https://www.cazypedia.org/api.php?action=feedcontributions&feedformat=atom&user=Al+BorastonCAZypedia - User contributions [en-ca]2026-05-05T14:09:54ZUser contributionsMediaWiki 1.35.10https://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_81&diff=15794Glycoside Hydrolase Family 812020-08-18T21:48:40Z<p>Al Boraston: </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]]: ^^^Julie Grondin^^^<br />
* [[Responsible Curator]]: ^^^Al Boraston^^^<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 GH81'''<br />
|-<br />
|'''Clan''' <br />
|none<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH81.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
GH81 members are endo-&beta;(1,3)-glucanases ([{{EClink}}3.2.1.39 EC 3.2.1.39]) with diverse physiological roles in, for example, plant biomass degradation, cell cycling, and pathogen defense. They are mostly found in bacteria and fungi, and are particularly abundant in ''Saccharomyces'' and ''Streptomyces'' species. Activity has been demonstrated on laminarin <cite>Fontaine1997, McGrath2006, Martin-Cuadrado2008, Zhou2013, Pluvinage2017, Kumar2018</cite>, curdlan <cite>Fontaine1997, Martin-Cuadrado2008, Pluvinage2017, Kumar2018</cite>, and pachyman <cite>McGrath2006, Pluvinage2017</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH81 enzymes follow an [[inverting]] mechanism, as first shown by <sup>1</sup>H-NMR during the hydrolysis of laminarin oligosaccharides <cite>Fliegmann2005</cite>, and laminarin <cite>McGrath2006</cite>, thus operating by a [[Glycoside_hydrolases#Inverting_glycoside_hydrolases|single-displacement mechanism]].<br />
<br />
== Catalytic Residues ==<br />
Primary sequence alignments of GH81 members reveal a number of highly conserved residues, including two glutamate residues and one aspartate residue, which are located in the active site cleft and are likely to serve as catalytic residues <cite>Martin-Cuadrado2008, McGrath2009, Zhou2013</cite>.<br />
<br />
Comprehensive mutagenesis experiments, azide rescue, structural analysis, and examination of the product conformational itinerary in ligand complexes show that one of the two glutamic acids (E542 in GH81 from ''Bacillus halodurans'' C-125) acts as the catalytic base by activating a catalytic water, and that the aspartic acid (D466 in ''Bh''GH81) acts as the catalytic acid <cite>McGrath2009, Pluvinage2017</cite>. Mutagenesis studies in ''T. fusca'' indicate that mutation of the second glutamic acid (E546 in ''Bh''GH81) results in a dramatic reduction in activity <cite>McGrath2009</cite>. Structural analysis of ''Bh''GH81 indicates that this residue is positioned during the catalytic cycle to interact with and stabilize a distorted product intermediate. The potential role of this residue as a base and in activating the catalytic water prior to substrate binding is presently unclear.<br />
<br />
== Three-dimensional structures ==<br />
[[File:figure1_4k3a.png|400px|thumb|right|'''Figure 1. Structure of Lam81A from ''Rhizomucor meihei''''' ([{{PDBlink}}4K3A PDB ID 4K3A]). Domain A (blue) and Domain C (green) comprise the core of the enzyme, with domain B (orange) acting as a stabilizer. The proposed catalytic residues are shown as red sticks.]]<br />
GH81 members are multimodular, although the composition of the domains can vary slightly. The first characterized structure, Lam81A from ''Rhizomucor miehei'' CAU432, comprises an N-terminal &beta;-sandwich domain (domain A), a small &alpha;/&beta; domain (domain B), and a C-terminal (&alpha;/&alpha;)<sub>6</sub> domain (domain C) <cite>Zhou2013</cite>. Domains A and C form the core of the enzyme, which is likely stabilized by domain B. ('''Figure 1'''). This architecture is largely conserved in the GH81 from ''Bacillus halodurans'' C-125 (''Bh''GH81) <cite>Pluvinage2017</cite>, and the cellulosomal GH81 from ''Clostridium themocellum'' ATCC 27405 (''Ct''Lam81A) <cite>Kumar2018</cite>, however, the C-terminal domain is a [[CBM56]] in ''Bh''GH81 and a cellulosomal dockerin in ''Ct''Lam81A.<br />
<br />
[[File:Figure2_helical.PNG|400px|thumb|right|'''Figure 2. The structure of GH81 from ''Bacillus halodurans'' suggests that GH81 are capable of binding helical forms of &beta;-glucan''' ([{{PDBlink}}5T4G PDB ID 5T4G]). The triple helical structure of curdlan (beige, yellow, cyan) is shown, with the pitch (16Å) and spacing (5.3Å) between strands indicated. Figure from <cite>Pluvinage2017</cite>.]]<br />
Spanning domains A and C is a large cleft (10Å deep, 10Å wide, 70Å long), in which the proposed catalytic residues are located. Co-crystallization of ''Bh''GH81 in complex with an extensive range of laminarin oligosaccharides provided structural evidence for the ability of this enzyme to generate a pool of oligosaccharide products <cite>Pluvinage2017</cite>. Notably, these structures clearly define catalytic and ancillary binding subsites, and reveal the ability of this enzyme to simultaneously bind oligosaccharides in these sites. Thus, GH81 is likely to bind and cleave helical forms of &beta;-1,3-glucans in an ''endo''-processive manner <cite>Pluvinage2017</cite> ('''Figure 2''').<br />
<br />
GH81 tertiary structures are unique among GHs, including other characterized endo-&beta;(1,3)-glucanase families. As such, GH81 is not classified into any GH [[clan]].<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: &beta;-glucan binding protein (GBP) from soybean (''Glycine max L.'') by <sup>1</sup>H-NMR <cite>Fliegmann2005</cite>. <br />
;First catalytic nucleophile identification: Lam81A from ''Thermobifida fusca'', by site-directed mutagenesis and azide rescue <cite>McGrath2009</cite>, later confirmed by structural analysis <cite>Pluvinage2017</cite>. <br />
;First general acid/base residue identification: Lam81A from ''Thermobifida fusca'', by site-directed mutagenesis <cite>McGrath2009</cite>, later confirmed by structural analysis <cite>Pluvinage2017</cite>. <br />
;First 3-D structure: Lam81A from ''Rhizomucor miehei'' CAU432 <cite>Zhou2013</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Fontaine1997 pmid=9030754<br />
#McGrath2006 pmid=17115704<br />
#Martin-Cuadrado2008 pmid=17933563<br />
#Zhou2013 pmid=24100321<br />
#Pluvinage2017 pmid=28781080<br />
#Kumar2018 pmid=29870811<br />
#Fliegmann2005 pmid=16297387<br />
#McGrath2009 pmid=19435780<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH081]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_81&diff=15700Glycoside Hydrolase Family 812020-08-06T23:44:18Z<p>Al Boraston: </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]]: ^^^Julie Grondin^^^<br />
* [[Responsible Curator]]: ^^^Al Boraston^^^<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 GH81'''<br />
|-<br />
|'''Clan''' <br />
|none<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH81.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
GH81 family are endo-&beta;(1,3)-glucanases ([{{EClink}}3.2.1.39 EC 3.2.1.39]) with diverse physiological roles, such as plant biomass degradation, cell cycling, and enzymatic pathogen defense. They are mostly found in bacteria and fungi, and are particularly abundant in ''Saccharomyces'' and ''Streptomyces'' species. Activity has been demonstrated on laminarin <cite>Fontaine1997, McGrath2006, Martin-Cuadrado2008, Zhou2013, Pluvinage2017, Kumar2018</cite>, curdlan <cite>Fontaine1997, Martin-Cuadrado2008, Pluvinage2017, Kumar2018</cite>, and pachyman <cite>McGrath2006, Pluvinage2017</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
GH81 enzymes follow an [[inverting]] mechanism, first shown by <sup>1</sup>H-NMR during the hydrolysis of laminarin oligosaccharides <cite>Fliegmann2005</cite>, and laminarin <cite>McGrath2006</cite>, thus operating by a [[Glycoside_hydrolases#Inverting_glycoside_hydrolases|single-displacement mechanism]].<br />
<br />
== Catalytic Residues ==<br />
Primary sequence alignments of GH81 reveal a number of highly conserved residues, including two glutamate residues and one aspartate residue which are located in the active site cleft and likely to serve as catalytic residues <cite>Martin-Cuadrado2008, McGrath2009, Zhou2013</cite>.<br />
<br />
Comprehensive mutagenesis experiments, azide rescue, structural analysis, and examination of the product conformational itinerary in ligand complexes show that one of the two glutamic acids (E542 in GH81 from ''Bacillus halodurans'' C-125) acts as the catalytic base by activating a catalytic water, and that the aspartic acid (D422 in ''Bh''GH81) acts as the catalytic acid <cite>McGrath2009, Pluvinage2017</cite>. Mutagenesis studies in T. fusca indicate that mutation of the second glutamic acid (E546 in ''Bh''GH81) results in a dramatic reduction in activity <cite>McGrath2009</cite>. Structural analysis in ''B. halodurans'' indicates that this residue is positioned during the catalytic cycle to interact with and stabilize a distorted product intermediate. As such, the potential role of this residue as a base and in activating the catalytic water prior to substrate binding is presently unclear.<br />
<br />
== Three-dimensional structures ==<br />
[[File:figure1_4k3a.png|400px|thumb|right|'''Figure 1. Structure of Lam81A from ''Rhizomucor meihei''''' ([{{PDBlink}}4K3A PDB ID 4K3A]). Domain A (blue) and Domain C (green) comprise the core of the enzyme, with domain B (orange) acting as a stabilizer. The proposed catalytic residues are shown as red sticks.]]<br />
GH81 are multimodular, although the composition of the domains can vary slightly. The first characterized structure, Lam81A from ''Rhizomucor miehei'' CAU432, comprises an N-terminal &beta;-sandwich domain (domain A), a small &alpha;/&beta; domain (domain B), and a C-terminal (&alpha;/&alpha;)<sub>6</sub> domain (domain C) <cite>Zhou2013</cite>. Domains A and C form the core of the enzyme, which is likely stabilized by domain B. ('''Figure 1'''). This architecture is largely conserved in the GH81 from ''Bacillus halodurans'' C-125 (''Bh''GH81) <cite>Pluvinage2017</cite>, and the cellulosomal GH81 from ''Clostridium themocellum'' ATCC 27405 (''Ct''Lam81A) <cite>Kumar2018</cite>, however, the C-terminal domain is a [[CBM56]] in ''Bh''GH81 and a cellulosomal dockerin in ''Ct''Lam81A.<br />
<br />
GH81 structures are unique among GHs and also differ from other characterized endo-&beta;(1,3)-glucanases in the PDB. As such, GH81 is not classified into any GH clan.<br />
<br />
[[File:Figure2_helical.PNG|400px|thumb|right|'''Figure 2. The structure of GH81 from ''Bacillus halodurans'' suggests that GH81 are capable of binding helical forms of &beta;-glucan''' ([{{PDBlink}}5T4G PDB ID 5T4G]). The triple helical structure of curdlan (beige, yellow, cyan) is shown, with the pitch (16Å) and spacing (5.3Å) between strands indicated. Figure from <cite>Pluvinage2017</cite>.]]<br />
Spanning domains A and C is a large cleft (10Å deep, 10Å wide, 70Å long), in which the proposed catalytic residues are located. Extensive co-crystallization of ''Bh''GH81 in complex with a range of laminarin oligosaccharides provides structural evidence for the ability of this enzyme for to generate a pool of oligosaccharide products <cite>Pluvinage2017</cite>. Notably, these structures clearly define catalytic and ancillary binding subsites, and reveal the ability of this enzyme to simultaneously bind oligosaccharides in these sites. Thus, GH81 is likely to bind and cleave helical forms of &beta;-1,3-glucans in an ''endo''-processive manner <cite>Pluvinage2017</cite> ('''Figure 2''').<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: &beta;-glucan binding protein (GBP) from soybean (''Glycine max L.'') by <sup>1</sup>H-NMR <cite>Fliegmann2005</cite>. <br />
;First catalytic nucleophile identification: Lam81A from ''Thermobifida fusca'', by site-directed mutagenesis and azide rescue <cite>McGrath2009</cite>, later confirmed by structural analysis <cite>Pluvinage2017</cite>. <br />
;First general acid/base residue identification: Lam81A from ''Thermobifida fusca'', by site-directed mutagenesis <cite>McGrath2009</cite>, later confirmed by structural analysis <cite>Pluvinage2017</cite>. <br />
;First 3-D structure: Lam81A from ''Rhizomucor miehei'' CAU432 <cite>Zhou2013</cite>. <br />
<br />
== References ==<br />
<biblio><br />
#Fontaine1997 pmid=9030754<br />
#McGrath2006 pmid=17115704<br />
#Martin-Cuadrado2008 pmid=17933563<br />
#Zhou2013 pmid=24100321<br />
#Pluvinage2017 pmid=28781080<br />
#Kumar2018 pmid=29870811<br />
#Fliegmann2005 pmid=16297387<br />
#McGrath2009 pmid=19435780<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH081]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=User:Al_Boraston&diff=14456User:Al Boraston2020-01-11T16:37:46Z<p>Al Boraston: </p>
<hr />
<div>'''Alisdair Boraston''', ''University of Victoria, Canada.''<br />
<br />
This is the user page of Alisdair ("Al") Boraston. I am a Professor in the [http://web.uvic.ca/biochem/ Department of Biochemistry and Microbiology] at the [http://www.uvic.ca/ University of Victoria], Victoria, Canada. I obtained by PhD working on [[carbohydrate-binding modules]] (CBMs - at the time they were cellulose-binding domains) under Dr. Douglas Kilburn and Dr. Tony Warren at the [http://www.ubc.ca/ University of British Columbia], Vancouver, Canada. After a Natural Sciences and Engineering Research Council of Canada funded post-doctoral fellowship with Dr. ^^^Gideon Davies^^^ in the YSBL at the University of York, UK, where I worked on the structures of [[Carbohydrate-binding_modules|CBMs]] and [[glycoside hydrolases]] (GHs), I returned to my hometown of Victoria to take up my current position. My research program currently focuses on the structures and functions of carbohydrate-active enzymes that are involved in marine algae polysaccharide depolymerization and microbial pathogenesis.<br />
[[Category:Contributors|Boraston, Alisdair]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_107&diff=14425Glycoside Hydrolase Family 1072019-12-16T17:08:07Z<p>Al Boraston: </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]]: ^^^David Teze^^^<br />
* [[Responsible Curator]]: ^^^Al Boraston^^^<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 GH107'''<br />
|-<br />
|'''Clan''' <br />
|GH-R<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}}GH107.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
The currently characterized [[glycoside hydrolases]] of this family are [[endo]]-acting α-fucosidases active on sulfated fucans (or fucoidans) from brown algae. All described GH107 family members are endo-1,4-fucanase of bacterial origin, and together with enzymes from the CAZY family [[GH29]], they form the clan GH-R. Sequences of GH107 family members were first reported in 2006,<cite>Colin2006</cite> even though the enzymatic activity was reported earlier.<br />
<br />
== Kinetics and Mechanism ==<br />
<br />
The mechanism was proven to be [[retaining]] by observation of the formation of an α-''O''-linked mercaptoethanol on a L-Fuc-2,3-disulfate-(α1-3)-L-Fuc-2-sulfate disaccharide by transglycosylation.<cite>Vickers2018</cite> It should then follow a [[classical Koshland double-displacement mechanism]] similarly to [[GH29]].<br />
<br />
[[Image:20191213 Gh107.png|thumb|left|800px|Figure 1: Mechanism of GH107 family. According to <cite>Vickers2018</cite>.]]<br />
<br style="clear: both" /><br />
<br />
== Catalytic Residues ==<br />
The catalytic nucleophile is an aspartate, while the catalytic acid-base is a histidine. The later is unusual in GHs, and a divergence from [[GH29]], but is likely necessary to avoid electronic repulsion with the substrate sulfate groups. These two residues have been identified by structural superimposition with GH29 enzymes, and are conserved within the few members of the GH107 family. The catalytic His has been further confirmed by the lack of activity of the H294Q mutant of ''Mariniflexile fucanivorans''.<cite>Vickers2018</cite> The catalytic aspartate was also proposed to be one of the catalytic residue on sequence analysis alone, in a simultaneously released paper.<cite>Shultz-Johansen2018</cite><br />
<br />
== Three-dimensional structures ==<br />
The crystal structures of ''Mariniflexile fucanivorans'' (PDB: [{{PDBlink}}6dns 6dns],[{{PDBlink}}6dms 6dms],[{{PDBlink}}6dlh 6dlh]) and ''Psychromonas sp.'' (PDB: [{{PDBlink}}6m8n 6m8n]) have been determined in 2018.<cite>Vickers2018</cite> The ''Psychromonas sp.'' (PDB: [{{PDBlink}}6m8n 6m8n]) enzyme showed a single catalytic domain with a (β/α)<sub>8</sub> / TIM-barrel fold, while in the ''Mariniflexile fucanivorans'' enzyme, this catalytic domain is followed by three Ig-like domains that wrap around the catalytic one.<cite>Vickers2018</cite><br />
<br />
[[Image:GH107_full.png|500px]]<br />
[[Image:20191213_GH107-zoom.png|500px]]<br />
<br style="clear: both" /><br />
Figure 2: ''Psychromonas sp.'' GH107 structure and catalytic residues (PDB: [{{PDBlink}}6m8n 6m8n]).<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: The retaining mechanism was determined in 2018.<cite>Vickers2018</cite><br />
;First catalytic nucleophile identification: An aspartic acid side chain acting as a catalytic nucleophile was identified by two simultaneous studies in the Autumn of 2018.<cite>Vickers2018</cite><cite>Shultz-Johansen2018</cite><br />
;First general acid/base residue identification: A histidine sidechain acting as a catalytic acid-base residue was identified in 2018.<cite>Vickers2018</cite><br />
;First 3-D structure: The crystal structures of ''Mariniflexile fucanivorans'' (PDB: [{{PDBlink}}6dns 6dns],[{{PDBlink}}6dms 6dms],[{{PDBlink}}6dlh 6dlh]) and ''Psychromonas sp.'' (PDB: [{{PDBlink}}6m8n 6m8n]) have been released at the same time, in 2018.<cite>Vickers2018</cite> <br />
<br />
== References ==<br />
<biblio><br />
#Colin2006 pmid=16880504<br />
#Vickers2018 pmid=30282808<br />
#Shultz-Johansen2018 pmid=30230202<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH107]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_107&diff=14424Glycoside Hydrolase Family 1072019-12-16T17:06:20Z<p>Al Boraston: </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]]: ^^^David Teze^^^<br />
* [[Responsible Curator]]: ^^^Al Boraston^^^<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 GH107'''<br />
|-<br />
|'''Clan''' <br />
|GH-R<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}}GH107.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
The currently characterized [[glycoside hydrolases]] of this family are [[endo]]-acting α-fucosidases active on sulfated fucans (or fucoidans) from brown algae. All described GH107 family members are endo-1,4-fucanase of bacterial origin, and together with enzymes from the CAZY family [[GH29]], they form the clan GH-R. Sequences of GH107 family members were first reported in 2006,<cite>Colin2006</cite> even though the enzymatic activity was reported earlier.<br />
<br />
== Kinetics and Mechanism ==<br />
<br />
The mechanism was proven to be [[retaining]] by observation of the formation of an α-''O''-linked mercaptoethanol on a L-Fuc-2,3-disulfate-(α1-3)-L-Fuc-2-sulfate disaccharide by transglycosylation.<cite>Vickers2018</cite> It should then follow a [[classical Koshland double-displacement mechanism]] similarly to [[GH29]].<br />
<br />
[[Image:20191213 Gh107.png|thumb|left|800px|Figure 1: Mechanism of GH107 family. According to <cite>Vickers2018</cite>.]]<br />
<br style="clear: both" /><br />
<br />
== Catalytic Residues ==<br />
The catalytic nucleophile is an aspartate, while the catalytic acid-base is a histidine. The later is unusual in GHs, and a divergence from [[GH29]], but is likely necessary to avoid electronic repulsion with the substrate sulfate groups. These two residues have been identified by structural superimposition with GH29 enzymes, and are conserved within the few members of the GH107 family. The catalytic His has been further confirmed by the lack of activity of the H294Q mutant of ''Mariniflexile fucanivorans''.<cite>Vickers2018</cite> The catalytic aspartate was also proposed to be one of the catalytic residue on sequence analysis alone, in a simultaneously released paper.<cite>Shultz-Johansen2018</cite><br />
<br />
== Three-dimensional structures ==<br />
The crystal structures of ''Mariniflexile fucanivorans'' (PDB: [{{PDBlink}}6dns 6dns],[{{PDBlink}}6dms 6dms],[{{PDBlink}}6dlh 6dlh]) and ''Psychromonas sp.'' (PDB: [{{PDBlink}}6m8n 6m8n]) have been determined in 2018.<cite>Vickers2018</cite> The ''Psychromonas sp.'' (PDB: [{{PDBlink}}6m8n 6m8n]) enzyme showed a single catalytic domain with a (β/α)<sub>8</sub> / TIM-barrel fold, while in the ''Mariniflexile fucanivorans'' enzyme, this catalytic domain is followed by three Ig-like domains that wrap around the catalytic one.<cite>Vickers2018</cite><br />
<br />
[[Image:GH107_full.png|500px]]<br />
[[Image:20191213_GH107-zoom.png|500px]]<br />
<br style="clear: both" /><br />
Figure 2: ''Psychromonas sp.'' GH107 structure and catalytic residues (PDB: [{{PDBlink}}6m8n 6m8n]).<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: The retaining mechanism was determined in 2018.<cite>Vickers2018</cite><br />
;First catalytic nucleophile identification: An aspartic acid side chain acting as a catalytic nucleophile was identified by two simultaneous studies in the Autumn of 2018.<cite>Vickers2018</cite><cite>Shultz-Johansen2018</cite><br />
;First general acid/base residue identification: A histidine sidechain acting as a catalytic acid-base residue was identified in 2018.<cite>Vickers2018</cite><br />
;First 3-D structure: The crystal structures of ''Mariniflexile fucanivorans'' (PDB: [{{PDBlink}}6dns 6dns],[{{PDBlink}}6dms 6dms],[{{PDBlink}}6dlh 6dlh]) and ''Psychromonas sp.'' (PDB: [{{PDBlink}}6m8n 6m8n]) have been released at the same time, in 2018.<cite>Vickers2018</cite> <br />
<br />
== References ==<br />
<biblio><br />
#Colin2006 pmid=16880504<br />
#Vickers2018 pmid=30282808<br />
#Shultz-Johansen2018 pmid=30230202<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH107]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_107&diff=14423Glycoside Hydrolase Family 1072019-12-16T17:05:22Z<p>Al Boraston: </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]]: ^^^David Teze^^^<br />
* [[Responsible Curator]]: ^^^Al Boraston^^^<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 GH107'''<br />
|-<br />
|'''Clan''' <br />
|GH-R<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}}GH107.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
The currently characterized [[glycoside hydrolases]] of this family are [[endo]]-acting α-fucosidases active on sulfated fucans (or fucoidans) from brown algae. All described GH107 family members are endo-1,4-fucanase of bacterial origin, and together with enzymes from the CAZY family [[GH29]], they form the clan GH-R. Sequences of GH107 family members were first reported in 2006,<cite>Colin2006</cite> even though the enzymatic activity was reported earlier.<br />
<br />
== Kinetics and Mechanism ==<br />
<br />
The mechanism was proven to be [[retaining]] by observation of the formation of an α-''O''-linked mercaptoethanol on a L-Fuc-2,3-disulfate-(α1-3)-L-Fuc-2-sulfate disaccharide by transglycosylation.<cite>Vickers2018</cite> It should then follow a [[classical Koshland double-displacement mechanism]] similarly to [[GH29]].<br />
<br />
[[Image:20191213 Gh107.png|thumb|left|800px|Figure 1: Mechanism of GH107 family. According to <cite>Vickers2018</cite>.]]<br />
<br style="clear: both" /><br />
<br />
== Catalytic Residues ==<br />
The catalytic nucleophile is an aspartate, while the catalytic acid-base is a histidine. The later is unusual in GHs, and a divergence from [[GH29]], but is likely necessary to avoid electronic repulsion with the substrate sulfate groups. These two residues have been identified by structural superimposition with GH29 enzymes, and are conserved within the few members of the GH107 family. The catalytic His has been further confirmed by the lack of activity of th H294Q mutant of ''Mariniflexile fucanivorans''.<cite>Vickers2018</cite> The catalytic aspartate was also proposed to be one of the catalytic residue on sequence analysis alone, in a simultaneously released paper.<cite>Shultz-Johansen2018</cite><br />
<br />
== Three-dimensional structures ==<br />
The crystal structures of ''Mariniflexile fucanivorans'' (PDB: [{{PDBlink}}6dns 6dns],[{{PDBlink}}6dms 6dms],[{{PDBlink}}6dlh 6dlh]) and ''Psychromonas sp.'' (PDB: [{{PDBlink}}6m8n 6m8n]) have been determined in 2018.<cite>Vickers2018</cite> The ''Psychromonas sp.'' (PDB: [{{PDBlink}}6m8n 6m8n]) enzyme showed a single catalytic domain with a (β/α)<sub>8</sub> / TIM-barrel fold, while in the ''Mariniflexile fucanivorans'' enzyme, this catalytic domain is followed by three Ig-like domains that wrap around the catalytic one.<cite>Vickers2018</cite><br />
<br />
[[Image:GH107_full.png|500px]]<br />
[[Image:20191213_GH107-zoom.png|500px]]<br />
<br style="clear: both" /><br />
Figure 2: ''Psychromonas sp.'' GH107 structure and catalytic residues (PDB: [{{PDBlink}}6m8n 6m8n]).<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: The retaining mechanism was determined in 2018.<cite>Vickers2018</cite><br />
;First catalytic nucleophile identification: An aspartic acid side chain acting as a catalytic nucleophile was identified by two simultaneous studies in the Autumn of 2018.<cite>Vickers2018</cite><cite>Shultz-Johansen2018</cite><br />
;First general acid/base residue identification: A histidine sidechain acting as a catalytic acid-base residue was identified in 2018.<cite>Vickers2018</cite><br />
;First 3-D structure: The crystal structures of ''Mariniflexile fucanivorans'' (PDB: [{{PDBlink}}6dns 6dns],[{{PDBlink}}6dms 6dms],[{{PDBlink}}6dlh 6dlh]) and ''Psychromonas sp.'' (PDB: [{{PDBlink}}6m8n 6m8n]) have been released at the same time, in 2018.<cite>Vickers2018</cite> <br />
<br />
== References ==<br />
<biblio><br />
#Colin2006 pmid=16880504<br />
#Vickers2018 pmid=30282808<br />
#Shultz-Johansen2018 pmid=30230202<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH107]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_107&diff=14422Glycoside Hydrolase Family 1072019-12-16T17:05:05Z<p>Al Boraston: </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]]: ^^^David Teze^^^<br />
* [[Responsible Curator]]: ^^^Al Boraston^^^<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 GH107'''<br />
|-<br />
|'''Clan''' <br />
|GH-R<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}}GH107.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
The currently characterizes [[glycoside hydrolases]] of this family are [[endo]]-acting α-fucosidases active on sulfated fucans (or fucoidans) from brown algae. All described GH107 family members are endo-1,4-fucanase of bacterial origin, and together with enzymes from the CAZY family [[GH29]], they form the clan GH-R. Sequences of GH107 family members were first reported in 2006,<cite>Colin2006</cite> even though the enzymatic activity was reported earlier.<br />
<br />
== Kinetics and Mechanism ==<br />
<br />
The mechanism was proven to be [[retaining]] by observation of the formation of an α-''O''-linked mercaptoethanol on a L-Fuc-2,3-disulfate-(α1-3)-L-Fuc-2-sulfate disaccharide by transglycosylation.<cite>Vickers2018</cite> It should then follow a [[classical Koshland double-displacement mechanism]] similarly to [[GH29]].<br />
<br />
[[Image:20191213 Gh107.png|thumb|left|800px|Figure 1: Mechanism of GH107 family. According to <cite>Vickers2018</cite>.]]<br />
<br style="clear: both" /><br />
<br />
== Catalytic Residues ==<br />
The catalytic nucleophile is an aspartate, while the catalytic acid-base is a histidine. The later is unusual in GHs, and a divergence from [[GH29]], but is likely necessary to avoid electronic repulsion with the substrate sulfate groups. These two residues have been identified by structural superimposition with GH29 enzymes, and are conserved within the few members of the GH107 family. The catalytic His has been further confirmed by the lack of activity of th H294Q mutant of ''Mariniflexile fucanivorans''.<cite>Vickers2018</cite> The catalytic aspartate was also proposed to be one of the catalytic residue on sequence analysis alone, in a simultaneously released paper.<cite>Shultz-Johansen2018</cite><br />
<br />
== Three-dimensional structures ==<br />
The crystal structures of ''Mariniflexile fucanivorans'' (PDB: [{{PDBlink}}6dns 6dns],[{{PDBlink}}6dms 6dms],[{{PDBlink}}6dlh 6dlh]) and ''Psychromonas sp.'' (PDB: [{{PDBlink}}6m8n 6m8n]) have been determined in 2018.<cite>Vickers2018</cite> The ''Psychromonas sp.'' (PDB: [{{PDBlink}}6m8n 6m8n]) enzyme showed a single catalytic domain with a (β/α)<sub>8</sub> / TIM-barrel fold, while in the ''Mariniflexile fucanivorans'' enzyme, this catalytic domain is followed by three Ig-like domains that wrap around the catalytic one.<cite>Vickers2018</cite><br />
<br />
[[Image:GH107_full.png|500px]]<br />
[[Image:20191213_GH107-zoom.png|500px]]<br />
<br style="clear: both" /><br />
Figure 2: ''Psychromonas sp.'' GH107 structure and catalytic residues (PDB: [{{PDBlink}}6m8n 6m8n]).<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: The retaining mechanism was determined in 2018.<cite>Vickers2018</cite><br />
;First catalytic nucleophile identification: An aspartic acid side chain acting as a catalytic nucleophile was identified by two simultaneous studies in the Autumn of 2018.<cite>Vickers2018</cite><cite>Shultz-Johansen2018</cite><br />
;First general acid/base residue identification: A histidine sidechain acting as a catalytic acid-base residue was identified in 2018.<cite>Vickers2018</cite><br />
;First 3-D structure: The crystal structures of ''Mariniflexile fucanivorans'' (PDB: [{{PDBlink}}6dns 6dns],[{{PDBlink}}6dms 6dms],[{{PDBlink}}6dlh 6dlh]) and ''Psychromonas sp.'' (PDB: [{{PDBlink}}6m8n 6m8n]) have been released at the same time, in 2018.<cite>Vickers2018</cite> <br />
<br />
== References ==<br />
<biblio><br />
#Colin2006 pmid=16880504<br />
#Vickers2018 pmid=30282808<br />
#Shultz-Johansen2018 pmid=30230202<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH107]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_107&diff=14421Glycoside Hydrolase Family 1072019-12-16T17:03:18Z<p>Al Boraston: </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]]: ^^^David Teze^^^<br />
* [[Responsible Curator]]: ^^^Al Boraston^^^<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 GH107'''<br />
|-<br />
|'''Clan''' <br />
|GH-R<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}}GH107.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
The [[glycoside hydrolases]] of this family are [[endo]]-acting α-fucosidases active on sulfated fucans (or fucoidans) from brown algae. All described GH107 family members are endo-1,4-fucanase of bacterial origin, and together with enzymes from the CAZY family [[GH29]], they form the clan GH-R. Sequences of GH107 family members were first reported in 2006,<cite>Colin2006</cite> even though the enzymatic activity was reported earlier.<br />
<br />
== Kinetics and Mechanism ==<br />
<br />
The mechanism was proven to be [[retaining]] by observation of the formation of an α-''O''-linked mercaptoethanol on a L-Fuc-2,3-disulfate-(α1-3)-L-Fuc-2-sulfate disaccharide by transglycosylation.<cite>Vickers2018</cite> It should then follow a [[classical Koshland double-displacement mechanism]] similarly to [[GH29]].<br />
<br />
[[Image:20191213 Gh107.png|thumb|left|800px|Figure 1: Mechanism of GH107 family. According to <cite>Vickers2018</cite>.]]<br />
<br style="clear: both" /><br />
<br />
== Catalytic Residues ==<br />
The catalytic nucleophile is an aspartate, while the catalytic acid-base is a histidine. The later is unusual in GHs, and a divergence from [[GH29]], but is likely necessary to avoid electronic repulsion with the substrate sulfate groups. These two residues have been identified by structural superimposition with GH29 enzymes, and are conserved within the few members of the GH107 family. The catalytic His has been further confirmed by the lack of activity of th H294Q mutant of ''Mariniflexile fucanivorans''.<cite>Vickers2018</cite> The catalytic aspartate was also proposed to be one of the catalytic residue on sequence analysis alone, in a simultaneously released paper.<cite>Shultz-Johansen2018</cite><br />
<br />
== Three-dimensional structures ==<br />
The crystal structures of ''Mariniflexile fucanivorans'' (PDB: [{{PDBlink}}6dns 6dns],[{{PDBlink}}6dms 6dms],[{{PDBlink}}6dlh 6dlh]) and ''Psychromonas sp.'' (PDB: [{{PDBlink}}6m8n 6m8n]) have been determined in 2018.<cite>Vickers2018</cite> The ''Psychromonas sp.'' (PDB: [{{PDBlink}}6m8n 6m8n]) enzyme showed a single catalytic domain with a (β/α)<sub>8</sub> / TIM-barrel fold, while in the ''Mariniflexile fucanivorans'' enzyme, this catalytic domain is followed by three Ig-like domains that wrap around the catalytic one.<cite>Vickers2018</cite><br />
<br />
[[Image:GH107_full.png|500px]]<br />
[[Image:20191213_GH107-zoom.png|500px]]<br />
<br style="clear: both" /><br />
Figure 2: ''Psychromonas sp.'' GH107 structure and catalytic residues (PDB: [{{PDBlink}}6m8n 6m8n]).<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: The retaining mechanism was determined in 2018.<cite>Vickers2018</cite><br />
;First catalytic nucleophile identification: An aspartic acid side chain acting as a catalytic nucleophile was identified by two simultaneous studies in the Autumn of 2018.<cite>Vickers2018</cite><cite>Shultz-Johansen2018</cite><br />
;First general acid/base residue identification: A histidine sidechain acting as a catalytic acid-base residue was identified in 2018.<cite>Vickers2018</cite><br />
;First 3-D structure: The crystal structures of ''Mariniflexile fucanivorans'' (PDB: [{{PDBlink}}6dns 6dns],[{{PDBlink}}6dms 6dms],[{{PDBlink}}6dlh 6dlh]) and ''Psychromonas sp.'' (PDB: [{{PDBlink}}6m8n 6m8n]) have been released at the same time, in 2018.<cite>Vickers2018</cite> <br />
<br />
== References ==<br />
<biblio><br />
#Colin2006 pmid=16880504<br />
#Vickers2018 pmid=30282808<br />
#Shultz-Johansen2018 pmid=30230202<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH107]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_71&diff=14403Carbohydrate Binding Module Family 712019-12-13T16:55:55Z<p>Al Boraston: </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]]: ^^^Ben Pluvinage^^^<br />
* [[Responsible Curator]]: ^^^Al Boraston^^^<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" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CBM71.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Ligand specificities ==<br />
<br />
[[File:CBM71-1.png|thumb|300px|right|'''Figure 1.''' Structure of CBM71-1. Cartoon representation of CBM71-1 in complex with LacNAc (green sticks). Color ramped red to blue from N- to C-terminus. A bound calcium atom is shown in magenta.]]<br />
<br />
The CBM family 71 was created in September 2014 with the characterization of the large multimodular β-galactosidase BgaA from ''Streptococcus pneumoniae'' <cite>Singh2014</cite>. Two CBMs, CBM71-1 (residues 1463-1645) and CBM71-2 (residues 1828-1998), were identified in the N-terminal region of this protein. The functional characterization of the CBMs reveals a binding specificity limited to lactose (galactopyranosyl-β-1,4-D-glucose) and LacNAc (galactopyranosyl-β-1,4-N-acetyl-D-glucosamine).<br />
<br />
== Structural Features ==<br />
The structure of CBM71-1 <cite>Singh2014</cite> solved by X-ray crystallography shows a β-sandwich fold comprising opposing sheets of 4- and 5-antiparallel β-strands and a bound structural metal ion modelled as a calcium (Figure 1). CBM71-1 structure in complex with LacNAc reveals a shallow <br />
binding site located at the apex of the β-fold opposite the N- and C-termini, making CBM71s [[Carbohydrate-binding_modules#Types|type C]] CBMs <cite>Boraston2004</cite>. The basis of CBM71-1 specificity for sugars with a terminal galactose resides in the W1514 side chain configuration, which provides CH-pi interactions with both β-linked pyranose rings of the disaccharide (Figure 2). CBM71-2, which possesses 35% sequence identity with CBM71-1, presents a very similar fold and an almost identical binding site <cite>Singh2014</cite>. <br />
<br />
[[File:CBM71-1CatSite.png|thumb|300px|right|'''Figure 2.''' CBM71-1 binding site. Residues involved in binding LacNAc (green) are shown as cyan sticks and waters as red spheres. Black dashed lines represent hydrogen bonds.]]<br />
<br />
== Functionalities ==<br />
The CBM71s are found as ancillary modules in the β-galactosidase BgaA from ''S. pneumoniae'' <cite>Singh2014</cite>. BgaA is a large multimodular cell surface exposed CAZyme comprising 17 modules of 7 different types. However, only the catalytic module belonging to the family 2 glycoside hydrolase <cite>Cantarel2009</cite> has been fully characterized along with the characterization of CBM71s <cite>Singh2014</cite>. In addition to their classical CBM role of focusing the enzyme to its substrate, the streptococcal CBM71s have been shown to contribute to pneumococcal adherence by binding lactose- and LacNAc-containing cell surface glycoconjugates <cite>Singh2014</cite>.<br />
<br />
== Family Firsts ==<br />
;First Identified: The CBM71 modules were first identified through the characterization of the β-galactosidase BgaA from ''S. pneumoniae'' <cite>Singh2014</cite>. CBM71-1 and CBM71-2 are the founding, and only characterized, members of the family.<br />
;First Structural Characterization: The first crystal structures of family CBM71s were from the streptococcal β-galactosidase BgaA <cite>Singh2014</cite>. The crystallographic structures of a seleno-methionine derivative of CBM71-1 (PDB ID [{{PDBlink}}4CUA 4CUA]), CBM71-1 in complex with LacNAc (PDB ID [{{PDBlink}}4CUB 4CUB]) and CBM71-2 (PDB ID [{{PDBlink}}4CU9 4CU9]) were deposited in the Protein Data Bank in September 2014. <br />
<br />
== References ==<br />
<biblio><br />
#Singh2014 pmid=25210925<br />
#Boraston2004 pmid=15214846<br />
#Cantarel2009 pmid=18838391<br />
</biblio><br />
<br />
[[Category:Carbohydrate Binding Module Families|CBM071]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Polysaccharide_Lyase_Family_2&diff=9319Polysaccharide Lyase Family 22013-09-23T21:52:43Z<p>Al Boraston: </p>
<hr />
<div><br />
<!-- RESPONSIBLE CURATORS: Please replace the {{UnderConstruction}} tag below with {{CuratorApproved}} when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Wade Abbott^^^<br />
* [[Responsible Curator]]: ^^^Wade Abbott^^^<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" |'''Polysaccharide Lyase Family PL2'''<br />
|-<br />
|'''Mechanism''' <br />
|&beta;-elimination<br />
|-<br />
|'''Metal Cofactor'''<br />
|manganese<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}PL2.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
PL2 activity has been demonstrated on &alpha;-(1,4)-linked polygalacturonic acid (i.e. homogalacturonan or pectate) and &alpha;-(1,4)-linked oligogalacturonides <cite>Abbott2007, Shevchik1999</cite>. <br />
<br />
== Kinetics and Mechanism ==<br />
Use of &beta;-elimination reaction to cleave the glycosidic bonds in pectate requires a Brønstead base for proton abstraction and a catalytic metal (e.g. Mn<sup>2+</sup> or Mg<sup>2+</sup>) for acidification of the &beta;-proton and oxyanion stabilization. PL2s have reported pH optimas in the range of 7.4 - 9.6 <cite>Abbott2007, Abbott2013</cite>, which is substantially lower than the pKa of arginine. These effects have been attributed to localized pKa effects within the active site. &beta;-elimination results in the production of a new reducing end (residue in the -1 subsite) and a 4,5-unsaturated bond in the other newly generated sugar chain end (residue in the +1 subsite).<br />
<br />
== Catalytic Residues ==<br />
The Brønstead base for the PL2 family is an ariginine, which is consistent with most pectate lyase families. R218 in YePL2A was the first catalytic base described for the family and it is completely conserved within the family <cite>Abbott2007, Abbott2013</cite>. The metal coordination pocket consists of two histidine residues (YePL2A: H109 and H172) and one glutamic acid (YePL2A: E130). <br />
<br />
== Subfamilies ==<br />
There are two PL2 subfamilies in PL2. Subfamily 1 is correlated with endolytic activity, whereas subfamily 2 is correlated with exolytic activity. Intriguingly, the majority of sequence entries are from the genomes of phytopathogenic or enteropathogenic bacteria, and are found in paralogous copies within each species <cite>Abbott2013</cite>. Several outliers exist, including the single copy PaePL2 from ''Paenibacillus sp.''Y412MC10, which may reflect the ancestral endolytic activity <cite>Abbott2013</cite>. <br />
<br />
== Three-dimensional structures ==<br />
The structure of the endolytic PL2A from ''Yersinia enterocolitica'' (YePL2A) is the only only PL2 structure to be reported <cite>Abbott2007</cite>. Three different models for YePL2A have been deposited, including a native-form (2V8I, 1.50 Å), and a complex with trigalacturonate (2V8K, 2.1 Å) and a transition metal bound form (2V8J, 2.01 Å). Family 2 PLs adopt a rare &alpha;/&alpha;-7 barrel fold, with an active site cleft extending along the surface of the enzyme between two catalytic arms. Substrate binding induces a conformational change and the arms close about the substrate. <br />
<br />
== Family Firsts ==<br />
;First catalytic activity: PelY from ''Yersinia pseudotuberculosis'' macerated cucumber <cite>Manulis1988</cite>. <br />
;First catalytic base identification: YePL2A (YE4069) R218 from ''Yersinia enterocolitica'' <cite>Abbott2007</cite>.<br />
;First catalytic divalent cation identification: DdPL2/PelW(Dda3937_03361) from ''Dickeya Dadantii'' 3937 (Previously ''Erwinia chrysanthemi''3937) <cite>Shevchik1999</cite>. <br />
<br />
;First 3-D structure: PL2A (YE4069) from ''Yersinia enterocolitica'' <cite>Abbott2007</cite> (2V8I, 2V8J, 2V8K).<br />
<br />
== References ==<br />
<biblio><br />
#Abbott2007 pmid=17881361<br />
#Shevchik1999 pmid=10383957<br />
#Manulis1988 pmid=2832382<br />
#Abbott2013 pmid=24013861<br />
</biblio><br />
<br />
[[Category:Polysaccharide Lyase Families|PL002]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_32&diff=8746Carbohydrate Binding Module Family 322013-05-22T16:19:05Z<p>Al Boraston: </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]]: ^^^Elizabeth Ficko-Blean^^^ and ^^^Al Boraston^^^<br />
* [[Responsible Curator]]: ^^^Elizabeth Ficko-Blean^^^<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" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CBM32.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Ligand specificities ==<br />
In 1994 the first CBM32 structure in complex with D-galactose was determined from a fungal galactose oxidase <cite>Ito1994</cite>. Following that, a CBM32 from a multi-modular sialidase produced by ''Micromonospora viridifaciens'' was shown to demonstrate galactose and lactose binding specificity <cite>Gaskell1995 Newstead2005</cite>. A CBM32 from a ''Cellvibrio mixtus'' family 16 glycoside hydrolase binds laminarin and pustulan <cite>Centeno2006</cite> while a CBM32 from a ''Clostridium thermocellum'' mannanase has demonstrated binding on the non-reducing end of β-mannans and β-1,4-linked mannooligosaccharides <cite>Mizutani2012</cite>. A periplasmic-binding protein, YeCBM32, from ''Yersinia enterolitica'' shares sequence identity with the CBM32 family and binds the polygalaturonic acid components of pectin <cite>Abbott2007</cite>. The ''Clostridium perfringens'' CBM32s have been well studied and many of their ligand specificities determined as follows: D-galactose, N-acetyl-D-galactosamine <cite>Boraston2007 Ficko-Blean2012 Ficko-Blean2006 </cite>, D-galactose-β-1,4-N-acetyl-D-glucosamine (LacNAc), L-fucose-α-1,2-D-galactose-β-1,4-N-acetyl-D-glucosamine (type II blood group H-trisaccharide) <cite>Ficko-Blean2006</cite>, N-acetyl-D-glucosamine, N-acetyl-D-glucosamine-β-1,3-N-acetyl-D-galactosamine, N-acetyl-D-glucosamine-β-1,2-D-mannose, N-acetyl-D-glucosamine-β-1,3-D-mannose (non-biological) <cite>Ficko-Blean2009</cite>, and N-acetyl-D-glucosamine-α-1,4-D-galactose <cite>Ficko-Blean2012</cite>. Some members of the family 32 CBMs have demonstrated a degree of promiscuity in their binding, these include CpCBM32-2 from the NagH enzyme and CpCBM32C from the NagJ enzyme, both produced by ''Clostridium perfringens'' <cite>Ficko-Blean2009 Ficko-Blean2006</cite>. This CBM family has a very diverse set of ligand specificities reflected in the notable amino acid sequence divergence throughout the family <cite>AbbottMolBiolEvol</cite>.<br />
<br />
Please see these references for an essential introduction to the CAZy classification system: <cite>DaviesSinnott2008 Cantarel2009</cite>. CBMs, in particular, have been extensively reviewed <cite>Boraston2004 Hashimoto2006 Shoseyov2006 Guillen2010</cite>.<br />
<br />
== Structural Features ==<br />
The CBM32s share the common beta sandwich fold and have a bound structural metal ion most often attributed to be calcium <cite>Boraston2004</cite>. Most family members have fairly weak binding affinities (''K''<sub>a</sub>s in the mM<sup>-1</sup> and low μM<sup>-1</sup> range) <cite>Ficko-Blean2009 Ficko-Blean2006 Mizutani2012</cite>. These binding site are located at the terminal loop region within the CBM32 family. The binding sites are in some cases quite shallow and designed to bind monosaccharides or short oligosaccharides <cite>Ficko-Blean2009 Ficko-Blean2006 Boraston2007 Ficko-Blean2012</cite>. Variability within the apical loop region within the family confers the different ligand specificities. Characteristically, there is one residue, commonly Trp but also Tyr, which provides an important hydrophobic platform for interaction with the ring of one of the sugar moieties <cite>Gaskell1995 Ficko-Blean2006 Ficko-Blean2012</cite>. In most cases the CBM32 members interact with the non-reducing end of oligosacchides <cite>Ficko-Blean2009 Ficko-Blean2006 Boraston2007 Ficko-Blean2012 Mizutani2012</cite>; however, this is not always the case as demonstrated by the periplasmic-binding protein from ''Y. enterocolitica'' - which shares sequence identity with the CBM32 family <cite>Cantarel2009</cite> - and binds polygalacturonic acid polymers <cite>Abbott2007</cite>. Some structural examples of the complex oligosaccharide binding sites of the CBM32s can be found in the following pdbs: 1EUU <cite>Gaskell1995</cite>, 2J7M <cite>Ficko-Blean2006</cite>, 4A45 <cite>Ficko-Blean2012</cite>, 4A6O <cite>Ficko-Blean2012</cite>, and 2W1U <cite>Ficko-Blean2009</cite>, to name just a few. <br />
<br />
== Functionalities == <br />
CBM32 modules are thought to target the catalytic modules to their respective substrates. CBM32s from the Gram positive pathogen ''C. perfringens'' may well have a dual role as many of the enzymes containing CBM32s have an LPXTG motif at their C-terminal end; this signals for sortase-mediated anchoring to the bacterial cell wall <cite>Mazmanian1999</cite>. Thus, not only would the catalytic modules be targeted to substrate, but also the bacterium as a whole, suggesting an adhesin-like activity for these CBMs <cite>Ficko-BleanPortraitOfAnEnzyme</cite>. <br />
<br />
The types of catalytic modules that the CBM32 members are associated with vary widely and include sialidases <cite>Boraston2007</cite>, β-N-acetylglucosaminidases <cite>Rao</cite>, α-N-acetylglucosaminidases <cite>Ficko-BleanGH89</cite>, mannanases <cite>Mizutani2012</cite> and galactose oxidases <cite>Ito1994</cite>. In enteric bacteria the CBM32 motif may occur more than once in the same enzyme and they may or may not share the same ligand specifities - suggesting the possibility of heterogenic multivalent binding events <cite>Boraston2007 Ficko-Blean2012 AbbottMolBiolEvol</cite>. Other modules that may be associated in the same enzymes are different families of CBMs, FNIII domains, and cohesin and dockerin domains <cite>Ficko-BleanPortraitOfAnEnzyme Chitayat2008 Adams2008 Ficko-Blean2012</cite>. <br />
<br />
There are now examples of CBM32s that are independant of a catalytic module, such as the YeCBM32 periplasmic-binding protein <cite>Abbott2007</cite>; however, with the application of a strict definition that CBMs are appended to carbohydrate-active enzymes <cite>Cantarel2009</cite> there is some debate as to whether the CBMs without covalently-bound carbohydrate-active enzymes are really CBMs. In any case, nature has found a way to use the CBM amino acid sequence, structural motif, modular character, and carbohydrate-binding functionality beyond the bounds of the definition of a CBM. <br />
<br />
Finally, the CBM32 family's "exotic" specificities for animal glycans suggest the possibility for novel application development, though, to date, none have been published. <br />
<br />
== Family Firsts ==<br />
;First Identified<br />
The first identification of the galactose carbohydrate-binding function of a CBM32 was from the fungus ''Fusarium graminearum'' <cite>Ito1994</cite> (previously ''Dactylium dendroides'' <cite>Ogel</cite>).<br />
;First Structural Characterization<br />
The first native crystal structure of a CBM32 from the fungus ''Fusarium graminearum'' was determined in 1991, although it had not yet been identified as a CBM <cite>Ito1991</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#AbbottMolBiolEvol pmid=18032406<br />
#Adams2008 pmid=18716000<br />
#Chitayat2008 pmid=17999932<br />
#Newstead2005 pmid=16239725<br />
#Ito1994 pmid=8182749<br />
#Gaskell1995 pmid=8591030<br />
#Centeno2006 pmid=17005007<br />
#Abbott2007 pmid=17292916<br />
#Boraston2007 pmid=17850114<br />
#Mizutani2012 pmid=22562994<br />
#Mazmanian1999 pmid=10427003<br />
#Ficko-BleanGH89 pmid=22479408 <br />
#Ficko-Blean2012 pmid=22479408<br />
#Ficko-Blean2009 pmid=19422833<br />
#Ficko-Blean2006 pmid=16990278<br />
#Ficko-BleanPortraitOfAnEnzyme pmid=19193644<br />
#Boraston2003 pmid=12634060<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. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
#Boraston2004 pmid=15214846<br />
#Hashimoto2006 pmid=17131061<br />
#Rao pmid=16541109<br />
#Shoseyov2006 pmid=16760304<br />
#Guillen2010 pmid=19908036<br />
#Ito1991 pmid=2002850 <br />
#Ogel Ögel, Z.B. Brayford, D. and McPherson, M.J. (1994) Cellulose-Triggered Sporulation in the Galactose Oxidase-Producing Fungus Cladobotryum (Dactylium) Dendroides Nrrl-2903 and Its Reidentification as a Species of Fusarium. Mycological Research. http://apps.webofknowledge.com/full_record.do?product=UA&search_mode=GeneralSearch&qid=6&SID=T257NBohnbhe1P6F9Dh&page=1&doc=1<br />
</biblio><br />
<br />
[[Category:Carbohydrate Binding Module Families|CBM032]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_32&diff=8745Carbohydrate Binding Module Family 322013-05-22T16:17:58Z<p>Al Boraston: </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 />
* [[Authors]]: ^^^Elizabeth Ficko-Blean and Al Boraston^^^<br />
* [[Responsible Curator]]: ^^^Elizabeth Ficko-Blean^^^<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" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CBM32.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Ligand specificities ==<br />
In 1994 the first CBM32 structure in complex with D-galactose was determined from a fungal galactose oxidase <cite>Ito1994</cite>. Following that, a CBM32 from a multi-modular sialidase produced by ''Micromonospora viridifaciens'' was shown to demonstrate galactose and lactose binding specificity <cite>Gaskell1995 Newstead2005</cite>. A CBM32 from a ''Cellvibrio mixtus'' family 16 glycoside hydrolase binds laminarin and pustulan <cite>Centeno2006</cite> while a CBM32 from a ''Clostridium thermocellum'' mannanase has demonstrated binding on the non-reducing end of β-mannans and β-1,4-linked mannooligosaccharides <cite>Mizutani2012</cite>. A periplasmic-binding protein, YeCBM32, from ''Yersinia enterolitica'' shares sequence identity with the CBM32 family and binds the polygalaturonic acid components of pectin <cite>Abbott2007</cite>. The ''Clostridium perfringens'' CBM32s have been well studied and many of their ligand specificities determined as follows: D-galactose, N-acetyl-D-galactosamine <cite>Boraston2007 Ficko-Blean2012 Ficko-Blean2006 </cite>, D-galactose-β-1,4-N-acetyl-D-glucosamine (LacNAc), L-fucose-α-1,2-D-galactose-β-1,4-N-acetyl-D-glucosamine (type II blood group H-trisaccharide) <cite>Ficko-Blean2006</cite>, N-acetyl-D-glucosamine, N-acetyl-D-glucosamine-β-1,3-N-acetyl-D-galactosamine, N-acetyl-D-glucosamine-β-1,2-D-mannose, N-acetyl-D-glucosamine-β-1,3-D-mannose (non-biological) <cite>Ficko-Blean2009</cite>, and N-acetyl-D-glucosamine-α-1,4-D-galactose <cite>Ficko-Blean2012</cite>. Some members of the family 32 CBMs have demonstrated a degree of promiscuity in their binding, these include CpCBM32-2 from the NagH enzyme and CpCBM32C from the NagJ enzyme, both produced by ''Clostridium perfringens'' <cite>Ficko-Blean2009 Ficko-Blean2006</cite>. This CBM family has a very diverse set of ligand specificities reflected in the notable amino acid sequence divergence throughout the family <cite>AbbottMolBiolEvol</cite>.<br />
<br />
Please see these references for an essential introduction to the CAZy classification system: <cite>DaviesSinnott2008 Cantarel2009</cite>. CBMs, in particular, have been extensively reviewed <cite>Boraston2004 Hashimoto2006 Shoseyov2006 Guillen2010</cite>.<br />
<br />
== Structural Features ==<br />
The CBM32s share the common beta sandwich fold and have a bound structural metal ion most often attributed to be calcium <cite>Boraston2004</cite>. Most family members have fairly weak binding affinities (''K''<sub>a</sub>s in the mM<sup>-1</sup> and low μM<sup>-1</sup> range) <cite>Ficko-Blean2009 Ficko-Blean2006 Mizutani2012</cite>. These binding site are located at the terminal loop region within the CBM32 family. The binding sites are in some cases quite shallow and designed to bind monosaccharides or short oligosaccharides <cite>Ficko-Blean2009 Ficko-Blean2006 Boraston2007 Ficko-Blean2012</cite>. Variability within the apical loop region within the family confers the different ligand specificities. Characteristically, there is one residue, commonly Trp but also Tyr, which provides an important hydrophobic platform for interaction with the ring of one of the sugar moieties <cite>Gaskell1995 Ficko-Blean2006 Ficko-Blean2012</cite>. In most cases the CBM32 members interact with the non-reducing end of oligosacchides <cite>Ficko-Blean2009 Ficko-Blean2006 Boraston2007 Ficko-Blean2012 Mizutani2012</cite>; however, this is not always the case as demonstrated by the periplasmic-binding protein from ''Y. enterocolitica'' - which shares sequence identity with the CBM32 family <cite>Cantarel2009</cite> - and binds polygalacturonic acid polymers <cite>Abbott2007</cite>. Some structural examples of the complex oligosaccharide binding sites of the CBM32s can be found in the following pdbs: 1EUU <cite>Gaskell1995</cite>, 2J7M <cite>Ficko-Blean2006</cite>, 4A45 <cite>Ficko-Blean2012</cite>, 4A6O <cite>Ficko-Blean2012</cite>, and 2W1U <cite>Ficko-Blean2009</cite>, to name just a few. <br />
<br />
== Functionalities == <br />
CBM32 modules are thought to target the catalytic modules to their respective substrates. CBM32s from the Gram positive pathogen ''C. perfringens'' may well have a dual role as many of the enzymes containing CBM32s have an LPXTG motif at their C-terminal end; this signals for sortase-mediated anchoring to the bacterial cell wall <cite>Mazmanian1999</cite>. Thus, not only would the catalytic modules be targeted to substrate, but also the bacterium as a whole, suggesting an adhesin-like activity for these CBMs <cite>Ficko-BleanPortraitOfAnEnzyme</cite>. <br />
<br />
The types of catalytic modules that the CBM32 members are associated with vary widely and include sialidases <cite>Boraston2007</cite>, β-N-acetylglucosaminidases <cite>Rao</cite>, α-N-acetylglucosaminidases <cite>Ficko-BleanGH89</cite>, mannanases <cite>Mizutani2012</cite> and galactose oxidases <cite>Ito1994</cite>. In enteric bacteria the CBM32 motif may occur more than once in the same enzyme and they may or may not share the same ligand specifities - suggesting the possibility of heterogenic multivalent binding events <cite>Boraston2007 Ficko-Blean2012 AbbottMolBiolEvol</cite>. Other modules that may be associated in the same enzymes are different families of CBMs, FNIII domains, and cohesin and dockerin domains <cite>Ficko-BleanPortraitOfAnEnzyme Chitayat2008 Adams2008 Ficko-Blean2012</cite>. <br />
<br />
There are now examples of CBM32s that are independant of a catalytic module, such as the YeCBM32 periplasmic-binding protein <cite>Abbott2007</cite>; however, with the application of a strict definition that CBMs are appended to carbohydrate-active enzymes <cite>Cantarel2009</cite> there is some debate as to whether the CBMs without covalently-bound carbohydrate-active enzymes are really CBMs. In any case, nature has found a way to use the CBM amino acid sequence, structural motif, modular character, and carbohydrate-binding functionality beyond the bounds of the definition of a CBM. <br />
<br />
Finally, the CBM32 family's "exotic" specificities for animal glycans suggest the possibility for novel application development, though, to date, none have been published. <br />
<br />
== Family Firsts ==<br />
;First Identified<br />
The first identification of the galactose carbohydrate-binding function of a CBM32 was from the fungus ''Fusarium graminearum'' <cite>Ito1994</cite> (previously ''Dactylium dendroides'' <cite>Ogel</cite>).<br />
;First Structural Characterization<br />
The first native crystal structure of a CBM32 from the fungus ''Fusarium graminearum'' was determined in 1991, although it had not yet been identified as a CBM <cite>Ito1991</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#AbbottMolBiolEvol pmid=18032406<br />
#Adams2008 pmid=18716000<br />
#Chitayat2008 pmid=17999932<br />
#Newstead2005 pmid=16239725<br />
#Ito1994 pmid=8182749<br />
#Gaskell1995 pmid=8591030<br />
#Centeno2006 pmid=17005007<br />
#Abbott2007 pmid=17292916<br />
#Boraston2007 pmid=17850114<br />
#Mizutani2012 pmid=22562994<br />
#Mazmanian1999 pmid=10427003<br />
#Ficko-BleanGH89 pmid=22479408 <br />
#Ficko-Blean2012 pmid=22479408<br />
#Ficko-Blean2009 pmid=19422833<br />
#Ficko-Blean2006 pmid=16990278<br />
#Ficko-BleanPortraitOfAnEnzyme pmid=19193644<br />
#Boraston2003 pmid=12634060<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. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
#Boraston2004 pmid=15214846<br />
#Hashimoto2006 pmid=17131061<br />
#Rao pmid=16541109<br />
#Shoseyov2006 pmid=16760304<br />
#Guillen2010 pmid=19908036<br />
#Ito1991 pmid=2002850 <br />
#Ogel Ögel, Z.B. Brayford, D. and McPherson, M.J. (1994) Cellulose-Triggered Sporulation in the Galactose Oxidase-Producing Fungus Cladobotryum (Dactylium) Dendroides Nrrl-2903 and Its Reidentification as a Species of Fusarium. Mycological Research. http://apps.webofknowledge.com/full_record.do?product=UA&search_mode=GeneralSearch&qid=6&SID=T257NBohnbhe1P6F9Dh&page=1&doc=1<br />
</biblio><br />
<br />
[[Category:Carbohydrate Binding Module Families|CBM032]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Carbohydrate_Binding_Module_Family_32&diff=8744Carbohydrate Binding Module Family 322013-05-22T15:41:33Z<p>Al Boraston: </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]]: ^^^Elizabeth Ficko-Blean^^^<br />
* [[Responsible Curator]]: ^^^Al Boraston^^^<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" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}CBM32.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
== Ligand specificities ==<br />
In 1994 the first CBM32 structure in complex with D-galactose was determined from a fungal galactose oxidase <cite>Ito1994</cite>. Following that, a CBM32 from a multi-modular sialidase produced by ''Micromonospora viridifaciens'' was shown to demonstrate galactose and lactose binding specificity <cite>Gaskell1995 Newstead2005</cite>. A CBM32 from a ''Cellvibrio mixtus'' family 16 glycoside hydrolase binds laminarin and pustulan <cite>Centeno2006</cite> while a CBM32 from a ''Clostridium thermocellum'' mannanase has demonstrated binding on the non-reducing end of β-mannans and β-1,4-linked mannooligosaccharides <cite>Mizutani2012</cite>. A periplasmic-binding protein, YeCBM32, from ''Yersinia enterolitica'' shares sequence identity with the CBM32 family and binds the polygalaturonic acid components of pectin <cite>Abbott2007</cite>. The ''Clostridium perfringens'' CBM32s have been well studied and many of their ligand specificities determined as follows: D-galactose, N-acetyl-D-galactosamine <cite>Boraston2007 Ficko-Blean2012 Ficko-Blean2006 </cite>, D-galactose-β-1,4-N-acetyl-D-glucosamine (LacNAc), L-fucose-α-1,2-D-galactose-β-1,4-N-acetyl-D-glucosamine (type II blood group H-trisaccharide) <cite>Ficko-Blean2006</cite>, N-acetyl-D-glucosamine, N-acetyl-D-glucosamine-β-1,3-N-acetyl-D-galactosamine, N-acetyl-D-glucosamine-β-1,2-D-mannose, N-acetyl-D-glucosamine-β-1,3-D-mannose (non-biological) <cite>Ficko-Blean2009</cite>, and N-acetyl-D-glucosamine-α-1,4-D-galactose <cite>Ficko-Blean2012</cite>. Some members of the family 32 CBMs have demonstrated a degree of promiscuity in their binding, these include CpCBM32-2 from the NagH enzyme and CpCBM32C from the NagJ enzyme, both produced by ''Clostridium perfringens'' <cite>Ficko-Blean2009 Ficko-Blean2006</cite>. This CBM family has a very diverse set of ligand specificities reflected in the notable amino acid sequence divergence throughout the family <cite>AbbottMolBiolEvol</cite>.<br />
<br />
Please see these references for an essential introduction to the CAZy classification system: <cite>DaviesSinnott2008 Cantarel2009</cite>. CBMs, in particular, have been extensively reviewed <cite>Boraston2004 Hashimoto2006 Shoseyov2006 Guillen2010</cite>.<br />
<br />
== Structural Features ==<br />
The CBM32s share the common beta sandwich fold and have a bound structural metal ion most often attributed to be calcium <cite>Boraston2004</cite>. Most family members have fairly weak binding affinities (''K''<sub>a</sub>s in the mM<sup>-1</sup> and low μM<sup>-1</sup> range) <cite>Ficko-Blean2009 Ficko-Blean2006 Mizutani2012</cite>. These binding site are located at the terminal loop region within the CBM32 family. The binding sites are in some cases quite shallow and designed to bind monosaccharides or short oligosaccharides <cite>Ficko-Blean2009 Ficko-Blean2006 Boraston2007 Ficko-Blean2012</cite>. Variability within the apical loop region within the family confers the different ligand specificities. Characteristically, there is one residue, commonly Trp but also Tyr, which provides an important hydrophobic platform for interaction with the ring of one of the sugar moieties <cite>Gaskell1995 Ficko-Blean2006 Ficko-Blean2012</cite>. In most cases the CBM32 members interact with the non-reducing end of oligosacchides <cite>Ficko-Blean2009 Ficko-Blean2006 Boraston2007 Ficko-Blean2012 Mizutani2012</cite>; however, this is not always the case as demonstrated by the periplasmic-binding protein from ''Y. enterocolitica'' - which shares sequence identity with the CBM32 family <cite>Cantarel2009</cite> - and binds polygalacturonic acid polymers <cite>Abbott2007</cite>. Some structural examples of the complex oligosaccharide binding sites of the CBM32s can be found in the following pdbs: 1EUU <cite>Gaskell1995</cite>, 2J7M <cite>Ficko-Blean2006</cite>, 4A45 <cite>Ficko-Blean2012</cite>, 4A6O <cite>Ficko-Blean2012</cite>, and 2W1U <cite>Ficko-Blean2009</cite>, to name just a few. <br />
<br />
== Functionalities == <br />
CBM32 modules are thought to target the catalytic modules to their respective substrates. CBM32s from the Gram positive pathogen ''C. perfringens'' may well have a dual role as many of the enzymes containing CBM32s have an LPXTG motif at their C-terminal end; this signals for sortase-mediated anchoring to the bacterial cell wall <cite>Mazmanian1999</cite>. Thus, not only would the catalytic modules be targeted to substrate, but also the bacterium as a whole, suggesting an adhesin-like activity for these CBMs <cite>Ficko-BleanPortraitOfAnEnzyme</cite>. <br />
<br />
The types of catalytic modules that the CBM32 members are associated with vary widely and include sialidases <cite>Boraston2007</cite>, β-N-acetylglucosaminidases <cite>Rao</cite>, α-N-acetylglucosaminidases <cite>Ficko-BleanGH89</cite>, mannanases <cite>Mizutani2012</cite> and galactose oxidases <cite>Ito1994</cite>. In enteric bacteria the CBM32 motif may occur more than once in the same enzyme and they may or may not share the same ligand specifities - suggesting the possibility of heterogenic multivalent binding events <cite>Boraston2007 Ficko-Blean2012 AbbottMolBiolEvol</cite>. Other modules that may be associated in the same enzymes are different families of CBMs, FNIII domains, and cohesin and dockerin domains <cite>Ficko-BleanPortraitOfAnEnzyme Chitayat2008 Adams2008 Ficko-Blean2012</cite>. <br />
<br />
There are now examples of CBM32s that are independant of a catalytic module, such as the YeCBM32 periplasmic-binding protein <cite>Abbott2007</cite>; however, with the application of a strict definition that CBMs are appended to carbohydrate-active enzymes <cite>Cantarel2009</cite> there is some debate as to whether the CBMs without covalently-bound carbohydrate-active enzymes are really CBMs. In any case, nature has found a way to use the CBM amino acid sequence, structural motif, modular character, and carbohydrate-binding functionality beyond the bounds of the definition of a CBM. <br />
<br />
Finally, the CBM32 family's "exotic" specificities for animal glycans suggest the possibility for novel application development, though, to date, none have been published. <br />
<br />
== Family Firsts ==<br />
;First Identified<br />
The first identification of the galactose carbohydrate-binding function of a CBM32 was from the fungus ''Fusarium graminearum'' <cite>Ito1994</cite> (previously ''Dactylium dendroides'' <cite>Ogel</cite>).<br />
;First Structural Characterization<br />
The first native crystal structure of a CBM32 from the fungus ''Fusarium graminearum'' was determined in 1991, although it had not yet been identified as a CBM <cite>Ito1991</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#AbbottMolBiolEvol pmid=18032406<br />
#Adams2008 pmid=18716000<br />
#Chitayat2008 pmid=17999932<br />
#Newstead2005 pmid=16239725<br />
#Ito1994 pmid=8182749<br />
#Gaskell1995 pmid=8591030<br />
#Centeno2006 pmid=17005007<br />
#Abbott2007 pmid=17292916<br />
#Boraston2007 pmid=17850114<br />
#Mizutani2012 pmid=22562994<br />
#Mazmanian1999 pmid=10427003<br />
#Ficko-BleanGH89 pmid=22479408 <br />
#Ficko-Blean2012 pmid=22479408<br />
#Ficko-Blean2009 pmid=19422833<br />
#Ficko-Blean2006 pmid=16990278<br />
#Ficko-BleanPortraitOfAnEnzyme pmid=19193644<br />
#Boraston2003 pmid=12634060<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. Biochem. J. (BJ Classic Paper, online only). [http://dx.doi.org/10.1042/BJ20080382 DOI: 10.1042/BJ20080382]<br />
#Boraston2004 pmid=15214846<br />
#Hashimoto2006 pmid=17131061<br />
#Rao pmid=16541109<br />
#Shoseyov2006 pmid=16760304<br />
#Guillen2010 pmid=19908036<br />
#Ito1991 pmid=2002850 <br />
#Ogel Ögel, Z.B. Brayford, D. and McPherson, M.J. (1994) Cellulose-Triggered Sporulation in the Galactose Oxidase-Producing Fungus Cladobotryum (Dactylium) Dendroides Nrrl-2903 and Its Reidentification as a Species of Fusarium. Mycological Research. http://apps.webofknowledge.com/full_record.do?product=UA&search_mode=GeneralSearch&qid=6&SID=T257NBohnbhe1P6F9Dh&page=1&doc=1<br />
</biblio><br />
<br />
[[Category:Carbohydrate Binding Module Families|CBM032]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_125&diff=7822Glycoside Hydrolase Family 1252012-11-16T21:50:30Z<p>Al Boraston: </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]]: ^^^Alisdair Boraston^^^<br />
* [[Responsible Curator]]: ^^^Alisdair Boraston^^^<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 GH125'''<br />
|-<br />
| '''Clan'''<br />
| GH-L<br />
|-<br />
| '''Mechanism'''<br />
| inverting<br />
|-<br />
| '''Active site residues'''<br />
| known<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH125.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
The currently characterized family 125 glycoside hydrolases, which include the examples from ''Streptococcus pneumoniae'' (SpGH125) and ''Clostridium perfringens'' (CpGH125), are α-mannosidases with specificity for α-1,6-linked non-reducing terminal mannose residues <cite>Gregg2011</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Kinetic characterization of 2,4-dinitrophenyl α-D-mannopyranoside hydrolysis by SpGH125 and CpGH125 revealed that this is a relatively poor substrate for these enzymes. Monitoring the hydrolysis of methyl 6-''O''-(α-D-mannopyranosyl)-β-D-mannopyranoside by <sup>1</sup>H NMR spectroscopy showed that CpGH125 and SpGH125 act with inversion of stereochemistry. The structural analysis of both enzymes detailed an arrangement of catalytic residues that was consistent with this mechanistic assignment <cite>Gregg2011</cite>.<br />
<br />
== Catalytic Residues ==<br />
The structural analysis of CpGH125 suggested it uses aspartate 220 as a catalytic acid and glutamate 393 as catalytic base. The corresponding residues in SpGH125 are aspartate 218 and glutamate 391 <cite>Gregg2011</cite>. The assignment of these residues was determined primarily from the structure of CpGH125 in complex with the non-hydrolyzable substrate-analog methyl-''S''-(α-D-mannopyranosyl)-(1–6)-α-D-mannopyranose (thiomannobiose), which spanned the -1 and +1 subsites and engaged the catalytic machinery. Additional support for the assignment was provided by structural alignment with other members of Clan GH-L, specifically GH15 and GH65, which revealed conservation of these catalytic residues among all of the clan members.<br />
<br />
== Three-dimensional structures ==<br />
The three dimensional structures of CpGH125 ([{{PDBlink}}3qt3 3qt3], [{{PDBlink}}3qt9 3qt9], and [{{PDBlink}}2nvp 2nvp]), SpGH125 ([{{PDBlink}}3qpf 3qpf], [{{PDBlink}}3qry 3qry], and [{{PDBlink}}3qsp 3qsp]) have been determined by X-ray crystallography and revealed the (α/α)<sub>6</sub>-fold of the family <cite>Gregg2011</cite>. The complexes of SpGH125 with the inhibitor 1-deoxymannojirimycin and CpGH125 with the non-hydrolyzable thiomannobiose provided insight into the mode of substrate recognition, the identity of the catalytic residues, and the catalytic mechanism. A non-productive complex of SpGH125 with α-D-mannopyranosyl-(1–6)-α-D-mannopyranose occupying the +1 and +2 subsites provided a view of how more extensive substrates may be recognized by these enzymes. The uncomplexed structures of two GH125 enzymes from ''Bacteroides ovatus'' ([{{PDBlink}}3on6 3on6], and [{{PDBlink}}3p2c 3p2c]) and one GH125 from ''Bacteroides thetaiotaomicron'' ([{{PDBlink}}2pov 2pov]) are notable as they were the first deposited structures for members of GH family 125; however, they were deposited prior to the determination of an activity for this family of enzymes and at present remain otherwise uncharacterized. <br />
<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: <sup>1</sup>H NMR spectroscopy revealed that CpGH125 and SpGH125 act with inversion of stereochemistry <cite>Gregg2011</cite>.<br />
;First [[general base]] identification: CpGH125 and SpGH125 (inferred from structure) <cite>Gregg2011</cite>.<br />
;First [[general acid]] identification: CpGH125 and SpGH125 (inferred from structure) <cite>Gregg2011</cite>.<br />
;First 3-D structure: The first deposited structure was that of CpGH125 ([{{PDBlink}}2nvp 2nvp]) closely followed by the deposition of structures of the ''Bacteroides'' sp. proteins ([{{PDBlink}}3on6 3on6], [{{PDBlink}}3p2c 3p2c], and [{{PDBlink}}2pov 2pov]). These structures were determined by the Structural Genomics Consortium but not published. The first published structures were those of CpGH125 and SpGH125, which also presented the first structures of these proteins in complex with carbohydrates <cite>Gregg2011</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Gregg2011 pmid=21388958<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH125]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_125&diff=7821Glycoside Hydrolase Family 1252012-11-16T21:49:34Z<p>Al Boraston: </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]]: ^^^Alisdair Boraston^^^<br />
* [[Responsible Curator]]: ^^^Alisdair Boraston^^^<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 GH125'''<br />
|-<br />
| '''Clan'''<br />
| GH-L<br />
|-<br />
| '''Mechanism'''<br />
| inverting<br />
|-<br />
| '''Active site residues'''<br />
| known<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH125.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
The currently characterized family 125 glycoside hydrolases, which include the examples from ''Streptococcus pneumoniae'' (SpGH125) and ''Clostridium perfringens'' (CpGH125), are α-mannosidases with specificity for α-1,6-linked non-reducing terminal mannose residues <cite>Gregg2011</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Kinetic characterization of 2,4-dinitrophenyl α-D-mannopyranoside hydrolysis by SpGH125 and CpGH125 revealed that this is a relatively poor substrate for these enzymes. Monitoring the hydrolysis of methyl 6-''O''-(α-D-mannopyranosyl)-β-D-mannopyranoside by <sup>1</sup>H NMR spectroscopy showed that CpGH125 and SpGH125 act with inversion of stereochemistry. The structural analysis of both enzymes detailed an arrangement of catalytic residues that was consistent with this mechanistic assignment <cite>Gregg2011</cite>.<br />
<br />
== Catalytic Residues ==<br />
The structural analysis of CpGH125 suggested it uses aspartate 220 as a catalytic acid and glutamate 393 as catalytic base. The corresponding residues in SpGH125 are aspartate 218 and glutamate 391 <cite>Gregg2011</cite>. The assignment of these residues was determined primarily from the structure of CpGH125 in complex with the non-hydrolyzable substrate-analog methyl-''S''-(α-D-mannopyranosyl)-(1–6)-α-D-mannopyranose (thiomannobiose), which spanned the -1 and +1 subsites and engaged the catalytic machinery. Additional support for the assignment was provided by structural alignment with other members of Clan GH-L, specifically GH15 and GH65, which revealed conservation of these catalytic residues among all of the clan members.<br />
<br />
== Three-dimensional structures ==<br />
The three dimensional structures of CpGH125 ([{{PDBlink}}3qt3 3qt3], [{{PDBlink}}3qt9 3qt9], and [{{PDBlink}}2nvp 2nvp]), SpGH125 ([{{PDBlink}}3qpf 3qpf], [{{PDBlink}}3qry 3qry], and [{{PDBlink}}3qsp 3qsp]) have been determined by X-ray crystallography and revealed the (α/α)<sub>6</sub>-fold of the family <cite>Gregg2011</cite>. The complexes of SpGH125 with the inhibitor 1-deoxymannojirimycin and CpGH125 with the non-hydrolyzable thiomannobiose provided insight into the mode of substrate recognition, the identity of the catalytic residues, and the catalytic mechanism. A non-productive complex of SpGH125 with α-D-mannopyranosyl-(1–6)-α-D-mannopyranose occupying the +1 and +2 subsites provided a view of how more extensive substrates may be recognized by these enzymes. The uncomplexed structures two GH125 enzymes from ''Bacteroides ovatus'' ([{{PDBlink}}3on6 3on6], and [{{PDBlink}}3p2c 3p2c]) and one GH125 from ''Bacteroides thetaiotaomicron'' ([{{PDBlink}}2pov 2pov]) are notable as they were the first deposited structures for members of GH family 125; however, they were deposited prior to the determination of an activity for this family of enzymes. <br />
<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: <sup>1</sup>H NMR spectroscopy revealed that CpGH125 and SpGH125 act with inversion of stereochemistry <cite>Gregg2011</cite>.<br />
;First [[general base]] identification: CpGH125 and SpGH125 (inferred from structure) <cite>Gregg2011</cite>.<br />
;First [[general acid]] identification: CpGH125 and SpGH125 (inferred from structure) <cite>Gregg2011</cite>.<br />
;First 3-D structure: The first deposited structure was that of CpGH125 ([{{PDBlink}}2nvp 2nvp]) closely followed by the deposition of structures of the ''Bacteroides'' sp. proteins ([{{PDBlink}}3on6 3on6], [{{PDBlink}}3p2c 3p2c], and [{{PDBlink}}2pov 2pov]). These structures were determined by the Structural Genomics Consortium but not published. The first published structures were those of CpGH125 and SpGH125, which also presented the first structures of these proteins in complex with carbohydrates <cite>Gregg2011</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Gregg2011 pmid=21388958<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH125]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_125&diff=7820Glycoside Hydrolase Family 1252012-11-16T21:48:01Z<p>Al Boraston: </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]]: ^^^Alisdair Boraston^^^<br />
* [[Responsible Curator]]: ^^^Alisdair Boraston^^^<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 GH125'''<br />
|-<br />
| '''Clan'''<br />
| GH-L<br />
|-<br />
| '''Mechanism'''<br />
| inverting<br />
|-<br />
| '''Active site residues'''<br />
| known<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH125.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
The currently characterized family 125 glycoside hydrolases, which include the examples from ''Streptococcus pneumoniae'' (SpGH125) and ''Clostridium perfringens'' (CpGH125), are α-mannosidases with specificity for α-1,6-linked non-reducing terminal mannose residues <cite>Gregg2011</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Kinetic characterization of 2,4-dinitrophenyl α-D-mannopyranoside hydrolysis by SpGH125 and CpGH125 revealed that this is a relatively poor substrate for these enzymes. Monitoring the hydrolysis of methyl 6-''O''-(α-D-mannopyranosyl)-β-D-mannopyranoside by <sup>1</sup>H NMR spectroscopy showed that CpGH125 and SpGH125 act with inversion of stereochemistry. The structural analysis of both enzymes detailed an arrangement of catalytic residues that was consistent with this mechanistic assignment <cite>Gregg2011</cite>.<br />
<br />
== Catalytic Residues ==<br />
The structural analysis of CpGH125 suggests it uses aspartate 220 as a catalytic acid and glutamate 393 as catalytic base. The corresponding residues in SpGH125 are aspartate 218 and glutamate 391 <cite>Gregg2011</cite>. The assignment of these residues was determined primarily from the structure of CpGH125 in complex with the non-hydrolyzable substrate-analog methyl-''S''-(α-D-mannopyranosyl)-(1–6)-α-D-mannopyranose (thiomannobiose), which spanned the -1 and +1 subsites and engaged the catalytic machinery. Additional support for the assignment was provided by structural alignment with other members of Clan GH-L, specifically GH15 and GH65, which revealed conservation of these catalytic residues among all of the clan members.<br />
<br />
== Three-dimensional structures ==<br />
The three dimensional structures of CpGH125 ([{{PDBlink}}3qt3 3qt3], [{{PDBlink}}3qt9 3qt9], and [{{PDBlink}}2nvp 2nvp]), SpGH125 ([{{PDBlink}}3qpf 3qpf], [{{PDBlink}}3qry 3qry], and [{{PDBlink}}3qsp 3qsp]) have been determined by X-ray crystallography and reveal the (α/α)<sub>6</sub>-fold of the family <cite>Gregg2011</cite>. The complexes of SpGH125 with the inhibitor 1-deoxymannojirimycin and CpGH125 with the non-hydrolyzable thiomannobiose provide insight into the mode of substrate recognition, the identity of the catalytic residues, and the catalytic mechanism. A non-productive complex of SpGH125 with α-D-mannopyranosyl-(1–6)-α-D-mannopyranose occupying the +1 and +2 subsites provides a view of how more extensive substrates may be recognized by these enzymes. The uncomplexed structures two GH125 enzymes from ''Bacteroides ovatus'' ([{{PDBlink}}3on6 3on6], and [{{PDBlink}}3p2c 3p2c]) and one GH125 from ''Bacteroides thetaiotaomicron'' ([{{PDBlink}}2pov 2pov]) are notable as they were the first deposited structures for members of GH family 125; however, they were deposited prior to the determination of an activity for this family of enzymes. <br />
<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: <sup>1</sup>H NMR spectroscopy revealed that CpGH125 and SpGH125 act with inversion of stereochemistry <cite>Gregg2011</cite>.<br />
;First [[general base]] identification: CpGH125 and SpGH125 (inferred from structure) <cite>Gregg2011</cite>.<br />
;First [[general acid]] identification: CpGH125 and SpGH125 (inferred from structure) <cite>Gregg2011</cite>.<br />
;First 3-D structure: The first deposited structure was that of CpGH125 ([{{PDBlink}}2nvp 2nvp]) closely followed by the deposition of structures of the ''Bacteroides'' sp. proteins ([{{PDBlink}}3on6 3on6], [{{PDBlink}}3p2c 3p2c], and [{{PDBlink}}2pov 2pov]). These structures were determined by the Structural Genomics Consortium but not published. The first published structures were those of CpGH125 and SpGH125, which also presented the first structures of these proteins in complex with carbohydrates <cite>Gregg2011</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Gregg2011 pmid=21388958<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH125]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_125&diff=7819Glycoside Hydrolase Family 1252012-11-16T21:46:21Z<p>Al Boraston: </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]]: ^^^Alisdair Boraston^^^<br />
* [[Responsible Curator]]: ^^^Alisdair Boraston^^^<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 GH125'''<br />
|-<br />
| '''Clan'''<br />
| GH-L<br />
|-<br />
| '''Mechanism'''<br />
| inverting<br />
|-<br />
| '''Active site residues'''<br />
| known<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH125.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
The currently characterized family 125 glycoside hydrolases, which include the examples from ''Streptococcus pneumoniae'' (SpGH125) and ''Clostridium perfringens'' (CpGH125), are α-mannosidases with specificity for α-1,6-linked non-reducing terminal mannose residues <cite>Gregg2011</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Kinetic characterization of 2,4-dinitrophenyl α-D-mannopyranoside hydrolysis by SpGH125 and CpGH125 revealed that this is a relatively poor substrate for these enzymes. Monitoring the hydrolysis of methyl 6-''O''-(α-D-mannopyranosyl)-β-D-mannopyranoside by <sup>1</sup>H NMR spectroscopy showed that CpGH125 and SpGH125 act with inversion of stereochemistry. The structural analysis of both enzymes detailed an arrangement of catalytic residues that was consistent with this mechanistic assignment <cite>Gregg2011</cite>.<br />
<br />
== Catalytic Residues ==<br />
The structural analysis of CpGH125 suggests it uses aspartate 220 as a catalytic acid and glutamate 393 as catalytic base. The corresponding residues in SpGH125 are aspartate 218 and glutamate 391 <cite>Gregg2011</cite>. The assignment of these residues was determined primarily from the structure of CpGH125 in complex with the non-hydrolyzable substrate-analog methyl-''S''-(α-D-mannopyranosyl)-(1–6)-α-D-mannopyranose, which spanned the -1 and +1 subsites and engaged the catalytic machinery. Additional support for the assignment was provided by structural alignment with other members of Clan GH-L, specifically GH15 and GH65, which revealed conservation of these catalytic residues among all of the clan members.<br />
<br />
== Three-dimensional structures ==<br />
The three dimensional structures of CpGH125 ([{{PDBlink}}3qt3 3qt3], [{{PDBlink}}3qt9 3qt9], and [{{PDBlink}}2nvp 2nvp]), SpGH125 ([{{PDBlink}}3qpf 3qpf], [{{PDBlink}}3qry 3qry], and [{{PDBlink}}3qsp 3qsp]) have been determined by X-ray crystallography and reveal the (α/α)<sub>6</sub>-fold of the family <cite>Gregg2011</cite>. The complexes of SpGH125 with the inhibitor 1-deoxymannojirimycin and CpGH125 with the non-hydrolyzable substrate-analog methyl-''S''-(α-D-mannopyranosyl)-(1–6)-α-D-mannopyranose (thiomannobiose), the latter of which spans the -1 and +1 sub sites and engages the catalytic machinery, provide insight into the mode of substrate recognition, the identity of the catalytic residues, and the catalytic mechanism. A non-productive complex of SpGH125 with α-D-mannopyranosyl-(1–6)-α-D-mannopyranose occupying the +1 and +2 subsites provides a view of how more extensive substrates may be recognized by these enzymes. The uncomplexed structures two GH125 enzymes from ''Bacteroides ovatus'' ([{{PDBlink}}3on6 3on6], and [{{PDBlink}}3p2c 3p2c]) and one GH125 from ''Bacteroides thetaiotaomicron'' ([{{PDBlink}}2pov 2pov]) are notable as they were the first deposited structures for members of GH family 125; however, they were deposited prior to the determination of an activity for this family of enzymes. <br />
<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: <sup>1</sup>H NMR spectroscopy revealed that CpGH125 and SpGH125 act with inversion of stereochemistry <cite>Gregg2011</cite>.<br />
;First [[general base]] identification: CpGH125 and SpGH125 (inferred from structure) <cite>Gregg2011</cite>.<br />
;First [[general acid]] identification: CpGH125 and SpGH125 (inferred from structure) <cite>Gregg2011</cite>.<br />
;First 3-D structure: The first deposited structure was that of CpGH125 ([{{PDBlink}}2nvp 2nvp]) closely followed by the deposition of structures of the ''Bacteroides'' sp. proteins ([{{PDBlink}}3on6 3on6], [{{PDBlink}}3p2c 3p2c], and [{{PDBlink}}2pov 2pov]). These structures were determined by the Structural Genomics Consortium but not published. The first published structures were those of CpGH125 and SpGH125, which also presented the first structures of these proteins in complex with carbohydrates <cite>Gregg2011</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Gregg2011 pmid=21388958<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH125]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_125&diff=7818Glycoside Hydrolase Family 1252012-11-16T21:44:54Z<p>Al Boraston: </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]]: ^^^Alisdair Boraston^^^<br />
* [[Responsible Curator]]: ^^^Alisdair Boraston^^^<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 GH125'''<br />
|-<br />
| '''Clan'''<br />
| GH-L<br />
|-<br />
| '''Mechanism'''<br />
| inverting<br />
|-<br />
| '''Active site residues'''<br />
| known<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH125.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
The currently characterized family 125 glycoside hydrolases, which include the examples from ''Streptococcus pneumoniae'' (SpGH125) and ''Clostridium perfringens'' (CpGH125), are α-mannosidases with specificity for α-1,6-linked non-reducing terminal mannose residues <cite>Gregg2011</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Kinetic characterization of 2,4-dinitrophenyl α-D-mannopyranoside hydrolysis by SpGH125 and CpGH125 revealed that this is a relatively poor substrate for these enzymes. Monitoring the hydrolysis of methyl 6-''O''-(α-D-mannopyranosyl)-β-D-mannopyranoside by <sup>1</sup>H NMR spectroscopy showed that CpGH125 and SpGH125 act with inversion of stereochemistry. The structural analysis of both enzymes detailed an arrangement of catalytic residues that was consistent with this mechanistic assignment <cite>Gregg2011</cite>.<br />
<br />
== Catalytic Residues ==<br />
The structural analysis of CpGH125 suggests it uses aspartate 220 as a catalytic acid and glutamate 393 as catalytic base. The corresponding residues in SpGH125 are aspartate 218 and glutamate 391 <cite>Gregg2011</cite>. The assignment of these residues was determined primarily from the structure of CpGH125 in complex with the non-hydrolyzable substrate-analog methyl-''S''-(α-D-mannopyranosyl)-(1–6)-α-D-mannopyranose, which spanned the -1 and +1 subsites and engaged the catalytic machinery. Additional support for the assignment was provided by structural alignment with other members of Clan GH-L, specifically GH15 and GH65, which revealed conservation of these catalytic residues among all of the clan members.<br />
<br />
== Three-dimensional structures ==<br />
The three dimensional structures of CpGH125 ([{{PDBlink}}3qt3 3qt3], [{{PDBlink}}3qt9 3qt9], and [{{PDBlink}}2nvp 2nvp]), SpGH125 ([{{PDBlink}}3qpf 3qpf], [{{PDBlink}}3qry 3qry], and [{{PDBlink}}3qsp 3qsp]) have been determined by X-ray crystallography and reveal the (α/α)<sub>6</sub>-fold of the family. The complexes of SpGH125 with the inhibitor 1-deoxymannojirimycin and CpGH125 with the non-hydrolyzable substrate-analog methyl-''S''-(α-D-mannopyranosyl)-(1–6)-α-D-mannopyranose (thiomannobiose), the latter of which spans the -1 and +1 sub sites and engages the catalytic machinery, provide insight into the mode of substrate recognition, the identity of the catalytic residues, and the catalytic mechanism. A non-productive complex of SpGH125 with α-D-mannopyranosyl-(1–6)-α-D-mannopyranose occupying the +1 and +2 subsites provides a view of how more extensive substrates may be recognized by these enzymes. The uncomplexed structures two GH125 enzymes from ''Bacteroides ovatus'' ([{{PDBlink}}3on6 3on6], and [{{PDBlink}}3p2c 3p2c]) and one GH125 from ''Bacteroides thetaiotaomicron'' ([{{PDBlink}}2pov 2pov]) are notable as they were the first deposited structures for members of GH family 125; however, they were deposited prior to the determination of an activity for this family of enzymes. <br />
<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: <sup>1</sup>H NMR spectroscopy revealed that CpGH125 and SpGH125 act with inversion of stereochemistry <cite>Gregg2011</cite>.<br />
;First [[general base]] identification: CpGH125 and SpGH125 (inferred from structure) <cite>Gregg2011</cite>.<br />
;First [[general acid]] identification: CpGH125 and SpGH125 (inferred from structure) <cite>Gregg2011</cite>.<br />
;First 3-D structure: The first deposited structure was that of CpGH125 ([{{PDBlink}}2nvp 2nvp]) closely followed by the deposition of structures of the ''Bacteroides'' sp. proteins ([{{PDBlink}}3on6 3on6], [{{PDBlink}}3p2c 3p2c], and [{{PDBlink}}2pov 2pov]). These structures were determined by the Structural Genomics Consortium but not published. The first published structures were those of CpGH125 and SpGH125, which also presented the first structures of these proteins in complex with carbohydrates <cite>Gregg2011</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Gregg2011 pmid=21388958<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH125]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_125&diff=7817Glycoside Hydrolase Family 1252012-11-16T21:37:48Z<p>Al Boraston: </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]]: ^^^Alisdair Boraston^^^<br />
* [[Responsible Curator]]: ^^^Alisdair Boraston^^^<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 GH125'''<br />
|-<br />
| '''Clan'''<br />
| GH-L<br />
|-<br />
| '''Mechanism'''<br />
| inverting<br />
|-<br />
| '''Active site residues'''<br />
| known<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH125.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
The currently characterized family 125 glycoside hydrolases, which include the examples from ''Streptococcus pneumoniae'' (SpGH125) and ''Clostridium perfringens'' (CpGH125), are α-mannosidases with specificity for α-1,6-linked non-reducing terminal mannose residues <cite>Gregg2011</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Kinetic characterization of 2,4-dinitrophenyl α-D-mannopyranoside hydrolysis by SpGH125 and CpGH125 revealed that this is a relatively poor substrate for these enzymes. Monitoring the hydrolysis of methyl 6-''O''-(α-D-mannopyranosyl)-β-D-mannopyranoside by <sup>1</sup>H NMR spectroscopy showed that CpGH125 and SpGH125 act with inversion of stereochemistry. The structural analysis of both enzymes detailed an arrangement of catalytic residues that was consistent with this mechanistic assignment <cite>Gregg2011</cite>.<br />
<br />
== Catalytic Residues ==<br />
The structural analysis of CpGH125 suggests it uses aspartate 220 as a catalytic acid and glutamate 393 as catalytic base. The corresponding residues in SpGH125 are aspartate 218 and glutamate 391 <cite>Gregg2011</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The three dimensional structures of CpGH125 ([{{PDBlink}}3qt3 3qt3], [{{PDBlink}}3qt9 3qt9], and [{{PDBlink}}2nvp 2nvp]), SpGH125 ([{{PDBlink}}3qpf 3qpf], [{{PDBlink}}3qry 3qry], and [{{PDBlink}}3qsp 3qsp]) have been determined by X-ray crystallography and reveal the (α/α)<sub>6</sub>-fold of the family. The complexes of SpGH125 with the inhibitor 1-deoxymannojirimycin and CpGH125 with the non-hydrolyzable substrate-analog methyl-''S''-(α-D-mannopyranosyl)-(1–6)-α-D-mannopyranose (thiomannobiose), the latter of which spans the -1 and +1 subsites, provide insight into the mode of substrate recognition, the identity of the catalytic residues, and the catalytic mechanism. A non-productive complex of SpGH125 with α-D-mannopyranosyl-(1–6)-α-D-mannopyranose occupying the +1 and +2 subsites provides a view of how more extensive substrates may be recognized by these enzymes. The uncomplexed structures two GH125 enzymes from ''Bacteroides ovatus'' ([{{PDBlink}}3on6 3on6], and [{{PDBlink}}3p2c 3p2c]) and one GH125 from ''Bacteroides thetaiotaomicron'' ([{{PDBlink}}2pov 2pov]) are also available. These latter structures are notable as they were the first deposited structures for members of GH family 125 but they were deposited prior to the determination of an activity for this family of enzymes. <br />
<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: <sup>1</sup>H NMR spectroscopy revealed that CpGH125 and SpGH125 act with inversion of stereochemistry <cite>Gregg2011</cite>.<br />
;First [[general base]] identification: CpGH125 and SpGH125 (inferred from structure) <cite>Gregg2011</cite>.<br />
;First [[general acid]] identification: CpGH125 and SpGH125 (inferred from structure) <cite>Gregg2011</cite>.<br />
;First 3-D structure: The first deposited structure was that of CpGH125 ([{{PDBlink}}2nvp 2nvp]) closely followed by the deposition of structures of the ''Bacteroides'' sp. proteins ([{{PDBlink}}3on6 3on6], [{{PDBlink}}3p2c 3p2c], and [{{PDBlink}}2pov 2pov]). These structures were determined by the Structural Genomics Consortium but not published. The first published structures were those of CpGH125 and SpGH125, which also presented the first structures of these proteins in complex with carbohydrates <cite>Gregg2011</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Gregg2011 pmid=21388958<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH125]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_125&diff=7816Glycoside Hydrolase Family 1252012-11-16T21:33:28Z<p>Al Boraston: </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]]: ^^^Alisdair Boraston^^^<br />
* [[Responsible Curator]]: ^^^Alisdair Boraston^^^<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 GH125'''<br />
|-<br />
| '''Clan'''<br />
| GH-L<br />
|-<br />
| '''Mechanism'''<br />
| inverting<br />
|-<br />
| '''Active site residues'''<br />
| known<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH125.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
The currently characterized family 125 glycoside hydrolases, which include the examples from ''Streptococcus pneumoniae'' (SpGH125) and ''Clostridium perfringens'' (CpGH125), are α-mannosidases with specificity for α-1,6-linked non-reducing terminal mannose residues <cite>Gregg2011</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Kinetic characterization of 2,4-dinitrophenyl α-D-mannopyranoside hydrolysis by SpGH125 and CpGH125 revealed that this is a relatively poor substrate for these enzymes. Monitoring the hydrolysis of methyl 6-''O''-(α-D-mannopyranosyl)-β-D-mannopyranoside by <sup>1</sup>H NMR spectroscopy showed that CpGH125 and SpGH125 act with inversion of stereochemistry. The structural analysis of both enzymes detailed an arrangement of catalytic residues that was consistent with this mechanistic assignment <cite>Gregg2011</cite>.<br />
<br />
== Catalytic Residues ==<br />
The structural analysis of CpGH125 suggests it uses aspartate 220 as a catalytic acid and glutamate 393 as catalytic base. The corresponding residues in SpGH125 are aspartate 218 and glutamate 391 <cite>Gregg2011</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The three dimensional structures of CpGH125 ([{{PDBlink}}3qt3 3qt3], [{{PDBlink}}3qt9 3qt9], and [{{PDBlink}}2nvp 2nvp]), SpGH125 ([{{PDBlink}}3qpf 3qpf], [{{PDBlink}}3qry 3qry], and [{{PDBlink}}3qsp 3qsp]) have been determined by X-ray crystallography and reveal the (α/α)<sub>6</sub>-fold of the family. The complexes of SpGH125 with the inhibitor 1-deoxymannojirimycin and CpGH125 with the non-hydrolyzable substrate-analog methyl-''S''-(α-D-mannopyranosyl)-(1–6)-α-D-mannopyranose (thiomannobiose), the latter of which spans the -1 and +1 subsites, provide insight into the mode of substrate recognition, the identity of the catalytic residues, and the catalytic mechanism. A non-productive complex of SpGH125 with α-D-mannopyranosyl-(1–6)-α-D-mannopyranose occupying the +1 and +2 subsites provides a view of how more extensive substrates may be recognized by these enzymes. The uncomplexed structures of presently uncharacterized family members, two GH125 enzymes from ''Bacteroides ovatus'' ([{{PDBlink}}3on6 3on6], and [{{PDBlink}}3p2c 3p2c]) and one GH125 from ''Bacteroides thetaiotaomicron'' ([{{PDBlink}}2pov 2pov]), are also available.<br />
<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: <sup>1</sup>H NMR spectroscopy revealed that CpGH125 and SpGH125 act with inversion of stereochemistry <cite>Gregg2011</cite>.<br />
;First [[general base]] identification: CpGH125 and SpGH125 (inferred from structure) <cite>Gregg2011</cite>.<br />
;First [[general acid]] identification: CpGH125 and SpGH125 (inferred from structure) <cite>Gregg2011</cite>.<br />
;First 3-D structure: The first deposited structure was that of CpGH125 ([{{PDBlink}}2nvp 2nvp]) closely followed by the deposition of structures of the ''Bacteroides'' sp. proteins ([{{PDBlink}}3on6 3on6], [{{PDBlink}}3p2c 3p2c], and [{{PDBlink}}2pov 2pov]). These structures were determined by the Structural Genomics Consortium but not published. The first published structures were those of CpGH125 and SpGH125, which also presented the first structures of these proteins in complex with carbohydrates <cite>Gregg2011</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Gregg2011 pmid=21388958<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH125]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_125&diff=7815Glycoside Hydrolase Family 1252012-11-16T21:29:16Z<p>Al Boraston: </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]]: ^^^Alisdair Boraston^^^<br />
* [[Responsible Curator]]: ^^^Alisdair Boraston^^^<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 GH125'''<br />
|-<br />
| '''Clan'''<br />
| GH-L<br />
|-<br />
| '''Mechanism'''<br />
| inverting<br />
|-<br />
| '''Active site residues'''<br />
| known<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH125.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
The currently characterized family 125 glycoside hydrolases, which include the examples from ''Streptococcus pneumoniae'' (SpGH125) and ''Clostridium perfringens'' (CpGH125), are α-mannosidases with specificity for α-1,6-linked non-reducing terminal mannose residues <cite>Gregg2011</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Kinetic characterization of 2,4-dinitrophenyl α-D-mannopyranoside hydrolysis by SpGH125 and CpGH125 revealed that this is a relatively poor substrate for these enzymes. Monitoring the hydrolysis of methyl 6-''O''-(α-D-mannopyranosyl)-β-D-mannopyranoside by <sup>1</sup>H NMR spectroscopy showed that CpGH125 and SpGH125 act with inversion of stereochemistry. The structural analysis of both enzymes detailed an arrangement of catalytic residues that was consistent with this mechanistic assignment <cite>Gregg2011</cite>.<br />
<br />
== Catalytic Residues ==<br />
The structural analysis of CpGH125 suggests it uses aspartate 220 as a catalytic acid and glutamate 393 as catalytic base. The corresponding residues in SpGH125 are aspartate 218 and glutamate 391 <cite>Gregg2011</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The three dimensional structures of CpGH125 ([{{PDBlink}}3qt3 3qt3], [{{PDBlink}}3qt9 3qt9], and [{{PDBlink}}2nvp 2nvp]), SpGH125 ([{{PDBlink}}3qpf 3qpf], [{{PDBlink}}3qry 3qry], and [{{PDBlink}}3qsp 3qsp]) have been determined by X-ray crystallography and reveal the (α/α)<sub>6</sub>-fold of the family. The complexes of SpGH125 with the inhibitor 1-deoxymannojirimycin and CpGH125 with the non-hydrolyzable substrate-analog methyl-''S''-(α-D-mannopyranosyl)-(1–6)-α-D-mannopyranose (thiomannobiose), the latter of which spans the -1 and +1 subsites, provide insight into the mode of substrate recognition, the identity of the catalytic residues, and the catalytic mechanism. A non-productive complex of SpGH125 with α-D-mannopyranosyl)-(1–6)-α-D-mannopyranose occupying the +1 and +2 subsites provides a view of how more extensive substrates may be recognized by these enzymes. Though the proteins are uncharacterized, structures are also available for two GH125 enzymes from ''Bacteroides ovatus'' ([{{PDBlink}}3on6 3on6], and [{{PDBlink}}3p2c 3p2c]) and one GH125 from ''Bacteroides thetaiotaomicron'' ([{{PDBlink}}2pov 2pov]).<br />
<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: <sup>1</sup>H NMR spectroscopy revealed that CpGH125 and SpGH125 act with inversion of stereochemistry <cite>Gregg2011</cite>.<br />
;First [[general base]] identification: CpGH125 and SpGH125 (inferred from structure) <cite>Gregg2011</cite>.<br />
;First [[general acid]] identification: CpGH125 and SpGH125 (inferred from structure) <cite>Gregg2011</cite>.<br />
;First 3-D structure: The first deposited structure was that of CpGH125 ([{{PDBlink}}2nvp 2nvp]) closely followed by the deposition of structures of the ''Bacteroides'' sp. proteins. These structures were determined by the Structural Genomics Consortium but not published. The first published structures were those of CpGH125 and SpGH125, which also presented the first structures of these proteins in complex with carbohydrates <cite>Gregg2011</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Gregg2011 pmid=21388958<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH125]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_125&diff=7814Glycoside Hydrolase Family 1252012-11-16T21:26:57Z<p>Al Boraston: </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]]: ^^^Alisdair Boraston^^^<br />
* [[Responsible Curator]]: ^^^Alisdair Boraston^^^<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 GH125'''<br />
|-<br />
| '''Clan'''<br />
| GH-L<br />
|-<br />
| '''Mechanism'''<br />
| inverting<br />
|-<br />
| '''Active site residues'''<br />
| known<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH125.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
The currently characterized family 125 glycoside hydrolases, which include the examples from ''Streptococcus pneumoniae'' (SpGH125) and ''Clostridium perfringens'' (CpGH125), are α-mannosidases with specificity for α-1,6-linked non-reducing terminal mannose residues <cite>Gregg2011</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Kinetic characterization of 2,4-dinitrophenyl α-D-mannopyranoside hydrolysis by SpGH125 and CpGH125 revealed that this is a relatively poor substrate for these enzymes. Monitoring the hydrolysis of methyl 6-''O''-(α-D-mannopyranosyl)-β-D-mannopyranoside by <sup>1</sup>H NMR spectroscopy showed that CpGH125 and SpGH125 act with inversion of stereochemistry. The structural analysis of both enzymes detailed an arrangement of catalytic residues that was consistent with this mechanistic assignment <cite>Gregg2011</cite>.<br />
<br />
== Catalytic Residues ==<br />
The structural analysis of CpGH125 suggests it uses aspartate 220 as a catalytic acid and glutamate 393 as catalytic base. The corresponding residues in SpGH125 are aspartate 218 and glutamate 391 <cite>Gregg2011</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The three dimensional structures of CpGH125 ([{{PDBlink}}3qt3 3qt3], [{{PDBlink}}3qt9 3qt9], and [{{PDBlink}}2nvp 2nvp]), SpGH125 ([{{PDBlink}}3qpf 3qpf], [{{PDBlink}}3qry 3qry], and [{{PDBlink}}3qsp 3qsp]) have been determined by X-ray crystallography and reveal the (α/α)<sub>6</sub>-fold of the family. The complexes of SpGH125 with the inhibitor 1-deoxymannojirimycin and CpGH125 with the non-hydrolyzable substrate-analog methyl-''S''-(α-D-mannopyranosyl)-(1–6)-α-D-mannopyranose (thiomannobiose), the latter of which spans the -1 and +1 subsites, provide insight into the mode of substrate recognition, the identity of the catalytic residues, and catalytic mechanism. Though the proteins are uncharacterized, structures are also available for two GH125 enzymes from ''Bacteroides ovatus'' ([{{PDBlink}}3on6 3on6], and [{{PDBlink}}3p2c 3p2c]) and one GH125 from ''Bacteroides thetaiotaomicron'' ([{{PDBlink}}2pov 2pov]).<br />
<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: <sup>1</sup>H NMR spectroscopy revealed that CpGH125 and SpGH125 act with inversion of stereochemistry <cite>Gregg2011</cite>.<br />
;First [[general base]] identification: CpGH125 and SpGH125 (inferred from structure) <cite>Gregg2011</cite>.<br />
;First [[general acid]] identification: CpGH125 and SpGH125 (inferred from structure) <cite>Gregg2011</cite>.<br />
;First 3-D structure: The first deposited structure was that of CpGH125 ([{{PDBlink}}2nvp 2nvp]) closely followed by the deposition of structures of the ''Bacteroides'' sp. proteins. These structures were determined by the Structural Genomics Consortium but not published. The first published structures were those of CpGH125 and SpGH125, which also presented the first structures of these proteins in complex with carbohydrates <cite>Gregg2011</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Gregg2011 pmid=21388958<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH125]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_125&diff=7813Glycoside Hydrolase Family 1252012-11-16T17:37:45Z<p>Al Boraston: </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]]: ^^^Alisdair Boraston^^^<br />
* [[Responsible Curator]]: ^^^Alisdair Boraston^^^<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 GH125'''<br />
|-<br />
| '''Clan'''<br />
| GH-L<br />
|-<br />
| '''Mechanism'''<br />
| inverting<br />
|-<br />
| '''Active site residues'''<br />
| known<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH125.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
The currently characterized family 125 glycoside hydrolases, which include the examples from ''Streptococcus pneumoniae'' (SpGH125) and ''Clostridium perfringens'' (CpGH125), are α-mannosidases with specificity for α-1,6-linked non-reducing terminal mannose residues <cite>Gregg2011</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Kinetic characterization of 2,4-dinitrophenyl α-D-mannopyranoside hydrolysis by SpGH125 and CpGH125 revealed that this is a relatively poor substrate for these enzymes. Monitoring the hydrolysis of methyl 6-''O''-(α-D-mannopyranosyl)-β-D-mannopyranoside by <sup>1</sup>H NMR spectroscopy showed that CpGH125 and SpGH125 act with inversion of stereochemistry. The structural analysis of both enzymes detailed an arrangement of catalytic residues that was consistent with this mechanistic assignment <cite>Gregg2011</cite>.<br />
<br />
== Catalytic Residues ==<br />
The structural analysis of CpGH125 suggests it uses aspartate 220 as a catalytic acid and glutamate 393 as catalytic base. The corresponding residues in SpGH125 are aspartame 218 and glutamate 391 <cite>Gregg2011</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The three dimensional structures of CpGH125 ([{{PDBlink}}3qt3 3qt3], [{{PDBlink}}3qt9 3qt9], and [{{PDBlink}}2nvp 2nvp]), SpGH125 ([{{PDBlink}}3qpf 3qpf], [{{PDBlink}}3qry 3qry], and [{{PDBlink}}3qsp 3qsp]) are available and reveal both the (α/α)<sub>6</sub>-fold of the family as well the details of inhibitor and substrate recognition. Though the proteins are uncharacterized, structures are also available for two GH125 enzymes from ''Bacteroides ovatus'' ([{{PDBlink}}3on6 3on6], and [{{PDBlink}}3p2c 3p2c]) and one GH125 from ''Bacteroides thetaiotaomicron'' ([{{PDBlink}}2pov 2pov]).<br />
<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: <sup>1</sup>H NMR spectroscopy revealed that CpGH125 and SpGH125 act with inversion of stereochemistry <cite>Gregg2011</cite>.<br />
;First [[general base]] identification: CpGH125 and SpGH125 (inferred from structure) <cite>Gregg2011</cite>.<br />
;First [[general acid]] identification: CpGH125 and SpGH125 (inferred from structure) <cite>Gregg2011</cite>.<br />
;First 3-D structure: The first deposited structure was that of CpGH125 ([{{PDBlink}}2nvp 2nvp]) closely followed by the deposition of structures of the ''Bacteroides'' sp. proteins. These structures were determined by the Structural Genomics Consortium but not published. The first published structures were those of CpGH125 and SpGH125, which also presented the first structures of these proteins in complex with carbohydrates <cite>Gregg2011</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Gregg2011 pmid=21388958<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH125]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_125&diff=7812Glycoside Hydrolase Family 1252012-11-16T17:36:06Z<p>Al Boraston: </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]]: ^^^Alisdair Boraston^^^<br />
* [[Responsible Curator]]: ^^^Alisdair Boraston^^^<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 GH125'''<br />
|-<br />
| '''Clan'''<br />
| GH-L<br />
|-<br />
| '''Mechanism'''<br />
| inverting<br />
|-<br />
| '''Active site residues'''<br />
| known<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH125.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
The currently characterized family 125 glycoside hydrolases, which include the examples from ''Streptococcus pneumoniae'' (SpGH125) and ''Clostridium perfringens'' (CpGH125), are α-mannosidases with specificity for α-1,6-linked non-reducing terminal mannose residues <cite>Gregg2011</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Kinetic characterization of 2,4-dinitrophenyl α-D-mannopyranoside hydrolysis by SpGH125 and Cp125 revealed that this is a poor substrate for these enzymes. Monitoring the hydrolysis of methyl 6-''O''-(α-D-mannopyranosyl)-β-D-mannopyranoside by <sup>1</sup>H NMR spectroscopy showed that CpGH125 and SpGH125 act with inversion of stereochemistry. The structural analysis of both enzymes detailed an arrangement of catalytic residues that was consistent with this mechanistic assignment <cite>Gregg2011</cite>.<br />
<br />
== Catalytic Residues ==<br />
The structural analysis of CpGH125 suggests it uses aspartate 220 as a catalytic acid and glutamate 393 as catalytic base. The corresponding residues in SpGH125 are aspartame 218 and glutamate 391 <cite>Gregg2011</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The three dimensional structures of CpGH125 ([{{PDBlink}}3qt3 3qt3], [{{PDBlink}}3qt9 3qt9], and [{{PDBlink}}2nvp 2nvp]), SpGH125 ([{{PDBlink}}3qpf 3qpf], [{{PDBlink}}3qry 3qry], and [{{PDBlink}}3qsp 3qsp]) are available and reveal both the (α/α)<sub>6</sub>-fold of the family as well the details of inhibitor and substrate recognition. Though the proteins are uncharacterized, structures are also available for two GH125 enzymes from ''Bacteroides ovatus'' ([{{PDBlink}}3on6 3on6], and [{{PDBlink}}3p2c 3p2c]) and one GH125 from ''Bacteroides thetaiotaomicron'' ([{{PDBlink}}2pov 2pov]).<br />
<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: <sup>1</sup>H NMR spectroscopy revealed that CpGH125 and SpGH125 act with inversion of stereochemistry <cite>Gregg2011</cite>.<br />
;First [[general base]] identification: CpGH125 and SpGH125 (inferred from structure) <cite>Gregg2011</cite>.<br />
;First [[general acid]] identification: CpGH125 and SpGH125 (inferred from structure) <cite>Gregg2011</cite>.<br />
;First 3-D structure: The first deposited structure was that of CpGH125 ([{{PDBlink}}2nvp 2nvp]) closely followed by the deposition of structures of the ''Bacteroides'' sp. proteins. These structures were determined by the Structural Genomics Consortium but not published. The first published structures were those of CpGH125 and SpGH125, which also presented the first structures of these proteins in complex with carbohydrates <cite>Gregg2011</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Gregg2011 pmid=21388958<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH125]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_125&diff=7811Glycoside Hydrolase Family 1252012-11-16T17:34:45Z<p>Al Boraston: </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]]: ^^^Alisdair Boraston^^^<br />
* [[Responsible Curator]]: ^^^Alisdair Boraston^^^<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 GH125'''<br />
|-<br />
| '''Clan'''<br />
| GH-L<br />
|-<br />
| '''Mechanism'''<br />
| inverting<br />
|-<br />
| '''Active site residues'''<br />
| known<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH125.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
The currently characterized family 125 glycoside hydrolases, which include the examples from ''Streptococcus pneumoniae'' (SpGH125) and ''Clostridium perfringens'' (CpGH125), are α-mannosidases with specificity for α-1,6-linked non-reducing terminal mannose residues <cite>Gregg2011</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Kinetic characterization of 2,4-dinitrophenyl α-D-mannopyranoside hydrolysis by SpGH125 and Cp125 revealed that this is a poor substrate for these enzymes. Monitoring the hydrolysis of methyl 6-''O''-(α-D-mannopyranosyl)-β-D-mannopyranoside by <sup>1</sup>H NMR spectroscopy showed that CpGH125 and SpGH125 act with inversion of stereochemistry. The structural analysis of both enzymes detailed an arrangement of catalytic residues that was consistent with this mechanistic assignment <cite>Gregg2011</cite>.<br />
<br />
== Catalytic Residues ==<br />
The structural analysis of CpGH125 suggests it uses aspartate 220 as a catalytic acid and glutamate 393 as catalytic base. The corresponding residues in SpGH125 are aspartame 218 and glutamate 391 <cite>Gregg2011</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The three dimensional structures of CpGH125 ([{{PDBlink}}3qt3 3qt3], [{{PDBlink}}3qt9 3qt9], and [{{PDBlink}}2nvp 2nvp]), SpGH125 ([{{PDBlink}}3qpf 3qpf], [{{PDBlink}}3qry 3qry], and [{{PDBlink}}3qsp 3qsp]) are available and reveal both the (α/α)<sub>6</sub>-fold of the family as well the details of inhibitor and substrate recognition. Though the proteins are uncharacterized, structures are also available for two GH125 enzymes from ''Bacteroides ovatus'' ([{{PDBlink}}3on6 3on6], and [{{PDBlink}}3p2c 3p2c]) and one GH125 from ''Bacteroides thetaiotaomicron'' ([{{PDBlink}}2pov 2pov]).<br />
<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: <sup>1</sup>H NMR spectroscopy revealed that CpGH125 and SpGH125 act with inversion of stereochemistry <cite>Gregg2011</cite>.<br />
;First [[general base]] identification: CpGH125 and SpGH125 <cite>Gregg2011</cite>.<br />
;First [[general acid]] identification: CpGH125 and SpGH125 <cite>Gregg2011</cite>.<br />
;First 3-D structure: The first deposited structure was that of CpGH125 ([{{PDBlink}}2nvp 2nvp]) closely followed by the deposition of structures of the ''Bacteroides'' sp. proteins. These structures were determined by the Structural Genomics Consortium but not published. The first published structures were those of CpGH125 and SpGH125, which also presented the first structures of these proteins in complex with carbohydrates <cite>Gregg2011</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Gregg2011 pmid=21388958<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH125]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_125&diff=7810Glycoside Hydrolase Family 1252012-11-16T17:33:24Z<p>Al Boraston: </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]]: ^^^Alisdair Boraston^^^<br />
* [[Responsible Curator]]: ^^^Alisdair Boraston^^^<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 GH125'''<br />
|-<br />
| '''Clan'''<br />
| GH-L<br />
|-<br />
| '''Mechanism'''<br />
| inverting<br />
|-<br />
| '''Active site residues'''<br />
| known<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH125.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
The currently characterized family 125 glycoside hydrolases, which include the examples from ''Streptococcus pneumoniae'' (SpGH125) and ''Clostridium perfringens'' (CpGH125), are α-mannosidases with specificity for α-1,6-linked non-reducing terminal mannose residues <cite>Gregg2011</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Kinetic characterization of 2,4-dinitrophenyl α-D-mannopyranoside hydrolysis by SpGH125 and Cp125 revealed that this is a poor substrate for these enzymes. Monitoring the hydrolysis of methyl 6-''O''-(α-D-mannopyranosyl)-β-D-mannopyranoside by <sup>1</sup>H NMR spectroscopy showed that CpGH125 and SpGH125 act with inversion of stereochemistry. The structural analysis of both enzymes detailed an arrangement of catalytic residues that was consistent with this mechanistic assignment <cite>Gregg2011</cite>.<br />
<br />
== Catalytic Residues ==<br />
The structural analysis of CpGH125 suggests it uses aspartate 220 as a catalytic acid and glutamate 393 as catalytic base. The corresponding residues in SpGH125 are aspartame 218 and glutamate 391 <cite>Gregg2011</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The three dimensional structures of CpGH125 ([{{PDBlink}}3qt3 3qt3], [{{PDBlink}}3qt9 3qt9], and [{{PDBlink}}2nvp 2nvp]), SpGH125 ([{{PDBlink}}3qpf 3qpf], [{{PDBlink}}3qry 3qry], and [{{PDBlink}}3qsp 3qsp]) are available and reveal both the (α/α)<sub>6</sub>-fold of the family as well the details of inhibitor and substrate recognition. Though the proteins are uncharacterized, structures are also available for two GH125 enzymes from ''Bacteroides ovatus'' ([{{PDBlink}}3on6 3on6], and [{{PDBlink}}3p2c 3p2c]) and one GH125 from ''Bacteroides thetaiotaomicron'' ([{{PDBlink}}2pov 2pov]).<br />
<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: <sup>1</sup>H NMR spectroscopy revealed that CpGH125 and SpGH125 act with inversion of stereochemistry <cite>Gregg2011</cite>.<br />
;First [[general base]] identification: CpGH125 and SpGH125 <cite>Gregg2011</cite>.<br />
;First [[general acid]] identification: CpGH125 and SpGH125 <cite>Gregg2011</cite>.<br />
;First 3-D structure: The first deposited structure was that of CpGH125 ([{{PDBlink}}2nvp 2nvp])closely followed by the examples from ''Bacteroides'' sp. These structures were determined by the Structural Genomics Consortium but not published. The first published structures were those of CpGH125 and SpGH125, which also presented the first structures of these proteins in complex with carbohydrates <cite>Gregg2011</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Gregg2011 pmid=21388958<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH125]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_125&diff=7809Glycoside Hydrolase Family 1252012-11-16T17:32:08Z<p>Al Boraston: </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]]: ^^^Alisdair Boraston^^^<br />
* [[Responsible Curator]]: ^^^Alisdair Boraston^^^<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 GH125'''<br />
|-<br />
| '''Clan'''<br />
| GH-L<br />
|-<br />
| '''Mechanism'''<br />
| inverting<br />
|-<br />
| '''Active site residues'''<br />
| known<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH125.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
The currently characterized family 125 glycoside hydrolases, which include the examples from ''Streptococcus pneumoniae'' (SpGH125) and ''Clostridium perfringens'' (CpGH125), are α-mannosidases with specificity for α-1,6-linked non-reducing terminal mannose residues <cite>Gregg2011</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Kinetic characterization of 2,4-dinitrophenyl α-D-mannopyranoside hydrolysis by SpGH125 and Cp125 revealed that this is a poor substrate for these enzymes. Monitoring the hydrolysis of methyl 6-''O''-(α-D-mannopyranosyl)-β-D-mannopyranoside by <sup>1</sup>H NMR spectroscopy showed that CpGH125 and SpGH125 act with inversion of stereochemistry. The structural analysis of both enzymes detailed an arrangement of catalytic residues that was consistent with this mechanistic assignment <cite>Gregg2011</cite>.<br />
<br />
== Catalytic Residues ==<br />
The structural analysis of CpGH125 suggests it uses aspartate 220 as a catalytic acid and glutamate 393 as catalytic base. The corresponding residues in SpGH125 are aspartame 218 and glutamate 391 <cite>Gregg2011</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The three dimensional structures of CpGH125 ([{{PDBlink}}3qt3 3qt3], [{{PDBlink}}3qt9 3qt9], and [{{PDBlink}}2nvp 2nvp]), SpGH125 ([{{PDBlink}}3qpf 3qpf], [{{PDBlink}}3qry 3qry], and [{{PDBlink}}3qsp 3qsp]) are available and reveal both the (α/α)<sub>6</sub>-fold of the family as well the details of inhibitor and substrate recognition. Though the proteins are uncharacterized, structures are also available for two GH125 enzymes from ''Bacteroides ovatus'' ([{{PDBlink}}3on6 3on6], and [{{PDBlink}}3p2c 3p2c]) and one GH125 from ''Bacteroides thetaiotaomicron'' ([{{PDBlink}}2pov 2pov]).<br />
<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: <sup>1</sup>H NMR spectroscopy revealed that CpGH125 and SpGH125 act with inversion of stereochemistry <cite>Gregg2011</cite>.<br />
;First [[general base]] identification: CpGH125 and SpGH125 <cite>Gregg2011</cite>.<br />
;First [[general acid]] identification: CpGH125 and SpGH125 <cite>Gregg2011</cite>.<br />
;First 3-D structure: The first deposited structure was that of CpGH125 closely followed by the examples from ''Bacteroides'' sp. These structures were determined by the Structural Genomics Consortium but not published. The first published structures were those of CpGH125 and SpGH125, which also presented the first structures of these proteins in complex with carbohydrates <cite>Gregg2011</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Gregg2011 pmid=21388958<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH125]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_125&diff=7808Glycoside Hydrolase Family 1252012-11-16T17:31:05Z<p>Al Boraston: </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]]: ^^^Alisdair Boraston^^^<br />
* [[Responsible Curator]]: ^^^Alisdair Boraston^^^<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 GH125'''<br />
|-<br />
| '''Clan'''<br />
| GH-L<br />
|-<br />
| '''Mechanism'''<br />
| inverting<br />
|-<br />
| '''Active site residues'''<br />
| known<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH125.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
The currently characterized family 125 glycoside hydrolases, which include the examples from ''Streptococcus pneumoniae'' (SpGH125) and ''Clostridium perfringens'' (CpGH125), are α-mannosidases with specificity for α-1,6-linked non-reducing terminal mannose residues <cite>Gregg2011</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Kinetic characterization of 2,4-dinitrophenyl α-D-mannopyranoside hydrolysis by SpGH125 and Cp125 revealed that this is a poor substrate for these enzymes. Monitoring the hydrolysis of methyl 6-''O''-(α-D-mannopyranosyl)-β-D-mannopyranoside by <sup>1</sup>H NMR spectroscopy showed that CpGH125 and SpGH125 act with inversion of stereochemistry. The structural analysis of both enzymes detailed an arrangement of catalytic residues that was consistent with this mechanistic assignment <cite>Gregg2011</cite>.<br />
<br />
== Catalytic Residues ==<br />
The structural analysis of CpGH125 suggests it uses aspartate 220 as a catalytic acid and glutamate 393 as catalytic base. The corresponding residues in SpGH125 are aspartame 218 and glutamate 391 <cite>Gregg2011</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The three dimensional structures of CpGH125 ([{{PDBlink}}3qt3 3qt3], [{{PDBlink}}3qt9 3qt9], and [{{PDBlink}}2nvp 2nvp]), SpGH125 ([{{PDBlink}}3qpf 3qpf], [{{PDBlink}}3qry 3qry], and [{{PDBlink}}3qsp 3qsp]) are available and reveal both the (α/α)<sub>6</sub>-fold of the family as well the details of inhibitor and substrate recognition. Though the proteins are uncharacterized, structures are also available for two GH125 enzymes from ''Bacteroides ovatus'' ([{{PDBlink}}3on6 3on6], and [{{PDBlink}}3p2c 3p2c]) and one GH125 from ''Bacteroides thetaiotaomicron'' ([{{PDBlink}}2pov 2pov]).<br />
<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: <sup>1</sup>H NMR spectroscopy revealed that CpGH125 and SpGH125 act with inversion of stereochemistry <cite>Gregg2011</cite>.<br />
;First [[general base]] identification: CpGH125 and SpGH125 <cite>Gregg2011</cite>.<br />
;First [[general acid]] identification: CpGH125 and SpGH125 <cite>Gregg2011</cite>.<br />
;First 3-D structure: The first deposited structure was that of CpGH125 closely followed by the examples from ''Bacteroides'' sp. These structures were determined by the Structural Genomics Consortium. The first published structures were those of CpGH125 and SpGH125, which represented the first structures of these proteins in complex with carbohydrates <cite>Gregg2011</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Gregg2011 pmid=21388958<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH125]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_125&diff=7807Glycoside Hydrolase Family 1252012-11-16T17:30:28Z<p>Al Boraston: </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]]: ^^^Alisdair Boraston^^^<br />
* [[Responsible Curator]]: ^^^Alisdair Boraston^^^<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 GH125'''<br />
|-<br />
| '''Clan'''<br />
| GH-L<br />
|-<br />
| '''Mechanism'''<br />
| inverting<br />
|-<br />
| '''Active site residues'''<br />
| known<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH125.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
The currently characterized family 125 glycoside hydrolases, which include the examples from ''Streptococcus pneumoniae'' (SpGH125) and ''Clostridium perfringens'' (CpGH125), are α-mannosidases with specificity for α-1,6-linked non-reducing terminal mannose residues <cite>Gregg2011</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Kinetic characterization of 2,4-dinitrophenyl α-D-mannopyranoside hydrolysis by SpGH125 and Cp125 revealed that this is a poor substrate for these enzymes. Monitoring the hydrolysis of methyl 6-''O''-(α-D-mannopyranosyl)-β-D-mannopyranoside by sup>1</sup>H NMR spectroscopy showed that CpGH125 and SpGH125 act with inversion of stereochemistry. The structural analysis of both enzymes detailed an arrangement of catalytic residues that was consistent with this mechanistic assignment <cite>Gregg2011</cite>.<br />
<br />
== Catalytic Residues ==<br />
The structural analysis of CpGH125 suggests it uses aspartate 220 as a catalytic acid and glutamate 393 as catalytic base. The corresponding residues in SpGH125 are aspartame 218 and glutamate 391 <cite>Gregg2011</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The three dimensional structures of CpGH125 ([{{PDBlink}}3qt3 3qt3], [{{PDBlink}}3qt9 3qt9], and [{{PDBlink}}2nvp 2nvp]), SpGH125 ([{{PDBlink}}3qpf 3qpf], [{{PDBlink}}3qry 3qry], and [{{PDBlink}}3qsp 3qsp]) are available and reveal both the (α/α)<sub>6</sub>-fold of the family as well the details of inhibitor and substrate recognition. Though the proteins are uncharacterized, structures are also available for two GH125 enzymes from ''Bacteroides ovatus'' ([{{PDBlink}}3on6 3on6], and [{{PDBlink}}3p2c 3p2c]) and one GH125 from ''Bacteroides thetaiotaomicron'' ([{{PDBlink}}2pov 2pov]).<br />
<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: <sup>1</sup>H NMR spectroscopy revealed that CpGH125 and SpGH125 act with inversion of stereochemistry <cite>Gregg2011</cite>.<br />
;First [[general base]] identification: CpGH125 and SpGH125 <cite>Gregg2011</cite>.<br />
;First [[general acid]] identification: CpGH125 and SpGH125 <cite>Gregg2011</cite>.<br />
;First 3-D structure: The first deposited structure was that of CpGH125 closely followed by the examples from ''Bacteroides'' sp. These structures were determined by the Structural Genomics Consortium. The first published structures were those of CpGH125 and SpGH125, which represented the first structures of these proteins in complex with carbohydrates <cite>Gregg2011</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Gregg2011 pmid=21388958<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH125]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_125&diff=7806Glycoside Hydrolase Family 1252012-11-16T17:29:27Z<p>Al Boraston: </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]]: ^^^Alisdair Boraston^^^<br />
* [[Responsible Curator]]: ^^^Alisdair Boraston^^^<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 GH125'''<br />
|-<br />
| '''Clan'''<br />
| GH-L<br />
|-<br />
| '''Mechanism'''<br />
| inverting<br />
|-<br />
| '''Active site residues'''<br />
| known<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH125.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
The currently characterized family 125 glycoside hydrolyses, which include the examples from ''Streptococcus pneumoniae'' (SpGH125) and ''Clostridium perfringens'' (CpGH125), are α-mannosidases with specificity for α-1,6-linked non-reducing terminal mannose residues <cite>Gregg2011</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Kinetic characterization of 2,4-dinitrophenyl α-D-mannopyranoside hydrolysis by SpGH125 and Cp125 revealed that this is a poor substrate for these enzymes. Monitoring the hydrolysis of methyl 6-''O''-(α-D-mannopyranosyl)-β-D-mannopyranoside by sup>1</sup>H NMR spectroscopy revealed that CpGH125 and SpGH125 act with inversion of stereochemistry. The structural analysis of both enzymes reveal an arrangement of catalytic residues that is consistent with this mechanistic assignment <cite>Gregg2011</cite>.<br />
<br />
== Catalytic Residues ==<br />
The structural analysis of CpGH125 suggests it uses aspartate 220 as a catalytic acid and glutamate 393 as catalytic base. The corresponding residues in SpGH125 are aspartame 218 and glutamate 391 <cite>Gregg2011</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The three dimensional structures of CpGH125 ([{{PDBlink}}3qt3 3qt3], [{{PDBlink}}3qt9 3qt9], and [{{PDBlink}}2nvp 2nvp]), SpGH125 ([{{PDBlink}}3qpf 3qpf], [{{PDBlink}}3qry 3qry], and [{{PDBlink}}3qsp 3qsp]) are available and reveal both the (α/α)<sub>6</sub>-fold of the family as well the details of inhibitor and substrate recognition. Though the proteins are uncharacterized, structures are also available for two GH125 enzymes from ''Bacteroides ovatus'' ([{{PDBlink}}3on6 3on6], and [{{PDBlink}}3p2c 3p2c]) and one GH125 from ''Bacteroides thetaiotaomicron'' ([{{PDBlink}}2pov 2pov]).<br />
<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: <sup>1</sup>H NMR spectroscopy revealed that CpGH125 and SpGH125 act with inversion of stereochemistry <cite>Gregg2011</cite>.<br />
;First [[general base]] identification: CpGH125 and SpGH125 <cite>Gregg2011</cite>.<br />
;First [[general acid]] identification: CpGH125 and SpGH125 <cite>Gregg2011</cite>.<br />
;First 3-D structure: The first deposited structure was that of CpGH125 closely followed by the examples from ''Bacteroides'' sp. These structures were determined by the Structural Genomics Consortium. The first published structures were those of CpGH125 and SpGH125, which represented the first structures of these proteins in complex with carbohydrates <cite>Gregg2011</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Gregg2011 pmid=21388958<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH125]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_125&diff=7805Glycoside Hydrolase Family 1252012-11-16T17:22:38Z<p>Al Boraston: </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]]: ^^^Alisdair Boraston^^^<br />
* [[Responsible Curator]]: ^^^Alisdair Boraston^^^<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 GH125'''<br />
|-<br />
| '''Clan'''<br />
| GH-L<br />
|-<br />
| '''Mechanism'''<br />
| inverting<br />
|-<br />
| '''Active site residues'''<br />
| known<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH125.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
The currently characterized family 125 glycoside hydrolyses, which include the examples from ''Streptococcus pneumoniae'' (SpGH125) and ''Clostridium perfringens'' (CpGH125), are α-mannosidases with specificity for α-1,6-linked non-reducing terminal mannose residues <cite>Gregg2011</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Kinetic characterization of 2,4-dinitrophenyl α-D-mannopyranoside hydrolysis by SpGH125 and Cp125 revealed that this is a poor substrate for these enzymes. Monitoring the hydrolysis of methyl 6-''O''-(α-D-mannopyranosyl)-β-D-mannopyranoside by sup>1</sup>H NMR spectroscopy revealed that CpGH125 and SpGH125 act with inversion of stereochemistry. The structural analysis of both enzymes reveal an arrangement of catalytic residues that is consistent with this mechanistic assignment <cite>Gregg2011</cite>.<br />
<br />
== Catalytic Residues ==<br />
The structural analysis of CpGH125 suggests it uses aspartate 220 as a catalytic acid and glutamate 393 as catalytic base. The corresponding residues in SpGH125 are aspartame 218 and glutamate 391.<br />
<br />
== Three-dimensional structures ==<br />
The three dimensional structures of CpGH125 ([{{PDBlink}}3qt3 3qt3], [{{PDBlink}}3qt9 3qt9], and [{{PDBlink}}2nvp 2nvp]), SpGH125 ([{{PDBlink}}3qpf 3qpf], [{{PDBlink}}3qry 3qry], and [{{PDBlink}}3qsp 3qsp]) are available and reveal both the (α/α)<sub>6</sub>-fold of the family as well the details of inhibitor and substrate recognition. Thought the proteins are uncharacterized structures are also available for two GH125 enzymes from BActeroides ovatus ([{{PDBlink}}3on6 3on6], and [{{PDBlink}}3p2c 3p2c]) and on GH125 from Bacteroides thetaiotaomicron ([{{PDBlink}}2pov 2pov]).<br />
<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: <sup>1</sup>H NMR spectroscopy revealed that CpGH125 and SpGH125 act with inversion of stereochemistry <cite>Gregg2011</cite>.<br />
;First catalytic nucleophile identification: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>Sinnott1990</cite>.<br />
;First general acid/base residue identification: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>He1999</cite>.<br />
;First 3-D structure: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>StickWilliams</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Gregg2011 pmid=21388958<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH125]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_125&diff=7804Glycoside Hydrolase Family 1252012-11-16T17:19:23Z<p>Al Boraston: </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]]: ^^^Alisdair Boraston^^^<br />
* [[Responsible Curator]]: ^^^Alisdair Boraston^^^<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 GH125'''<br />
|-<br />
| '''Clan'''<br />
| GH-L<br />
|-<br />
| '''Mechanism'''<br />
| inverting<br />
|-<br />
| '''Active site residues'''<br />
| known<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH125.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
The currently characterized family 125 glycoside hydrolyses, which include the examples from ''Streptococcus pneumoniae'' (SpGH125) and ''Clostridium perfringens'' (CpGH125), are α-mannosidases with specificity for α-1,6-linked non-reducing terminal mannose residues <cite>Gregg2011</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Kinetic characterization of 2,4-dinitrophenyl α-D-mannopyranoside hydrolysis by SpGH125 and Cp125 revealed that this is a poor substrate for these enzymes. Monitoring the hydrolysis of methyl 6-''O''-(α-D-mannopyranosyl)-β-D-mannopyranoside by sup>1</sup>H NMR spectroscopy revealed that CpGH125 and SpGH125 act with inversion of stereochemistry. The structural analysis of both enzymes reveal an arrangement of catalytic residues that is consistent with this mechanistic assignment <cite>Gregg2011</cite>.<br />
<br />
<br />
== Catalytic Residues ==<br />
The structural analysis of CpGH125 suggests it uses aspartate 220 as a catalytic acid and glutamate 393 as catalytic base. The corresponding residues in SpGH125 are aspartame 218 and glutamate 391.<br />
<br />
== Three-dimensional structures ==<br />
The three dimensional structures of CpGH125 ([{{PDBlink}}3qt3 3qt3], [{{PDBlink}}3qt9 3qt9], and [{{PDBlink}}2nvp 2nvp]), SpGH125 ([{{PDBlink}}3qpf 3qpf], [{{PDBlink}}3qry 3qry], and [{{PDBlink}}3qsp 3qsp]) are available and reveal both the (α/α)<sub>6</sub>fold of the family as well the details of inhibitor and substrate recognition. <br />
<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: <sup>1</sup>H NMR spectroscopy revealed that CpGH125 and SpGH125 act with inversion of stereochemistry <cite>Gregg2011</cite>.<br />
;First catalytic nucleophile identification: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>Sinnott1990</cite>.<br />
;First general acid/base residue identification: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>He1999</cite>.<br />
;First 3-D structure: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>StickWilliams</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Gregg2011 pmid=21388958<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH125]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_125&diff=7803Glycoside Hydrolase Family 1252012-11-16T17:18:11Z<p>Al Boraston: </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]]: ^^^Alisdair Boraston^^^<br />
* [[Responsible Curator]]: ^^^Alisdair Boraston^^^<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 GH125'''<br />
|-<br />
| '''Clan'''<br />
| GH-L<br />
|-<br />
| '''Mechanism'''<br />
| inverting<br />
|-<br />
| '''Active site residues'''<br />
| known<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH125.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
The currently characterized family 125 glycoside hydrolyses, which include the examples from ''Streptococcus pneumoniae'' (SpGH125) and ''Clostridium perfringens'' (CpGH125), are α-mannosidases with specificity for α-1,6-linked non-reducing terminal mannose residues <cite>Gregg2011</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Kinetic characterization of 2,4-dinitrophenyl α-D-mannopyranoside hydrolysis by SpGH125 and Cp125 revealed that this is a poor substrate for these enzymes. Monitoring the hydrolysis of methyl 6-''O''-(α-D-mannopyranosyl)-β-D-mannopyranoside by sup>1</sup>H NMR spectroscopy revealed that CpGH125 and SpGH125 act with inversion of stereochemistry. The structural analysis of both enzymes reveal an arrangement of catalytic residues that is consistent with this mechanistic assignment <cite>Gregg2011</cite>.<br />
<br />
<br />
== Catalytic Residues ==<br />
The structural analysis of CpGH125 suggests it uses aspartate 220 as a catalytic acid and glutamate 393 as catalytic base. The corresponding residues in SpGH125 are aspartame 218 and glutamate 391.<br />
<br />
== Three-dimensional structures ==<br />
The three dimensional structures of CpGH125 ([{{PDBlink}}3qt3 3qt3], [{{PDBlink}}3qt9 3qt9], and [{{PDBlink}}2nvp 2nvp]), SpGH125 ([{{PDBlink}}3qpf 3qpf], [{{PDBlink}}3qry 3qry], and [{{PDBlink}}3qsp 3qsp]) <cite>1</cite>. <br />
<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: <sup>1</sup>H NMR spectroscopy revealed that CpGH125 and SpGH125 act with inversion of stereochemistry <cite>Gregg2011</cite>.<br />
;First catalytic nucleophile identification: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>Sinnott1990</cite>.<br />
;First general acid/base residue identification: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>He1999</cite>.<br />
;First 3-D structure: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>StickWilliams</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Gregg2011 pmid=21388958<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH125]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_125&diff=7802Glycoside Hydrolase Family 1252012-11-16T17:16:42Z<p>Al Boraston: </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]]: ^^^Alisdair Boraston^^^<br />
* [[Responsible Curator]]: ^^^Alisdair Boraston^^^<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 GH125'''<br />
|-<br />
| '''Clan'''<br />
| GH-L<br />
|-<br />
| '''Mechanism'''<br />
| inverting<br />
|-<br />
| '''Active site residues'''<br />
| known<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH125.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
The currently characterized family 125 glycoside hydrolyses, which include the examples from ''Streptococcus pneumoniae'' (SpGH125) and ''Clostridium perfringens'' (CpGH125), are α-mannosidases with specificity for α-1,6-linked non-reducing terminal mannose residues <cite>Gregg2011</cite>.<br />
<br />
== Kinetics and Mechanism ==<br />
Kinetic characterization of 2,4-dinitrophenyl α-D-mannopyranoside hydrolysis by SpGH125 and Cp125 revealed that this is a poor substrate for these enzymes. Monitoring the hydrolysis of methyl 6-''O''-(α-D-mannopyranosyl)-β-D-mannopyranoside by sup>1</sup>H NMR spectroscopy revealed that CpGH125 and SpGH125 act with inversion of stereochemistry. The structural analysis of both enzymes reveal an arrangement of catalytic residues that is consistent with this mechanistic assignment <cite>Gregg2011</cite>.<br />
<br />
<br />
== Catalytic Residues ==<br />
The structural analysis of CpGH125 suggests it uses aspartate 220 as a catalytic acid and glutamate 393 as catalytic base. The corresponding residues in SpGH125 are aspartame 218 and glutamate 391.<br />
<br />
== Three-dimensional structures ==<br />
The three dimensional structures of CpGH125 [{{PDBlink}}3qt3 3qt3], [{{PDBlink}}3qt9 3qt9], [{{PDBlink}}2nvp 2nvp] and [{{PDBlink}}2vcc 2vcc] <cite>1</cite>. <br />
<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: <sup>1</sup>H NMR spectroscopy revealed that CpGH125 and SpGH125 act with inversion of stereochemistry <cite>Gregg2011</cite>.<br />
;First catalytic nucleophile identification: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>Sinnott1990</cite>.<br />
;First general acid/base residue identification: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>He1999</cite>.<br />
;First 3-D structure: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>StickWilliams</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Gregg2011 pmid=21388958<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH125]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_125&diff=7801Glycoside Hydrolase Family 1252012-11-16T17:08:17Z<p>Al Boraston: </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]]: ^^^Alisdair Boraston^^^<br />
* [[Responsible Curator]]: ^^^Alisdair Boraston^^^<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 GH125'''<br />
|-<br />
| '''Clan'''<br />
| GH-L<br />
|-<br />
| '''Mechanism'''<br />
| inverting<br />
|-<br />
| '''Active site residues'''<br />
| known<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH125.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
The currently characterized family 125 glycoside hydrolyses, which include the examples from ''Streptococcus pneumoniae'' (SpGH125) and ''Clostridium perfringens'' (CpGH125), are a-mannosidases with specificity for a-1,6-linked non-reducing terminal mannose residues.<br />
<br />
== Kinetics and Mechanism ==<br />
Kinetic characterization of 2,4-dinitrophenyl a-D-mannopyranoside hydrolysis by SpGH125 and Cp125 revealed that this is a poor substrate for these enzymes. Monitoring the hydrolysis of methyl 6-''O''-(α-D-mannopyranosyl)-β-D-mannopyranoside sup>1</sup>H NMR spectroscopy revealed that CpGH125 and SpGH125 act with inversion of stereochemistry<br />
<br />
<br />
== Catalytic Residues ==<br />
Content is to be added here.<br />
<br />
<br />
== Three-dimensional structures ==<br />
Content is to be added here.<br />
<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: <sup>1</sup>H NMR spectroscopy revealed that CpGH125 and SpGH125 act with inversion of stereochemistry <cite>Gregg2011</cite>..<br />
;First catalytic nucleophile identification: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>Sinnott1990</cite>.<br />
;First general acid/base residue identification: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>He1999</cite>.<br />
;First 3-D structure: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>StickWilliams</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Gregg2011 pmid=21388958<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH125]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_125&diff=7800Glycoside Hydrolase Family 1252012-11-16T17:04:59Z<p>Al Boraston: </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]]: ^^^Alisdair Boraston^^^<br />
* [[Responsible Curator]]: ^^^Alisdair Boraston^^^<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 GH125'''<br />
|-<br />
| '''Clan'''<br />
| GH-L<br />
|-<br />
| '''Mechanism'''<br />
| inverting<br />
|-<br />
| '''Active site residues'''<br />
| known<br />
|-<br />
| {{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH125.html<br />
|}<br />
<br />
</div><br />
<br />
<!-- This is the end of the table --><br />
<br />
== Substrate specificities ==<br />
The currently characterized family 125 glycoside hydrolyses, which include the examples from ''Streptococcus pneumoniae'' (SpGH125) and ''Clostridium perfringens'' (CpGH125), are a-mannosidases with specificity for a-1,6-linked non-reducing terminal mannose residues.<br />
<br />
== Kinetics and Mechanism ==<br />
Content is to be added here.<br />
<br />
<br />
== Catalytic Residues ==<br />
Content is to be added here.<br />
<br />
<br />
== Three-dimensional structures ==<br />
Content is to be added here.<br />
<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: <sup>1</sup>H NMR spectroscopy revealed that CpGH125 and SpGH125 act with inversion of stereochemistry <cite>Gregg2011</cite>..<br />
;First catalytic nucleophile identification: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>Sinnott1990</cite>.<br />
;First general acid/base residue identification: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>He1999</cite>.<br />
;First 3-D structure: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>StickWilliams</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Gregg2011 pmid=21388958<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH125]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_125&diff=7799Glycoside Hydrolase Family 1252012-11-16T17:00:12Z<p>Al Boraston: </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]]: ^^^Alisdair Boraston^^^<br />
* [[Responsible Curator]]: ^^^Alisdair Boraston^^^<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 GH125'''<br />
|-<br />
|'''Clan''' <br />
|GH-L<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH125.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
The currently characterized family 125 glycoside hydrolyses, which include the examples from ''Streptococcus pneumoniae'' (SpGH125) and ''Clostridium perfringens'' (CpGH125), are a-mannosidases with specificity for a-1,6-linked non-reducing terminal mannose residues. <br />
<br />
<br />
== Kinetics and Mechanism ==<br />
Content is to be added here.<br />
<br />
<br />
== Catalytic Residues ==<br />
Content is to be added here.<br />
<br />
<br />
== Three-dimensional structures ==<br />
Content is to be added here.<br />
<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: <sup>1</sup>H NMR spectroscopy revealed that CpGH125 and SpGH125 act with inversion of stereochemistry <cite>Gregg2011</cite>..<br />
;First catalytic nucleophile identification: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>Sinnott1990</cite>.<br />
;First general acid/base residue identification: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>He1999</cite>.<br />
;First 3-D structure: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>StickWilliams</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Gregg2011 pmid=21388958<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH125]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_125&diff=7798Glycoside Hydrolase Family 1252012-11-16T16:56:38Z<p>Al Boraston: </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]]: ^^^Alisdair Boraston^^^<br />
* [[Responsible Curator]]: ^^^Alisdair Boraston^^^<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 GH125'''<br />
|-<br />
|'''Clan''' <br />
|GH-L<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH125.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
The currently characterized family 125 glycoside hydrolyses, which include the examples from ''Streptococcus pneumoniae'' (SpGH125) and ''Clostridium perfringens'' (CpGH125), are a-mannosidases with specificity for a-1,6-linked non-reducing terminal mannose residues.<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
Content is to be added here.<br />
<br />
<br />
== Catalytic Residues ==<br />
Content is to be added here.<br />
<br />
<br />
== Three-dimensional structures ==<br />
Content is to be added here.<br />
<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: <sup>1</sup>H NMR spectroscopy revealed that CpGH125 and SpGH125 act with inversion of stereochemistry <cite>Gregg2011</cite>..<br />
;First catalytic nucleophile identification: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>Sinnott1990</cite>.<br />
;First general acid/base residue identification: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>He1999</cite>.<br />
;First 3-D structure: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>StickWilliams</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Gregg2011 pmid=21388958<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH125]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_125&diff=7797Glycoside Hydrolase Family 1252012-11-16T16:52:51Z<p>Al Boraston: </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]]: ^^^Alisdair Boraston^^^<br />
* [[Responsible Curator]]: ^^^Alisdair Boraston^^^<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 GH125'''<br />
|-<br />
|'''Clan''' <br />
|GH-L<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH125.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Content is to be added here.<br />
<br />
This is an example of how to make references to a journal article <cite>Comfort2007</cite>, together with the References section below. Multiple references can go in the same place like this <cite>Comfort2007 He1999</cite>. You can even cite books using just the ISBN <cite>StickWilliams</cite>. References that are not in PubMed can be typed in by hand <cite>Sinnott1990</cite>. See the help page [[Help:References]] for more detailed instructions.<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
Content is to be added here.<br />
<br />
<br />
== Catalytic Residues ==<br />
Content is to be added here.<br />
<br />
<br />
== Three-dimensional structures ==<br />
Content is to be added here.<br />
<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: <sup>1</sup>H NMR spectroscopy revealed that CpGH125 and SpGH125 act with inversion of stereochemistry <cite>Gregg2011</cite>..<br />
;First catalytic nucleophile identification: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>Sinnott1990</cite>.<br />
;First general acid/base residue identification: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>He1999</cite>.<br />
;First 3-D structure: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>StickWilliams</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Gregg2011 pmid=21388958<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH125]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_125&diff=7796Glycoside Hydrolase Family 1252012-11-16T16:50:46Z<p>Al Boraston: </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]]: ^^^Alisdair Boraston^^^<br />
* [[Responsible Curator]]: ^^^Alisdair Boraston^^^<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 GH125'''<br />
|-<br />
|'''Clan''' <br />
|GH-L<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH125.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Content is to be added here.<br />
<br />
This is an example of how to make references to a journal article <cite>Comfort2007</cite>, together with the References section below. Multiple references can go in the same place like this <cite>Comfort2007 He1999</cite>. You can even cite books using just the ISBN <cite>StickWilliams</cite>. References that are not in PubMed can be typed in by hand <cite>Sinnott1990</cite>. See the help page [[Help:References]] for more detailed instructions.<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
Content is to be added here.<br />
<br />
<br />
== Catalytic Residues ==<br />
Content is to be added here.<br />
<br />
<br />
== Three-dimensional structures ==<br />
Content is to be added here.<br />
<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>Comfort2007</cite>.<br />
;First catalytic nucleophile identification: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>Sinnott1990</cite>.<br />
;First general acid/base residue identification: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>He1999</cite>.<br />
;First 3-D structure: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>StickWilliams</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Gregg2011 pmid=21388958<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH125]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_125&diff=7795Glycoside Hydrolase Family 1252012-11-16T16:49:54Z<p>Al Boraston: </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]]: ^^^Alisdair Boraston^^^<br />
* [[Responsible Curator]]: ^^^Alisdair Boraston^^^<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 GH125'''<br />
|-<br />
|'''Clan''' <br />
|GH-L<br />
|-<br />
|'''Mechanism'''<br />
|inverting<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |{{CAZyDBlink}}GH125.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Content is to be added here.<br />
<br />
This is an example of how to make references to a journal article <cite>Comfort2007</cite>, together with the References section below. Multiple references can go in the same place like this <cite>Comfort2007 He1999</cite>. You can even cite books using just the ISBN <cite>StickWilliams</cite>. References that are not in PubMed can be typed in by hand <cite>Sinnott1990</cite>. See the help page [[Help:References]] for more detailed instructions.<br />
<br />
<br />
== Kinetics and Mechanism ==<br />
Content is to be added here.<br />
<br />
<br />
== Catalytic Residues ==<br />
Content is to be added here.<br />
<br />
<br />
== Three-dimensional structures ==<br />
Content is to be added here.<br />
<br />
<br />
== Family Firsts ==<br />
;First stereochemistry determination: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>Comfort2007</cite>.<br />
;First catalytic nucleophile identification: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>Sinnott1990</cite>.<br />
;First general acid/base residue identification: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>He1999</cite>.<br />
;First 3-D structure: Cite some reference here, with a ''short'' (1-2 sentence) explanation <cite>StickWilliams</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#Comfort2007 pmid=17323919<br />
#He1999 pmid=9312086<br />
#StickWilliams isbn=978-0-240-52118-3<br />
#Sinnott1990 Sinnott, M.L. (1990) Catalytic mechanisms of enzymic glycosyl transfer. Chem. Rev. 90, 1171-1202. [http://dx.doi.org/10.1021/cr00105a006 DOI: 10.1021/cr00105a006]<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH125]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_85&diff=2529Glycoside Hydrolase Family 852009-10-27T21:54:32Z<p>Al Boraston: </p>
<hr />
<div><!-- CURATORS: Please delete the {{UnderConstruction}} tag below when the page is ready for wider public consumption --><br />
* [[Author]]: ^^^Wade Abbott^^^<br />
* [[Responsible Curator]]: ^^^Al Boraston^^^<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 GH85'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH85.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Endo-beta-N-acetylglucosaminidases (ENGse) cleave the chitobiose core (GlcNAc-beta-1,4-GlcNac) of N-linked glycans. Examples of ENGases have been shown to be active on high-mannose type N-glycans (Endo-H, Endo-A, Endo-Fsp, Endo-F1, Endo-D and Endo-E), bi- and tri-antennary complex type N-glycans (Endo-F2 and Endo-F3), and both substrates (Endo-M) and belong to glycoside hydrolase families 18 and 85. Although specificity appears to be primarily determined by the oligosaccharide glycone <cite>#1</cite>, there is evidence that structural features within the carbohydrate-protein aglycone region (GlcNAc-Asn) may also play a role in substrate recognition. GH85s, represented by Endo-D, Endo-A, and Endo-M, are broadly distributed in nature having been described in bacteria <cite>#2 #3 #4 #5 </cite>, fungi <cite>#6</cite>, plants <cite>#7</cite> and animals <cite>#8</cite>. In several cases, including Endo-A from ''Arthrobacter protophormiae'' (''Ap''GH85) and Endo-M from ''Mucor hiemalis'' (''Mh''GH85), ENGases have been shown to catalyze transglycosylation reactions, making them useful candidates in the bioengineering of glycoproteins <cite>#1</cite> and biologic pharmaceuticals <cite>#9</cite>.<br />
<br />
== Kinetics and Mechanism == <br />
GH85s were originally proposed to utilize a substrate-assisted mechanism resulting in the retention of anomeric configuration on the basis of transglycosylation reactions that deployed oxazoline substrates as donor sugars <cite>#10</cite>. Further support was provided by the three-dimensional structure of Endo-A <cite>#11</cite> and Endo-D <cite>#5</cite> in complex with thiazoline-based inhibitors. NMR spectroscopy was to monitor the Endo-D catalyzed cleavage of a synthetic aryl-glycoside to demonstrate retention of the anomeric configuration <cite>#5</cite>. GH85s appear to deploy a rare form of substrate-assisted catalysis as a candidate asparagine, operating in an imidic tautomer form, facilitates a “proton shuttle” that results in acid-base catalysis of the glycosidic bond, a role similar to the catalytic aspartates in family 18 and 56 glycoside hydrolases <cite>#5</cite>.<br />
<br />
== Catalytic Residues == <br />
Exploiting the transglycosylation capabilities of Endo-M from ''M. hiemalis'', three residues were identified by site directed mutagenesis to be central to the catalytic reaction: N175, E177, and Y217 <cite>#10</cite>. Mutation of the tyrosine to phenylalanine diminished hydrolytic capability but enhanced transglycosylation. The role of N175 was demonstrated to be fundamental for hydrolysis as substitution with alanine ablated hydrolysis; however, transglycosylation could be performed using oxazoline substrates. Interactions between homologous asparagines residues in Endo-A (N171) and Endo-D (N335) were confirmed by structural studies, which observed each in contact with the modified 2-acetamido group of NAG-thiazoline inhibitors <cite>#5 #11</cite>. E177 operates as the catalytic acid and donates a protein to the glycosidic oxygen <cite>#10</cite>.<br />
<br />
== Family Firsts == <br />
'''First stereochemistry determination''': <sup>1</sup>H NMR spectroscopy was used on the products of 3-fluoro-4-nitrophenyl 2-acetamido-2-deoxy-beta-D-glucopyranoside cleavage by Endo-D from ''S. pneumoniae TIGR4'' (''Sp''GH85) <cite>#5</cite>.<br />
<br />
'''First catalytic nucleophile identification''': the 2-acetamido group acting as a nucleophile was suggested by <cite>#13</cite> following transglycosylation of a disaccharide oxazoline substrate.<br />
<br />
'''First general acid/base residue identification''': The “catalytic base” that deprotonates the 2-acetamido group was identified by the site-directed mutagenesis of N175 in Endo-M <cite>#10</cite>.<br />
<br />
'''First 3-D structure''': ''S. pneumoniae TIGR4'' Endo-D PDB IDs: 2W91 and 2W92 (release date: 2009-01-27). <cite>#5</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#1 pmid=16805557 <br />
#2 pmid=8525060<br />
#3 pmid=7860600<br />
#4 pmid=2511903<br />
#5 pmid=19181667<br />
#6 pmid=15519295<br />
#7 pmid=6793075<br />
#8 pmid=8340428<br />
#9 pmid=16960007<br />
#10 pmid=18096701<br />
#11 pmid=19252736<br />
#12 pmid=19327363<br />
#13 pmid=11514092<br />
</biblio><br />
<br />
<!-- ATTN CURATOR: Please delete the "<nowiki>" and "</nowiki>" tags below when you are ready for the page to be included in the "GH Families" category, which is linked on the Main Page; ALSO: REPLACE "nnn" with the family number) --><br />
[[Category:Glycoside Hydrolase Families|GH085]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_85&diff=2528Glycoside Hydrolase Family 852009-10-27T21:51:17Z<p>Al Boraston: </p>
<hr />
<div><!-- CURATORS: Please delete the {{UnderConstruction}} tag below when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Wade Abbott^^^<br />
* [[Responsible Curator]]: ^^^Al Boraston^^^<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 GH85'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH85.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Endo-beta-N-acetylglucosaminidases (ENGse) cleave the chitobiose core (GlcNAc-beta-1,4-GlcNac) of N-linked glycans. Examples of ENGases have been shown to be active on high-mannose type N-glycans (Endo-H, Endo-A, Endo-Fsp, Endo-F1, Endo-D and Endo-E), bi- and tri-antennary complex type N-glycans (Endo-F2 and Endo-F3), and both substrates (Endo-M) and belong to glycoside hydrolase families 18 and 85. Although specificity appears to be primarily determined by the oligosaccharide glycone <cite>#1</cite>, there is evidence that structural features within the carbohydrate-protein aglycone region (GlcNAc-Asn) may also play a role in substrate recognition. GH85s, represented by Endo-D, Endo-A, and Endo-M, are broadly distributed in nature having been described in bacteria <cite>#2 #3 #4 #5 </cite>, fungi <cite>#6</cite>, plants <cite>#7</cite> and animals <cite>#8</cite>. In several cases, including Endo-A from ''Arthrobacter protophormiae'' (''Ap''GH85) and Endo-M from ''Mucor hiemalis'' (''Mh''GH85), ENGases have been shown to catalyze transglycosylation reactions, making them useful candidates in the bioengineering of glycoproteins <cite>#1</cite> and biologic pharmaceuticals <cite>#9</cite>.<br />
<br />
== Kinetics and Mechanism == <br />
GH85s were originally proposed to utilize a substrate-assisted mechanism resulting in the retention of anomeric configuration on the basis of transglycosylation reactions that deployed oxazoline substrates as donor sugars <cite>#10</cite>. Further support was provided by the three-dimensional structure of Endo-A <cite>#11</cite> and Endo-D <cite>#5</cite> in complex with thiazoline-based inhibitors. NMR spectroscopy was to monitor the Endo-D catalyzed cleavage of a synthetic aryl-glycoside to demonstrate retention of the anomeric configuration <cite>#5</cite>. GH85s appear to deploy a rare form of substrate-assisted catalysis as a candidate asparagine, operating in an imidic tautomer form, facilitates a “proton shuttle” that results in acid-base catalysis of the glycosidic bond, a role similar to the catalytic aspartates in family 18 and 56 glycoside hydrolases <cite>#5</cite>.<br />
<br />
== Catalytic Residues == <br />
Exploiting the transglycosylation capabilities of Endo-M from ''M. hiemalis'', three residues were identified by site directed mutagenesis to be central to the catalytic reaction: N175, E177, and Y217 <cite>#10</cite>. Mutation of the tyrosine to phenylalanine diminished hydrolytic capability but enhanced transglycosylation. The role of N175 was demonstrated to be fundamental for hydrolysis as substitution with alanine ablated hydrolysis; however, transglycosylation could be performed using oxazoline substrates. Interactions between homologous asparagines residues in Endo-A (N171) and Endo-D (N335) were confirmed by structural studies, which observed each in contact with the modified 2-acetamido group of NAG-thiazoline inhibitors <cite>#5 #11</cite>. E177 operates as the catalytic acid and donates a protein to the glycosidic oxygen <cite>#10</cite>.<br />
<br />
== Family Firsts == <br />
'''First stereochemistry determination''': <sup>1</sup>H NMR spectroscopy was used on the products of 3-fluoro-4-nitrophenyl 2-acetamido-2-deoxy-beta-D-glucopyranoside cleavage by Endo-D from ''S. pneumoniae TIGR4'' (''Sp''GH85) <cite>#5</cite>.<br />
<br />
'''First catalytic nucleophile identification''': the 2-acetamido group acting as a nucleophile was suggested by <cite>#13</cite> following transglycosylation of a disaccharide oxazoline substrate.<br />
<br />
'''First general acid/base residue identification''': The “catalytic base” that deprotonates the 2-acetamido group was identified by the site-directed mutagenesis of N175 in Endo-M <cite>#10</cite>.<br />
<br />
'''First 3-D structure''': ''S. pneumoniae TIGR4'' Endo-D PDB IDs: 2W91 and 2W92 (release date: 2009-01-27). <cite>#5</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#1 pmid=16805557 <br />
#2 pmid=8525060<br />
#3 pmid=7860600<br />
#4 pmid=2511903<br />
#5 pmid=19181667<br />
#6 pmid=15519295<br />
#7 pmid=6793075<br />
#8 pmid=8340428<br />
#9 pmid=16960007<br />
#10 pmid=18096701<br />
#11 pmid=19252736<br />
#12 pmid=19327363<br />
#13 pmid=11514092<br />
</biblio><br />
<br />
<!-- ATTN CURATOR: Please delete the "<nowiki>" and "</nowiki>" tags below when you are ready for the page to be included in the "GH Families" category, which is linked on the Main Page; ALSO: REPLACE "nnn" with the family number) --><br />
<nowiki>[[Category:Glycoside Hydrolase Families|GH085]]</nowiki></div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_85&diff=2527Glycoside Hydrolase Family 852009-10-27T21:49:29Z<p>Al Boraston: </p>
<hr />
<div><!-- CURATORS: Please delete the {{UnderConstruction}} tag below when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Wade Abbott^^^<br />
* [[Responsible Curator]]: ^^^Al Boraston^^^<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 GH85'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH85.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Endo-beta-N-acetylglucosaminidases (ENGse) cleave the chitobiose core (GlcNAc-beta-1,4-GlcNac) of N-linked glycans. Examples of ENGases have been shown to be active on high-mannose type N-glycans (Endo-H, Endo-A, Endo-Fsp, Endo-F1, Endo-D and Endo-E), bi- and tri-antennary complex type N-glycans (Endo-F2 and Endo-F3), and both substrates (Endo-M) and belong to glycoside hydrolase families 18 and 85. Although specificity appears to be primarily determined by the oligosaccharide glycone <cite>#1</cite>, there is evidence that structural features within the carbohydrate-protein aglycone region (GlcNAc-Asn) may also play a role in substrate recognition. GH85s, represented by Endo-D, Endo-A, and Endo-M, are broadly distributed in nature having been described in bacteria <cite>#2 #3 #4 #5 </cite>, fungi <cite>#6</cite>, plants <cite>#7</cite> and animals <cite>#8</cite>. In several cases, including Endo-A from ''Arthrobacter protophormiae'' (''Ap''GH85) and Endo-M from ''Mucor hiemalis'' (''Mh''GH85), ENGases have been shown to catalyze transglycosylation reactions, making them useful candidates in the bioengineering of glycoproteins <cite>#1</cite> and biologic pharmaceuticals <cite>#9</cite>.<br />
<br />
== Kinetics and Mechanism == <br />
GH85s were originally proposed to utilize a substrate-assisted mechanism resulting in the retention of anomeric configuration on the basis of transglycosylation reactions that deployed oxazoline substrates as donor sugars <cite>#10</cite>. Further support was provided by the three-dimensional structure of Endo-A <cite>#11</cite> and Endo-D <cite>#5</cite> in complex with thiazoline-based inhibitors. NMR spectroscopy was to monitor the Endo-D catalyzed cleavage of a synthetic aryl-glycoside to demonstrate retention of the anomeric configuration <cite>#5</cite>. GH85s appear to deploy a rare form of substrate-assisted catalysis as a candidate asparagine, operating in an imidic tautomer form, facilitates a “proton shuttle” that results in acid-base catalysis of the glycosidic bond, a role similar to the catalytic aspartates in family 18 and 56 glycoside hydrolases <cite>#5</cite>.<br />
<br />
== Catalytic Residues == <br />
Exploiting the transglycosylation capabilities of Endo-M from ''M. hiemalis'', three residues were identified by site directed mutagenesis to be central to the catalytic reaction: N175, E177, and Y217 <cite>#10</cite>. Mutation of the tyrosine to phenylalanine diminished hydrolytic capability but enhanced transglycosylation. The role of N175 was demonstrated to be fundamental for hydrolysis as substitution with alanine ablated hydrolysis; however, transglycosylation could be performed using oxazoline substrates. Interactions between homologous asparagines residues in Endo-A (N171) and Endo-D (N335) were confirmed by structural studies, which observed each in contact with the modified 2-acetamido group of NAG-thiazoline inhibitors <cite>#5 #11</cite>. E177 operates as the catalytic acid and donates a protein to the glycosidic oxygen <cite>#10</cite>.<br />
<br />
== Family Firsts == <br />
'''First stereochemistry determination''': <sup>1</sup>H NMR spectroscopy was used on the products of 3-fluoro-4-nitrophenyl 2-acetamido-2-deoxy-beta-D-glucopyranoside cleavage by Endo-D from ''S. pneumoniae TIGR4'' (''Sp''GH85) <cite>#5</cite>.<br />
<br />
'''First catalytic nucleophile identification''': the 2-acetamido group acting as a nucleophile was suggested by <cite>#14</cite> following transglycosylation of a disaccharide oxazoline substrate.<br />
<br />
'''First general acid/base residue identification''': catalytic acid was identified by the site-directed mutagenesis of E174 in Endo-H <cite>#12</cite>. The “catalytic base” that deprotonates the 2-acetamido group was identified by the site-directed mutagenesis of N175 in Endo-M <cite>#10</cite>.<br />
<br />
'''First 3-D structure''': ''S. pneumoniae TIGR4'' Endo-D PDB IDs: 2W91 and 2W92 (release date: 2009-01-27). <cite>#5</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#1 pmid=16805557 <br />
#2 pmid=8525060<br />
#3 pmid=7860600<br />
#4 pmid=2511903<br />
#5 pmid=19181667<br />
#6 pmid=15519295<br />
#7 pmid=6793075<br />
#8 pmid=8340428<br />
#9 pmid=16960007<br />
#10 pmid=18096701<br />
#11 pmid=19252736<br />
#12 pmid=7911292<br />
#13 pmid=19327363<br />
#14 pmid=11514092<br />
</biblio><br />
<br />
<!-- ATTN CURATOR: Please delete the "<nowiki>" and "</nowiki>" tags below when you are ready for the page to be included in the "GH Families" category, which is linked on the Main Page; ALSO: REPLACE "nnn" with the family number) --><br />
<nowiki>[[Category:Glycoside Hydrolase Families|GH085]]</nowiki></div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_85&diff=2526Glycoside Hydrolase Family 852009-10-27T21:44:07Z<p>Al Boraston: </p>
<hr />
<div><!-- CURATORS: Please delete the {{UnderConstruction}} tag below when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Wade Abbott^^^<br />
* [[Responsible Curator]]: ^^^Al Boraston^^^<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 GH85'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH85.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Endo-beta-N-acetylglucosaminidases (ENGse) cleave the chitobiose core (GlcNAc-beta-1,4-GlcNac) of N-linked glycans. Examples of ENGases have been shown to be active on high-mannose type N-glycans (Endo-H, Endo-A, Endo-Fsp, Endo-F1, Endo-D and Endo-E), bi- and tri-antennary complex type N-glycans (Endo-F2 and Endo-F3), and both substrates (Endo-M) and belong to glycoside hydrolase families 18 and 85. Although specificity appears to be primarily determined by the oligosaccharide glycone <cite>#1</cite>, there is evidence that structural features within the carbohydrate-protein aglycone region (GlcNAc-Asn) may also play a role in substrate recognition. GH85s, represented by Endo-D, Endo-A, and Endo-M, are broadly distributed in nature having been described in bacteria <cite>#2 #3 #4 #5 </cite>, fungi <cite>#6</cite>, plants <cite>#7</cite> and animals <cite>#8</cite>. In several cases, including Endo-A from ''Arthrobacter protophormiae'' (''Ap''GH85) and Endo-M from ''Mucor hiemalis'' (''Mh''GH85), ENGases have been shown to catalyze transglycosylation reactions, making them useful candidates in the bioengineering of glycoproteins <cite>#1</cite> and biologic pharmaceuticals <cite>#9</cite>.<br />
<br />
== Kinetics and Mechanism == <br />
GH85s were originally proposed to utilize a substrate-assisted mechanism resulting in the retention of anomeric configuration on the basis of transglycosylation reactions that deployed oxazoline substrates as donor sugars <cite>#10</cite>. Further support was provided by the three-dimensional structure of Endo-A <cite>#11</cite> and Endo-D <cite>#5</cite> in complex with thiazoline-based inhibitors. NMR spectroscopy was to monitor the Endo-D catalyzed cleavage of a synthetic aryl-glycoside to demonstrate retention of the anomeric configuration <cite>#5</cite>. GH85s appear to deploy a rare form of substrate-assisted catalysis as a candidate asparagine, operating in an imidic tautomer form, facilitates a “proton shuttle” that results in acid-base catalysis of the glycosidic bond, a role similar to the catalytic aspartates in family 18 and 56 glycoside hydrolases <cite>#5</cite>.<br />
<br />
== Catalytic Residues == <br />
Exploiting the transglycosylation capabilities of Endo-M from ''M. hiemalis'', three residues were identified by site directed mutagenesis to be central to the catalytic reaction: N175, E177, and Y217 <cite>#10</cite>. Mutation of the tyrosine to phenylalanine diminished hydrolytic capability but enhanced transglycosylation. The role of N175 was demonstrated to be fundamental for hydrolysis as substitution with alanine ablated hydrolysis; however, transglycosylation could be performed using oxazoline substrates. Interactions between homologous asparagines residues in Endo-A (N171) and Endo-D (N335) were confirmed by structural studies, which observed each in contact with the modified 2-acetamido group of NAG-thiazoline inhibitors <cite>#5 #11</cite>. E177 operates as the catalytic acid and donates a protein to the glycosidic oxygen <cite>#10</cite>, a role first suggested following the mutagenesis of E174 in Endo-H from ''Streptomyces plicatus'' <cite>#12</cite>.<br />
<br />
== Family Firsts == <br />
'''First stereochemistry determination''': <sup>1</sup>H NMR spectroscopy was used on the products of 3-fluoro-4-nitrophenyl 2-acetamido-2-deoxy-beta-D-glucopyranoside cleavage by Endo-D from ''S. pneumoniae TIGR4'' (''Sp''GH85) <cite>#5</cite>.<br />
<br />
'''First catalytic nucleophile identification''': the 2-acetamido group acting as a nucleophile was suggested by <cite>#14</cite> following transglycosylation of a disaccharide oxazoline substrate.<br />
<br />
'''First general acid/base residue identification''': catalytic acid was identified by the site-directed mutagenesis of E174 in Endo-H <cite>#12</cite>. The “catalytic base” that deprotonates the 2-acetamido group was identified by the site-directed mutagenesis of N175 in Endo-M <cite>#10</cite>.<br />
<br />
'''First 3-D structure''': ''S. pneumoniae TIGR4'' Endo-D PDB IDs: 2W91 and 2W92 (release date: 2009-01-27). <cite>#5</cite>.<br />
<br />
== References ==<br />
<biblio><br />
#1 pmid=16805557 <br />
#2 pmid=8525060<br />
#3 pmid=7860600<br />
#4 pmid=2511903<br />
#5 pmid=19181667<br />
#6 pmid=15519295<br />
#7 pmid=6793075<br />
#8 pmid=8340428<br />
#9 pmid=16960007<br />
#10 pmid=18096701<br />
#11 pmid=19252736<br />
#12 pmid=7911292<br />
#13 pmid=19327363<br />
#14 pmid=11514092<br />
</biblio><br />
<br />
<!-- ATTN CURATOR: Please delete the "<nowiki>" and "</nowiki>" tags below when you are ready for the page to be included in the "GH Families" category, which is linked on the Main Page; ALSO: REPLACE "nnn" with the family number) --><br />
<nowiki>[[Category:Glycoside Hydrolase Families|GH085]]</nowiki></div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_85&diff=2525Glycoside Hydrolase Family 852009-10-27T21:42:53Z<p>Al Boraston: </p>
<hr />
<div><!-- CURATORS: Please delete the {{UnderConstruction}} tag below when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Wade Abbott^^^<br />
* [[Responsible Curator]]: ^^^Al Boraston^^^<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 GH85'''<br />
|-<br />
|'''Clan''' <br />
|GH-K<br />
|-<br />
|'''Mechanism'''<br />
|retaining<br />
|-<br />
|'''Active site residues'''<br />
|known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH85.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
Endo-beta-N-acetylglucosaminidases (ENGse) cleave the chitobiose core (GlcNAc-beta-1,4-GlcNac) of N-linked glycans. Examples of ENGases have been shown to be active on high-mannose type N-glycans (Endo-H, Endo-A, Endo-Fsp, Endo-F1, Endo-D and Endo-E), bi- and tri-antennary complex type N-glycans (Endo-F2 and Endo-F3), and both substrates (Endo-M) and belong to glycoside hydrolase families 18 and 85. Although specificity appears to be primarily determined by the oligosaccharide glycone <cite>#1</cite>, there is evidence that structural features within the carbohydrate-protein aglycone region (GlcNAc-Asn) may also play a role in substrate recognition. GH85s, represented by Endo-D, Endo-A, and Endo-M, are broadly distributed in nature having been described in bacteria <cite>#2 #3 #4 #5 </cite>, fungi <cite>#6</cite>, plants <cite>#7</cite> and animals <cite>#8</cite>. In several cases, including Endo-A from ''Arthrobacter protophormiae'' (''Ap''GH85) and Endo-M from ''Mucor hiemalis'' (''Mh''GH85), ENGases have been shown to catalyze transglycosylation reactions, making them useful candidates in the bioengineering of glycoproteins <cite>#1</cite> and biologic pharmaceuticals <cite>#9</cite>.<br />
<br />
== Kinetics and Mechanism == <br />
GH85s were originally proposed to utilize a substrate-assisted mechanism resulting in the retention of anomeric configuration on the basis of transglycosylation reactions that deployed oxazoline substrates as donor sugars <cite>#10</cite>. Further support was provided by the three-dimensional structure of Endo-A <cite>#11</cite> and Endo-D <cite>#5</cite> in complex with thiazoline-based inhibitors. NMR spectroscopy was to monitor the Endo-D catalyzed cleavage of a synthetic aryl-glycoside to demonstrate retention of the anomeric configuration <cite>#5</cite>. GH85s appear to deploy a rare form of substrate-assisted catalysis as a candidate asparagine, operating in an imidic tautomer form, facilitates a “proton shuttle” that results in acid-base catalysis of the glycosidic bond, a role similar to the catalytic aspartates in family 18 and 56 glycoside hydrolases <cite>#5</cite>.<br />
<br />
== Catalytic Residues == <br />
Exploiting the transglycosylation capabilities of Endo-M from ''M. hiemalis'', three residues were identified by site directed mutagenesis to be central to the catalytic reaction: N175, E177, and Y217 <cite>#10</cite>. Mutation of the tyrosine to phenylalanine diminished hydrolytic capability but enhanced transglycosylation. The role of N175 was demonstrated to be fundamental for hydrolysis as substitution with alanine ablated hydrolysis; however, transglycosylation could be performed using oxazoline substrates. Interactions between homologous asparagines residues in Endo-A (N171) and Endo-D (N335) were confirmed by structural studies, which observed each in contact with the modified 2-acetamido group of NAG-thiazoline inhibitors <cite>#5 #11</cite>. E177 operates as the catalytic acid and donates a protein to the glycosidic oxygen <cite>#10</cite>, a role first suggested following the mutagenesis of E174 in Endo-H from ''Streptomyces plicatus'' <cite>#12</cite>.<br />
<br />
== Family Firsts == <br />
'''First stereochemistry determination''': <sup>1</sup>H NMR spectroscopy was used on the products of 3-fluoro-4-nitrophenyl 2-acetamido-2-deoxy-beta-D-glucopyranoside cleavage by Endo-D from ''S. pneumoniae TIGR4'' (''Sp''GH85) <cite>#5</cite>.<br />
<br />
'''First catalytic nucleophile identification''': the 2-acetamido group acting as a nucleophile was suggested by <cite>#14</cite> following transglycosylation of a disaccharide oxazoline substrate.<br />
<br />
'''First general acid/base residue identification''': catalytic acid was identified by the site-directed mutagenesis of E174 in Endo-H <cite>#12</cite>. The “catalytic base” that deprotonates the 2-acetamido group was identified by the site-directed mutagenesis of N175 in Endo-M <cite>#10</cite>.<br />
<br />
'''First 3-D structure''': ''S. pneumoniae TIGR4'' Endo-D PDB IDs: 2W91 and 2W92 (release date: 2009-03-17). Unpublished.<br />
<br />
== References ==<br />
<biblio><br />
#1 pmid=16805557 <br />
#2 pmid=8525060<br />
#3 pmid=7860600<br />
#4 pmid=2511903<br />
#5 pmid=19181667<br />
#6 pmid=15519295<br />
#7 pmid=6793075<br />
#8 pmid=8340428<br />
#9 pmid=16960007<br />
#10 pmid=18096701<br />
#11 pmid=19252736<br />
#12 pmid=7911292<br />
#13 pmid=19327363<br />
#14 pmid=11514092<br />
</biblio><br />
<br />
<!-- ATTN CURATOR: Please delete the "<nowiki>" and "</nowiki>" tags below when you are ready for the page to be included in the "GH Families" category, which is linked on the Main Page; ALSO: REPLACE "nnn" with the family number) --><br />
<nowiki>[[Category:Glycoside Hydrolase Families|GH085]]</nowiki></div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_98&diff=2524Glycoside Hydrolase Family 982009-10-27T21:34:03Z<p>Al Boraston: </p>
<hr />
<div><!-- CURATORS: Please delete the {{UnderConstruction}} tag below when the page is ready for wider public consumption --><br />
* [[Author]]: ^^^Fathima Shaikh^^^<br />
* [[Responsible Curator]]: ^^^Al Boraston^^^<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 GH98'''<br />
|-<br />
|'''Clan''' <br />
|Not assigned<br />
|-<br />
|'''Mechanism'''<br />
|Inverting<br />
|-<br />
|'''Active site residues'''<br />
|Known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH98.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
The [[glycoside hydrolase]]s of this family are [[endo]]-β-galactosidases. No other activities have been reported. Family 98 glycoside hydrolases are unique in their specificity towards cleavage of the type II core [gal(β1-4)glcNAc] in the AB blood group antigens (EABase, Sp3GH98) and Lewis<sup>Y</sup> antigens (SpGH98) <cite>Ashida2005 Higgins2009 Shaikh2009</cite>. These enzymes are capable of processing these glycans when presented on cell surfaces thus destroying the antigens <cite>Ashida2005 Higgins2009</cite>. <br />
<br />
== Kinetics and Mechanism ==<br />
Family GH98 galactosidases are [[inverting]] enzymes, as first shown by NMR monitoring of the Sp4GH98-catalyzed hydrolysis of the Lewis<sup>Y</sup> tetrasaccharide <cite>Higgins2009</cite>. EABase was also shown to act through an inverting enzyme by NMR monitoring of the EABase catalysed hydrolysis of an artificial substrate, DNP-A-trisaccharide <cite>Shaikh2009</cite>. These results are contrary to the initial predictions made by Rigden <cite>Rigden2005</cite>. EABase follows normal Michaelis-Menten kinetics <cite>Shaikh2009</cite>.<br />
<br />
== Catalytic Residues ==<br />
The [[general base]], an aspartate and glutamate diad, and the [[general acid]], glutamate, were identified through the crystal structures of Sp3GH98 and Sp4GH98 in complex with the A trisaccharide and H disaccharide, respectively, and confirmed by site-directed mutagenesis <cite>Higgins2009</cite>. Similar results were obtained through kinetic studies of the corresponding acid and base mutants of EABase with the artificial substrate DNP-A-trisaccharide. Further biochemical evidence for the catalytic acid residue was obtained by comparison between the activity of the acid mutant and the ''p''K<sub>a</sub> of the leaving group of the substrate <cite>Shaikh2009</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The first crystal structures from family 98 were the Sp3GH98 and Sp4GH98 enzymes from ''S. pneumoniae'' in complex with the A trisaccharide and H disaccharide respectively <cite>Higgins2009</cite>. Both structures feature a (α/β)<sub>8</sub> barrel in the catalytic domain with an adjoining β-sandwich domain that contributes to the architecture of the active site and helps define the respective specificities of the enzymes <cite>Higgins2009</cite><br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination <br />
:''Streptococcus pneumoniae'' TIGR4 endo-beta-galactosidase Sp4GH98 by NMR <cite>Higgins2009</cite>.<br />
;First [[general base]] identification<br />
:''Streptococcus pneumoniae'' SP3-BS71 endo-beta-galactosidase Sp3GH98 <cite>Higgins2009</cite>.<br />
:''Streptococcus pneumoniae'' TIGR4 endo-beta-galactosidase Sp4GH98 <cite>Higgins2009</cite>.<br />
<br />
;First [[general acid]] identification<br />
:''Streptococcus pneumoniae'' SP3-BS71 endo-beta-galactosidase Sp3GH98 <cite>Higgins2009</cite>.<br />
:''Streptococcus pneumoniae'' TIGR4 endo-beta-galactosidase Sp4GH98 <cite>Higgins2009</cite>.<br />
<br />
;First 3-D structures<br />
:''Streptococcus pneumoniae'' SP3-BS71 endo-beta-galactosidase Sp3GH98 <cite>Higgins2009</cite>.<br />
:''Streptococcus pneumoniae'' TIGR4 endo-beta-galactosidase Sp4GH98 <cite>Higgins2009</cite>.<br />
<br />
== References ==<br />
<biblio><br />
# Ashida2005 pmid=15618227<br />
# Higgins2009 pmid=19608744<br />
# Shaikh2009 pmid=19630404<br />
# Rigden2005 pmid=16212961<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH098]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_98&diff=2523Glycoside Hydrolase Family 982009-10-27T21:33:14Z<p>Al Boraston: </p>
<hr />
<div><!-- CURATORS: Please delete the {{UnderConstruction}} tag below when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Fathima Shaikh^^^<br />
* [[Responsible Curator]]: ^^^Al Boraston^^^<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 GH98'''<br />
|-<br />
|'''Clan''' <br />
|Not assigned<br />
|-<br />
|'''Mechanism'''<br />
|Inverting<br />
|-<br />
|'''Active site residues'''<br />
|Known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH98.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
The [[glycoside hydrolase]]s of this family are [[endo]]-β-galactosidases. No other activities have been reported. Family 98 glycoside hydrolases are unique in their specificity towards cleavage of the type II core [gal(β1-4)glcNAc] in the AB blood group antigens (EABase, Sp3GH98) and Lewis<sup>Y</sup> antigens (SpGH98) <cite>Ashida2005 Higgins2009 Shaikh2009</cite>. These enzymes are capable of processing these glycans when presented on cell surfaces thus destroying the antigens <cite>Ashida2005 Higgins2009</cite>. <br />
<br />
== Kinetics and Mechanism ==<br />
Family GH98 galactosidases are [[inverting]] enzymes, as first shown by NMR monitoring of the Sp4GH98-catalyzed hydrolysis of the Lewis<sup>Y</sup> tetrasaccharide <cite>Higgins2009</cite>. EABase was also shown to act through an inverting enzyme by NMR monitoring of the EABase catalysed hydrolysis of an artificial substrate, DNP-A-trisaccharide <cite>Shaikh2009</cite>. These results are contrary to the initial predictions made by Rigden <cite>Rigden2005</cite>. EABase follows normal Michaelis-Menten kinetics <cite>Shaikh2009</cite>.<br />
<br />
== Catalytic Residues ==<br />
The [[general base]], an aspartate and glutamate diad, and the [[general acid]], glutamate, were identified through the crystal structures of Sp3GH98 and Sp4GH98 in complex with the A trisaccharide and H disaccharide, respectively, and confirmed by site-directed mutagenesis <cite>Higgins2009</cite>. Similar results were obtained through kinetic studies of the corresponding acid and base mutants of EABase with the artificial substrate DNP-A-trisaccharide. Further biochemical evidence for the catalytic acid residue was obtained by comparison between the activity of the acid mutant and the ''p''K<sub>a</sub> of the leaving group of the substrate <cite>Shaikh2009</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The first crystal structures from family 98 were the Sp3GH98 and Sp4GH98 enzymes from ''S. pneumoniae'' in complex with the A trisaccharide and H disaccharide respectively <cite>Higgins2009</cite>. Both structures feature a (α/β)<sub>8</sub> barrel in the catalytic domain with an adjoining β-sandwich domain that contributes to the architecture of the active site and helps define the respective specificities of the enzymes <cite>Higgins2009</cite><br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination <br />
:''Streptococcus pneumoniae'' TIGR4 endo-beta-galactosidase Sp4GH98 by NMR <cite>Higgins2009</cite>.<br />
;First [[general base]] identification<br />
:''Streptococcus pneumoniae'' SP3-BS71 endo-beta-galactosidase Sp3GH98 <cite>Higgins2009</cite>.<br />
:''Streptococcus pneumoniae'' TIGR4 endo-beta-galactosidase Sp4GH98 <cite>Higgins2009</cite>.<br />
<br />
;First [[general acid]] identification<br />
:''Streptococcus pneumoniae'' SP3-BS71 endo-beta-galactosidase Sp3GH98 <cite>Higgins2009</cite>.<br />
:''Streptococcus pneumoniae'' TIGR4 endo-beta-galactosidase Sp4GH98 <cite>Higgins2009</cite>.<br />
<br />
;First 3-D structures<br />
:''Streptococcus pneumoniae'' SP3-BS71 endo-beta-galactosidase Sp3GH98 <cite>Higgins2009</cite>.<br />
:''Streptococcus pneumoniae'' TIGR4 endo-beta-galactosidase Sp4GH98 <cite>Higgins2009</cite>.<br />
<br />
== References ==<br />
<biblio><br />
# Ashida2005 pmid=15618227<br />
# Higgins2009 pmid=19608744<br />
# Shaikh2009 pmid=19630404<br />
# Rigden2005 pmid=16212961<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH098]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_98&diff=2522Glycoside Hydrolase Family 982009-10-27T21:31:16Z<p>Al Boraston: </p>
<hr />
<div><!-- CURATORS: Please delete the {{UnderConstruction}} tag below when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Fathima Shaikh^^^<br />
* [[Responsible Curator]]: ^^^Al Boraston^^^<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 GH98'''<br />
|-<br />
|'''Clan''' <br />
|Not assigned<br />
|-<br />
|'''Mechanism'''<br />
|Inverting<br />
|-<br />
|'''Active site residues'''<br />
|Known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH98.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
The [[glycoside hydrolase]]s of this family are [[endo]]-β-galactosidases. No other activities have been reported. Family 98 glycoside hydrolases are unique in their specificity towards cleavage of the type II core [gal(β1-4)glcNAc] in the AB blood group antigens (EABase, Sp3GH98) and Lewis<sup>Y</sup> antigens (SpGH98) <cite>Ashida2005 Higgins2009 Shaikh2009</cite>. <br />
<br />
== Kinetics and Mechanism ==<br />
Family GH98 galactosidases are [[inverting]] enzymes, as first shown by NMR monitoring of the Sp4GH98-catalyzed hydrolysis of the Lewis<sup>Y</sup> tetrasaccharide <cite>Higgins2009</cite>. EABase was also shown to act through an inverting enzyme by NMR monitoring of the EABase catalysed hydrolysis of an artificial substrate, DNP-A-trisaccharide <cite>Shaikh2009</cite>. These results are contrary to the initial predictions made by Rigden <cite>Rigden2005</cite>. EABase follows normal Michaelis-Menten kinetics <cite>Shaikh2009</cite>.<br />
<br />
== Catalytic Residues ==<br />
The [[general base]], an aspartate and glutamate diad, and the [[general acid]], glutamate, were identified through the crystal structures of Sp3GH98 and Sp4GH98 in complex with the A trisaccharide and H disaccharide, respectively, and confirmed by site-directed mutagenesis <cite>Higgins2009</cite>. Similar results were obtained through kinetic studies of the corresponding acid and base mutants of EABase with the artificial substrate DNP-A-trisaccharide. Further biochemical evidence for the catalytic acid residue was obtained by comparison between the activity of the acid mutant and the ''p''K<sub>a</sub> of the leaving group of the substrate <cite>Shaikh2009</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The first crystal structures from family 98 were the Sp3GH98 and Sp4GH98 enzymes from ''S. pneumoniae'' in complex with the A trisaccharide and H disaccharide respectively <cite>Higgins2009</cite>. Both structures feature a (α/β)<sub>8</sub> barrel in the catalytic domain with an adjoining β-sandwich domain that contributes to the architecture of the active site and helps define the respective specificities of the enzymes <cite>Higgins2009</cite><br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination <br />
:''Streptococcus pneumoniae'' TIGR4 endo-beta-galactosidase Sp4GH98 by NMR <cite>Higgins2009</cite>.<br />
;First [[general base]] identification<br />
:''Streptococcus pneumoniae'' SP3-BS71 endo-beta-galactosidase Sp3GH98 <cite>Higgins2009</cite>.<br />
:''Streptococcus pneumoniae'' TIGR4 endo-beta-galactosidase Sp4GH98 <cite>Higgins2009</cite>.<br />
<br />
;First [[general acid]] identification<br />
:''Streptococcus pneumoniae'' SP3-BS71 endo-beta-galactosidase Sp3GH98 <cite>Higgins2009</cite>.<br />
:''Streptococcus pneumoniae'' TIGR4 endo-beta-galactosidase Sp4GH98 <cite>Higgins2009</cite>.<br />
<br />
;First 3-D structures<br />
:''Streptococcus pneumoniae'' SP3-BS71 endo-beta-galactosidase Sp3GH98 <cite>Higgins2009</cite>.<br />
:''Streptococcus pneumoniae'' TIGR4 endo-beta-galactosidase Sp4GH98 <cite>Higgins2009</cite>.<br />
<br />
== References ==<br />
<biblio><br />
# Ashida2005 pmid=15618227<br />
# Higgins2009 pmid=19608744<br />
# Shaikh2009 pmid=19630404<br />
# Rigden2005 pmid=16212961<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH098]]</div>Al Borastonhttps://www.cazypedia.org/index.php?title=Glycoside_Hydrolase_Family_98&diff=2521Glycoside Hydrolase Family 982009-10-27T21:30:42Z<p>Al Boraston: </p>
<hr />
<div><!-- CURATORS: Please delete the {{UnderConstruction}} tag below when the page is ready for wider public consumption --><br />
{{UnderConstruction}}<br />
* [[Author]]: ^^^Fathima Shaikh^^^<br />
* [[Responsible Curator]]: ^^^Al Boraston^^^<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 GH98'''<br />
|-<br />
|'''Clan''' <br />
|Not assigned<br />
|-<br />
|'''Mechanism'''<br />
|Inverting<br />
|-<br />
|'''Active site residues'''<br />
|Known<br />
|-<br />
|{{Hl2}} colspan="2" align="center" |'''CAZy DB link'''<br />
|-<br />
| colspan="2" |http://www.cazy.org/fam/GH98.html<br />
|}<br />
</div><br />
<!-- This is the end of the table --><br />
<br />
<br />
== Substrate specificities ==<br />
The [[glycoside hydrolase]]s of this family are [[endo]]-β-galactosidases. No other activities have been reported. Family 98 glycoside hydrolases are unique in their specificity towards cleavage of the type II core [gal(b1-4)glcNAc] inthe AB blood group antigens (EABase, Sp3GH98) and Lewis<sup>Y</sup> antigens (SpGH98) <cite>Ashida2005 Higgins2009 Shaikh2009</cite>. <br />
<br />
== Kinetics and Mechanism ==<br />
Family GH98 galactosidases are [[inverting]] enzymes, as first shown by NMR monitoring of the Sp4GH98-catalyzed hydrolysis of the Lewis<sup>Y</sup> tetrasaccharide <cite>Higgins2009</cite>. EABase was also shown to act through an inverting enzyme by NMR monitoring of the EABase catalysed hydrolysis of an artificial substrate, DNP-A-trisaccharide <cite>Shaikh2009</cite>. These results are contrary to the initial predictions made by Rigden <cite>Rigden2005</cite>. EABase follows normal Michaelis-Menten kinetics <cite>Shaikh2009</cite>.<br />
<br />
== Catalytic Residues ==<br />
The [[general base]], an aspartate and glutamate diad, and the [[general acid]], glutamate, were identified through the crystal structures of Sp3GH98 and Sp4GH98 in complex with the A trisaccharide and H disaccharide, respectively, and confirmed by site-directed mutagenesis <cite>Higgins2009</cite>. Similar results were obtained through kinetic studies of the corresponding acid and base mutants of EABase with the artificial substrate DNP-A-trisaccharide. Further biochemical evidence for the catalytic acid residue was obtained by comparison between the activity of the acid mutant and the ''p''K<sub>a</sub> of the leaving group of the substrate <cite>Shaikh2009</cite>.<br />
<br />
== Three-dimensional structures ==<br />
The first crystal structures from family 98 were the Sp3GH98 and Sp4GH98 enzymes from ''S. pneumoniae'' in complex with the A trisaccharide and H disaccharide respectively <cite>Higgins2009</cite>. Both structures feature a (α/β)<sub>8</sub> barrel in the catalytic domain with an adjoining β-sandwich domain that contributes to the architecture of the active site and helps define the respective specificities of the enzymes <cite>Higgins2009</cite><br />
<br />
== Family Firsts ==<br />
;First sterochemistry determination <br />
:''Streptococcus pneumoniae'' TIGR4 endo-beta-galactosidase Sp4GH98 by NMR <cite>Higgins2009</cite>.<br />
;First [[general base]] identification<br />
:''Streptococcus pneumoniae'' SP3-BS71 endo-beta-galactosidase Sp3GH98 <cite>Higgins2009</cite>.<br />
:''Streptococcus pneumoniae'' TIGR4 endo-beta-galactosidase Sp4GH98 <cite>Higgins2009</cite>.<br />
<br />
;First [[general acid]] identification<br />
:''Streptococcus pneumoniae'' SP3-BS71 endo-beta-galactosidase Sp3GH98 <cite>Higgins2009</cite>.<br />
:''Streptococcus pneumoniae'' TIGR4 endo-beta-galactosidase Sp4GH98 <cite>Higgins2009</cite>.<br />
<br />
;First 3-D structures<br />
:''Streptococcus pneumoniae'' SP3-BS71 endo-beta-galactosidase Sp3GH98 <cite>Higgins2009</cite>.<br />
:''Streptococcus pneumoniae'' TIGR4 endo-beta-galactosidase Sp4GH98 <cite>Higgins2009</cite>.<br />
<br />
== References ==<br />
<biblio><br />
# Ashida2005 pmid=15618227<br />
# Higgins2009 pmid=19608744<br />
# Shaikh2009 pmid=19630404<br />
# Rigden2005 pmid=16212961<br />
<br />
</biblio><br />
<br />
[[Category:Glycoside Hydrolase Families|GH098]]</div>Al Boraston