose-α1,2-D-galacturonic acid-O-methyl in the presence of 10 % methanol. This experiment performed with BT1012 generated the product L-rhamnose-β1,3-D-apiose-O-methyl suggesting a retaining mechanism <cite>Ndeh2017</cite>. Glycoside hydrolases that utilise a retaining mechanism, but not those that use an inverting mechanism, can utilise methanol as an external nucleophile and thus generate a methylated product. <br />
<br />
== Catalytic Residues ==<br />
The catalytic residues are an aspartate and glutamate located on the top of β-strands 4 and 7, respectively <cite>Ndeh2017</cite>. This could mean GH140 is a distant relative of Clan GH-A enzymes, however in with GH-A the catalytic residue atop of β-strands 4 and 7 are both glutamates. In the absence of a ligand bound complex or more detailed biochemical analysis <cite>Shallom2002</cite> (preferably both) it is not possible to say which of the catalytic residues is the nucleophile or acid/base.<br />
<br />
== Three-dimensional structures ==<br />
GH140 adopts a (β/α)<sub>8</sub> , TIM barrel, where a central barrel of eight β strands are encircled by eight α helices <cite>Ndeh2017</cite>. BT1012, the only GH140 structure available, also has a Ig like domain that stacks against the TIM barrel likely providing structural stability, similar to the role of Ig like domains in [[GH43]] enzymes <cite>McKee2012 Cartmell2011</cite>. <br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Methanolysis experiments suggest a retaining mechanism <cite>Ndeh2017</cite>.<br />
;First catalytic nucleophile identification: Not known.<br />
;First general acid/base residue identification: Not Known.<br />
;First 3-D structure: BT1012 from ''Bacteroides thetaiotaomicron'' <cite>Ndeh2017</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Ndeh2017 pmid=28329766<br />
#Shallom2002 pmid=12221104<br />
#McKee2012 pmid=22492980<br />
#Cartmell2011 pmid=21339299<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH140]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_140&diff=14830Glycoside Hydrolase Family 1402020-05-11T19:15:27Z<p>Alan Cartmell: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<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 GH140'''<br />
|-<br />
|'''Clan''' <br />
|GH-x<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}}GH140.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Thus far only one member of the family has been characterised, BT1012 from bacteroides thetaiotaomicron. BT1012 displays endo-apiosidase activity targeting α1,2 linked apiose at the base of the sidechains A and B in the complex glycan rhamnogalacturonan ii (RGII) <cite>Ndeh2017</cite>. Cleavage of the RGII backbone must occur before BT1012 can act <cite>Ndeh2017</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH140 likely uses a, retaining, double displacement mechanism. This is strongly supported by methanolysis experiments where BT1012 was incubated with trisaccharide L-rhamnose-β1,3-D-apiose-α1,2-D-galacturonic acid-O-methyl in the presence of 10 % methanol. This experiment performed with BT1012 generated the product L-rhamnose-β1,3-D-apiose-O-methyl suggesting a retaining mechanism <cite>Ndeh2017</cite>. Glycoside hydrolases that utilise a retaining mechanism, but not those that use an inverting mechanism, can utilise methanol as an external nucleophile and thus generate a methylated product. <br />
<br />
== Catalytic Residues ==<br />
The catalytic residues are an aspartate and glutamate located on the top of β-strands 4 and 7, respectively <cite>Ndeh2017</cite>. This could mean GH140 is a distant relative of Clan GH-A enzymes, however in with GH-A the catalytic residue atop of β-strands 4 and 7 are both glutamates. In the absence of a ligand bound complex or more detailed biochemical analysis <cite>Shallom2002</cite> (preferably both) it is not possible to say which of the catalytic residues is the nucleophile or acid/base.<br />
<br />
== Three-dimensional structures ==<br />
GH140 adopts a (β/α)<sub>8</sub> , TIM barrel, where a central barrel of eight β strands are encircled by eight α helices <cite>Ndeh2017</cite>. BT1012, the only GH140 structure available, also has a Ig like domain that stacks against the TIM barrel likely providing structural stability, similar to the role of Ig like domains in [[GH43]] enzymes <cite>McKee2012 Cartmell2011</cite>. <br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Methanolysis experiments suggest a retaining mechanism <cite>Ndeh2017</cite>.<br />
;First catalytic nucleophile identification: Not known.<br />
;First general acid/base residue identification: Not Known.<br />
;First 3-D structure: BT1012 from ''Bacteroides thetaiotaomicron'' <cite>Ndeh2017</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Ndeh2017 pmid=28329766<br />
#Shallom2002 pmid=12221104<br />
#McKee2012 pmid=22492980<br />
#Cartmell2011 pmid=21339299<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH140]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_145&diff=14829Glycoside Hydrolase Family 1452020-05-11T19:10:54Z<p>Alan Cartmell: </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]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Alan Cartmell^^^<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 />
<br />
{| {{Prettytable}}<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH145'''<br />
|-<br />
| '''Clan'''<br />
| No clan assigned<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}}GH145.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
== Substrate specificities ==<br />
Two members of this family have been shown to be an exo-α-L-rhamnosidases, targeting rhamnose linked α-1,4 to glucuronic acid in the complex arabinogalactan protein gum arabic <cite>Munoz-Munoz2017 Cartmell2019</cite>. <br />
<br />
== Kinetics and Mechanism ==<br />
NMR, using the arabinogalactan protein (AGP) gum arabic as the substrate, revealed the family operates via a retaining mechanism <cite>Munoz-Munoz2017</cite>. Rather than using a standard double displacement mechanism the enzyme is speculatively predicted to perform catalysis via an epoxide intermediate, similar to GH99 enzymes <cite>Thompson2012 Fernandes2018</cite>. GH145, however, is proposed to perform catalysis via a substrate assisted mechanism, requiring the carboxyl group of the glucuronic acid and a single catalytic histidine; both acting as an acid/base. This histidine is predicted to deprotonate the O2 of rhamnose, allowing O2 to attack C1 and form an epoxide. Simultaneously the carboxyl group of the glucuronic acid may deprotonate a water molecule generating a hydroxyl group to attach the C1 of rhamnose and allowing protonation of its own O4 thus, leading to glycosidic bond cleavage <cite>Munoz-Munoz2017</cite>. Further work is needed to confirm the mechanism by which GH145 operates. <br />
<br />
== Catalytic Residues ==<br />
A single catalytic histidine has been shown to be critical for activity. The introduction of the catalytic histidine into related enzymes, which lack the histidine and rhamnosidase activity, is sufficient to introduce rhamnosidase activity into these enzymes <cite>Munoz-Munoz2017</cite>.<br />
<br />
== Three-dimensional structures ==<br />
GH145 comprise a single domain which is a seven bladed β-propeller fold. Each blade is composed of four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. The active site of these α-L-rhamnosidases is located on the opposite side, termed the posterior surface, of CAZymes with similar β-propeller folds. The "normal" side, termed the anterior surface, of the β-propeller bears the highest residue conservation and may well have another function. GH145 is distantly related to [[PL25]] which utilise the anterior surface suggesting that the this surface in GH145 may have another activity <cite>Munoz-Munoz2017 Ulaganathan2017</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Determined for the ''bacteroides thetaiotaomicron'' enzyme BT3686 <cite>Munoz-Munoz2017</cite>.<br />
;First catalytic acid/base residue identification: Predicted to be a histidine <cite>Munoz-Munoz2017</cite>.<br />
;Second general acid/base residue identification: Predicted to be provided by the substrate <cite>Munoz-Munoz2017</cite>.<br />
;First 3-D structure: BT3686, BACINT_00347 and BACCELL_00856 were the first enzymes to have their structures solved from the organisms ''bacteroides thetaiotaomicron'', ''bacteroides intestinalis'' and ''bacteroides cellulosilyticus'', respectively. <cite>Munoz-Munoz2017</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Munoz-Munoz2017 pmid=28396425<br />
#Cartmell2019 pmid=31541200<br />
#Thompson2012 pmid=22219371<br />
#Fernandes2018 pmid=29508463<br />
#Ulaganathan2017 pmid=28290654<br />
</biblio><br />
<br />
<br />
[[Category:Glycoside Hydrolase Families|GH145]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_145&diff=14828Glycoside Hydrolase Family 1452020-05-11T19:09:26Z<p>Alan Cartmell: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Alan Cartmell^^^<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 />
<br />
{| {{Prettytable}}<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH145'''<br />
|-<br />
| '''Clan'''<br />
| No clan assigned<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}}GH145.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
== Substrate specificities ==<br />
Two members of this family have been shown to be an exo-α-L-rhamnosidases, targeting rhamnose linked α-1,4 to glucuronic acid in the complex arabinogalactan protein gum arabic <cite>Munoz-Munoz2017 Cartmell2019</cite>. <br />
<br />
== Kinetics and Mechanism ==<br />
NMR, using the arabinogalactan protein (AGP) gum arabic as the substrate, revealed the family operates via a retaining mechanism <cite>Munoz-Munoz2017</cite>. Rather than using a standard double displacement mechanism the enzyme is speculatively predicted to perform catalysis via an epoxide intermediate, similar to GH99 enzymes <cite>Thompson2012 Fernandes2018</cite>. GH145, however, is proposed to perform catalysis via a substrate assisted mechanism, requiring the carboxyl group of the glucuronic acid and a single catalytic histidine; both acting as an acid/base. This histidine is predicted to deprotonate the O2 of rhamnose, allowing O2 to attack C1 and form an epoxide. Simultaneously the carboxyl group of the glucuronic acid may deprotonate a water molecule generating a hydroxyl group to attach the C1 of rhamnose and allowing protonation of its own O4 thus, leading to glycosidic bond cleavage <cite>Munoz-Munoz2017</cite>. Further work is needed to confirm the mechanism by which GH145 operates. <br />
<br />
== Catalytic Residues ==<br />
A single catalytic histidine has been shown to be critical for activity. The introduction of the catalytic histidine into related enzymes, which lack the histidine and rhamnosidase activity, is sufficient to introduce rhamnosidase activity into these enzymes <cite>Munoz-Munoz2017</cite>.<br />
<br />
== Three-dimensional structures ==<br />
GH145 comprise a single domain which is a seven bladed β-propeller fold. Each blade is composed of four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. The active site of these α-L-rhamnosidases is located on the opposite side, termed the posterior surface, of CAZymes with similar β-propeller folds. The "normal" side, termed the anterior surface, of the β-propeller bears the highest residue conservation and may well have another function. GH145 is distantly related to [[PL25]] which utilise the anterior surface suggesting that the this surface in GH145 may have another activity <cite>Munoz-Munoz2017 Ulaganathan2017</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Determined for the ''bacteroides thetaiotaomicron'' enzyme BT3686 <cite>Munoz-Munoz2017</cite>.<br />
;First catalytic acid/base residue identification: Predicted to be a histidine <cite>Munoz-Munoz2017</cite>.<br />
;Second general acid/base residue identification: Predicted to be provided by the substrate <cite>Munoz-Munoz2017</cite>.<br />
;First 3-D structure: BT3686, BACINT_00347 and BACCELL_00856 were the first enzymes to have their structures solved from the organisms ''bacteroides thetaiotaomicron'', ''bacteroides intestinalis'' and ''bacteroides cellulosilyticus'', respectively. <cite>Munoz-Munoz2017</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Munoz-Munoz2017 pmid=28396425<br />
#Cartmell2019 pmid=31541200<br />
#Thompson2012 pmid=22219371<br />
#Fernandes2018 pmid=29508463<br />
#Ulaganathan2017 pmid=28290654<br />
</biblio><br />
<br />
<br />
[[Category:Glycoside Hydrolase Families|GH145]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_145&diff=14827Glycoside Hydrolase Family 1452020-05-11T19:09:03Z<p>Alan Cartmell: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<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 />
<br />
{| {{Prettytable}}<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH145'''<br />
|-<br />
| '''Clan'''<br />
| No clan assigned<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}}GH145.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
== Substrate specificities ==<br />
Two members of this family have been shown to be an exo-α-L-rhamnosidases, targeting rhamnose linked α-1,4 to glucuronic acid in the complex arabinogalactan protein gum arabic <cite>Munoz-Munoz2017 Cartmell2019</cite>. <br />
<br />
== Kinetics and Mechanism ==<br />
NMR, using the arabinogalactan protein (AGP) gum arabic as the substrate, revealed the family operates via a retaining mechanism <cite>Munoz-Munoz2017</cite>. Rather than using a standard double displacement mechanism the enzyme is speculatively predicted to perform catalysis via an epoxide intermediate, similar to GH99 enzymes <cite>Thompson2012 Fernandes2018</cite>. GH145, however, is proposed to perform catalysis via a substrate assisted mechanism, requiring the carboxyl group of the glucuronic acid and a single catalytic histidine; both acting as an acid/base. This histidine is predicted to deprotonate the O2 of rhamnose, allowing O2 to attack C1 and form an epoxide. Simultaneously the carboxyl group of the glucuronic acid may deprotonate a water molecule generating a hydroxyl group to attach the C1 of rhamnose and allowing protonation of its own O4 thus, leading to glycosidic bond cleavage <cite>Munoz-Munoz2017</cite>. Further work is needed to confirm the mechanism by which GH145 operates. <br />
<br />
== Catalytic Residues ==<br />
A single catalytic histidine has been shown to be critical for activity. The introduction of the catalytic histidine into related enzymes, which lack the histidine and rhamnosidase activity, is sufficient to introduce rhamnosidase activity into these enzymes <cite>Munoz-Munoz2017</cite>.<br />
<br />
== Three-dimensional structures ==<br />
GH145 comprise a single domain which is a seven bladed β-propeller fold. Each blade is composed of four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. The active site of these α-L-rhamnosidases is located on the opposite side, termed the posterior surface, of CAZymes with similar β-propeller folds. The "normal" side, termed the anterior surface, of the β-propeller bears the highest residue conservation and may well have another function. GH145 is distantly related to [[PL25]] which utilise the anterior surface suggesting that the this surface in GH145 may have another activity <cite>Munoz-Munoz2017 Ulaganathan2017</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Determined for the ''bacteroides thetaiotaomicron'' enzyme BT3686 <cite>Munoz-Munoz2017</cite>.<br />
;First catalytic acid/base residue identification: Predicted to be a histidine <cite>Munoz-Munoz2017</cite>.<br />
;Second general acid/base residue identification: Predicted to be provided by the substrate <cite>Munoz-Munoz2017</cite>.<br />
;First 3-D structure: BT3686, BACINT_00347 and BACCELL_00856 were the first enzymes to have their structures solved from the organisms ''bacteroides thetaiotaomicron'', ''bacteroides intestinalis'' and ''bacteroides cellulosilyticus'', respectively. <cite>Munoz-Munoz2017</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Munoz-Munoz2017 pmid=28396425<br />
#Cartmell2019 pmid=31541200<br />
#Thompson2012 pmid=22219371<br />
#Fernandes2018 pmid=29508463<br />
#Ulaganathan2017 pmid=28290654<br />
</biblio><br />
<br />
<br />
[[Category:Glycoside Hydrolase Families|GH145]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_145&diff=14826Glycoside Hydrolase Family 1452020-05-11T19:08:07Z<p>Alan Cartmell: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<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 />
<br />
{| {{Prettytable}}<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH145'''<br />
|-<br />
| '''Clan'''<br />
| No assigned clan<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}}GH145.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
== Substrate specificities ==<br />
Two members of this family have been shown to be an exo-α-L-rhamnosidases, targeting rhamnose linked α-1,4 to glucuronic acid in the complex arabinogalactan protein gum arabic <cite>Munoz-Munoz2017 Cartmell2019</cite>. <br />
<br />
== Kinetics and Mechanism ==<br />
NMR, using the arabinogalactan protein (AGP) gum arabic as the substrate, revealed the family operates via a retaining mechanism <cite>Munoz-Munoz2017</cite>. Rather than using a standard double displacement mechanism the enzyme is speculatively predicted to perform catalysis via an epoxide intermediate, similar to GH99 enzymes <cite>Thompson2012 Fernandes2018</cite>. GH145, however, is proposed to perform catalysis via a substrate assisted mechanism, requiring the carboxyl group of the glucuronic acid and a single catalytic histidine; both acting as an acid/base. This histidine is predicted to deprotonate the O2 of rhamnose, allowing O2 to attack C1 and form an epoxide. Simultaneously the carboxyl group of the glucuronic acid may deprotonate a water molecule generating a hydroxyl group to attach the C1 of rhamnose and allowing protonation of its own O4 thus, leading to glycosidic bond cleavage <cite>Munoz-Munoz2017</cite>. Further work is needed to confirm the mechanism by which GH145 operates. <br />
<br />
== Catalytic Residues ==<br />
A single catalytic histidine has been shown to be critical for activity. The introduction of the catalytic histidine into related enzymes, which lack the histidine and rhamnosidase activity, is sufficient to introduce rhamnosidase activity into these enzymes <cite>Munoz-Munoz2017</cite>.<br />
<br />
== Three-dimensional structures ==<br />
GH145 comprise a single domain which is a seven bladed β-propeller fold. Each blade is composed of four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. The active site of these α-L-rhamnosidases is located on the opposite side, termed the posterior surface, of CAZymes with similar β-propeller folds. The "normal" side, termed the anterior surface, of the β-propeller bears the highest residue conservation and may well have another function. GH145 is distantly related to [[PL25]] which utilise the anterior surface suggesting that the this surface in GH145 may have another activity <cite>Munoz-Munoz2017 Ulaganathan2017</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Determined for the ''bacteroides thetaiotaomicron'' enzyme BT3686 <cite>Munoz-Munoz2017</cite>.<br />
;First catalytic acid/base residue identification: Predicted to be a histidine <cite>Munoz-Munoz2017</cite>.<br />
;Second general acid/base residue identification: Predicted to be provided by the substrate <cite>Munoz-Munoz2017</cite>.<br />
;First 3-D structure: BT3686, BACINT_00347 and BACCELL_00856 were the first enzymes to have their structures solved from the organisms ''bacteroides thetaiotaomicron'', ''bacteroides'intestinalis'' and ''bacteroides cellulosilyticus'', <cite>Munoz-Munoz2017</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Munoz-Munoz2017 pmid=28396425<br />
#Cartmell2019 pmid=31541200<br />
#Thompson2012 pmid=22219371<br />
#Fernandes2018 pmid=29508463<br />
#Ulaganathan2017 pmid=28290654<br />
</biblio><br />
<br />
<br />
[[Category:Glycoside Hydrolase Families|GH145]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=User:Alan_Cartmell&diff=14490User:Alan Cartmell2020-01-25T16:35:29Z<p>Alan Cartmell: </p>
<hr />
<div>[[Image:Blank_user-200px.png|200px|right]]<br />
Alan Cartmell did his B.Sc. in Biochemistry at Newcastle University and then completed both an M.Res and Ph.D under the supervision of Professor Harry Gilbert. The work during his doctoral studies focused on structure/function studies of novel glycoside hydrolases from GH26, GH43 and GH124 families. He then undertook a two year postdoctoral fellowship at the La Jolla institute for Allergy and Immunology in the laboratory of Professor Dirk Zajonc. The position was funded by a juvenile diabetes research foundation junior postdoctoral fellowship and focussed on the class I tyrosine phosphatase PTPN22 involved in type 1 diabetes. He then had a temporary 3 month position in the laboratory of Professor Spencer Williams focusing on elucidating the mechanism of action of GH76 enzymes. After this short spell with Professor Williams he returned to Professor Gilberts laboratory where he worked on elucidating how members of the human gut microbiota (HGM) catabolised plant glycans (Pectins and Arabinogalactans) from the human diet. I am currently a Tenure-Track Fellow at the University of Liverpool with a recent focus on exploring how sulfated glycans, such as glycosaminoglycans and sulfomucin, are metabolised by the HGM and the host itself.<br />
<br />
----<br />
<br />
<biblio><br />
#Gilbert2008 pmid=18430603<br />
<br />
</biblio><br />
<br />
<!-- Do not remove this Category tag --><br />
[[Category:Contributors|Cartmell,Alan]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=User:Alan_Cartmell&diff=14489User:Alan Cartmell2020-01-25T16:33:21Z<p>Alan Cartmell: </p>
<hr />
<div>[[Image:Blank_user-200px.png|200px|right]]<br />
Alan Cartmell did his B.Sc. in Biochemistry at Newcastle University and then completed both an M.Res and Ph.D under the supervision of Professor Harry Gilbert. The work during his doctoral studies focused on structure/function studies of novel glycoside hydrolases from GH26, GH43 and GH124 families. He then undertook a two year postdoctoral fellowship at the La Jolla institute for Allergy and Immunology in the laboratory of Professor Dirk Zajonc. The position was funded by a juvenile diabetes research foundation junior postdoctoral fellowship and focussed on the class I tyrosine phosphatase PTPN22 involved in type 1 diabetes. He then had a temporary 3 month position in the laboratory of Professor Spencer Williams focusing on elucidating the mechanism of action of GH76 enzymes. After this short spell with Professor Williams he returned to Professor Gilberts laboratory where he work on elucidating how members of the human gut microbiota (HGM) catabolised plant glycans (Pectins and Arabinogalactans) from the human diet. I am currently a Tenure-Track Fellow at the University of Liverpool with a recent focus on exploring how sulfated glycans such as glycosaminoglycans and sulfomucin are metabolised by the HGM and the host itself.<br />
<br />
----<br />
<br />
<biblio><br />
#Gilbert2008 pmid=18430603<br />
<br />
</biblio><br />
<br />
<!-- Do not remove this Category tag --><br />
[[Category:Contributors|Cartmell,Alan]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_145&diff=14488Glycoside Hydrolase Family 1452020-01-25T16:05:52Z<p>Alan Cartmell: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<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 />
<br />
{| {{Prettytable}}<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH145'''<br />
|-<br />
| '''Clan'''<br />
| GH-x<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}}GH145.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
== Substrate specificities ==<br />
Two members of this family have been shown to be an exo-α-L-rhamnosidases, targeting rhamnose linked α-1,4 to glucuronic acid in the complex arabinogalactan protein gum arabic <cite>Munoz-Munoz2017 Cartmell2019</cite>. <br />
<br />
== Kinetics and Mechanism ==<br />
NMR, using the arabinogalactan protein (AGP) gum arabic as the substrate, revealed the family operates via a retaining mechanism<cite>Munoz-Munoz2017</cite>. Rather than using a standard double displacement mechanism the enzyme is speculatively predicted to perform catalysis via an epoxide intermediate, similar to GH99 enzymes<cite>Thompson2012 Fernandes2018</cite>. GH145, however, is proposed to perform catalysis via a substrate assisted mechanism, requiring the carboxyl group of the glucuronic acid and a single catalytic histidine; both acting as an acid/base. This histidine is predicted to deprotonate the O2 of rhamnose, allowing O2 to attack C1 and form an epoxide. Simultaneously the carboxyl group of the glucuronic acid may deprotonate a water molecule generating a hydroxyl group to attach the C1 of rhamnose and allowing protonation of its own O4 thus, leading to glycosidic bond cleavage<cite>Munoz-Munoz2017</cite>. Further work is needed to confirm the mechanism by which GH145 operates. <br />
<br />
<br />
== Catalytic Residues ==<br />
A single catalytic histidine has been shown to be critical for activity. The introduction of the catalytic histidine into related enzymes, which lack the histidine and rhamnosidase activity, is sufficient to introduce rhamnosidase activity into these enzymes<cite>Munoz-Munoz2017</cite>.<br />
<br />
== Three-dimensional structures ==<br />
GH145 comprise a single domain which is a seven bladed β-propeller fold. Each blade is composed of four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. The active site of these α-L-rhamnosidases is located on the opposite side, termed the posterior surface, of CAZymes with similar β-propeller folds. The "normal" side, termed the anterior surface, of the β-propeller bears the highest residue conservation and may well have another function. GH145 is distantly related to PL25 which utilise the anterior surface suggesting that the this surface in GH145 may have another activity<cite>Munoz-Munoz2017 Ulaganathan2017</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Determined for the bacteroides thetaiotaomicron enzyme BT3686<cite>Munoz-Munoz2017</cite>.<br />
;First catalytic acid/base residue identification: Predicted to be a histidine<cite>Munoz-Munoz2017</cite>.<br />
;Second general acid/base residue identification: Predicted to be provided by the substrate<cite>Munoz-Munoz2017</cite>.<br />
;First 3-D structure: BT3686, BACINT_00347 and BACCELL_00856 were the first enzymes to have their structures solved<cite>Munoz-Munoz2017</cite>.<br />
<br />
<br />
<br />
== References ==<br />
<biblio><br />
#Munoz-Munoz2017 pmid=28396425<br />
#Cartmell2019 pmid=31541200<br />
#Thompson2012 pmid=22219371<br />
#Fernandes2018 pmid=29508463<br />
#Ulaganathan2017 pmid=28290654<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].<br />
</biblio><br />
<br />
<br />
[[Category:Glycoside Hydrolase Families|GH145]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_145&diff=14487Glycoside Hydrolase Family 1452020-01-25T16:05:34Z<p>Alan Cartmell: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<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 />
<br />
{| {{Prettytable}}<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH145'''<br />
|-<br />
| '''Clan'''<br />
| GH-x<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}}GH145.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
== Substrate specificities ==<br />
Two members of this family have been shown to be an exo-α-L-rhamnosidases, targeting rhamnose linked α-1,4 to glucuronic acid in the complex arabinogalactan protein gum arabic <cite>Munoz-Munoz2017 Cartmell2019</cite>. <br />
<br />
== Kinetics and Mechanism ==<br />
NMR, using the arabinogalactan protein (AGP) gum arabic as the substrate, revealed the family operates via a retaining mechanism<cite>Munoz-Munoz2017</cite>. Rather than using a standard double displacement mechanism the enzyme is speculatively predicted to perform catalysis via an epoxide intermediate, similar to GH99 enzymes<cite>Thompson2012 Fernandes2018</cite>. GH145, however, is proposed to perform catalysis via a substrate assisted mechanism, requiring the carboxyl group of the glucuronic acid and a single catalytic histidine; both acting as an acid/base. This histidine is predicted to deprotonate the O2 of rhamnose, allowing O2 to attack C1 and form an epoxide. Simultaneously the carboxyl group of the glucuronic acid may deprotonate a water molecule generating a hydroxyl group to attach the C1 of rhamnose and allowing protonation of its own O4 thus, leading to glycosidic bond cleavage<cite>Munoz-Munoz2017</cite>. Further work is needed to confirm the mechanism by which GH145 operates. <br />
<br />
<br />
== Catalytic Residues ==<br />
A single catalytic histidine has been shown to be critical for activity. The introduction of the catalytic histidine into related enzymes, which lack the histidine and rhamnosidase activity, is sufficient to introduce rhamnosidase activity into these enzymes<cite>Munoz-Munoz2017</cite>.<br />
<br />
== Three-dimensional structures ==<br />
GH145 comprise a single domain which is a seven bladed β-propeller fold. Each blade is composed of four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. The active site of these α-L-rhamnosidases is located on the opposite side, termed the posterior surface, of CAZymes with similar β-propeller folds. The "normal" side, termed the anterior surface, of the β-propeller bears the highest residue conservation and may well have another function. GH145 is distantly related to PL25 which utilise the anterior surface suggesting that the this surface in GH145 may have another activity<cite>Munoz-Munoz2017 Ulaganathan2017</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Determined for the bacteroides thetaiotaomicron enzyme BT3686<cite>Munoz-Munoz2017</cite>.<br />
;First catalytic acid/base residue identification: Predicted to be a histidine<cite>Munoz-Munoz2017</cite>.<br />
;Second general acid/base residue identification: Predicted to be provided by the substrate<cite>Munoz-Munoz2017</cite>.<br />
;First 3-D structure: BT3686, BACINT_00347 and BACCELL_00856 were the first enzymes to have their structures solved<cite>Munoz-Munoz2017</cite>.<br />
<br />
<br />
<br />
== References ==<br />
<references/><biblio><br />
#Munoz-Munoz2017 pmid=28396425<br />
#Cartmell2019 pmid=31541200<br />
#Thompson2012 pmid=22219371<br />
#Fernandes2018 pmid=29508463<br />
#Ulaganathan2017 pmid=28290654<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].<br />
</biblio><br />
<br />
<br />
[[Category:Glycoside Hydrolase Families|GH145]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_140&diff=14486Glycoside Hydrolase Family 1402020-01-25T16:04:59Z<p>Alan Cartmell: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<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 GH140'''<br />
|-<br />
|'''Clan''' <br />
|GH-x<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}}GH140.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Thus far only one member of the family has been characterised, BT1012 from bacteroides thetaiotaomicron. BT1012 displays endo-apiosidase activity targeting α1,2 linked apiose at the base of the sidechains A and B in the complex glycan rhamnogalacturonan ii (RGII)<cite>Ndeh2017</cite>. Cleavage of the RGII backbone must occur before BT1012 can act<cite>Ndeh2017</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH140 likely uses a, retaining, double displacement mechanism. This is strongly supported by methanolysis experiments where BT1012 was incubated with trisaccharide L-rhamnose-β1,3-D-apiose-α1,2-D-galacturonic acid-O-methyl in the presence of 10 % methanol. This experiment performed with BT1012 generated the product L-rhamnose-β1,3-D-apiose-O-methyl suggesting a retaining mechanism<cite>Ndeh2017</cite>. Glycoside hydrolases that utilise a retaining mechanism, but not those that use an inverting mechanism, can utilise methanol as an external nucleophile and thus generate a methylated product. <br />
<br />
== Catalytic Residues ==<br />
The catalytic residues are an aspartate and glutamate located on the top of β-strands 4 and 7, respectively<cite>Ndeh2017</cite>. This could mean GH140 is a distant relative of Clan GH-A enzymes, however in with GH-A the catalytic residue atop of β-strands 4 and 7 are both glutamates. In the absence of a ligand bound complex or more detailed biochemical analysis <cite>Shallom2002</cite> (preferably both) it is not possible to say which of the catalytic residues is the nucleophile or acid/base.<br />
<br />
== Three-dimensional structures ==<br />
GH140 adopts a (β/α)<sub>8</sub> , TIM barrel, where a central barrel of eight β strands are encircled by eight α helices<cite>Ndeh2017</cite>. BT1012, the only GH140 structure available, also has a Ig like domain that stacks against the TIM barrel likely providing structural stability, similar to the role of Ig like domains in GH43 enzymes<cite>McKee2012 Cartmell2011</cite>. <br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Methanolysis experiments suggest a retaining mechanism<cite>Ndeh2017</cite>.<br />
;First catalytic nucleophile identification: Not known.<br />
;First general acid/base residue identification: Not Known.<br />
;First 3-D structure: BT1012 from bacteroides thetaiotaomicron<cite>Ndeh2017</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Ndeh2017 pmid=28329766<br />
#Shallom2002 pmid=12221104<br />
#McKee2012 pmid=22492980<br />
#Cartmell2011 pmid=21339299<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH140]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_137&diff=14485Glycoside Hydrolase Family 1372020-01-25T16:02:06Z<p>Alan Cartmell: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<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 GH137'''<br />
|-<br />
|'''Clan''' <br />
|GH-x<br />
|-<br />
|'''Mechanism'''<br />
|Unknown<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH137.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
The only activity identified to date is β-L-arabinofuranosidase activity displayed by the enzyme BT0996. This enzyme removes β linked L-arabinose from the terminus of side chain B in the complex glycan rhamnogalacturonan ii (RGII)<cite>Ndeh2017</cite>.<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
Unknown <br />
<br />
== Catalytic Residues ==<br />
The catalytic residues were shown to be a pair of glutamates. They sit around 6 Angstroms apart. Typically retaining enzymes are expected to have their catalytic residues ~5.5 Angstroms apart, whilst in inverting enzymes they are expected to be ~10 Angstroms apart. Glu159 sits beneath the alpha face of the -1 β-linked arabinose, 3.2 Angstroms from the anomeric carbon, placing it in a an ideal position to act as a catalytic nucleophile. Glu240 resides 5 Angstroms from the glycosidic oxygen which somewhat far to act as catalytic acid/base in a retaining mechanism. Alternatively, one could also speculate that at a distance of 4.6 Angstroms from the anomeric carbon Glu240 could potentially act as a catalytic base in an inverting mechanism, with Glu159 acting as the catalytic acid being at a distance of 3.7 Angstroms from the glycosidic oxygen<cite>Ndeh2017</cite>. <br />
<br />
== Three-dimensional structures ==<br />
The structure of BT0996 comprises a single domain which is a five bladed β-propeller fold. Each blade is composed of three to four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. It should be noted that BT0996 is appended to a GH2 from clan GHA. This GH2 targets β-D-GlcA linkage in Chain A of RGII<cite>Ndeh2017</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Not Known.<br />
;First catalytic nucleophile/base identification: Inferred to be Glu159 in BT0996 <cite>Ndeh2017</cite>.<br />
;First general acid/base residue identification: Inferred to be Glu240 in BT0996<cite>Ndeh2017</cite>.<br />
;First 3-D structure: The first structure determination for GH137 was of BT0996 from the organism ''Bacteroides thetaiotaomicon''<cite>Ndeh2017</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Ndeh2017 pmid=28329766<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].<br />
<br />
[[Category:Glycoside Hydrolase Families|GH137]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_137&diff=14484Glycoside Hydrolase Family 1372020-01-25T15:57:33Z<p>Alan Cartmell: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<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 GH137'''<br />
|-<br />
|'''Clan''' <br />
|GH-x<br />
|-<br />
|'''Mechanism'''<br />
|Unknown<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH137.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
Unknown <br />
<br />
== Catalytic Residues ==<br />
The catalytic residues were shown to be a pair of glutamates. They sit around 6 Angstroms apart. Typically retaining enzymes are expected to have their catalytic residues ~5.5 Angstroms apart, whilst in inverting enzymes they are expected to be ~10 Angstroms apart. Glu159 sits beneath the alpha face of the -1 β-linked arabinose, 3.2 Angstroms from the anomeric carbon, placing it in a an ideal position to act as a catalytic nucleophile. Glu240 resides 5 Angstroms from the glycosidic oxygen which somewhat far to act as catalytic acid/base in a retaining mechanism. Alternatively, one could also speculate that at a distance of 4.6 Angstroms from the anomeric carbon Glu240 could potentially act as a catalytic base in an inverting mechanism, with Glu159 acting as the catalytic acid being at a distance of 3.7 Angstroms from the glycosidic oxygen. <br />
<br />
== Three-dimensional structures ==<br />
The structure of BT0996 comprises a single domain which is a five bladed β-propeller fold. Each blade is composed of three to four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. It should be noted that BT0996 is appended to a GH2 from clan GHA. This GH2 targets β-D-GlcA linkage in Chain A of RGII.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Not Known.<br />
;First catalytic nucleophile/base identification: Inferred to be Glu159 in BT0996 <cite>Ndeh2017</cite>.<br />
;First general acid/base residue identification: Inferred to be Glu240 in BT0996<cite>Ndeh2017</cite>.<br />
;First 3-D structure: The first structure determination for GH137 was of BT0996 from the organism ''Bacteroides thetaiotaomicon''<cite>Ndeh2017</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Ndeh2017 pmid=28329766<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].<br />
<br />
[[Category:Glycoside Hydrolase Families|GH137]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_137&diff=14483Glycoside Hydrolase Family 1372020-01-25T15:56:53Z<p>Alan Cartmell: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<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 GH137'''<br />
|-<br />
|'''Clan''' <br />
|GH-x<br />
|-<br />
|'''Mechanism'''<br />
|Unknown<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH137.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 />
Authors may get an idea of what to put in each field from ''Curator Approved'' [[Glycoside Hydrolase Families]]. ''(TIP: Right click with your mouse and open this link in a new browser window...)''<br />
<br />
In the meantime, please see these references for an essential introduction to the CAZy classification system: <cite>DaviesSinnott2008 Cantarel2009</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Unknown <br />
<br />
== Catalytic Residues ==<br />
The catalytic residues were shown to be a pair of glutamates. They sit around 6 Angstroms apart. Typically retaining enzymes are expected to have their catalytic residues ~5.5 Angstroms apart, whilst in inverting enzymes they are expected to be ~10 Angstroms apart. Glu159 sits beneath the alpha face of the -1 β-linked arabinose, 3.2 Angstroms from the anomeric carbon, placing it in a an ideal position to act as a catalytic nucleophile. Glu240 resides 5 Angstroms from the glycosidic oxygen which somewhat far to act as catalytic acid/base in a retaining mechanism. Alternatively, one could also speculate that at a distance of 4.6 Angstroms from the anomeric carbon Glu240 could potentially act as a catalytic base in an inverting mechanism, with Glu159 acting as the catalytic acid being at a distance of 3.7 Angstroms from the glycosidic oxygen. <br />
<br />
== Three-dimensional structures ==<br />
The structure of BT0996 comprises a single domain which is a five bladed β-propeller fold. Each blade is composed of three to four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. It should be noted that BT0996 is appended to a GH2 from clan GHA. This GH2 targets β-D-GlcA linkage in Chain A of RGII.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Not Known.<br />
;First catalytic nucleophile/base identification: Inferred to be Glu159 in BT0996 <cite>Ndeh2017</cite>.<br />
;First general acid/base residue identification: Inferred to be Glu240 in BT0996<cite>Ndeh2017</cite>.<br />
;First 3-D structure: The first structure determination for GH137 was of BT0996 from the organism ''Bacteroides thetaiotaomicon''<cite>Ndeh2017</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Ndeh2017 pmid=28329766<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].<br />
<br />
[[Category:Glycoside Hydrolase Families|GH137]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_137&diff=14482Glycoside Hydrolase Family 1372020-01-25T15:55:55Z<p>Alan Cartmell: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<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 GH137'''<br />
|-<br />
|'''Clan''' <br />
|GH-x<br />
|-<br />
|'''Mechanism'''<br />
|Unknown<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH137.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 />
Authors may get an idea of what to put in each field from ''Curator Approved'' [[Glycoside Hydrolase Families]]. ''(TIP: Right click with your mouse and open this link in a new browser window...)''<br />
<br />
In the meantime, please see these references for an essential introduction to the CAZy classification system: <cite>DaviesSinnott2008 Cantarel2009</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Unknown <br />
<br />
== Catalytic Residues ==<br />
The catalytic residues were shown to be a pair of glutamates. They sit around 6 Angstroms apart. Typically retaining enzymes are expected to have their catalytic residues ~5.5 Angstroms apart, whilst in inverting enzymes they are expected to be ~10 Angstroms apart. Glu159 sits beneath the alpha face of the -1 β-linked arabinose, 3.2 Angstroms from the anomeric carbon, placing it in a an ideal position to act as a catalytic nucleophile. Glu240 resides 5 Angstroms from the glycosidic oxygen which somewhat far to act as catalytic acid/base in a retaining mechanism. Alternatively, one could also speculate that at a distance of 4.6 Angstroms from the anomeric carbon Glu240 could potentially act as a catalytic base in an inverting mechanism, with Glu159 acting as the catalytic acid being at a distance of 3.7 Angstroms from the glycosidic oxygen. <br />
<br />
== Three-dimensional structures ==<br />
The structure of BT0996 comprises a single domain which is a five bladed β-propeller fold. Each blade is composed of three to four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. It should be noted that BT0996 is appended to a GH2 from clan GHA. This GH2 targets β-D-GlcA linkage in Chain A of RGII.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Not Known.<br />
;First catalytic nucleophile/base identification: Inferred to be Glu159 in BT0996 <cite>Ndeh2017</cite>.<br />
;First general acid/base residue identification: Inferred to be Glu240 in BT0996<cite>Ndeh2017</cite>.<br />
;First 3-D structure: The first structure determination for GH137 was of BT0996 from the organism ''Bacteroides thetaiotaomicon''<cite>Ndeh2017</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Ndeh2017 pmid=28329766<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH137]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_137&diff=14481Glycoside Hydrolase Family 1372020-01-25T15:28:45Z<p>Alan Cartmell: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<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 GH137'''<br />
|-<br />
|'''Clan''' <br />
|GH-x<br />
|-<br />
|'''Mechanism'''<br />
|retaining/inverting<br />
|-<br />
|'''Active site residues'''<br />
|known/not known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH137.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 />
Authors may get an idea of what to put in each field from ''Curator Approved'' [[Glycoside Hydrolase Families]]. ''(TIP: Right click with your mouse and open this link in a new browser window...)''<br />
<br />
In the meantime, please see these references for an essential introduction to the CAZy classification system: <cite>DaviesSinnott2008 Cantarel2009</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Content is to be added here.<br />
<br />
== Catalytic Residues ==<br />
Content is to be added here.<br />
<br />
== Three-dimensional structures ==<br />
The structure of BT0996 comprises a single domain which is a five bladed β-propeller fold. Each blade is composed of three to four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. <br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Not Known.<br />
;First catalytic nucleophile/base identification: Inferred to be Glu159 in BT0996 <cite>Ndeh2017</cite>.<br />
;First general acid/base residue identification: Inferred to be Glu240 in BT0996<cite>Ndeh2017</cite>.<br />
;First 3-D structure: The first structure determination for GH137 was of BT0996 from the organism ''Bacteroides thetaiotaomicon''<cite>Ndeh2017</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Ndeh2017 pmid=28329766<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH137]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_140&diff=14480Glycoside Hydrolase Family 1402020-01-25T15:17:47Z<p>Alan Cartmell: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<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 GH140'''<br />
|-<br />
|'''Clan''' <br />
|GH-x<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}}GH140.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Thus far only one member of the family has been characterised, BT1012 from bacteroides thetaiotaomicron. BT1012 displays endo-apiosidase activity targeting α1,2 linked apiose at the base of the sidechains A and B in the complex glycan rhamnogalacturonan ii (RGII)<cite>Ndeh2017</cite>. Cleavage of the RGII backbone must occur for BT1012 to then act<cite>Ndeh2017</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH140 likely uses a, retaining, double displacement mechanism. This is strongly supported by methanolysis experiments where BT1012 was incubated with trisaccharide L-rhamnose-β1,3-D-apiose-α1,2-D-galacturonic acid-O-methyl in the presence of 10 % methanol. This experiment performed with BT1012 generated the product L-rhamnose-β1,3-D-apiose-O-methyl suggesting a retaining mechanism<cite>Ndeh2017</cite>. Glycoside hydrolases that utilise a retaining mechanism, but not those that use an inverting mechanism, can utilise methanol as an external nucleophile and thus generate a methylated product. <br />
<br />
== Catalytic Residues ==<br />
The catalytic residues are an aspartate and glutamate located on the top of β-strands 4 and 7, respectively<cite>Ndeh2017</cite>. This could mean GH140 is a distant relative of Clan GH-A enzymes, however in with GH-A the catalytic residue atop of β-strands 4 and 7 are both glutamates. In the absence of a ligand bound complex or more detailed biochemical analysis <cite>Shallom2002</cite> (preferably both) it is not possible to say which of the catalytic residues is the nucleophile or acid/base.<br />
<br />
== Three-dimensional structures ==<br />
GH140 adopts a (β/α)<sub>8</sub> , TIM barrel, where a central barrel of eight β strands are encircled by eight α helices<cite>Ndeh2017</cite>. BT1012, the only GH140 structure available, also has a Ig like domain that stacks against the TIM barrel likely providing structural stability, similar to the role of Ig like domains in GH43 enzymes<cite>McKee2012 Cartmell2011</cite>. <br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Methanolysis experiments suggest a retaining mechanism<cite>Ndeh2017</cite>.<br />
;First catalytic nucleophile identification: Not known.<br />
;First general acid/base residue identification: Not Known.<br />
;First 3-D structure: BT1012 from bacteroides thetaiotaomicron<cite>Ndeh2017</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Ndeh2017 pmid=28329766<br />
#Shallom2002 pmid=12221104<br />
#McKee2012 pmid=22492980<br />
#Cartmell2011 pmid=21339299<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH140]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_140&diff=14479Glycoside Hydrolase Family 1402020-01-25T15:17:00Z<p>Alan Cartmell: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<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 GH140'''<br />
|-<br />
|'''Clan''' <br />
|GH-x<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}}GH140.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Thus far only one member of the family has been characterised, BT1012 from bacteroides thetaiotaomicron. BT1012 displays endo-apiosidase activity targeting α1,2 linked apiose at the base of the sidechains A and B in the complex glycan rhamnogalacturonan ii (RGII)<cite>Ndeh2017</cite>. Cleavage of the RGII backbone must occur for BT1012 to then act<cite>Ndeh2017</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH140 likely uses a, retaining, double displacement mechanism. This is strongly supported by methanolysis experiments where BT1012 was incubated with trisaccharide L-rhamnose-β1,3-D-apiose-α1,2-D-galacturonic acid-O-methyl in the presence of 10 % methanol. This experiment performed with BT1012 generated the product L-rhamnose-β1,3-D-apiose-O-methyl suggesting a retaining mechanism<cite>Ndeh2017</cite>. Glycoside hydrolases that utilise a retaining mechanism, but not those that use an inverting mechanism, can utilise methanol as an external nucleophile and thus generate a methylated product. <br />
<br />
== Catalytic Residues ==<br />
The catalytic residues are an aspartate and glutamate located on the top of β-strands 4 and 7, respectively<cite>Ndeh2017</cite>. This could mean GH140 is a distant relative of Clan GH-A enzymes, however in with GH-A the catalytic residue atop of β-strands 4 and 7 are both glutamates. In the absence of a ligand bound complex or more detailed biochemical analysis <cite>Shallom2002</cite> (preferably both) it is not possible to say which of the catalytic residues is the nucleophile or acid/base.<br />
<br />
== Three-dimensional structures ==<br />
GH140 adopts a (β/α)<sub>8</sub> , TIM barrel, where a central barrel of eight β strands are encircled by eight α helices<cite>Ndeh2017</cite>. BT1012, the only GH140 structure available, also has a Ig like domain that stacks against the TIM barrel likely providing structural stability, similar to the role of Ig like domains in GH43 enzymes<cite>McKee2012 Cartmell2011</cite>. <br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Content is to be added here.<br />
Methanolysis experiments suggest a retaining mechanism<cite>Ndeh2017</cite>.<br />
;First catalytic nucleophile identification: Content is to be added here.<br />
;First general acid/base residue identification: Content is to be added here.<br />
;First 3-D structure: BT1012 from bacteroides thetaiotaomicron<cite>Ndeh2017</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Ndeh2017 pmid=28329766<br />
#Shallom2002 pmid=12221104<br />
#McKee2012 pmid=22492980<br />
#Cartmell2011 pmid=21339299<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH140]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_140&diff=14478Glycoside Hydrolase Family 1402020-01-25T15:15:33Z<p>Alan Cartmell: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<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 GH140'''<br />
|-<br />
|'''Clan''' <br />
|GH-x<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}}GH140.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Thus far only one member of the family has been characterised, BT1012 from bacteroides thetaiotaomicron. BT1012 displays endo-apiosidase activity targeting α1,2 linked apiose at the base of the sidechains A and B in the complex glycan rhamnogalacturonan ii (RGII)<cite>Ndeh2017</cite>. Cleavage of the RGII backbone must occur for BT1012 to then act<cite>Ndeh2017</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH140 likely uses a, retaining, double displacement mechanism. This is strongly supported by methanolysis experiments where BT1012 was incubated with trisaccharide L-rhamnose-β1,3-D-apiose-α1,2-D-galacturonic acid-O-methyl in the presence of 10 % methanol. This experiment performed with BT1012 generated the product L-rhamnose-β1,3-D-apiose-O-methyl suggesting a retaining mechanism<cite>Ndeh2017</cite>. Glycoside hydrolases that utilise a retaining mechanism, but not those that use an inverting mechanism, can utilise methanol as an external nucleophile and thus generate a methylated product. <br />
<br />
== Catalytic Residues ==<br />
The catalytic residues are an aspartate and glutamate located on the top of β-strands 4 and 7, respectively<cite>Ndeh2017</cite>. This could mean GH140 is a distant relative of Clan GH-A enzymes, however in with GH-A the catalytic residue atop of β-strands 4 and 7 are both glutamates. In the absence of a ligand bound complex or more detailed biochemical analysis <cite>Shallom2002</cite> (preferably both) it is not possible to say which of the catalytic residues is the nucleophile or acid/base.<br />
<br />
== Three-dimensional structures ==<br />
GH140 adopts a (β/α)<sub>8</sub> , TIM barrel, where a central barrel of eight β strands are encircled by eight α helices. BT1012, the only GH140 structure available, also has a Ig like domain that stacks against the TIM barrel likely providing structural stability, similar to the role of Ig like domains in GH43 enzymes<cite>McKee2012 Cartmell2011</cite>. <br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Content is to be added here.<br />
Methanolysis experiments suggest a retaining mechanism<cite>Ndeh2017</cite>.<br />
;First catalytic nucleophile identification: Content is to be added here.<br />
;First general acid/base residue identification: Content is to be added here.<br />
;First 3-D structure: BT1012 from bacteroides thetaiotaomicron<cite>Ndeh2017</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Ndeh2017 pmid=28329766<br />
#Shallom2002 pmid=12221104<br />
#McKee2012 pmid=22492980<br />
#Cartmell2011 pmid=21339299<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH140]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_140&diff=14477Glycoside Hydrolase Family 1402020-01-25T15:08:48Z<p>Alan Cartmell: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<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 GH140'''<br />
|-<br />
|'''Clan''' <br />
|GH-x<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}}GH140.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Thus far only one member of the family has been characterised, BT1012 from bacteroides thetaiotaomicron. BT1012 displays endo-apiosidase activity targeting α1,2 linked apiose at the base of the sidechains A and B in the complex glycan rhamnogalacturonan ii (RGII)<cite>Ndeh2017</cite>. Cleavage of the RGII backbone must occur for BT1012 to then act<cite>Ndeh2017</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH140 likely uses a, retaining, double displacement mechanism. This is strongly supported by methanolysis experiments where BT1012 was incubated with trisaccharide L-rhamnose-β1,3-D-apiose-α1,2-D-galacturonic acid-O-methyl in the presence of 10 % methanol. This experiment performed with BT1012 generated the product L-rhamnose-β1,3-D-apiose-O-methyl suggesting a retaining mechanism<cite>Ndeh2017</cite>. Glycoside hydrolases that utilise a retaining mechanism, but not those that use an inverting mechanism, can utilise methanol as an external nucleophile and thus generate a methylated product. <br />
<br />
== Catalytic Residues ==<br />
The catalytic residues are an aspartate and glutamate located on the top of β-strands 4 and 7, respectively<cite>Ndeh2017</cite>. This could mean GH140 is a distant relative of Clan GH-A enzymes, however in with GH-A the catalytic residue atop of β-strands 4 and 7 are both glutamates. In the absence of a ligand bound complex or more detailed biochemical analysis <cite>Shallom2002</cite> (preferably both) it is not possible to say which of the catalytic residues is the nucleophile or acid/base.<br />
<br />
== Three-dimensional structures ==<br />
GH140 adopts a (β/α)<sub>8</sub> , TIM barrel, where a central barrel of eight β strands are encircled by eight α helices. BT1012, the only GH140 structure available, also has a Ig like domain that stacks against the TIM barrel likely providing structural stability, similar to the role of Ig like domains in GH43 enzymes. <br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Content is to be added here.<br />
Methanolysis experiments suggest a retaining mechanism<cite>Ndeh2017</cite>.<br />
;First catalytic nucleophile identification: Content is to be added here.<br />
;First general acid/base residue identification: Content is to be added here.<br />
;First 3-D structure: BT1012 from bacteroides thetaiotaomicron<cite>Ndeh2017</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Ndeh2017 pmid=28329766<br />
#Shallom2002 pmid=12221104<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH140]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_140&diff=14476Glycoside Hydrolase Family 1402020-01-25T15:06:12Z<p>Alan Cartmell: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<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 GH140'''<br />
|-<br />
|'''Clan''' <br />
|GH-x<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}}GH140.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Thus far only one member of the family has been characterised, BT1012 from bacteroides thetaiotaomicron. BT1012 displays endo-apiosidase activity targeting α1,2 linked apiose at the base of the sidechains A and B in the complex glycan rhamnogalacturonan ii (RGII)<cite>Ndeh2017</cite>. Cleavage of the RGII backbone must occur for BT1012 to then act<cite>Ndeh2017</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH140 likely uses a, retaining, double displacement mechanism. This is strongly supported by methanolysis experiments where BT1012 was incubated with trisaccharide L-rhamnose-β1,3-D-apiose-α1,2-D-galacturonic acid-O-methyl in the presence of 10 % methanol. This experiment performed with BT1012 generated the product L-rhamnose-β1,3-D-apiose-O-methyl suggesting a retaining mechanism<cite>Ndeh2017</cite>. Glycoside hydrolases that utilise a retaining mechanism, but not those that use an inverting mechanism, can utilise methanol as an external nucleophile and thus generate a methylated product. <br />
<br />
== Catalytic Residues ==<br />
The catalytic residues are an aspartate and glutamate located on the top of β-strands 4 and 7, respectively<cite>Ndeh2017</cite>. This could mean GH140 is a distant relative of Clan GH-A enzymes, however in with GH-A the catalytic residue atop of β-strands 4 and 7 are both glutamates. In the absence of a ligand bound complex or more detailed biochemical analysis <cite>Shallom2002</cite> (preferably both) it is not possible to say which of the catalytic residues is the nucleophile or acid/base.<br />
<br />
== Three-dimensional structures ==<br />
GH140 adopts a (β/α)<sub>8</sub> , TIM barrel, where a central barrel of eight β strands are encircled by eight α helices. BT1012, the only GH140 structure available, also has a Ig like domain that stacks against the TIM barrel likely providing structural stability, similar to the role of Ig like domains in GH43 enzymes. <br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Content is to be added here.<br />
;First catalytic nucleophile identification: Content is to be added here.<br />
;First general acid/base residue identification: Content is to be added here.<br />
;First 3-D structure: BT1012 from bacteroides thetaiotaomicron<cite>Ndeh2017</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Ndeh2017 pmid=28329766<br />
#Shallom2002 pmid=12221104<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH140]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_140&diff=14475Glycoside Hydrolase Family 1402020-01-25T14:54:39Z<p>Alan Cartmell: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<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 GH140'''<br />
|-<br />
|'''Clan''' <br />
|GH-x<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}}GH140.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Thus far only one member of the family has been characterised, BT1012 from bacteroides thetaiotaomicron. BT1012 displays endo-apiosidase activity targeting α1,2 linked apiose at the base of the sidechains A and B in the complex glycan rhamnogalacturonan ii (RGII)<cite>Ndeh2017</cite>. Cleavage of the RGII backbone must occur for BT1012 to then act<cite>Ndeh2017</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH140 likely uses a, retaining, double displacement mechanism. This is strongly supported by methanolysis experiments using the trisaccharide L-rhamnose-β1,3-D-apiose-α1,2-D-galacturonic acid-O-methyl in the presence of 10 % methanol. This experiment generated the product L-rhamnose-β1,3-D-apiose-O-methyl which is only possible via a retaining mechanism<cite>Ndeh2017</cite>.<br />
<br />
== Catalytic Residues ==<br />
The catalytic residues are an aspartate and glutamate located on the top of β-strands 4 and 7, respectively. This could mean GH140 is a distant relative of Clan GH-A enzymes, however in with GH-A the catalytic residue atop of β-strands 4 and 7 are both glutamates. In the absence of a ligand bound complex or more detailed biochemical analysis (preferably both) it is not possible to say which of the catalytic residues is the nucleophile or acid/base.<br />
<br />
== Three-dimensional structures ==<br />
GH140 adopts a (β/α)<sub>8</sub> , TIM barrel, where a central barrel of eight β strands are encircled by eight α helices. BT1012, the only GH140 strcuture available, also has a Ig like domain that stacks against the TIM barrel likely providing structural stability, similar to the role of Ig like domains in GH43 enzymes. <br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Content is to be added here.<br />
;First catalytic nucleophile identification: Content is to be added here.<br />
;First general acid/base residue identification: Content is to be added here.<br />
;First 3-D structure: BT1012 from bacteroides thetaiotaomicron.<br />
<br />
== References ==<br />
<biblio><br />
#Ndeh2017 pmid=28329766<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH140]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_145&diff=14474Glycoside Hydrolase Family 1452020-01-25T14:40:41Z<p>Alan Cartmell: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<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 />
<br />
{| {{Prettytable}}<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH145'''<br />
|-<br />
| '''Clan'''<br />
| GH-x<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}}GH145.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
== Substrate specificities ==<br />
Two members of this family have been shown to be an exo-α-L-rhamnosidases, targeting rhamnose linked α-1,4 to glucuronic acid in the complex arabinogalactan protein gum arabic <cite>Munoz-Munoz2017 Cartmell2019</cite>. <br />
<br />
== Kinetics and Mechanism ==<br />
NMR, using the arabinogalactan protein (AGP) gum arabic as the substrate, revealed the family operates via a retaining mechanism<cite>Munoz-Munoz2017</cite>. Rather than using a standard double displacement mechanism the enzyme is speculatively predicted to perform catalysis via an epoxide intermediate, similar to GH99 enzymes<cite>Thompson2012 Fernandes2018</cite>. GH145, however, is proposed to perform catalysis via a substrate assisted mechanism, requiring the carboxyl group of the glucuronic acid and a single catalytic histidine; both acting as an acid/base. This histidine is predicted to deprotonate the O2 of rhamnose, allowing O2 to attack C1 and form an epoxide. Simultaneously the carboxyl group of the glucuronic acid may deprotonate a water molecule generating a hydroxyl group to attach the C1 of rhamnose and allowing protonation of its own O4 thus, leading to glycosidic bond cleavage<cite>Munoz-Munoz2017</cite>. Further work is needed to confirm the mechanism by which GH145 operates. <br />
<br />
<br />
== Catalytic Residues ==<br />
A single catalytic histidine has been shown to be critical for activity. The introduction of the catalytic histidine into related enzymes, which lack the histidine and rhamnosidase activity, is sufficient to introduce rhamnosidase activity into these enzymes<cite>Munoz-Munoz2017</cite>.<br />
<br />
== Three-dimensional structures ==<br />
GH145 comprise a single domain which is a seven bladed β-propeller fold. Each blade is composed of four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. The active site of these α-L-rhamnosidases is located on the opposite side, termed the posterior surface, of CAZymes with similar β-propeller folds. The "normal" side, termed the anterior surface, of the β-propeller bears the highest residue conservation and may well have another function. GH145 is distantly related to PL25 which utilise the anterior surface suggesting that the this surface in GH145 may have another activity<cite>Munoz-Munoz2017 Ulaganathan2017</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Determined for the bacteroides thetaiotaomicron enzyme BT3686<cite>Munoz-Munoz2017</cite>.<br />
;First catalytic acid/base residue identification: Predicted to be a histidine<cite>Munoz-Munoz2017</cite>.<br />
;Second general acid/base residue identification: Predicted to be provided by the substrate<cite>Munoz-Munoz2017</cite>.<br />
;First 3-D structure: BT3686, BACINT_00347 and BACCELL_00856 were the first enzymes to have their structures solved<cite>Munoz-Munoz2017</cite>.<br />
<br />
<br />
<br />
== References ==<br />
<references/><biblio><br />
#Munoz-Munoz2017 pmid=28396425<br />
#Cartmell2019 pmid=31541200<br />
#Thompson2012 pmid=22219371<br />
#Fernandes2018 pmid=29508463<br />
#Ulaganathan2017 pmid=28290654<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].<br />
<br />
<br />
<br />
[[Category:Glycoside Hydrolase Families|GH145]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_140&diff=14473Glycoside Hydrolase Family 1402020-01-25T14:40:13Z<p>Alan Cartmell: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<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 GH140'''<br />
|-<br />
|'''Clan''' <br />
|GH-x<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}}GH140.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Thus far only one member of the family has been characterised, BT1012 from bacteroides thetaiotaomicron. BT1012 displays endo-apiosidase activity targeting apiose in the complex glycan rhamnogalacturonan ii (RGII). The apiose is found at the base of Chains A and B in RGII and linked α1,2 to the galacturonic acid backbone. Cleavage of the backbone must occur for BT1012 to then act.<br />
<br />
== Kinetics and Mechanism ==<br />
GH140 likely uses a, retaining, double displacement mechanism. This is strongly supported by methanolysis experiments using the trisaccharide L-rhamnose-β1,3-D-apiose-α1,2-D-galacturonic acid-O-methyl in the presence of 10 % methanol. This experiment generates the product L-rhamnose-β1,3-D-apiose-O-methyl which is only possible via a retaining mechanism.<br />
<br />
== Catalytic Residues ==<br />
The catalytic residues are an aspartate and glutamate located on beta strands 4 and 7, respectively. <br />
<br />
== Three-dimensional structures ==<br />
GH140 adopts a (β/α)<sub>8</sub> , TIM barrel, where a central barrel of eight β strands are encircled by eight α helices. BT1012, the only GH140 strcuture available, also has a Ig like domain that stacks against the TIM barrel likely providing structural stability, similar to the role of Ig like domains in GH43 enzymes. <br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Content is to be added here.<br />
;First catalytic nucleophile identification: Content is to be added here.<br />
;First general acid/base residue identification: Content is to be added here.<br />
;First 3-D structure: BT1012 from bacteroides thetaiotaomicron.<br />
<br />
== References ==<br />
<biblio><br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH140]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_145&diff=14472Glycoside Hydrolase Family 1452020-01-25T14:37:12Z<p>Alan Cartmell: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<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 />
<br />
{| {{Prettytable}}<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH145'''<br />
|-<br />
| '''Clan'''<br />
| GH-x<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}}GH145.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
== Substrate specificities ==<br />
Two members of this family have been shown to be α-L-rhamnosidases, targeting rhamnose linked α-1,4 to glucuronic acid in the complex arabinogalactan protein gum arabic <cite>Munoz-Munoz2017 Cartmell2019</cite>. <br />
<br />
== Kinetics and Mechanism ==<br />
NMR, using the arabinogalactan protein (AGP) gum arabic as the substrate, revealed the family operates via a retaining mechanism<cite>Munoz-Munoz2017</cite>. Rather than using a standard double displacement mechanism the enzyme is speculatively predicted to perform catalysis via an epoxide intermediate, similar to GH99 enzymes<cite>Thompson2012 Fernandes2018</cite>. GH145, however, is proposed to perform catalysis via a substrate assisted mechanism, requiring the carboxyl group of the glucuronic acid and a single catalytic histidine; both acting as an acid/base. This histidine is predicted to deprotonate the O2 of rhamnose, allowing O2 to attack C1 and form an epoxide. Simultaneously the carboxyl group of the glucuronic acid may deprotonate a water molecule generating a hydroxyl group to attach the C1 of rhamnose and allowing protonation of its own O4 thus, leading to glycosidic bond cleavage<cite>Munoz-Munoz2017</cite>. Further work is needed to confirm the mechanism by which GH145 operates. <br />
<br />
<br />
== Catalytic Residues ==<br />
A single catalytic histidine has been shown to be critical for activity. The introduction of the catalytic histidine into related enzymes, which lack the histidine and rhamnosidase activity, is sufficient to introduce rhamnosidase activity into these enzymes<cite>Munoz-Munoz2017</cite>.<br />
<br />
== Three-dimensional structures ==<br />
GH145 comprise a single domain which is a seven bladed β-propeller fold. Each blade is composed of four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. The active site of these α-L-rhamnosidases is located on the opposite side, termed the posterior surface, of CAZymes with similar β-propeller folds. The "normal" side, termed the anterior surface, of the β-propeller bears the highest residue conservation and may well have another function. GH145 is distantly related to PL25 which utilise the anterior surface suggesting that the this surface in GH145 may have another activity<cite>Munoz-Munoz2017 Ulaganathan2017</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Determined for the bacteroides thetaiotaomicron enzyme BT3686<cite>Munoz-Munoz2017</cite>.<br />
;First catalytic acid/base residue identification: Predicted to be a histidine<cite>Munoz-Munoz2017</cite>.<br />
;Second general acid/base residue identification: Predicted to be provided by the substrate<cite>Munoz-Munoz2017</cite>.<br />
;First 3-D structure: BT3686, BACINT_00347 and BACCELL_00856 were the first enzymes to have their structures solved<cite>Munoz-Munoz2017</cite>.<br />
<br />
<br />
<br />
== References ==<br />
<references/><biblio><br />
#Munoz-Munoz2017 pmid=28396425<br />
#Cartmell2019 pmid=31541200<br />
#Thompson2012 pmid=22219371<br />
#Fernandes2018 pmid=29508463<br />
#Ulaganathan2017 pmid=28290654<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].<br />
<br />
<br />
<br />
[[Category:Glycoside Hydrolase Families|GH145]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_145&diff=14471Glycoside Hydrolase Family 1452020-01-25T14:36:07Z<p>Alan Cartmell: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<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 />
<br />
{| {{Prettytable}}<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH145'''<br />
|-<br />
| '''Clan'''<br />
| GH-x<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}}GH145.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
== Substrate specificities ==<br />
Two members of this family have been shown to be α-L-rhamnosidases, targeting rhamnose linked α-1,4 to glucuronic acid in the complex arabinogalactan protein gum arabic <cite>Munoz-Munoz2017 Cartmell2019</cite>. <br />
<br />
== Kinetics and Mechanism ==<br />
NMR, using the arabinogalactan protein (AGP) gum arabic as the substrate, revealed the family operates via a retaining mechanism<cite>Munoz-Munoz2017</cite>. Rather than using a standard double displacement mechanism the enzyme is speculatively predicted to perform catalysis via an epoxide intermediate, similar to GH99 enzymes<cite>Thompson2012 Fernandes2018</cite>. GH145, however, is proposed to perform catalysis via a substrate assisted mechanism, requiring the carboxyl group of the glucuronic acid and a single catalytic histidine; both acting as an acid/base. This histidine is predicted to deprotonate the O2 of rhamnose, allowing O2 to attack C1 and form an epoxide. Simultaneously the carboxyl group of the glucuronic acid may deprotonate a water molecule generating a hydroxyl group to attach the C1 of rhamnose and allowing protonation of its own O4 thus, leading to glycosidic bond cleavage<cite>Munoz-Munoz2017</cite>. Further work is needed to confirm the mechanism by which GH145 operates. <br />
<br />
<br />
== Catalytic Residues ==<br />
A single catalytic histidine has been shown to be critical for activity. The introduction of the catalytic histidine into related enzymes, which lack the histidine and rhamnosidase activity, is sufficient to introduce rhamnosidase activity into these enzymes<cite>Munoz-Munoz2017</cite>.<br />
<br />
== Three-dimensional structures ==<br />
GH145 comprise a single domain which is a seven bladed β-propeller fold. Each blade is composed of four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. The active site of these α-L-rhamnosidases is located on the opposite side, termed the posterior surface, of CAZymes with similar β-propeller folds. The "normal" side, termed the anterior surface, of the β-propeller bears the highest residue conservation and may well have another function. GH145 is distantly related to PL25 which utilise the anterior surface suggesting that the this surface in GH145 may have another activity<cite>Munoz-Munoz2017 Ulaganathan2017</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Determined for the bacteroides thetaiotaomicron enzyme BT3686<br />
;First catalytic acid/base residue identification: Predicted to be a histidine <br />
;Second general acid/base residue identification: Predicted to be provided by the substrate.<br />
;First 3-D structure: BT3686, BACINT_00347 and BACCELL_00856 were the first enzymes to have their structures solved.<br />
<br />
<br />
<br />
== References ==<br />
<references/><biblio><br />
#Munoz-Munoz2017 pmid=28396425<br />
#Cartmell2019 pmid=31541200<br />
#Thompson2012 pmid=22219371<br />
#Fernandes2018 pmid=29508463<br />
#Ulaganathan2017 pmid=28290654<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].<br />
<br />
<br />
<br />
[[Category:Glycoside Hydrolase Families|GH145]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_145&diff=14470Glycoside Hydrolase Family 1452020-01-25T14:34:36Z<p>Alan Cartmell: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<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 />
<br />
{| {{Prettytable}}<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH145'''<br />
|-<br />
| '''Clan'''<br />
| GH-x<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}}GH145.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
== Substrate specificities ==<br />
Two members of this family have been shown to be α-L-rhamnosidases, targeting rhamnose linked α-1,4 to glucuronic acid in the complex arabinogalactan protein gum arabic <cite>Munoz-Munoz2017 Cartmell2019</cite>. <br />
<br />
== Kinetics and Mechanism ==<br />
NMR, using the arabinogalactan protein (AGP) gum arabic as the substrate, revealed the family operates via a retaining mechanism<cite>Munoz-Munoz2017</cite>. Rather than using a standard double displacement mechanism the enzyme is speculatively predicted to perform catalysis via an epoxide intermediate, similar to GH99 enzymes<cite>Thompson=2012 Fernandes2018</cite>. GH145, however, is proposed to perform catalysis via a substrate assisted mechanism, requiring the carboxyl group of the glucuronic acid and a single catalytic histidine; both acting as an acid/base. This histidine is predicted to deprotonate the O2 of rhamnose, allowing O2 to attack C1 and form an epoxide. Simultaneously the carboxyl group of the glucuronic acid may deprotonate a water molecule generating a hydroxyl group to attach the C1 of rhamnose and allowing protonation of its own O4 thus, leading to glycosidic bond cleavage<cite>Munoz-Munoz2017</cite>. Further work is needed to confirm the mechanism by which GH145 operates. <br />
<br />
<br />
== Catalytic Residues ==<br />
A single catalytic histidine has been shown to be critical for activity. The introduction of the catalytic histidine into related enzymes, which lack the histidine and rhamnosidase activity, is sufficient to introduce rhamnosidase activity into these enzymes<cite>Munoz-Munoz2017</cite>.<br />
<br />
== Three-dimensional structures ==<br />
GH145 comprise a single domain which is a seven bladed β-propeller fold. Each blade is composed of four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. The active site of these α-L-rhamnosidases is located on the opposite side, termed the posterior surface, of CAZymes with similar β-propeller folds. The "normal" side, termed the anterior surface, of the β-propeller bears the highest residue conservation and may well have another function. GH145 is distantly related to PL25 which utilise the anterior surface suggesting that the this surface in GH145 may have another activity<cite>Munoz-Munoz2017 Ulaganathan2017</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Determined for the bacteroides thetaiotaomicron enzyme BT3686<br />
;First catalytic acid/base residue identification: Predicted to be a histidine <br />
;Second general acid/base residue identification: Predicted to be provided by the substrate.<br />
;First 3-D structure: BT3686, BACINT_00347 and BACCELL_00856 were the first enzymes to have their structures solved.<br />
<br />
<br />
<br />
== References ==<br />
<references/><biblio><br />
#Munoz-Munoz2017 pmid=28396425<br />
#Cartmell2019 pmid=31541200<br />
#Thompson2012 pmid=22219371<br />
#Fernandes2018 pmid=29508463<br />
#Ulaganathan2017 pmid=28290654<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].<br />
<br />
<br />
<br />
[[Category:Glycoside Hydrolase Families|GH145]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_145&diff=14469Glycoside Hydrolase Family 1452020-01-25T14:34:21Z<p>Alan Cartmell: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<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 />
<br />
{| {{Prettytable}}<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH145'''<br />
|-<br />
| '''Clan'''<br />
| GH-x<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}}GH145.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
== Substrate specificities ==<br />
Two members of this family have been shown to be α-L-rhamnosidases, targeting rhamnose linked α-1,4 to glucuronic acid in the complex arabinogalactan protein gum arabic <cite>Munoz-Munoz2017 Cartmell2019</cite>. <br />
<br />
== Kinetics and Mechanism ==<br />
NMR, using the arabinogalactan protein (AGP) gum arabic as the substrate, revealed the family operates via a retaining mechanism<cite>Munoz-Munoz2017</cite>. Rather than using a standard double displacement mechanism the enzyme is speculatively predicted to perform catalysis via an epoxide intermediate, similar to GH99 enzymes<cite>Thompson=2012 Fernandes2018</cite>. GH145, however, is proposed to perform catalysis via a substrate assisted mechanism, requiring the carboxyl group of the glucuronic acid and a single catalytic histidine; both acting as an acid/base. This histidine is predicted to deprotonate the O2 of rhamnose, allowing O2 to attack C1 and form an epoxide. Simultaneously the carboxyl group of the glucuronic acid may deprotonate a water molecule generating a hydroxyl group to attach the C1 of rhamnose and allowing protonation of its own O4 thus, leading to glycosidic bond cleavage<cite>Munoz-Munoz2017</cite>. Further work is needed to confirm the mechanism by which GH145 operates. <br />
<br />
<br />
== Catalytic Residues ==<br />
A single catalytic histidine has been shown to be critical for activity. The introduction of the catalytic histidine into related enzymes, which lack the histidine and rhamnosidase activity, is sufficient to introduce rhamnosidase activity into these enzymes<cite>Munoz-Munoz2017</cite>.<br />
<br />
== Three-dimensional structures ==<br />
GH145 comprise a single domain which is a seven bladed β-propeller fold. Each blade is composed of four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. The active site of these α-L-rhamnosidases is located on the opposite side, termed the posterior surface, of CAZymes with similar β-propeller folds. The "normal" side, termed the anterior surface, of the β-propeller bears the highest residue conservation and may well have another function. GH145 is distantly related to PL25 which utilise the anterior surface suggesting that the this surface in GH145 may have another activity<cite>Munoz-Munoz2017 Ulaganathan2017</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Determined for the bacteroides thetaiotaomicron enzyme BT3686<br />
;First catalytic acid/base residue identification: Predicted to be a histidine <br />
;Second general acid/base residue identification: Predicted to be provided by the substrate.<br />
;First 3-D structure: BT3686, BACINT_00347 and BACCELL_00856 were the first enzymes to have their structures solved.<br />
<br />
<br />
<br />
== References ==<br />
<references/><biblio><br />
#Munoz-Munoz2017 pmid=28396425<br />
#Cartmell2019 pmid=31541200<br />
#Thompson2012 pmid=22219371<br />
#Fernandes2018 pmid=29508463<br />
#Ulaganathan2017 pmid=28290654<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].<br />
<biblio><br />
<br />
<br />
[[Category:Glycoside Hydrolase Families|GH145]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_145&diff=14468Glycoside Hydrolase Family 1452020-01-25T14:32:57Z<p>Alan Cartmell: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<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 />
<br />
{| {{Prettytable}}<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH145'''<br />
|-<br />
| '''Clan'''<br />
| GH-x<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}}GH145.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
== Substrate specificities ==<br />
Two members of this family have been shown to be α-L-rhamnosidases, targeting rhamnose linked α-1,4 to glucuronic acid in the complex arabinogalactan protein gum arabic <cite>Munoz-Munoz2017 Cartmell2019</cite>. <br />
<br />
== Kinetics and Mechanism ==<br />
NMR, using the arabinogalactan protein (AGP) gum arabic as the substrate, revealed the family operates via a retaining mechanism<cite>Munoz-Munoz2017</cite>. Rather than using a standard double displacement mechanism the enzyme is speculatively predicted to perform catalysis via an epoxide intermediate, similar to GH99 enzymes<cite>Thompson=2012 Fernandes2018</cite>. GH145, however, is proposed to perform catalysis via a substrate assisted mechanism, requiring the carboxyl group of the glucuronic acid and a single catalytic histidine; both acting as an acid/base. This histidine is predicted to deprotonate the O2 of rhamnose, allowing O2 to attack C1 and form an epoxide. Simultaneously the carboxyl group of the glucuronic acid may deprotonate a water molecule generating a hydroxyl group to attach the C1 of rhamnose and allowing protonation of its own O4 thus, leading to glycosidic bond cleavage<cite>Munoz-Munoz2017</cite>. Further work is needed to confirm the mechanism by which GH145 operates. <br />
<br />
<br />
== Catalytic Residues ==<br />
A single catalytic histidine has been shown to be critical for activity. The introduction of the catalytic histidine into related enzymes, which lack the histidine and rhamnosidase activity, is sufficient to introduce rhamnosidase activity into these enzymes<cite>Munoz-Munoz2017</cite>.<br />
<br />
== Three-dimensional structures ==<br />
GH145 comprise a single domain which is a seven bladed β-propeller fold. Each blade is composed of four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. The active site of these α-L-rhamnosidases is located on the opposite side, termed the posterior surface, of CAZymes with similar β-propeller folds. The "normal" side, termed the anterior surface, of the β-propeller bears the highest residue conservation and may well have another function. GH145 is distantly related to PL25 which utilise the anterior surface suggesting that the this surface in GH145 may have another activity<cite>Munoz-Munoz2017 Ulaganathan2017</cite>.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Determined for the bacteroides thetaiotaomicron enzyme BT3686<br />
;First catalytic acid/base residue identification: Predicted to be a histidine <br />
;Second general acid/base residue identification: Predicted to be provided by the substrate.<br />
;First 3-D structure: BT3686, BACINT_00347 and BACCELL_00856 were the first enzymes to have their structures solved.<br />
<br />
<br />
<br />
== References ==<br />
<references/><biblio><br />
#Munoz-Munoz2017 pmid=28396425<br />
#Cartmell2019 pmid=31541200<br />
#Thompson2012 pmid=22219371<br />
#Fernandes2018 pmid=29508463<br />
#Ulaganathan2017 pmid=28290654<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].<br />
<br />
<br />
<br />
[[Category:Glycoside Hydrolase Families|GH145]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_145&diff=14467Glycoside Hydrolase Family 1452020-01-25T14:30:50Z<p>Alan Cartmell: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<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 />
<br />
{| {{Prettytable}}<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH145'''<br />
|-<br />
| '''Clan'''<br />
| GH-x<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}}GH145.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
== Substrate specificities ==<br />
Two members of this family have been shown to be α-L-rhamnosidases, targeting rhamnose linked α-1,4 to glucuronic acid in the complex arabinogalactan protein gum arabic <cite>Munoz-Munoz2017 Cartmell2019</cite>. <br />
<br />
== Kinetics and Mechanism ==<br />
NMR, using the arabinogalactan protein (AGP) gum arabic as the substrate, revealed the family operates via a retaining mechanism<cite>Munoz-Munoz2017</cite>. Rather than using a standard double displacement mechanism the enzyme is speculatively predicted to perform catalysis via an epoxide intermediate, similar to GH99 enzymes<cite>Thompson=2012 Fernandes2018</cite>. GH145, however, is proposed to perform catalysis via a substrate assisted mechanism, requiring the carboxyl group of the glucuronic acid and a single catalytic histidine; both acting as an acid/base. This histidine is predicted to deprotonate the O2 of rhamnose, allowing O2 to attack C1 and form an epoxide. Simultaneously the carboxyl group of the glucuronic acid may deprotonate a water molecule generating a hydroxyl group to attach the C1 of rhamnose and allowing protonation of its own O4 thus, leading to glycosidic bond cleavage<cite>Munoz-Munoz2017</cite>. Further work is needed to confirm the mechanism by which GH145 operates. <br />
<br />
<br />
== Catalytic Residues ==<br />
A single catalytic histidine has been shown to be critical for activity. The introduction of the catalytic histidine into related enzymes, which lack the histidine and rhamnosidase activity, is sufficient to introduce rhamnosidase activity into these enzymes<cite>Munoz-Munoz2017</cite>.<br />
<br />
== Three-dimensional structures ==<br />
GH145 comprise a single domain which is a seven bladed β-propeller fold. Each blade is composed of four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. The active site of these α-L-rhamnosidases is located on the opposite side, termed the posterior surface, of CAZymes with similar β-propeller folds. The "normal" side, termed the anterior surface, of the β-propeller bears the highest residue conservation and may well have another function. GH145 is distantly related to PL25 which utilise the anterior surface suggesting that the this surface in GH145 may have another activity.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Determined for the bacteroides thetaiotaomicron enzyme BT3686<br />
;First catalytic acid/base residue identification: Predicted to be a histidine <br />
;Second general acid/base residue identification: Predicted to be provided by the substrate.<br />
;First 3-D structure: BT3686, BACINT_00347 and BACCELL_00856 were the first enzymes to have their structures solved.<br />
<br />
<br />
<br />
== References ==<br />
<references/><biblio><br />
#Munoz-Munoz2017 pmid=28396425<br />
#Cartmell2019 pmid=31541200<br />
#Thompson2012 pmid=22219371<br />
#Fernandes2018 pmid=29508463<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].<br />
<br />
<br />
<br />
[[Category:Glycoside Hydrolase Families|GH145]]</div>Alan Cartmellhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_145&diff=14466Glycoside Hydrolase Family 1452020-01-25T14:28:18Z<p>Alan Cartmell: </p>
<hr />
<div><!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Alan Cartmell^^^<br />
* [[Responsible Curator]]: ^^^Harry Gilbert^^^<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 />
<br />
{| {{Prettytable}}<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''Glycoside Hydrolase Family GH145'''<br />
|-<br />
| '''Clan'''<br />
| GH-x<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}}GH145.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
== Substrate specificities ==<br />
Two members of this family have been shown to be α-L-rhamnosidases, targeting rhamnose linked α-1,4 to glucuronic acid in the complex arabinogalactan protein gum arabic <cite>Munoz-Munoz2017</cite>. <br />
<br />
== Kinetics and Mechanism ==<br />
NMR, using the arabinogalactan protein (AGP) gum arabic as the substrate, revealed the family operates via a retaining mechanism<cite>Munoz-Munoz2017</cite>. Rather than using a standard double displacement mechanism the enzyme is speculatively predicted to perform catalysis via an epoxide intermediate, similar to GH99 enzymes<cite>Thompson=2012 Fernandes2018</cite>. GH145, however, is proposed to perform catalysis via a substrate assisted mechanism, requiring the carboxyl group of the glucuronic acid and a single catalytic histidine; both acting as an acid/base. This histidine is predicted to deprotonate the O2 of rhamnose, allowing O2 to attack C1 and form an epoxide. Simultaneously the carboxyl group of the glucuronic acid may deprotonate a water molecule generating a hydroxyl group to attach the C1 of rhamnose and allowing protonation of its own O4 thus, leading to glycosidic bond cleavage<cite>Munoz-Munoz2017</cite>. Further work is needed to confirm the mechanism by which GH145 operates. <br />
<br />
<br />
== Catalytic Residues ==<br />
A single catalytic histidine has been shown to be critical for activity. The introduction of the catalytic histidine into related enzymes, which lack the histidine and rhamnosidase activity, is sufficient to introduce rhamnosidase activity into these enzymes<cite>Munoz-Munoz2017</cite>.<br />
<br />
== Three-dimensional structures ==<br />
GH145 comprise a single domain which is a seven bladed β-propeller fold. Each blade is composed of four anti parallel β-strands that extend out radially from the central core. The final blade is formed by strands from both the N- and C-terminus of the protein which is termed as 'molecular velcro' and is believed to add considerable stability to the fold. The active site of these α-L-rhamnosidases is located on the opposite side, termed the posterior surface, of CAZymes with similar β-propeller folds. The "normal" side, termed the anterior surface, of the β-propeller bears the highest residue conservation and may well have another function. GH145 is distantly related to PL25 which utilise the anterior surface suggesting that the this surface in GH145 may have another activity.<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Determined for the bacteroides thetaiotaomicron enzyme BT3686<br />
;First catalytic acid/base residue identification: Predicted to be a histidine <br />
;Second general acid/base residue identification: Predicted to be provided by the substrate.<br />
;First 3-D structure: BT3686, BACINT_00347 and BACCELL_00856 were the first enzymes to have their structures solved.<br />
<br />
<br />
<br />
== References ==<br />
<references/><biblio><br />
#Munoz-Munoz2017 pmid=28396425<br />
#Thompson=2012 pmid=22219371<br />
#Fernandes2018 pmid=29508463<br />
#Cantarel2009 pmid=18838391<br />
#DaviesSinnott2008 Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. ''The Biochemist'', vol. 30, no. 4., pp. 26-32. [http://www.biochemist.org/bio/03004/0026/030040026.pdf Download PDF version].<br />
<br />
<br />
<br />
[[Category:Glycoside Hydrolase Families|GH145]]</div>Alan Cartmell