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Difference between revisions of "Syn/anti lateral protonation"

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<!-- CURATORS: Please delete the {{UnderConstruction}} tag below when the page is ready for wider public consumption -->
+
{{CuratorApproved}}
{{UnderConstruction}}
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* [[Author]]: [[User:Wim Nerinckx|Wim Nerinckx]]
* [[Author]]: ^^^Wim Nerinckx^^^
+
* [[Responsible Curator]]:  [[User:Spencer Williams|Spencer Williams]]
* [[Responsible Curator]]:  ^^^Spencer Williams^^^
+
 
 
----
 
----
  
 
== Overview ==
 
== Overview ==
This page will provide a table (and eventually a full lexicon article) on the spatial positioning of the catalytic general acid residue in the active sites of glycoside hydrolases.  The table below updates those found in the seminal paper on this concept by Heightman and Vasella <cite>HeightmanVasella1999</cite>, and the more recent summary by Nerinckx ''et al.'' <cite>Nerinckx2005</cite>.
 
  
== Table ==
+
This page provides a table that summarizes the spatial positioning of the catalytic [[general acid]] residue in the active sites of [[glycoside hydrolase]]s, relative to the substrate. The table below updates those found in the seminal paper on this concept by Heightman and Vasella <cite>HeightmanVasella1999</cite>, and a following paper by Nerinckx ''et al.'' <cite>Nerinckx2005</cite>.
This table can be re-sorted by clicking on the icons in the header (''javascript must be turned on in your browser'').  To reset the page to be sorted by GH family, click the ''page'' above the page title.  
+
 
 +
== Background ==
 +
 
 +
The ''"not from above, but from the side"'' concept of semi-lateral glycosidic oxygen [[General_acid/base|protonation]] by [[glycoside hydrolase]]s was introduced by Heightman and Vasella <cite>HeightmanVasella1999</cite>. It was originally only described for [[Anomeric centre (alpha and beta)|beta]]-equatorial [[glycoside hydrolase]]s, but appears to be equally applicable to enzymes acting on an [[Anomeric centre (alpha and beta)|alpha]]-axial glycosidic bond <cite>Nerinckx2005</cite>. When dividing [[Sub-site nomenclature|subsite -1]] into half-spaces by a plane defined by the glycosidic oxygen and C1' and H1' of the –1 glycoside, many ligand-complexed structures reveal that the [[General_acid/base|proton donor]] is positioned either in the ''syn'' half-space (near the ring-oxygen of the –1 glycoside), or in the ''anti'' half-space (on the opposite side of the ring-oxygen). Members of the same GH [[Families|family]] appear to share a common ''syn'' or ''anti'' [[General_acid/base|protonator]] arrangement and further, this specificity appears to be preserved within [[Clans|Clans]] of [[Families|families]]. This page's compilation of [[Sub-site nomenclature|subsite -1]] occupied complexes shows that about 70% of all GH [[Families|families]] are ''anti'' [[General_acid/base|protonators]].
 +
 
 +
Closer inspection of crystal structures of [[Sub-site nomenclature|–1/+1 subsite]]-spanning substrates, or substrate-analogue ligands, in complex with enzymes reveals a further intriguing corollary <cite>Nerinckx2005 Wu2012</cite>. In substrate-bound complexes with ''anti'' [[General_acid/base|protonating]] GH enzymes, the scissile [[Anomeric centre (alpha and beta)|anomeric bond]] (often studied using the thio-analogue) shows a dihedral angle φ (O5'-C1'-[O,S]x-Cx) that is in the lowest-energy synclinal (gauche) conformation. The rationale for this is that a minus synclinal dihedral angle φ for an equatorial glycosidic bond, or plus synclinal for an axial glycosidic bond <cite>Perez1978</cite>, allows for hyperconjugative overlap of the C1'-O5' antibonding orbital with an antiperiplanar-oriented lone pair orbital lobe of the glycosidic oxygen, thereby creating partial double bond character and stabilization of the glycosidic bond by 4–5 kcal/mol; this ground-state stabilizing phenomenon is known as the ‘exo-anomeric effect’ <cite>Cramer1997 Johnson2009 Alonso2016</cite>. ''Anti'' [[General_acid/base|protonation]] occurs on the glycosidic oxygen’s antiperiplanar lone pair, thereby removing the stabilizing exo-anomeric effect. This suggests that ''anti'' [[General_acid/base|protonation]] is an enzymic approach for lowering the activation barrier leading to the [[Transition state|transition state]] (Figure 1 centre).
 +
 
 +
''Syn'' [[General_acid/base|protonating]] [[glycoside hydrolase]]s apparently make use of a different approach <cite>Nerinckx2005 Wu2012</cite>. In many [[Sub-site nomenclature|–1/+1 subsite]]-spanning ligand complexes, the dihedral angle φ of the scissile anomeric bond has been rotated away from its lowest-energy synclinal position: clockwise to minus-anticlinal or antiperiplanar for beta-equatorial; counterclockwise to plus-anticlinal or antiperiplanar for alpha-axial [[Anomeric centre (alpha and beta)|anomeric bonds]]. This removes the hyperconjugative overlap and thus also the stabilizing exo-anomeric effect. And because of this rotation, a lone pair of the glycosidic oxygen is directed into the ''syn'' half-space, allowing it to be protonated by the ''syn''-positioned [[General_acid/base|proton donor]] (Figure 1 right).
 +
 
 +
[[File:Syn_anti.jpg|800px|thumb|center|Figure 1. Newman projections, with the glycosidic oxygen as proximal atom and the anomeric carbon as distal atom, showing ''anti'' (centre) versus ''syn'' (right) semi-lateral [[General_acid/base|protonation]] in beta-equatorial (top) and alpha-axial (bottom) [[glycoside hydrolase]]s. The indicated φ is the dihedral angle for O5'-C1'-O4-C4.]]
 +
 
 +
== Table of ''syn/anti'' protonation examples ==
 +
 
 +
This table contains only one example per GH [[Families|family]] of a ligand-complexed protein structure where the ''syn'' or ''anti'' positioning of the [[General_acid/base|proton donor]] can be clearly observed; other examples may be available on a [[Families|family-by-family]] basis. The reader is thus advised to consult the [http://www.cazy.org/fam/acc_GH.html#table CAZy database] for a current, comprehensive list of CAZyme structures. Where available, the selected examples are Michaelis-type complexes with the ligand spanning the [[Sub-site nomenclature|-1/+1 subsites]], since these have an intact glycosidic or thioglycosidic bond, or are ''N''-analogs of the substrate (''e.g.'' acarbose). In some examples, the [[General_acid/base|proton donor]] has been mutated (''e.g.'', to the corresponding amide or to an alanine), and in those cases one may wish to look at a superposition of the given PDB example with the structure of the native enzyme. If a Michaelis-type complex is not yet available, the second and third example choices, respectively, are trapped glycosyl-enzyme [[intermediate]]s and product complexes where [[Sub-site nomenclature|subsite -1]] is occupied.
 +
 
 +
''Please also be aware that this is a large table with many data. Please contact the page Author or Responsible Curator with corrections.''
 +
 
 +
=== Table ===
 +
This table can be re-sorted by clicking on the icons in the header (''javascript must be turned on in your browser'').  To reset the page to be sorted by GH family, click the ''View'' tab at the very top of the page.
 +
 
 
{| {{Prettytable}} class="sortable"
 
{| {{Prettytable}} class="sortable"
|-valign="top"
+
|- valign="top"
 
! '''Family'''
 
! '''Family'''
 
! '''Clan'''
 
! '''Clan'''
 +
! '''Structure fold  '''
 
! '''Anomeric specificity'''
 
! '''Anomeric specificity'''
 
! '''Mechanism'''
 
! '''Mechanism'''
 +
! '''''Syn/anti'' protonator'''
 +
! '''Example PDB ID'''
 +
! '''Enzyme'''
 +
! '''Organism'''
 +
! '''Ligand'''
 
! '''General acid'''
 
! '''General acid'''
! '''''syn/anti'''''
 
 
! '''Nucleophile or General base'''
 
! '''Nucleophile or General base'''
! '''Ligand'''
+
! '''Reference'''
! '''Organism'''
 
! '''Enzyme'''
 
! '''PDB ID'''
 
! '''Primary reference'''
 
 
|-
 
|-
 
| [[GH1]]
 
| [[GH1]]
 
| A
 
| A
| beta
+
| (β/α)<sub>8</sub>
 +
| beta-{{Smallcaps|d}}
 
| retaining
 
| retaining
| Glu160
+
| '''''anti'''''
| ''anti''
+
| [{{PDBlink}}2cer 2cer]
| Glu375
+
| β-glycosidase S
| product
+
| ''Sulfolobus solfataricus'' P2
| ''Lactococcus lactis''
+
| phenethyl glucoimidazole
| 6-phosopho-beta-galactosidase
+
| '''Glu206'''
| 4pbg
+
| Glu387
| <cite>Wiesmann1997</cite>
+
| <cite>Gloster2006</cite>
 
|-
 
|-
 
| [[GH2]]
 
| [[GH2]]
 
| A
 
| A
| beta
+
| (β/α)<sub>8</sub>
 +
| beta-{{Smallcaps|d}} / alpha-{{Smallcaps|l}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}2vzu 2vzu]
 +
| exo-β-glucosaminidase
 +
| ''Amicolatopsis orientalis''
 +
| PNP-β-{{Smallcaps|d}}-glucosamine
 +
| '''Glu469'''
 +
| Glu541
 +
| <cite>van_Bueren2009</cite>
 +
|-
 +
| [[GH3]]
 +
| none
 +
| (β/α)<sub>8</sub>
 +
| beta-{{Smallcaps|d}} / alpha-{{Smallcaps|l}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}1iex 1iex]
 +
| exo-1,3-1,4-glucanase
 +
| ''Hordeum vulgare''
 +
| thiocellobiose
 +
| '''Glu491'''
 +
| Asp285
 +
| <cite>Hrmova2001</cite>
 +
|-
 +
| [[GH4]]
 +
| none
 +
| Rossmann + α6/β3 + β3/α4
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}1u8x 1u8x]
 +
| 6-P-α-glucosidase
 +
| ''Bacillus subtilis''
 +
| alpha-{{Smallcaps|d}}-glucose-6-phosphate
 +
| '''Asp172'''
 +
| not applicable
 +
| <cite>Rajan2004</cite>
 +
|-
 +
| [[GH5]]
 +
| A
 +
| (β/α)<sub>8</sub>
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}1h2j 1h2j]
 +
| endo-β-1,4-glucanase
 +
| ''Bacillus agaradhaerens''
 +
| 2',4'-DNP-2-F-cellobioside
 +
| '''Glu129'''
 +
| Glu228
 +
| <cite>Varrot2003</cite>
 +
|-
 +
| [[GH6]]
 +
| none
 +
| (β/α)<sub>8</sub>
 +
| beta-{{Smallcaps|d}}
 +
| inverting
 +
| '''''syn'''''
 +
| [{{PDBlink}}1qjw 1qjw]
 +
| cellobiohydrolase 2
 +
| ''Hypocrea jecorina''
 +
| (Glc)<sub>2</sub>-S-(Glc)<sub>2</sub>
 +
| '''Asp221'''
 +
| debated
 +
| <cite>Zhou1999</cite>
 +
|-
 +
| [[GH7]]
 +
| B
 +
| β-jelly roll
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| '''''syn'''''
 +
| [{{PDBlink}}1ovw 1ovw]
 +
| endo-1,4-glucanase
 +
| ''Fusarium oxysporum''
 +
| thio-(Glc)<sub>5</sub>
 +
| '''Glu202'''
 +
| Glu197
 +
| <cite>Sulzenbacher1999</cite>
 +
|-
 +
| [[GH8]]
 +
| M
 +
| (α/α)<sub>6</sub>
 +
| beta-{{Smallcaps|d}}
 +
| inverting
 +
| '''''anti'''''
 +
| [{{PDBlink}}1kwf 1kwf]
 +
| endo-1,4-glucanase
 +
| ''Clostridium thermocellum''
 +
| cellopentaose
 +
| '''Glu95'''
 +
| Asp278
 +
| <cite>Guerin2002</cite>
 +
|-
 +
| [[GH9]]
 +
| none
 +
| (α/α)<sub>6</sub>
 +
| beta-{{Smallcaps|d}}
 +
| inverting
 +
| '''''syn'''''
 +
| [{{PDBlink}}1rq5 1rq5]
 +
| cellobiohydrolase
 +
| ''Clostridium thermocellum''
 +
| cellotetraose
 +
| '''Glu795'''
 +
| Asp383
 +
| <cite>Schubot2004</cite>
 +
|-
 +
| [[GH10]]
 +
| A
 +
| (β/α)<sub>8</sub>
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}2d24 2d24]
 +
| β-1,4-xylanase
 +
| ''Streptomyces olivaceoviridis'' E-86
 +
| xylopentaose
 +
| '''Glu128'''
 +
| Glu236
 +
| <cite>Suzuki2009</cite>
 +
|-
 +
| [[GH11]]
 +
| C
 +
| β-jelly roll
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| '''''syn'''''
 +
| [{{PDBlink}}4hk8 4hk8]
 +
| endo-β-1,4-xylanase
 +
| ''Hypocrea jecorina''
 +
| xylohexaose
 +
| '''Glu177'''
 +
| Glu86
 +
| <cite>Wan2014</cite>
 +
|-
 +
| [[GH12]]
 +
| C
 +
| β-jelly roll
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| '''''syn'''''
 +
| [{{PDBlink}}1w2u 1w2u]
 +
| endoglucanase
 +
| ''Humicola grisea''
 +
| thiocellotetraose
 +
| '''Glu205'''
 +
| Glu120
 +
| <cite>Sandgren2004</cite>
 +
|-
 +
| [[GH13]]
 +
| H
 +
| (β/α)<sub>8</sub>
 +
| alpha-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}1cxk 1cxk]
 +
| β-cyclodextrin glucanotransferase
 +
| ''Bacillus circulans''
 +
| maltononaose
 +
| '''Glu257'''
 +
| Asp229
 +
| <cite>Uitdehaag1999</cite>
 +
|-
 +
| [[GH14]]
 +
| none
 +
| (β/α)<sub>8</sub>
 +
| alpha-{{Smallcaps|d}}
 +
| inverting
 +
| '''''syn'''''
 +
| [{{PDBlink}}1itc 1itc]
 +
| β-amylase
 +
| ''Bacillus cereus''
 +
| maltopentaose
 +
| '''Glu172'''
 +
| Glu367
 +
| <cite>Miyake2003</cite>
 +
|-
 +
| [[GH15]]
 +
| L
 +
| (α/α)<sub>6</sub>
 +
| alpha-{{Smallcaps|d}}
 +
| inverting
 +
| '''''anti'''''
 +
| [{{PDBlink}}1dog 1dog]
 +
| glucoamylase
 +
| ''Aspergillus awamori''
 +
| 1-deoxynojirimycin
 +
| '''Glu179'''
 +
| Glu400
 +
| <cite>Harris1993</cite>
 +
|-
 +
| [[GH16]]
 +
| B
 +
| β-jelly roll
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| '''''syn'''''
 +
| [{{PDBlink}}1urx 1urx]
 +
| β-agarase A
 +
| ''Zobellia galactanivorans''
 +
| oligoagarose
 +
| '''Glu152'''
 +
| Glu147
 +
| <cite>Allouch2004</cite>
 +
|-
 +
| [[GH17]]
 +
| A
 +
| (β/α)<sub>8</sub>
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}4gzj 4gzj]
 +
| endo-β-1,3-glucanase
 +
| ''Solanum tuberosum''
 +
| laminaratriose + laminarabiose
 +
| '''Glu118'''
 +
| Glu259
 +
| <cite>Wojtkowiak2013</cite>
 +
|-
 +
| [[GH18]]
 +
| K
 +
| (β/α)<sub>8</sub>
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}1ffr 1ffr]
 +
| chitinase A
 +
| ''Serratia marcescens''
 +
| (NAG)<sub>6</sub>
 +
| '''Glu315'''
 +
| internal
 +
| <cite>Papanikolau2001</cite>
 +
|-
 +
| [[GH19]]
 +
| none
 +
| lysozyme type
 +
| beta-{{Smallcaps|d}}
 +
| inverting
 +
| '''''syn'''''
 +
| [{{PDBlink}}3wh1 3wh1]
 +
| chitinase
 +
| ''Bryum coronatum''
 +
| (GlcNAc)<sub>4</sub>
 +
| '''Glu61'''
 +
| Glu70
 +
| <cite>Ohnuma2014</cite>
 +
|-
 +
| [[GH20]]
 +
| K
 +
| (β/α)<sub>8</sub>
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}1c7s 1c7s]
 +
| chitobiase
 +
| ''Serratia marcescens''
 +
| chitobiose
 +
| '''Glu540'''
 +
| internal
 +
| <cite>Prag2000</cite>
 +
|-
 +
| [[GH22]]
 +
| none
 +
| lysozyme type
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| '''''syn'''''
 +
| [{{PDBlink}}1h6m 1h6m]
 +
| lysozyme C
 +
| ''Gallus gallus''
 +
| Chit-2-F-chitosyl
 +
| '''Glu35'''
 +
| Asp52
 +
| <cite>Vocadlo2001</cite>
 +
|-
 +
| [[GH23]]
 +
| none
 +
| lysozyme type
 +
| beta-{{Smallcaps|d}}
 +
| inverting
 +
| '''''syn'''''
 +
| [{{PDBlink}}1lsp 1lsp]
 +
| lysozyme G
 +
| ''Cygnus atratus''
 +
| Bulgecin A
 +
| '''Glu73'''
 +
| internal
 +
| <cite>Karlsen1996</cite>
 +
|-
 +
| [[GH24]]
 +
| I
 +
| α + β
 +
| beta-{{Smallcaps|d}}
 +
| inverting
 +
| '''''syn'''''
 +
| [{{PDBlink}}148l 148l]
 +
| lysozyme E
 +
| Bacteriophage T4
 +
| chitobiosyl
 +
| '''Glu11'''
 +
| Glu26
 +
| <cite>Baldwin1993</cite>
 +
|-
 +
| [[GH26]]
 +
| A
 +
| (β/α)<sub>8</sub>
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}2vx6 2vx6]
 +
| exo-β-mannanase
 +
| ''Cellvibrio japonicus'' Ueda107
 +
| Gal1Man4
 +
| '''Glu221'''
 +
| Glu338
 +
| <cite>Cartmell2008</cite>
 +
|-
 +
| [[GH27]]
 +
| D
 +
| (β/α)<sub>8</sub>
 +
| alpha-{{Smallcaps|d}} / beta-{{Smallcaps|l}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}3lrm 3lrm]
 +
| α-galactosidase
 +
| ''Saccharomyces cerevisiae''
 +
| raffinose
 +
| '''Asp209'''
 +
| Asp141
 +
| <cite>Fernandez-Leiro2010</cite>
 +
|-
 +
| [[GH28]]
 +
| N
 +
| β-helix
 +
| alpha-{{Smallcaps|d}} (and α-{{Smallcaps|l}}-rham)
 +
| inverting
 +
| '''''anti'''''
 +
| [{{PDBlink}}2uvf 2uvf]
 +
| exo-polygalacturonosidase
 +
| ''Yersinia enterocolitica'' ATCC9610D
 +
| digalacturonic acid
 +
| '''Asp402'''
 +
| Asp381 Asp403
 +
| <cite>Abbott2007</cite>
 +
|-
 +
| [[GH29]]
 +
| R
 +
| (β/α)<sub>8</sub>
 +
| alpha-{{Smallcaps|l}}
 +
| retaining
 +
| '''''syn'''''
 +
| [{{PDBlink}}3uet 3uet]
 +
| α-1,3/4-fucosidase
 +
| ''Bifidobacterium longum'' subsp. infantis
 +
| lacto-''N''-fucopentaose II
 +
| '''Glu217'''
 +
| Asp172
 +
| <cite>Sakurama2012</cite>
 +
|-
 +
| [[GH30]]
 +
| A
 +
| (β/α)<sub>8</sub>
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}2y24 2y24]
 +
| glucurono-xylanase
 +
| ''Dickea chrysanthemi'' D1
 +
| glucuronoxylan tetrasaccharide
 +
| '''Glu163'''
 +
| Glu253
 +
| <cite>Urbanikova2011</cite>
 +
|-
 +
| [[GH31]]
 +
| D
 +
| (β/α)<sub>8</sub>
 +
| alpha-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}2qmj 2qmj]
 +
| maltase-glucoamylase
 +
| ''Homo sapiens''
 +
| acarbose
 +
| '''Asp542'''
 +
| Asp443
 +
| <cite>Sim2008</cite>
 +
|-
 +
| [[GH32]]
 +
| J
 +
| 5-fold β-propeller
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}2add 2add]
 +
| fructan β-(2,1)-fructosidase
 +
| ''Cichorium intybus''
 +
| sucrose
 +
| '''Glu201'''
 +
| Asp22
 +
| <cite>Verhaest2007</cite>
 +
|-
 +
| [[GH33]]
 +
| E
 +
| 6-fold β-propeller
 +
| alpha-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}1s0i 1s0i]
 +
| transsialidase
 +
| ''Trypanosoma cruzi''
 +
| sialyllactose
 +
| '''Asp59'''
 +
| Tyr342
 +
| <cite>Amaya2004</cite>
 +
|-
 +
| [[GH34]]
 +
| E
 +
| 6-fold β-propeller
 +
| alpha-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}4gzw 4gzw]
 +
| N2 neuraminidase
 +
| ''Influenza'' A Tanzania/205/2010 H3N2
 +
| α-{{Smallcaps|d}}-Neup5Ac-(2,3)-β-{{Smallcaps|d}}-Galp-(1,4)-β-{{Smallcaps|d}}-GlcpNAc
 +
| '''Asp151'''
 +
| Tyr406
 +
| <cite>Zhu2012</cite>
 +
|-
 +
| [[GH35]]
 +
| A
 +
| (β/α)<sub>8</sub>
 +
| beta-{{Smallcaps|d}}
 
| retaining
 
| retaining
| Glu461
+
| '''''anti'''''
| ''anti''
+
| [{{PDBlink}}3ogv 3ogv]
 +
| β-galactosidase
 +
| ''Hypocrea jecorina''
 +
| 2-phenylethyl 1-thio-β-{{Smallcaps|d}}-galactopyranoside
 +
| '''Glu200'''
 +
| Glu298
 +
| <cite>Maksimainen2011</cite>
 +
|-
 +
| [[GH36]]
 +
| D
 +
| (β/α)<sub>8</sub>
 +
| alpha-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}4fnu 4fnu]
 +
| β-galactosidase
 +
| ''Geobacillus stearothermophilus''
 +
| stachyose
 +
| '''Asp584'''
 +
| Asp478
 +
| <cite>Merceron2012</cite>
 +
|-
 +
| [[GH37]]
 +
| G
 +
| (α/α)<sub>6</sub>
 +
| alpha-{{Smallcaps|d}}
 +
| inverting
 +
| '''''anti'''''
 +
| [{{PDBlink}}2jf4 2jf4]
 +
| trehalase
 +
| ''Escherichia coli''
 +
| validoxylamine
 +
| '''Asp312'''
 +
| Glu496
 +
| <cite>Gibson2007</cite>
 +
|-
 +
| [[GH38]]
 +
| none
 +
| (β/α)<sub>7</sub>
 +
| alpha-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}3czn 3czn]
 +
| Golgi α-mannosidase II
 +
| ''Drosophila melanogaster''
 +
| GlcNAcMan(5)GlcNAc(2)
 +
| '''Asp341'''
 +
| Asp204
 +
| <cite>Shah2008</cite>
 +
|-
 +
| [[GH39]]
 +
| A
 +
| (β/α)<sub>8</sub>
 +
| beta-{{Smallcaps|d}} / alpha-{{Smallcaps|l}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}2bfg 2bfg]
 +
| β-xylosidase
 +
| ''Geobacillus stearothermophilus''
 +
| 2,5-dinitrophenyl-β-{{Smallcaps|d}}-xyloside
 +
| '''Glu160'''
 +
| Glu278
 +
| <cite>Czjzek2005</cite>
 +
|-
 +
| [[GH42]]
 +
| A
 +
| (β/α)<sub>8</sub>
 +
| beta-{{Smallcaps|d}} / alpha-{{Smallcaps|l}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}4ucf 4ucf]
 +
| β-galactosidase
 +
| ''Bifidobacterium bifidum''
 +
| {{Smallcaps|d}}-galactose
 +
| '''Glu161'''
 +
| Glu320
 +
| <cite>Godoy2016</cite>
 +
|-
 +
| [[GH43]]
 +
| F
 +
| 5-fold β-propeller
 +
| beta-{{Smallcaps|d}} / alpha-{{Smallcaps|l}}
 +
| inverting
 +
| '''''anti'''''
 +
| [{{PDBlink}}3akh 3akh]
 +
| exo-1,5-α-{{Smallcaps|l}}-arabinofuranosidase
 +
| ''Streptomyces avermitilis''
 +
| α-1,5-arabinofuranotriose
 +
| '''Glu196'''
 +
| Asp220
 +
| <cite>Fujimoto2010</cite>
 +
|-
 +
| [[GH44]]
 +
| none
 +
| (β/α)<sub>8</sub>
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}2eqd 2eqd]
 +
| endoglucanase
 +
| ''Clostridium thermocellum''
 +
| cellooctaose
 +
| '''Glu186'''
 +
| Glu359
 +
| <cite>Kitago2007</cite>
 +
|-
 +
| [[GH45]]
 +
| none
 +
| 6-stranded β-barrel
 +
| beta-{{Smallcaps|d}}
 +
| inverting
 +
| '''''syn'''''
 +
| [{{PDBlink}}4eng 4eng]
 +
| endo-1,4-glucanase
 +
| ''Humicola insolens''
 +
| cellohexaose
 +
| '''Asp121'''
 +
| Asp10
 +
| <cite>Davies1996</cite>
 +
|-
 +
| [[GH46]]
 +
| I
 +
| lysozyme type
 +
| beta-{{Smallcaps|d}}
 +
| inverting
 +
| '''''syn'''''
 +
| [{{PDBlink}}4olt 4olt]
 +
| chitosanase
 +
| ''Microbacterium sp.'' OU01
 +
| hexa-glucosamine
 +
| '''Glu25'''
 +
| Asp43
 +
| <cite>Lyu2014</cite>
 +
|-
 +
| [[GH47]]
 +
| none
 +
| (α/α)<sub>7</sub>
 +
| alpha-{{Smallcaps|d}}
 +
| inverting
 +
| '''''anti'''''
 +
| [{{PDBlink}}1x9d 1x9d]
 +
| α-mannosidase I
 +
| ''Homo sapiens''
 +
| Me-2-S-(α-Man)-2-thio-α-Man
 +
| '''Asp463'''
 +
| Glu599
 +
| <cite>Karaveg2005</cite>, <cite>Nerinckx2008</cite>
 +
|-
 +
| [[GH48]]
 +
| M
 +
| (α/α)<sub>6</sub>
 +
| beta-{{Smallcaps|d}}
 +
| inverting
 +
| ''predicted anti by clan''
 +
| ''see at GH8''
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|-
 +
| [[GH49]]
 +
| N
 +
| β-helix
 +
| alpha-{{Smallcaps|d}}
 +
| inverting
 +
| ''predicted anti by clan''
 +
| ''see at GH28''
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|-
 +
| [[GH50]]
 +
| A
 +
| (β/α)<sub>8</sub>
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}4bq5 4bq5]
 +
| exo-β-agarase
 +
| ''Saccharophagus degradans''
 +
| neoagarotetraose
 +
| '''Glu535'''
 +
| Glu695
 +
| <cite>Pluvinage2013</cite>
 +
|-
 +
| [[GH51]]
 +
| A
 +
| (β/α)<sub>8</sub>
 +
| beta-{{Smallcaps|d}} / alpha-{{Smallcaps|l}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}1qw9 1qw9]
 +
| α-{{Smallcaps|l}}-arabinofuranosidase
 +
| ''Geobacillus stearothermophilus''
 +
| PNP-{{Smallcaps|l}}-arabinofuranoside
 +
| '''Glu175'''
 +
| Glu294
 +
| <cite>Hoevel2003</cite>
 +
|-
 +
| [[GH52]]
 +
| O
 +
| (α/α)<sub>6</sub>
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}4c1p 4c1p]
 +
| β-xylosidase
 +
| ''Geobacillus thermoglucosidasius''
 +
| xylobiose
 +
| '''Asp517'''
 
| Glu537
 
| Glu537
| GalF-glycenz.
+
| <cite>Espina2014</cite>
| ''Escherechia coli''
+
|-
| beta-galactosidase
+
| [[GH53]]
| 1jz0
+
| A
| <cite>Juers2001</cite>
+
| (β/α)<sub>8</sub>
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}2ccr 2ccr]
 +
| β-1,4-galactanase
 +
| ''Bacillus licheniformis''
 +
| galactotriose
 +
| '''Glu165'''
 +
| Glu263
 +
| <cite>Le_Nours2009</cite>
 +
|-
 +
| [[GH54]]
 +
| none
 +
| β-sandwich
 +
| beta-{{Smallcaps|d}} / alpha-{{Smallcaps|l}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}1wd4 1wd4]
 +
| α-{{Smallcaps|l}}-arabinofuranosidase B
 +
| ''Aspergillus kawachii''
 +
| {{Smallcaps|l}}-arabinofuranose
 +
| '''Asp297'''
 +
| Glu221
 +
| <cite>Miyanaga2004</cite>
 +
|-
 +
| [[GH55]]
 +
| none
 +
| β-helix
 +
| beta-{{Smallcaps|d}}
 +
| inverting
 +
| '''''syn'''''
 +
| [{{PDBlink}}4tz5 4tz5]
 +
| exo-β-1,3-glucanase
 +
| ''Streptomyces sp.'' SirexAA-E
 +
| laminarihexaose
 +
| '''Glu502'''
 +
| unknown
 +
| <cite>Bianchetti2015</cite>
 +
|-
 +
| [[GH56]]
 +
| none
 +
| (β/α)<sub>7</sub>
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}1fcv 1fcv]
 +
| hyaluronidase
 +
| ''Apis mellifera''
 +
| (hyaluron.)<sub>4</sub>
 +
| '''Glu113'''
 +
| internal
 +
| <cite>Markovic-Housley2000</cite>
 +
|-
 +
| [[GH57]]
 +
| none
 +
| (β/α)<sub>7</sub>
 +
| alpha-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}1k1y 1k1y]
 +
| glucanotransferase
 +
| ''Thermococcus litoralis''
 +
| acarbose
 +
| '''Asp214'''
 +
| Glu123
 +
| <cite>Imamura2003</cite>
 +
|-
 +
| [[GH59]]
 +
| A
 +
| (β/α)<sub>8</sub>
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}4ccc 4ccc]
 +
| β-galactocerebrosidase
 +
| ''Mus musculus''
 +
| PNP-β-{{Smallcaps|d}}-galactoside
 +
| '''Glu182'''
 +
| Glu258
 +
| <cite>Hill2013</cite>
 +
|-
 +
| [[GH62]]
 +
| F
 +
| 5-fold β-propeller
 +
| alpha-{{Smallcaps|l}}
 +
| inverting
 +
| '''''anti'''''
 +
| [{{PDBlink}}3wn0 3wn0]
 +
| α-{{Smallcaps|l}}-arabinofuranosidase
 +
| ''Streptomyces coelicolor''
 +
| β-{{Smallcaps|l}}-Arabinofuranose
 +
| '''Glu361'''
 +
| Asp202
 +
| <cite>Maehara2014</cite>
 +
|-
 +
| [[GH63]]
 +
| G
 +
| (α/α)<sub>6</sub>
 +
| alpha-{{Smallcaps|d}}
 +
| inverting
 +
| '''''anti'''''
 +
| [{{PDBlink}}5ca3 5ca3]
 +
| α-glucosidase
 +
| ''Escherichia coli''
 +
| glucose and lactose
 +
| '''Asp501'''
 +
| Glu727
 +
| <cite>Miyazaki2016</cite>
 +
|-
 +
| [[GH65]]
 +
| L
 +
| (α/α)<sub>6</sub>
 +
| alpha-{{Smallcaps|d}} (and α-{{Smallcaps|l}}-rham)
 +
| inverting
 +
| '''''anti'''''
 +
| [{{PDBlink}}4ktr 4ktr]
 +
| 2-O-α-glucosylglycerol phosphorylase
 +
| ''Bacillus selenitireducens''
 +
| isofagomine
 +
| '''Glu475'''
 +
| phosphate
 +
| <cite>Touhara2014</cite>
 +
|-
 +
| [[GH66]]
 +
| none
 +
| (β/α)<sub>8</sub>
 +
| alpha-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}5axh 5axh]
 +
| dextranase
 +
| ''Thermoanaerobacter pseudethanolicus''
 +
| isomaltohexaose
 +
| '''Glu374'''
 +
| Asp312
 +
| <cite>Suzuki2016</cite>
 +
|-
 +
| [[GH67]]
 +
| none
 +
| (β/α)<sub>8</sub>
 +
| alpha-{{Smallcaps|d}}
 +
| inverting
 +
| '''''syn'''''
 +
| [{{PDBlink}}1l8n 1l8n]
 +
| α-glucuronidase
 +
| ''Geobacillus stearothermophilus''
 +
| 4-O-methyl-{{Smallcaps|d}}-glucuronic acid and xylotriose
 +
| '''Glu286'''
 +
| Asp364 Glu392
 +
| <cite>Golan2004</cite>
 +
|-
 +
| [[GH68]]
 +
| J
 +
| 5-fold β-propeller
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}1pt2 1pt2]
 +
| levansucrase
 +
| ''Bacillus subtilis''
 +
| sucrose
 +
| '''Glu342'''
 +
| Asp86
 +
| <cite>Meng2003</cite>
 +
|-
 +
| [[GH70]]
 +
| H
 +
| (β/α)<sub>8</sub>
 +
| alpha-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}3aic 3aic]
 +
| glucansucrase
 +
| ''Streptococcus mutans''
 +
| α-acarbose
 +
| '''Glu515'''
 +
| Asp477
 +
| <cite>Ito2011</cite>
 +
|-
 +
| [[GH72]]
 +
| A
 +
| (β/α)<sub>8</sub>
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}2w62 2w62]
 +
| β-1,3-glucanotransferase
 +
| ''Saccharomyces cerevisiae'' S288C
 +
| laminaripentaose
 +
| '''Glu176'''
 +
| Glu275
 +
| <cite>Hurtado-Gerrero2009</cite>
 +
|-
 +
| [[GH74]]
 +
| none
 +
| 7-fold β-propeller
 +
| beta-{{Smallcaps|d}}
 +
| inverting
 +
| '''''syn'''''
 +
| [{{PDBlink}}2ebs 2ebs]
 +
| cellobiohydrolase (OXG-RCBH)
 +
| ''Geotrichum sp.'' m128
 +
| xyloglucan heptasaccharide
 +
| '''Asp465'''
 +
| Asp35
 +
| <cite>Yaoi2007</cite>
 +
|-
 +
| [[GH76]]
 +
| none
 +
| (α/α)<sub>6</sub>
 +
| alpha-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}5agd 5agd]
 +
| endo-α-1,6-mannanase
 +
| ''Bacillus circulans''
 +
| α-1,6-mannopentaose
 +
| '''Asp125'''
 +
| Asp124
 +
| <cite>Thompson2015</cite>
 +
|-
 +
| [[GH77]]
 +
| H
 +
| (β/α)<sub>8</sub>
 +
| alpha-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}2oww 2oww]
 +
| 4-α-glucanotransferase
 +
| ''Thermus thermofilus''
 +
| acarbose + 4-deoxy-α-{{Smallcaps|d}}-glucose
 +
| '''Glu340'''
 +
| Asp293
 +
| <cite>Barends2007</cite>
 +
|-
 +
| [[GH78]]
 +
| H
 +
| (α/α)<sub>6</sub>
 +
| alpha-{{Smallcaps|l}}
 +
| inverting
 +
| '''''anti'''''
 +
| [{{PDBlink}}3w5n 3w5n]
 +
| α-{{Smallcaps|l}}-rhamnosidase
 +
| ''Streptomyces avermitilis''
 +
| {{Smallcaps|l}}-rhamnose
 +
| '''Glu636'''
 +
| Glu895
 +
| <cite>Fujimoto2013</cite>
 +
|-
 +
| [[GH79]]
 +
| A
 +
| (β/α)<sub>8</sub>
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}5e9c 5e9c]
 +
|  heparanase
 +
| ''Homo sapiens''
 +
| heparin tetrasaccharide
 +
| '''Glu225'''
 +
| Glu343
 +
| <cite>Wu2015</cite>
 +
|-
 +
| [[GH80]]
 +
| I
 +
| α + β
 +
| beta-{{Smallcaps|d}}
 +
| inverting
 +
| ''predicted syn by clan''
 +
| ''see at GH24''
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|-
 +
| [[GH81]]
 +
| none
 +
| β-sandwich
 +
| beta-{{Smallcaps|d}}
 +
| inverting
 +
| '''''syn'''''
 +
| [{{PDBlink}}5t4g 5t4g]
 +
| endo-β-1,3-glucanase
 +
| ''Bacillus halodurans'' C-125
 +
| laminarin
 +
| '''Asp466'''
 +
| Glu542
 +
| <cite>Pluvinage2017</cite>
 +
|-
 +
| [[GH83]]
 +
| E
 +
| 6-fold β-propeller
 +
| alpha-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}1z4x 1z4x]
 +
| hemagglutinin-neuraminidase
 +
| Simian virus 5
 +
| α-2,3-sialyllactose
 +
| '''Glu247''' relay
 +
| Tyr523
 +
| <cite>Yuan2005</cite>
 +
|-
 +
| [[GH84]]
 +
| none
 +
| (β/α)<sub>8</sub>
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}2chn 2chn]
 +
| β-''N''-acetyl-glucosaminidase
 +
| ''Bacteroides thetaiotaomicron'' VPI-5482
 +
| NAG-thiazoline
 +
| '''Glu242'''
 +
| internal
 +
| <cite>Dennis2006</cite>
 +
|-
 +
| [[GH85]]
 +
| K
 +
| (β/α)<sub>8</sub>
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}2w92 2w92]
 +
| endo-β-''N''-acetyl-glucosaminidase D
 +
| ''Streptococcus pneumoniae'' TIGR4
 +
| NAG-thiazoline
 +
| '''Glu337'''
 +
| internal
 +
| <cite>Abbott2009</cite>
 +
|-
 +
| [[GH86]]
 +
| A
 +
| (β/α)<sub>8</sub>
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}4aw7 4aw7]
 +
| β-porphyranase
 +
| ''Bacteroides plebeius''
 +
| porphyran fragment
 +
| '''Glu152'''
 +
| Glu279
 +
| <cite>Hehemann_1_2012</cite>
 +
|-
 +
| [[GH89]]
 +
| none
 +
| (β/α)<sub>8</sub>
 +
| alpha-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}2vcb 2vcb]
 +
| α-''N''-acetyl-glucosaminidase
 +
| ''Clostridium perfringens''
 +
| PUGNAc
 +
| '''Glu483'''
 +
| Glu601
 +
| <cite>Ficko-Blean2008</cite>
 +
|-
 +
| [[GH92]]
 +
| none
 +
| (α/α)<sub>6</sub> and β-sandwich
 +
| alpha-{{Smallcaps|d}}
 +
| inverting
 +
| '''''anti'''''
 +
| [{{PDBlink}}2ww1 2ww1]
 +
| α-1,2-mannosidase
 +
| ''Bacteroides thetaiotaomicron'' VPI-5482
 +
| thiomannobioside
 +
| '''Glu533'''
 +
| Asp644 Asp642
 +
| <cite>Zhu2009</cite>
 +
|-
 +
| [[GH93]]
 +
| E
 +
| 6-fold β-propeller
 +
| alpha-{{Smallcaps|l}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}3a72 3a72]
 +
| exo-arabinanase
 +
| ''Penicillium chrysogenum''
 +
| arabinobiose
 +
| '''Glu246'''
 +
| Glu174
 +
| <cite>Sogabe2011</cite>
 +
|-
 +
| [[GH94]]
 +
| Q
 +
| (α/α)<sub>6</sub>
 +
| beta-{{Smallcaps|d}}
 +
| inverting
 +
| '''''syn'''''
 +
| [{{PDBlink}}4zli 4zli]
 +
| cellobionic acid phosphorylase
 +
| ''Saccharophagus degradans''
 +
| 3-O-β-{{Smallcaps|d}}-glucopyranosyl-α-{{Smallcaps|d}}-glucopyranuronic acid
 +
| '''Asp472'''
 +
| phosphate
 +
| <cite>Nam2015</cite>
 +
|-
 +
| [[GH95]]
 +
| none
 +
| (α/α)<sub>6</sub>
 +
| alpha-{{Smallcaps|l}}
 +
| inverting
 +
| '''''anti'''''
 +
| [{{PDBlink}}2ead 2ead]
 +
| α-1,2-{{Smallcaps|l}}-fucosidase
 +
| ''Bifidobacterium bifidum''
 +
| Fuc-α-1,2-Gal
 +
| '''Glu566'''
 +
| Asn423 Asp766
 +
| <cite>Nagae2007</cite>
 +
|-
 +
| [[GH97]]
 +
| none
 +
| (β/α)<sub>8</sub>
 +
| alpha-{{Smallcaps|d}}
 +
| retaining + inverting
 +
| '''''anti'''''
 +
| [{{PDBlink}}2zq0 2zq0]
 +
| α-glucosidase
 +
| ''Bacteroides thetaiotaomicron'' VPI-5482
 +
| acarbose
 +
| '''Glu532'''
 +
| Glu508
 +
| <cite>Kitamura2008</cite>
 +
|-
 +
| [[GH98]]
 +
| none
 +
| (β/α)<sub>8</sub> and β-sandwich
 +
| beta-{{Smallcaps|d}}
 +
| inverting
 +
| '''''anti'''''
 +
| [{{PDBlink}}2wmg 2wmg]
 +
| endo-β-1,4-galactosidase
 +
| ''Streptococcus pneumoniae''
 +
| A-Lewis<sup>Y</sup> pentasaccharide
 +
| '''Glu158'''
 +
| Asp251 Glu301
 +
| <cite>Higgins2009</cite>
 +
|-
 +
| [[GH99]]
 +
| none
 +
| (β/α)<sub>8</sub>
 +
| alpha-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}4ad4 4ad4]
 +
| endo-α-mannosidase
 +
| ''Bacteroides xylanisolvens''
 +
| glucose-1,3-isofagomine and α-1,2- mannobiose
 +
| '''Glu336'''
 +
| debated
 +
| <cite>Thompson2012</cite>
 +
|-
 +
| [[GH100]]
 +
| none
 +
| (α/α)<sub>6</sub> core
 +
| beta-{{Smallcaps|d}}
 +
| inverting
 +
| '''''anti'''''
 +
| [{{PDBlink}}5gop 5gop]
 +
| invertase
 +
| ''Anabaena (Nostoc) sp.'' pcc7120
 +
| sucrose
 +
| '''Asp188'''
 +
| Glu414
 +
| <cite>Xie2016</cite>
 +
|-
 +
| [[GH102]]
 +
| none
 +
| double-ψ β-barrel
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| '''''syn'''''
 +
| [{{PDBlink}}2pi8 2pi8]
 +
| lytic transglycosylase A
 +
| ''Escherichia coli''
 +
| chitohexaose
 +
| '''Asp308'''
 +
| none
 +
| <cite>van_Straaten2007</cite>
 +
|-
 +
| [[GH103]]
 +
| none
 +
| lysozyme type
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| '''''syn'''''
 +
| [{{PDBlink}}1d0k 1d0k]
 +
| lytic transglycosylase SLT35
 +
| ''Escherichia coli''
 +
| murodipeptides
 +
| '''Glu162'''
 +
| internal
 +
| <cite>van_Asselt2000</cite>
 +
|-
 +
| [[GH106]]
 +
| none
 +
| (β/α)<sub>8</sub>
 +
| alpha-{{Smallcaps|l}}
 +
| inverting
 +
| '''''anti'''''
 +
| [{{PDBlink}}5mwk 5mwk]
 +
| α-{{Smallcaps|l}}-rhamnosidase BT_0986
 +
| ''Bacteroides thetaiotaomicron''
 +
| pectin heptasaccharide
 +
| '''Glu461'''
 +
| Glu593 or Glu561
 +
| <cite>Ndeh2017</cite>
 +
|-
 +
| [[GH107]]
 +
| R
 +
| (β/α)<sub>8</sub>
 +
| alpha-{{Smallcaps|l}}
 +
| retaining
 +
| ''predicted syn by clan''
 +
| ''see at GH29''
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|-
 +
| [[GH110]]
 +
| none
 +
| parallel β-helix
 +
| alpha-{{Smallcaps|d}}
 +
| inverting
 +
| '''''anti'''''
 +
| [{{PDBlink}}7jwf 7jwf]
 +
| α-1,3-galactosidase
 +
| ''Pseudoalteromonas distincta''
 +
| Gal-α1,3-Gal
 +
| '''Asp344'''
 +
| Asp321 Asp345
 +
| <cite>McGuire2020</cite>
 +
|-
 +
| [[GH113]]
 +
| A
 +
| (β/α)<sub>8</sub>
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}4cd8 4cd8]
 +
| β-mannanase
 +
| ''Alicyclobacillus acidocaldarius''
 +
| mannobioimidazole
 +
| '''Glu151'''
 +
| Glu231
 +
| <cite>Williams2014</cite>
 +
|-
 +
| [[GH116]]
 +
| O
 +
| (α/α)<sub>6</sub> and β-sandwich
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| ''predicted anti by clan''
 +
| ''see at GH52''
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|-
 +
| [[GH117]]
 +
| none
 +
| 5-fold β-propeller
 +
| alpha-{{Smallcaps|l}}
 +
| inverting
 +
| '''''anti'''''
 +
| [{{PDBlink}}4ak7 4ak7]
 +
| α-1,3-3,6-anhydro-{{Smallcaps|l}}-galactosidase
 +
| ''Bacteroides plebeius''
 +
| neoagarobiose
 +
| '''His302''' (relay from Asp320)
 +
| Asp90
 +
| <cite>Hehemann_2_2012</cite>
 +
|-
 +
| [[GH120]]
 +
| none
 +
| parallel β-helix and β-sandwich
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}3vsv 3vsv]
 +
| β-xylosidase XylC
 +
| ''Thermoanaerobacterium saccharolyticum'' JW/SL-YS485
 +
| {{Smallcaps|d}}-xylose
 +
| '''Glu405'''
 +
| Asp382
 +
| <cite>Huang2012</cite>
 +
|-
 +
| [[GH123]]
 +
| none
 +
| (β/α)<sub>8</sub> and β-sandwich
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}5fr0 5fr0]
 +
| exo-β-N-acetyl-galactosaminidase
 +
| ''Clostridium perfringens''
 +
| ''N''-difluoroacetyl-{{Smallcaps|d}}-galactosamine
 +
| '''Glu345'''
 +
| internal
 +
| <cite>Noach2016</cite>
 +
|-
 +
| [[GH125]]
 +
| L
 +
| (α/α)<sub>6</sub>
 +
| alpha-{{Smallcaps|d}}
 +
| inverting
 +
| '''''anti'''''
 +
| [{{PDBlink}}5m7y 5m7y]
 +
| exo-α-1,6-mannosidase
 +
| ''Clostridium perfringens''
 +
| 1,6-α-mannotriose
 +
| '''Asp220'''
 +
| Glu393
 +
| <cite>Alonso-Gil2016</cite>
 +
|-
 +
| [[GH127]]
 +
| P
 +
| (α/α)<sub>6</sub> and β-sandwich
 +
| beta-{{Smallcaps|l}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}3wrg 3wrg]
 +
| β-{{Smallcaps|l}}-arabinofuranosidase
 +
| ''Bifidobacterium longum''
 +
| {{Smallcaps|l}}-arabinose
 +
| '''Glu322'''
 +
| Cys417
 +
| <cite>Huang2014</cite>
 +
|-
 +
| [[GH128]]
 +
| A
 +
| (β/α)<sub>8</sub>
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}6ufl 6ufl]
 +
| β-1,3-glucanase
 +
| ''Amycolatopsis mediterranei''
 +
| laminarihexaose
 +
| '''Glu102'''
 +
| Glu199
 +
| <cite>Santos2020</cite>
 
|-
 
|-
| [[GH9]]
+
| [[GH130]]
 +
| none
 +
| 5-fold β-propeller
 +
| beta-{{Smallcaps|d}}
 +
| inverting
 +
| '''''anti'''''
 +
| [{{PDBlink}}5b0s 5b0s]
 +
| β-1,2-mannobiose phosphorylase
 +
| ''Listeria innocua''
 +
| β-1,2-mannotriose
 +
| '''Asp141''' relay
 +
| phosphate
 +
| <cite>Tsuda2015</cite>
 +
|-
 +
|  [[GH134]]
 +
| none
 +
| β + α
 +
| beta-{{Smallcaps|d}}
 +
| inverting
 +
| '''''syn'''''
 +
| [{{PDBlink}}5jug 5jug]
 +
| β-mannanase
 +
| ''Streptomyces sp.''
 +
| mannopentaose
 +
| '''Glu45'''
 +
| Asp57
 +
| <cite>Jin2016</cite>
 +
|-
 +
|  [[GH136]]
 +
| none
 +
| β-helix
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| '''''syn'''''
 +
| [{{PDBlink}}5gqf 5gqf]
 +
| lacto-N-biosidase
 +
| ''Bifidobacterium longum''
 +
| lacto-N-biose
 +
| '''Asp411'''
 +
| Asp418
 +
| <cite>Yamada2017</cite>
 +
|-
 +
|  [[GH137]]
 +
| none
 +
| 5-fold β-propeller
 +
| beta-{{Smallcaps|l}}
 +
| unknown
 +
| '''''anti'''''
 +
| [{{PDBlink}}5mui 5mui]
 +
| β-{{Smallcaps|l}}-arabinofuranosidase BT_0996
 +
| ''Bacteroides thetaiotaomicron''
 +
| pectin oligosaccharide
 +
| '''Glu240'''
 +
| Glu159
 +
| <cite>Ndeh2017</cite>
 +
|-
 +
|  [[GH138]]
 +
| none
 +
| (β/α)<sub>8</sub>
 +
| alpha-{{Smallcaps|d}}
 +
| retaining
 +
| '''''syn'''''
 +
| [{{PDBlink}}6hzg 6hzg]
 +
| α-1,2-{{Smallcaps|d}}-galacturonidase
 +
| ''Bacteroides paurosaccharolyticus''
 +
| alpha-{{Smallcaps|d}}-galactopyranuronic
 +
| '''Glu294'''
 +
| Glu361
 +
| <cite>Labourel2019</cite>
 +
|-
 +
| [[GH146]]
 +
| P
 +
| (α/α)<sub>6</sub> and β-sandwich
 +
| beta-{{Smallcaps|l}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}5opj 5opj]
 +
| β-{{Smallcaps|l}}-arabinofuranosidase BT_0349
 +
| ''Bacteroides thetaiotaomicron''
 +
| {{Smallcaps|l}}-arabinose
 +
| '''Glu320'''
 +
| Cys416
 +
| <cite>Luis2018</cite>
 +
|-
 +
| [[GH147]]
 +
| A
 +
| (β/α)<sub>8</sub>
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| ''predicted anti by clan''
 +
| ''see at e.g. GH1''
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|-
 +
| [[GH148]]
 +
| A
 +
| (β/α)<sub>8</sub>
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| ''predicted anti by clan''
 +
| ''see at e.g. GH1''
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|-
 +
| [[GH149]]
 +
| Q
 +
| (α/α)<sub>6</sub>
 +
| beta-{{Smallcaps|d}}
 +
| inverting
 +
| ''predicted syn by clan''
 +
| ''see at GH94''
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|-
 +
| [[GH156]]
 +
| none
 +
| (β/α)<sub>8</sub>
 +
| alpha-{{Smallcaps|d}}
 +
| inverting
 +
| '''''syn'''''
 +
| [{{PDBlink}}6s0e 6s0e]
 +
| exo-α-sialidase
 +
| uncultured bacterium pG7
 +
| N-acetyl-2,3-dehydro-2-deoxyneuraminic acid
 +
| '''His134''' (relay from Asp132)
 +
| Asp14
 +
| <cite>Bule2019</cite>
 +
|-
 +
| [[GH157]]
 +
| A
 +
| (β/α)<sub>8</sub>
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| ''predicted anti by clan''
 +
| ''see at e.g. GH1''
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|-
 +
| [[GH158]]
 +
| A
 +
| (β/α)<sub>8</sub>
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| ''predicted anti by clan''
 +
| ''see at e.g. GH1''
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|-
 +
| [[GH161]]
 +
| Q
 +
| (α/α)<sub>6</sub>
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| ''predicted syn by clan''
 +
| ''see at GH94''
 +
|
 +
|
 +
|
 +
|
 +
|
 
|  
 
|  
| beta
+
|-
 +
| [[GH162]]
 +
| none
 +
| (α/α)<sub>6</sub>
 +
| beta-{{Smallcaps|d}}
 +
| inverting
 +
| '''''syn'''''
 +
| [{{PDBlink}}6imw 6imw]
 +
| endo-β-1,2-glucanase
 +
| ''Talaromyces funiculosus''
 +
| beta-1,2-glucan
 +
| '''Glu262''' via C3-OH of glc at subs. +2
 +
| Asp446
 +
| <cite>Tanaka2019</cite>
 +
|-
 +
| [[GH164]]
 +
| A
 +
| (β/α)<sub>8</sub>
 +
| beta-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}6t75 6t75]
 +
| β-mannosidase
 +
| ''Bacteroides salyersiae''
 +
| 2-deoxy-2-F-mannosyl
 +
| '''Glu160'''
 +
| Glu297
 +
| <cite>Armstrong2020</cite>
 +
|-
 +
| [[GH172]]
 +
| none
 +
| β-jelly roll
 +
| alpha-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}7v1w 7v1w]
 +
| difructose-anhydride synthase
 +
| ''Bifidobacterium dentum''
 +
| beta-{{Smallcaps|d}}-arabinofuranose
 +
| '''Glu270'''
 +
| Glu291
 +
| <cite>Kashima2021</cite>
 +
|-
 +
| [[GH181]]
 +
| E
 +
| 6-fold β-propeller
 +
| alpha-{{Smallcaps|d}}
 +
| inverting
 +
| '''''anti'''''
 +
| [{{PDBlink}}8axi 8axi]
 +
| exo-α-sialidase
 +
| ''Akkermansia muciniphila''
 +
| 2-deoxy-2,3-dehydro-''N''-acetyl-neuraminic acid + T-antigen disaccharide
 +
| '''Asp345'''
 +
| Glu218
 +
| <cite>Shuoker2023</cite>
 +
|-
 +
| [[GH183]]
 +
| none
 +
| 5-bladed β-propeller
 +
| alpha-{{Smallcaps|d}}
 +
| retaining
 +
| '''''anti'''''
 +
| [{{PDBlink}}8ic1 8ic1]
 +
| endo-α-1,5-{{Smallcaps|d}}-arabinofuranosidase
 +
| ''Microbacterium arabinogalactanolyticum'' JCM 9171
 +
| α-{{Smallcaps|d}}-Araf-(1,5)-α-{{Smallcaps|d}}-Araf-(1,5)-α-{{Smallcaps|d}}-Araf-(1,5)-α-{{Smallcaps|d}}-Araf
 +
| '''Asp51'''
 +
| Asp33
 +
| <cite>Shimokawa2023</cite>
 +
|-
 +
| [http://www.cazy.org/GH0.html n.c.*]
 +
| none
 +
| parallel β-helix
 +
| alpha-{{Smallcaps|d}}
 
| inverting
 
| inverting
| Glu424
+
| '''''anti'''''
| ''anti''
+
| [{{PDBlink}}2vjj 2vjj]
| Asp55,Asp58
+
| endo-α-N-acetylglucosaminidase
| product
+
| Bacteriophage HK620
| ''Thermomonospora fusca''
+
| O18A1 O-antigen hexasaccharide
| cellulase
+
| '''Asp339'''
| 3tf4,4tf4
+
| Glu372
| <cite>Irwin1998</cite>
+
| <cite>Barbirz2008</cite>
 
|}
 
|}
 +
<nowiki>*</nowiki> n.c.: Found among the collection of [http://www.cazy.org/GH0.html non-classified GH sequences in the CAZy Database].
  
 
== References ==
 
== References ==
 +
 
<biblio>
 
<biblio>
#HeightmanVasella1999 Heightman, T.D. and Vasella, A.T. (1999) Recent Insights into Inhibition, Structure, and Mechanism of Configuration-Retaining Glycosidases. Angewandte Chemie-International Edition 38(6), 750-770. [http://www3.interscience.wiley.com/journal/55000581/abstract Article online].
+
# HeightmanVasella1999 Heightman TD and Vasella AT. ''Recent Insights into Inhibition, Structure, and Mechanism of Configuration-Retaining Glycosidases.'' Angew Chem Int Ed. 1999 38(6):750-770. [http://www3.interscience.wiley.com/journal/55000581/abstract Article online].
#Nerinckx2005 pmid=15642336
+
# Nerinckx2005 pmid=15642336
#Wiesmann1997 pmid=9223646
+
# Wu2012 pmid=23137336
#Juers2001 pmid=11732897
+
# Perez1978 Pérez S and Marchessault RH. ''The exo-anomeric effect: experimental evidence from crystal structures.'' Carbohydr res. 1978 65:114-120. [http://dx.doi.org/10.1016/S0008-6215(00)84218-4 DOI:10.1016/S0008-6215(00)84218-4]
#Irwin1998 pmid=9537366
+
# Cramer1997 Cramer CJ, Truhlar DG, and French AD. ''Exo-anomeric effects on energies and geometries of different conformations of glucose and related systems in the gas phase and aqueous solution.'' Carbohydr res. 1997 298:1-14. [http://dx.doi.org/10.1016/S0008-6215(96)00297-2 DOI:10.1016/S0008-6215(96)00297-2]
 +
# Johnson2009 pmid=19733839
 +
# Alonso2016 pmid=26889578
 +
# Gloster2006 pmid=17002288
 +
# van_Bueren2009 pmid=18976664
 +
# Hrmova2001 pmid=11709165
 +
# Rajan2004 pmid=15341727
 +
# Varrot2003 pmid=12595701
 +
# Zhou1999 pmid=10508787
 +
# Sulzenbacher1999 pmid=10200171
 +
# Urbanikova2011 pmid=21501386
 +
# Guerin2002 pmid=11884144
 +
# Schubot2004 pmid=14756552
 +
# Suzuki2009 pmid=19279191
 +
# Wan2014 pmid=24419374
 +
# Sandgren2004 pmid=15364577
 +
# Uitdehaag1999 pmid=10331869
 +
# Miyake2003 pmid=12741813
 +
# Harris1993 pmid=8431441
 +
# Allouch2004 pmid=15062085
 +
# Wojtkowiak2013 pmid=23275163
 +
# Papanikolau2001 pmid=11560481
 +
# Prag2000 pmid=10884356
 +
# Vocadlo2001 pmid=11518970
 +
# Karlsen1996 pmid=15299731
 +
# Baldwin1993 pmid=8259514
 +
# Cartmell2008 pmid=18799462
 +
# Fernandez-Leiro2010 pmid=20592022
 +
# Abbott2007 pmid=17397864
 +
# Sakurama2012 pmid=22451675
 +
# Sim2008 pmid=18036614
 +
# Verhaest2007 pmid=17335500
 +
# Amaya2004 pmid=15130470
 +
# Zhu2012 pmid=23015718
 +
# Maksimainen2011 pmid=21130883
 +
# Merceron2012 pmid=23012371
 +
# Gibson2007 pmid=17455176
 +
# Shah2008 pmid=18599462
 +
# Czjzek2005 pmid=16212978
 +
# Godoy2016 pmid=27685756
 +
# Fujimoto2010 pmid=20739278
 +
# Kitago2007 pmid=17905739
 +
# Davies1996 pmid=15299721
 +
# Lyu2014 pmid=24766439
 +
# Karaveg2005 pmid=15713668
 +
# Nerinckx2008 pmid=18619586
 +
# Pluvinage2013 pmid=23921382
 +
# Yuan2005 pmid=15893670
 +
# Hoevel2003 pmid=14517232
 +
# Espina2014 pmid=24816105
 +
# Le_Nours2009 pmid=19089956
 +
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# Jin2016 Jin Y, Petricevic M, John A, Raich L, Jenkins H, Portela De Souza L, Cuskin F, Gilbert HJ, Rovira C, Goddard-Borger ED, Williams SJ, and Davies GJ. ''A β-Mannanase with a Lysozyme-like Fold and a Novel Molecular Catalytic Mechanism.'' ACS Cent Sci. 2016 Nov [http://dx.doi.org/10.1021/acscentsci.6b00232 DOI:10.1021/acscentsci.6b00232]
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</biblio>
 
</biblio>
 
  
 
[[Category:Definitions and explanations]]
 
[[Category:Definitions and explanations]]

Revision as of 00:29, 26 October 2023

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This page has been approved by the Responsible Curator as essentially complete. CAZypedia is a living document, so further improvement of this page is still possible. If you would like to suggest an addition or correction, please contact the page's Responsible Curator directly by e-mail.


Overview

This page provides a table that summarizes the spatial positioning of the catalytic general acid residue in the active sites of glycoside hydrolases, relative to the substrate. The table below updates those found in the seminal paper on this concept by Heightman and Vasella [1], and a following paper by Nerinckx et al. [2].

Background

The "not from above, but from the side" concept of semi-lateral glycosidic oxygen protonation by glycoside hydrolases was introduced by Heightman and Vasella [1]. It was originally only described for beta-equatorial glycoside hydrolases, but appears to be equally applicable to enzymes acting on an alpha-axial glycosidic bond [2]. When dividing subsite -1 into half-spaces by a plane defined by the glycosidic oxygen and C1' and H1' of the –1 glycoside, many ligand-complexed structures reveal that the proton donor is positioned either in the syn half-space (near the ring-oxygen of the –1 glycoside), or in the anti half-space (on the opposite side of the ring-oxygen). Members of the same GH family appear to share a common syn or anti protonator arrangement and further, this specificity appears to be preserved within Clans of families. This page's compilation of subsite -1 occupied complexes shows that about 70% of all GH families are anti protonators.

Closer inspection of crystal structures of –1/+1 subsite-spanning substrates, or substrate-analogue ligands, in complex with enzymes reveals a further intriguing corollary [2, 3]. In substrate-bound complexes with anti protonating GH enzymes, the scissile anomeric bond (often studied using the thio-analogue) shows a dihedral angle φ (O5'-C1'-[O,S]x-Cx) that is in the lowest-energy synclinal (gauche) conformation. The rationale for this is that a minus synclinal dihedral angle φ for an equatorial glycosidic bond, or plus synclinal for an axial glycosidic bond [4], allows for hyperconjugative overlap of the C1'-O5' antibonding orbital with an antiperiplanar-oriented lone pair orbital lobe of the glycosidic oxygen, thereby creating partial double bond character and stabilization of the glycosidic bond by 4–5 kcal/mol; this ground-state stabilizing phenomenon is known as the ‘exo-anomeric effect’ [5, 6, 7]. Anti protonation occurs on the glycosidic oxygen’s antiperiplanar lone pair, thereby removing the stabilizing exo-anomeric effect. This suggests that anti protonation is an enzymic approach for lowering the activation barrier leading to the transition state (Figure 1 centre).

Syn protonating glycoside hydrolases apparently make use of a different approach [2, 3]. In many –1/+1 subsite-spanning ligand complexes, the dihedral angle φ of the scissile anomeric bond has been rotated away from its lowest-energy synclinal position: clockwise to minus-anticlinal or antiperiplanar for beta-equatorial; counterclockwise to plus-anticlinal or antiperiplanar for alpha-axial anomeric bonds. This removes the hyperconjugative overlap and thus also the stabilizing exo-anomeric effect. And because of this rotation, a lone pair of the glycosidic oxygen is directed into the syn half-space, allowing it to be protonated by the syn-positioned proton donor (Figure 1 right).

Figure 1. Newman projections, with the glycosidic oxygen as proximal atom and the anomeric carbon as distal atom, showing anti (centre) versus syn (right) semi-lateral protonation in beta-equatorial (top) and alpha-axial (bottom) glycoside hydrolases. The indicated φ is the dihedral angle for O5'-C1'-O4-C4.

Table of syn/anti protonation examples

This table contains only one example per GH family of a ligand-complexed protein structure where the syn or anti positioning of the proton donor can be clearly observed; other examples may be available on a family-by-family basis. The reader is thus advised to consult the CAZy database for a current, comprehensive list of CAZyme structures. Where available, the selected examples are Michaelis-type complexes with the ligand spanning the -1/+1 subsites, since these have an intact glycosidic or thioglycosidic bond, or are N-analogs of the substrate (e.g. acarbose). In some examples, the proton donor has been mutated (e.g., to the corresponding amide or to an alanine), and in those cases one may wish to look at a superposition of the given PDB example with the structure of the native enzyme. If a Michaelis-type complex is not yet available, the second and third example choices, respectively, are trapped glycosyl-enzyme intermediates and product complexes where subsite -1 is occupied.

Please also be aware that this is a large table with many data. Please contact the page Author or Responsible Curator with corrections.

Table

This table can be re-sorted by clicking on the icons in the header (javascript must be turned on in your browser). To reset the page to be sorted by GH family, click the View tab at the very top of the page.

Family Clan Structure fold Anomeric specificity Mechanism Syn/anti protonator Example PDB ID Enzyme Organism Ligand General acid Nucleophile or General base Reference
GH1 A (β/α)8 beta-d retaining anti 2cer β-glycosidase S Sulfolobus solfataricus P2 phenethyl glucoimidazole Glu206 Glu387 [8]
GH2 A (β/α)8 beta-d / alpha-l retaining anti 2vzu exo-β-glucosaminidase Amicolatopsis orientalis PNP-β-d-glucosamine Glu469 Glu541 [9]
GH3 none (β/α)8 beta-d / alpha-l retaining anti 1iex exo-1,3-1,4-glucanase Hordeum vulgare thiocellobiose Glu491 Asp285 [10]
GH4 none Rossmann + α6/β3 + β3/α4 beta-d retaining anti 1u8x 6-P-α-glucosidase Bacillus subtilis alpha-d-glucose-6-phosphate Asp172 not applicable [11]
GH5 A (β/α)8 beta-d retaining anti 1h2j endo-β-1,4-glucanase Bacillus agaradhaerens 2',4'-DNP-2-F-cellobioside Glu129 Glu228 [12]
GH6 none (β/α)8 beta-d inverting syn 1qjw cellobiohydrolase 2 Hypocrea jecorina (Glc)2-S-(Glc)2 Asp221 debated [13]
GH7 B β-jelly roll beta-d retaining syn 1ovw endo-1,4-glucanase Fusarium oxysporum thio-(Glc)5 Glu202 Glu197 [14]
GH8 M (α/α)6 beta-d inverting anti 1kwf endo-1,4-glucanase Clostridium thermocellum cellopentaose Glu95 Asp278 [15]
GH9 none (α/α)6 beta-d inverting syn 1rq5 cellobiohydrolase Clostridium thermocellum cellotetraose Glu795 Asp383 [16]
GH10 A (β/α)8 beta-d retaining anti 2d24 β-1,4-xylanase Streptomyces olivaceoviridis E-86 xylopentaose Glu128 Glu236 [17]
GH11 C β-jelly roll beta-d retaining syn 4hk8 endo-β-1,4-xylanase Hypocrea jecorina xylohexaose Glu177 Glu86 [18]
GH12 C β-jelly roll beta-d retaining syn 1w2u endoglucanase Humicola grisea thiocellotetraose Glu205 Glu120 [19]
GH13 H (β/α)8 alpha-d retaining anti 1cxk β-cyclodextrin glucanotransferase Bacillus circulans maltononaose Glu257 Asp229 [20]
GH14 none (β/α)8 alpha-d inverting syn 1itc β-amylase Bacillus cereus maltopentaose Glu172 Glu367 [21]
GH15 L (α/α)6 alpha-d inverting anti 1dog glucoamylase Aspergillus awamori 1-deoxynojirimycin Glu179 Glu400 [22]
GH16 B β-jelly roll beta-d retaining syn 1urx β-agarase A Zobellia galactanivorans oligoagarose Glu152 Glu147 [23]
GH17 A (β/α)8 beta-d retaining anti 4gzj endo-β-1,3-glucanase Solanum tuberosum laminaratriose + laminarabiose Glu118 Glu259 [24]
GH18 K (β/α)8 beta-d retaining anti 1ffr chitinase A Serratia marcescens (NAG)6 Glu315 internal [25]
GH19 none lysozyme type beta-d inverting syn 3wh1 chitinase Bryum coronatum (GlcNAc)4 Glu61 Glu70 [26]
GH20 K (β/α)8 beta-d retaining anti 1c7s chitobiase Serratia marcescens chitobiose Glu540 internal [27]
GH22 none lysozyme type beta-d retaining syn 1h6m lysozyme C Gallus gallus Chit-2-F-chitosyl Glu35 Asp52 [28]
GH23 none lysozyme type beta-d inverting syn 1lsp lysozyme G Cygnus atratus Bulgecin A Glu73 internal [29]
GH24 I α + β beta-d inverting syn 148l lysozyme E Bacteriophage T4 chitobiosyl Glu11 Glu26 [30]
GH26 A (β/α)8 beta-d retaining anti 2vx6 exo-β-mannanase Cellvibrio japonicus Ueda107 Gal1Man4 Glu221 Glu338 [31]
GH27 D (β/α)8 alpha-d / beta-l retaining anti 3lrm α-galactosidase Saccharomyces cerevisiae raffinose Asp209 Asp141 [32]
GH28 N β-helix alpha-d (and α-l-rham) inverting anti 2uvf exo-polygalacturonosidase Yersinia enterocolitica ATCC9610D digalacturonic acid Asp402 Asp381 Asp403 [33]
GH29 R (β/α)8 alpha-l retaining syn 3uet α-1,3/4-fucosidase Bifidobacterium longum subsp. infantis lacto-N-fucopentaose II Glu217 Asp172 [34]
GH30 A (β/α)8 beta-d retaining anti 2y24 glucurono-xylanase Dickea chrysanthemi D1 glucuronoxylan tetrasaccharide Glu163 Glu253 [35]
GH31 D (β/α)8 alpha-d retaining anti 2qmj maltase-glucoamylase Homo sapiens acarbose Asp542 Asp443 [36]
GH32 J 5-fold β-propeller beta-d retaining anti 2add fructan β-(2,1)-fructosidase Cichorium intybus sucrose Glu201 Asp22 [37]
GH33 E 6-fold β-propeller alpha-d retaining anti 1s0i transsialidase Trypanosoma cruzi sialyllactose Asp59 Tyr342 [38]
GH34 E 6-fold β-propeller alpha-d retaining anti 4gzw N2 neuraminidase Influenza A Tanzania/205/2010 H3N2 α-d-Neup5Ac-(2,3)-β-d-Galp-(1,4)-β-d-GlcpNAc Asp151 Tyr406 [39]
GH35 A (β/α)8 beta-d retaining anti 3ogv β-galactosidase Hypocrea jecorina 2-phenylethyl 1-thio-β-d-galactopyranoside Glu200 Glu298 [40]
GH36 D (β/α)8 alpha-d retaining anti 4fnu β-galactosidase Geobacillus stearothermophilus stachyose Asp584 Asp478 [41]
GH37 G (α/α)6 alpha-d inverting anti 2jf4 trehalase Escherichia coli validoxylamine Asp312 Glu496 [42]
GH38 none (β/α)7 alpha-d retaining anti 3czn Golgi α-mannosidase II Drosophila melanogaster GlcNAcMan(5)GlcNAc(2) Asp341 Asp204 [43]
GH39 A (β/α)8 beta-d / alpha-l retaining anti 2bfg β-xylosidase Geobacillus stearothermophilus 2,5-dinitrophenyl-β-d-xyloside Glu160 Glu278 [44]
GH42 A (β/α)8 beta-d / alpha-l retaining anti 4ucf β-galactosidase Bifidobacterium bifidum d-galactose Glu161 Glu320 [45]
GH43 F 5-fold β-propeller beta-d / alpha-l inverting anti 3akh exo-1,5-α-l-arabinofuranosidase Streptomyces avermitilis α-1,5-arabinofuranotriose Glu196 Asp220 [46]
GH44 none (β/α)8 beta-d retaining anti 2eqd endoglucanase Clostridium thermocellum cellooctaose Glu186 Glu359 [47]
GH45 none 6-stranded β-barrel beta-d inverting syn 4eng endo-1,4-glucanase Humicola insolens cellohexaose Asp121 Asp10 [48]
GH46 I lysozyme type beta-d inverting syn 4olt chitosanase Microbacterium sp. OU01 hexa-glucosamine Glu25 Asp43 [49]
GH47 none (α/α)7 alpha-d inverting anti 1x9d α-mannosidase I Homo sapiens Me-2-S-(α-Man)-2-thio-α-Man Asp463 Glu599 [50], [51]
GH48 M (α/α)6 beta-d inverting predicted anti by clan see at GH8
GH49 N β-helix alpha-d inverting predicted anti by clan see at GH28
GH50 A (β/α)8 beta-d retaining anti 4bq5 exo-β-agarase Saccharophagus degradans neoagarotetraose Glu535 Glu695 [52]
GH51 A (β/α)8 beta-d / alpha-l retaining anti 1qw9 α-l-arabinofuranosidase Geobacillus stearothermophilus PNP-l-arabinofuranoside Glu175 Glu294 [53]
GH52 O (α/α)6 beta-d retaining anti 4c1p β-xylosidase Geobacillus thermoglucosidasius xylobiose Asp517 Glu537 [54]
GH53 A (β/α)8 beta-d retaining anti 2ccr β-1,4-galactanase Bacillus licheniformis galactotriose Glu165 Glu263 [55]
GH54 none β-sandwich beta-d / alpha-l retaining anti 1wd4 α-l-arabinofuranosidase B Aspergillus kawachii l-arabinofuranose Asp297 Glu221 [56]
GH55 none β-helix beta-d inverting syn 4tz5 exo-β-1,3-glucanase Streptomyces sp. SirexAA-E laminarihexaose Glu502 unknown [57]
GH56 none (β/α)7 beta-d retaining anti 1fcv hyaluronidase Apis mellifera (hyaluron.)4 Glu113 internal [58]
GH57 none (β/α)7 alpha-d retaining anti 1k1y glucanotransferase Thermococcus litoralis acarbose Asp214 Glu123 [59]
GH59 A (β/α)8 beta-d retaining anti 4ccc β-galactocerebrosidase Mus musculus PNP-β-d-galactoside Glu182 Glu258 [60]
GH62 F 5-fold β-propeller alpha-l inverting anti 3wn0 α-l-arabinofuranosidase Streptomyces coelicolor β-l-Arabinofuranose Glu361 Asp202 [61]
GH63 G (α/α)6 alpha-d inverting anti 5ca3 α-glucosidase Escherichia coli glucose and lactose Asp501 Glu727 [62]
GH65 L (α/α)6 alpha-d (and α-l-rham) inverting anti 4ktr 2-O-α-glucosylglycerol phosphorylase Bacillus selenitireducens isofagomine Glu475 phosphate [63]
GH66 none (β/α)8 alpha-d retaining anti 5axh dextranase Thermoanaerobacter pseudethanolicus isomaltohexaose Glu374 Asp312 [64]
GH67 none (β/α)8 alpha-d inverting syn 1l8n α-glucuronidase Geobacillus stearothermophilus 4-O-methyl-d-glucuronic acid and xylotriose Glu286 Asp364 Glu392 [65]
GH68 J 5-fold β-propeller beta-d retaining anti 1pt2 levansucrase Bacillus subtilis sucrose Glu342 Asp86 [66]
GH70 H (β/α)8 alpha-d retaining anti 3aic glucansucrase Streptococcus mutans α-acarbose Glu515 Asp477 [67]
GH72 A (β/α)8 beta-d retaining anti 2w62 β-1,3-glucanotransferase Saccharomyces cerevisiae S288C laminaripentaose Glu176 Glu275 [68]
GH74 none 7-fold β-propeller beta-d inverting syn 2ebs cellobiohydrolase (OXG-RCBH) Geotrichum sp. m128 xyloglucan heptasaccharide Asp465 Asp35 [69]
GH76 none (α/α)6 alpha-d retaining anti 5agd endo-α-1,6-mannanase Bacillus circulans α-1,6-mannopentaose Asp125 Asp124 [70]
GH77 H (β/α)8 alpha-d retaining anti 2oww 4-α-glucanotransferase Thermus thermofilus acarbose + 4-deoxy-α-d-glucose Glu340 Asp293 [71]
GH78 H (α/α)6 alpha-l inverting anti 3w5n α-l-rhamnosidase Streptomyces avermitilis l-rhamnose Glu636 Glu895 [72]
GH79 A (β/α)8 beta-d retaining anti 5e9c heparanase Homo sapiens heparin tetrasaccharide Glu225 Glu343 [73]
GH80 I α + β beta-d inverting predicted syn by clan see at GH24
GH81 none β-sandwich beta-d inverting syn 5t4g endo-β-1,3-glucanase Bacillus halodurans C-125 laminarin Asp466 Glu542 [74]
GH83 E 6-fold β-propeller alpha-d retaining anti 1z4x hemagglutinin-neuraminidase Simian virus 5 α-2,3-sialyllactose Glu247 relay Tyr523 [75]
GH84 none (β/α)8 beta-d retaining anti 2chn β-N-acetyl-glucosaminidase Bacteroides thetaiotaomicron VPI-5482 NAG-thiazoline Glu242 internal [76]
GH85 K (β/α)8 beta-d retaining anti 2w92 endo-β-N-acetyl-glucosaminidase D Streptococcus pneumoniae TIGR4 NAG-thiazoline Glu337 internal [77]
GH86 A (β/α)8 beta-d retaining anti 4aw7 β-porphyranase Bacteroides plebeius porphyran fragment Glu152 Glu279 [78]
GH89 none (β/α)8 alpha-d retaining anti 2vcb α-N-acetyl-glucosaminidase Clostridium perfringens PUGNAc Glu483 Glu601 [79]
GH92 none (α/α)6 and β-sandwich alpha-d inverting anti 2ww1 α-1,2-mannosidase Bacteroides thetaiotaomicron VPI-5482 thiomannobioside Glu533 Asp644 Asp642 [80]
GH93 E 6-fold β-propeller alpha-l retaining anti 3a72 exo-arabinanase Penicillium chrysogenum arabinobiose Glu246 Glu174 [81]
GH94 Q (α/α)6 beta-d inverting syn 4zli cellobionic acid phosphorylase Saccharophagus degradans 3-O-β-d-glucopyranosyl-α-d-glucopyranuronic acid Asp472 phosphate [82]
GH95 none (α/α)6 alpha-l inverting anti 2ead α-1,2-l-fucosidase Bifidobacterium bifidum Fuc-α-1,2-Gal Glu566 Asn423 Asp766 [83]
GH97 none (β/α)8 alpha-d retaining + inverting anti 2zq0 α-glucosidase Bacteroides thetaiotaomicron VPI-5482 acarbose Glu532 Glu508 [84]
GH98 none (β/α)8 and β-sandwich beta-d inverting anti 2wmg endo-β-1,4-galactosidase Streptococcus pneumoniae A-LewisY pentasaccharide Glu158 Asp251 Glu301 [85]
GH99 none (β/α)8 alpha-d retaining anti 4ad4 endo-α-mannosidase Bacteroides xylanisolvens glucose-1,3-isofagomine and α-1,2- mannobiose Glu336 debated [86]
GH100 none (α/α)6 core beta-d inverting anti 5gop invertase Anabaena (Nostoc) sp. pcc7120 sucrose Asp188 Glu414 [87]
GH102 none double-ψ β-barrel beta-d retaining syn 2pi8 lytic transglycosylase A Escherichia coli chitohexaose Asp308 none [88]
GH103 none lysozyme type beta-d retaining syn 1d0k lytic transglycosylase SLT35 Escherichia coli murodipeptides Glu162 internal [89]
GH106 none (β/α)8 alpha-l inverting anti 5mwk α-l-rhamnosidase BT_0986 Bacteroides thetaiotaomicron pectin heptasaccharide Glu461 Glu593 or Glu561 [90]
GH107 R (β/α)8 alpha-l retaining predicted syn by clan see at GH29
GH110 none parallel β-helix alpha-d inverting anti 7jwf α-1,3-galactosidase Pseudoalteromonas distincta Gal-α1,3-Gal Asp344 Asp321 Asp345 [91]
GH113 A (β/α)8 beta-d retaining anti 4cd8 β-mannanase Alicyclobacillus acidocaldarius mannobioimidazole Glu151 Glu231 [92]
GH116 O (α/α)6 and β-sandwich beta-d retaining predicted anti by clan see at GH52
GH117 none 5-fold β-propeller alpha-l inverting anti 4ak7 α-1,3-3,6-anhydro-l-galactosidase Bacteroides plebeius neoagarobiose His302 (relay from Asp320) Asp90 [93]
GH120 none parallel β-helix and β-sandwich beta-d retaining anti 3vsv β-xylosidase XylC Thermoanaerobacterium saccharolyticum JW/SL-YS485 d-xylose Glu405 Asp382 [94]
GH123 none (β/α)8 and β-sandwich beta-d retaining anti 5fr0 exo-β-N-acetyl-galactosaminidase Clostridium perfringens N-difluoroacetyl-d-galactosamine Glu345 internal [95]
GH125 L (α/α)6 alpha-d inverting anti 5m7y exo-α-1,6-mannosidase Clostridium perfringens 1,6-α-mannotriose Asp220 Glu393 [96]
GH127 P (α/α)6 and β-sandwich beta-l retaining anti 3wrg β-l-arabinofuranosidase Bifidobacterium longum l-arabinose Glu322 Cys417 [97]
GH128 A (β/α)8 beta-d retaining anti 6ufl β-1,3-glucanase Amycolatopsis mediterranei laminarihexaose Glu102 Glu199 [98]
GH130 none 5-fold β-propeller beta-d inverting anti 5b0s β-1,2-mannobiose phosphorylase Listeria innocua β-1,2-mannotriose Asp141 relay phosphate [99]
GH134 none β + α beta-d inverting syn 5jug β-mannanase Streptomyces sp. mannopentaose Glu45 Asp57 [100]
GH136 none β-helix beta-d retaining syn 5gqf lacto-N-biosidase Bifidobacterium longum lacto-N-biose Asp411 Asp418 [101]
GH137 none 5-fold β-propeller beta-l unknown anti 5mui β-l-arabinofuranosidase BT_0996 Bacteroides thetaiotaomicron pectin oligosaccharide Glu240 Glu159 [90]
GH138 none (β/α)8 alpha-d retaining syn 6hzg α-1,2-d-galacturonidase Bacteroides paurosaccharolyticus alpha-d-galactopyranuronic Glu294 Glu361 [102]
GH146 P (α/α)6 and β-sandwich beta-l retaining anti 5opj β-l-arabinofuranosidase BT_0349 Bacteroides thetaiotaomicron l-arabinose Glu320 Cys416 [103]
GH147 A (β/α)8 beta-d retaining predicted anti by clan see at e.g. GH1
GH148 A (β/α)8 beta-d retaining predicted anti by clan see at e.g. GH1
GH149 Q (α/α)6 beta-d inverting predicted syn by clan see at GH94
GH156 none (β/α)8 alpha-d inverting syn 6s0e exo-α-sialidase uncultured bacterium pG7 N-acetyl-2,3-dehydro-2-deoxyneuraminic acid His134 (relay from Asp132) Asp14 [104]
GH157 A (β/α)8 beta-d retaining predicted anti by clan see at e.g. GH1
GH158 A (β/α)8 beta-d retaining predicted anti by clan see at e.g. GH1
GH161 Q (α/α)6 beta-d retaining predicted syn by clan see at GH94
GH162 none (α/α)6 beta-d inverting syn 6imw endo-β-1,2-glucanase Talaromyces funiculosus beta-1,2-glucan Glu262 via C3-OH of glc at subs. +2 Asp446 [105]
GH164 A (β/α)8 beta-d retaining anti 6t75 β-mannosidase Bacteroides salyersiae 2-deoxy-2-F-mannosyl Glu160 Glu297 [106]
GH172 none β-jelly roll alpha-d retaining anti 7v1w difructose-anhydride synthase Bifidobacterium dentum beta-d-arabinofuranose Glu270 Glu291 [107]
GH181 E 6-fold β-propeller alpha-d inverting anti 8axi exo-α-sialidase Akkermansia muciniphila 2-deoxy-2,3-dehydro-N-acetyl-neuraminic acid + T-antigen disaccharide Asp345 Glu218 [108]
GH183 none 5-bladed β-propeller alpha-d retaining anti 8ic1 endo-α-1,5-d-arabinofuranosidase Microbacterium arabinogalactanolyticum JCM 9171 α-d-Araf-(1,5)-α-d-Araf-(1,5)-α-d-Araf-(1,5)-α-d-Araf Asp51 Asp33 [109]
n.c.* none parallel β-helix alpha-d inverting anti 2vjj endo-α-N-acetylglucosaminidase Bacteriophage HK620 O18A1 O-antigen hexasaccharide Asp339 Glu372 [110]

* n.c.: Found among the collection of non-classified GH sequences in the CAZy Database.

References

  1. Heightman TD and Vasella AT. Recent Insights into Inhibition, Structure, and Mechanism of Configuration-Retaining Glycosidases. Angew Chem Int Ed. 1999 38(6):750-770. Article online.

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