Syn/anti lateral protonation - Revision history

Wim Nerinckx at 14:46, 16 April 2026

2026-04-16T14:46:50Z

Wim Nerinckx: added example for GH71, GH109 and GH135

2026-04-16T12:04:48Z

added example for GH71, GH109 and GH135

Wim Nerinckx: GH192-3-4 predicted syn by clan

2026-04-15T12:14:50Z

GH192-3-4 predicted syn by clan

Wim Nerinckx: proton donor residue number correction in GH30: Glu165 (not 163)

2025-10-08T18:18:10Z

proton donor residue number correction in GH30: Glu165 (not 163)

Wim Nerinckx: All pdb IDs in the new 12-character format

2025-08-22T12:10:23Z

All pdb IDs in the new 12-character format

Show changes

Wim Nerinckx at 12:36, 15 April 2025

2025-04-15T12:36:52Z

Wim Nerinckx: GH73 syn, GH124 syn, GH129 anti, GH133 anti, GH168 syn.

2025-04-15T12:33:22Z

GH73 syn, GH124 syn, GH129 anti, GH133 anti, GH168 syn.

Wim Nerinckx: Update clan-O GH52 and GH116

2025-04-08T08:14:45Z

Update clan-O GH52 and GH116

Wim Nerinckx: GH144 syn protonator (with temporary BioRxiv2024 reference)

2025-04-03T09:35:30Z

GH144 syn protonator (with temporary BioRxiv2024 reference)

Wim Nerinckx: Correction at GH83 after re-check with its pub and reviewing 3D-examples from Clan-E's GH33 and GH34

2025-04-03T08:07:24Z

Correction at GH83 after re-check with its pub and reviewing 3D-examples from Clan-E's GH33 and GH34

@@ Line 1,297: / Line 1,297: @@
 | '''''anti'''''
 | [{{PDBlink}}pdb_00006t2b pdb_00006t2b]
-| a/β-N-acetylgalactosaminidase
+| α/β-N-acetylgalactosaminidase
 | ''Akkermansia muciniphila''
 | α-{{Smallcaps|d}}-GalpNAc

@@ Line 897: / Line 897: @@
 | Asp477
 | <cite>Ito2011</cite>
 |-
 | [[GH72]]
@@ Line 1,275: / Line 1,289: @@
+|
+|
 |-
 | [[GH110]]
@@ Line 1,486: / Line 1,514: @@
 | <cite>Jin2016</cite>
 |-
 |  [[GH136]]
 | none
@@ Line 1,706: / Line 1,750: @@
+|
+|
 | |
+|
 |-
 | [[GH168]]
@@ Line 1,951: / Line 1,996: @@
 # Meng2003 pmid=14517548
 # Ito2011 pmid=21354427
 # Hurtado-Gerrero2009 pmid=19097997
 # Yaoi2007 pmid=17498741
 # Martinez-Caballero2023 pmid=37418323
@@ Line 1,978: / Line 2,027: @@
 # 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]
 # Yamada2017 pmid=28392148
 # Ohnuma2014 pmid=24582745
 # Thompson2012 pmid=22219371
 # Xie2016 pmid=27777307
@@ Line 1,999: / Line 2,052: @@
 # Sato2017 pmid=28546425
 # Kashima2021 pmid=34688653
 # McGuire2020 pmid=33127644
 # Shuoker2023 pmid=37005422
 # Shimokawa2023 pmid=37726269

@@ Line 1,530: / Line 1,530: @@
 | [[GH140]]
 | A
-| (β/α)<sub>8</sub>
+| (β/α)<sub>6</sub>
 | beta-{{Smallcaps|d}}
 | retaining
@@ Line 1,706: / Line 1,706: @@
+|
+|
+|
-−
 |-
 | [[GH168]]
@@ Line 1,735: / Line 1,737: @@
+|
+|
-−
+|
 |-
 | [[GH172]]
@@ Line 1,763: / Line 1,765: @@
+|
+|
-−
+|
 |-
 | [[GH178]]
@@ Line 1,777: / Line 1,779: @@
+|
+|
 |-
 | [[GH181]]
@@ Line 1,819: / Line 1,822: @@
 | Asp300 + 3 waters
 | <cite>Motouchi2023</cite>
 |-
 | [http://www.cazy.org/GH0.html n.c.*]

@@ Line 432: / Line 432: @@
 | ''Dickea chrysanthemi'' D1
 | glucuronoxylan tetrasaccharide
-| '''Glu163'''
+| '''Glu165'''
 | Glu253
 | <cite>Urbanikova2011</cite>

@@ Line 912: / Line 912: @@
 | <cite>Hurtado-Gerrero2009</cite>
 |-
 | [[GH73]]
 | none
@@ Line 927: / Line 926: @@
 | <cite>Martinez-Caballero2023</cite>
 |-
 | [[GH74]]
 | none
 | 7-fold β-propeller
@@ Line 1,377: / Line 1,374: @@
 | <cite>Noach2016</cite>
 |-
 | [[GH124]]
 | none
@@ Line 1,392: / Line 1,388: @@
 | <cite>Urresti2018</cite>
 |-
 | [[GH125]]
 | L
 | (α/α)<sub>6</sub>
@@ Line 1,436: / Line 1,430: @@
 | <cite>Santos2020</cite>
 |-
 | [[GH129]]
 | none
@@ Line 1,451: / Line 1,444: @@
 | <cite>Sato2017</cite>
 |-
 | [[GH130]]
 | none
 | 5-fold β-propeller
@@ Line 1,467: / Line 1,458: @@
 | <cite>Tsuda2015</cite>
 |-
 | [[GH133]]
 | none
@@ Line 1,482: / Line 1,472: @@
 | <cite>Zhai2016</cite>
 |-
 |  [[GH134]]
 | none
 | β + α
@@ Line 1,721: / Line 1,709: @@
+|
 |-
 | [[GH168]]
 | none
@@ Line 1,736: / Line 1,723: @@
 | <cite>Chen2024</cite>
 |-
 | [[GH169]]
 | A
 | (β/α)<sub>8</sub>
@@ Line 1,923: / Line 1,908: @@
 # Hurtado-Gerrero2009 pmid=19097997
 # Yaoi2007 pmid=17498741
 # Martinez-Caballero2023 pmid=37418323
 # Thompson2015 pmid=25772148
 # Barends2007 pmid=17420245
 # Fujimoto2013 pmid=23486481
@@ Line 1,960: / Line 1,942: @@
 # Huang2012 pmid=22992047
 # Noach2016 pmid=27038508
 # Urresti2018 pmid=30084399
 # Alonso-Gil2016 pmid=28026180
 # Huang2014 Huang CH, Zhu Z, Cheng YS, Chan HC, Ko TP, Chen CC, Wang I, Ho MR, Hsu ST, Zeng YF, Huang YN, Liu JR, Guo RT. ''Structure and Catalytic Mechanism of a Glycoside Hydrolase Family-127 β-L-Arabinofuranosidase (HypBA1).'' J Bioprocess Biotech. 2014 4:171 [http://dx.doi.org/10.4172/2155-9821.1000171 DOI:10.4172/2155-9821.1000171]
 # Tsuda2015 pmid=26632508
 # Zhai2016 pmid=27088557
 # Barbirz2008 pmid=18547389
 # Tanaka2019 pmid=30926603
 # Armstrong2020 pmid=31871050
 # Chen2024 pmid=38795894
 # Santos2020 pmid=32451508
 # Sato2017 pmid=28546425
 # Kashima2021 pmid=34688653
 # McGuire2020 pmid=33127644
 # Shuoker2023 pmid=37005422

@@ Line 707: / Line 707: @@
 | beta-{{Smallcaps|d}}
 | retaining
-| '''''anti'''''
+| '' predicted perpendicular by clan, see at GH116''
 | [{{PDBlink}}4c1p 4c1p]
 | β-xylosidase
@@ Line 1,295: / Line 1,295: @@
 | beta-{{Smallcaps|d}}
 | retaining
-| ''predicted anti by clan''
+| '''''perpendicular''''' (anomaly)
-| ''see at GH52''
+| [{{PDBlink}}8i5u 8i5u]
+| β-glucosidase
+| ''Thermoanaerobacterium xylanolyticum'' LX-11
+| laminaribiose
+| '''Asp593'''
+| Glu441
+| <cite>Pengthaisong2023</cite>
 |-
 | [[GH117]]
@@ Line 1,867: / Line 1,867: @@
 # Gregg2015 pmid=26304114
 # Williams2014 pmid=24339341
 # Hehemann_2_2012 pmid=22393053
 # Huang2012 pmid=22992047
 # Noach2016 pmid=27038508

@@ Line 1,191: / Line 1,191: @@
 | Glu414
 | <cite>Xie2016</cite>
 |-
 | [[GH101]]
@@ Line 1,205: / Line 1,204: @@
 | '''Glu796''' +water
 | Asp764
 | <cite>Gregg2015</cite>
 |-
 | [[GH102]]
 | none
@@ Line 1,489: / Line 1,485: @@
+|
+|
 |-
 | [[GH146]]
@@ Line 1,497: / Line 1,507: @@
 | '''''anti'''''
 | [{{PDBlink}}5opj 5opj]
-| β-{{Smallcaps|l}}-arabinofuranosidase BT_0349
+| β-{{Smallcaps|l}}-arabinofuranosidase
 | ''Bacteroides thetaiotaomicron''
 | {{Smallcaps|l}}-arabinose
@@ Line 1,696: / Line 1,706: @@
+|
+|
+|
 |-
@@ Line 1,848: / Line 1,857: @@
 # Ndeh2017 pmid=28329766
 # Labourel2019 pmid=30877196
 # Luis2018 pmid=29255254
 # Bule2019 pmid=31645552
@@ Line 1,855: / Line 1,865: @@
 # Thompson2012 pmid=22219371
 # Xie2016 pmid=27777307
 # Gregg2015 pmid=26304114
 # Williams2014 pmid=24339341
 # Hehemann_2_2012 pmid=22393053

@@ Line 475: / Line 475: @@
 | sialyllactose
 | '''Asp59'''
-| Tyr342
+| Tyr342 (with Glu230)
 | <cite>Amaya2004</cite>
 |-
@@ Line 489: / Line 489: @@
 | α-{{Smallcaps|d}}-Neup5Ac-(2,3)-β-{{Smallcaps|d}}-Galp-(1,4)-β-{{Smallcaps|d}}-GlcpNAc
 | '''Asp151'''
-| Tyr406
+| Tyr406 (with Glu277)
 | <cite>Zhu2012</cite>
 |-
@@ Line 1,020: / Line 1,020: @@
 | Simian virus 5
 | α-2,3-sialyllactose
-| '''Glu247''' relay
+| '''Asp187''' on flexible loop
-| Tyr523
+| Tyr523 (with Glu390)
 | <cite>Yuan2005</cite>
 |-