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Syn/anti lateral protonation

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Contents

Overview

This page provides 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 [1], and the more recent summary by Nerinckx et al. [2].

Table of syn/anti protonation examples

Note

This table contains only one example per GH-family of a ligand-complexed protein structure where the syn positioning (close to the ring-oxygen of the sugar moiety at subsite -1) or anti positioning (at the opposite side of the ring-oxygen, close to C-2) 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 with the subsite -1 correctly occupied.

Please also be aware that this is a large table with many data, so some (hopefully few) errors may have sneaked in. 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 page 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 retaining anti 2cer β-glycosidase S Sulfolobus solfataricus P2 phenethyl glucoimidazol Glu206 Glu387 [3]
GH2 A (β/α)8 beta retaining anti 2vzu exo-β-glucosaminidase Amicolatopsis orientalis PNP-β-d-glucosamine Glu469 Glu541 [4]
GH3 none (β/α)8 beta retaining anti 1iex exo-1,3-1,4-glucanase Hordeum vulgare thiocellobiose Glu491 Asp285 [5]
GH5 A (β/α)8 beta retaining anti 1h2j endo-β-1,4-glucanase Bacillus agaradhaerens 2',4'-DNP-2-F-cellobioside Glu129 Glu228 [6]
GH6 none (β/α)8 beta inverting syn 1qjw cellobiohydrolase 2 Hypocrea jecorina (Glc)2-S-(Glc)2 Asp221 debated [7]
GH7 B β-jelly roll beta retaining syn 1ovw endo-1,4-glucanase Fusarium oxysporum thio-(Glc)5 Glu202 Glu197 [8]
GH8 M (α/α)6 beta inverting anti 1kwf endo-1,4-glucanase Clostridium thermocellum cellopentaose Glu95 Asp278 [9]
GH9 none (α/α)6 beta inverting syn 1rq5 cellobiohydrolase Clostridium thermocellum cellotetraose Glu795 Asp383 [10]
GH10 A (β/α)8 beta retaining anti 2d24 β-1,4-xylanase Streptomyces olivaceoviridis E-86 xylopentaose Glu128 Glu236 [11]
GH11 C β-jelly roll beta retaining syn 1bvv xylanase Bacillus circulans Xyl-2-F-xylosyl Glu172 Glu78 [12]
GH12 C β-jelly roll beta retaining syn 1w2u endoglucanase Humicola grisea thiocellotetraose Glu205 Glu120 [13]
GH13 H (β/α)8 alpha retaining anti 1cxk β-cyclodextrin glucanotransferase Bacillus circulans maltononaose Glu257 Asp229 [14]
GH14 none (β/α)8 alpha inverting syn 1itc β-amylase Bacillus cereus maltopentaose Glu172 Glu367 [15]
GH15 L (α/α)6 alpha inverting syn 1gah glucoamylase Aspergillus awamori acarbose Glu179 Glu400 [16]
GH16 B β-jelly roll beta retaining syn 1urx β-agarase A Zobellia galactanivorans oligoagarose Glu152 Glu147 [17]
GH17 A (β/α)8 beta retaining predicted anti by clan see e.g. at GH1
GH18 K (β/α)8 beta retaining anti 1ffr chitinase A Serratia marcescens (NAG)6 Glu315 internal [18]
GH20 K (β/α)8 beta retaining anti 1c7s chitobiase Serratia marcescens chitobiose Glu540 internal [19]
GH22 none lysozyme type beta retaining syn 1h6m lysozyme C Gallus gallus Chit-2-F-chitosyl Glu35 Asp52 [20]
GH23 none lysozyme type beta inverting syn 1lsp lysozyme G Cygnus atratus Bulgecin A Glu73 internal [21]
GH24 I α + β beta inverting syn 148l lysozyme E Bacteriophage T4 chitobiosyl Glu11 Glu26 [22]
GH26 A (β/α)8 beta retaining anti 1gw1 mannanase A Cellvibrio japonicus 2',4'-DNP-2-F-cellotrioside Glu212 Glu320 [23]
GH27 D (β/α)8 alpha retaining anti 1ktc α-N-acetyl galactosaminidase Gallus gallus NAGal Asp201 Asp410 [24]
GH28 N β-helix alpha inverting anti 2uvf exo-polygalacturonosidase Yersinia enterocolitica ATCC9610D digalacturonic acid Asp402 Asp381 Asp403 [25]
GH29 none (β/α)8 alpha retaining syn 1hl9 α-l-fucosidase Thermotoga maritima 2-F-fuco- pyranosyl Glu266 Asp224 [26]
GH30 A (β/α)8 beta retaining anti 2v3d glucocerebrosidase 1 Homo sapiens N-butyl-deoxynojirimycin Glu235 Glu340 [27]
GH31 D (β/α)8 alpha retaining anti 2qmj maltase-glucoamylase Homo sapiens acarbose Asp542 Asp443 [28]
GH32 J 5-fold β-propeller beta retaining anti 2add fructan β-(2,1)-fructosidase Cichorium intybus sucrose Glu201 Asp22 [29]
GH33 E 6-fold β-propeller alpha retaining anti 1s0i trans-sialidase Trypanosoma cruzi sialyl-lactose Asp59 Tyr342 [30]
GH34 E 6-fold β-propeller alpha retaining anti 2bat neuraminidase Influenza A virus sialic acid Asp151 Tyr406 [31]
GH35 A (β/α)8 beta retaining anti 1xc6 β-galactosidase Penicillium sp. d-galactose Glu200 Glu299 [32]
GH37 G (α/α)6 alpha inverting anti 2jf4 trehalase Escherechia coli validoxylamine Asp312 Glu496 [33]
GH38 none (β/α)7 alpha retaining anti 1qwn α-mannosidase II Drosophila melanogaster 5-F-β-l-gulosyl Asp341 Asp204 [34]
GH39 A (β/α)8 beta retaining anti 1uhv β-xylosidase Thermoanaerobacterium saccharolyticum 2-F-xylosyl Glu160 Glu277 [35]
GH42 A (β/α)8 beta retaining anti 1kwk β-galactosidase Thermus thermophylus A4 d-galactose Glu141 Glu312 [36]
GH44 none (β/α)8 beta retaining anti 2eqd endoglucanase Clostridium thermocellum cellooctaose Glu186 Glu359 [37]
GH45 none 6-strand. β-barrel beta inverting syn 4eng endo-1,4-glucanase Humicola insolens cellohexaose Asp121 Asp10 [38]
GH46 I α + β beta inverting predicted syn by clan see at GH24
GH47 none (α/α)7 alpha inverting anti 1x9d α-mannosidase I Homo sapiens Me-2-S-(α-Man)-2-thio-α-Man Asp463 Glu599 [39], [40]
GH48 M (α/α)6 beta inverting predicted anti by clan see at GH8
GH49 N β-helix alpha inverting predicted anti by clan see at GH28
GH50 A (β/α)8 beta retaining predicted anti by clan see e.g. at GH1
GH51 A (β/α)8 alpha retaining anti 1qw9 α-l-arabino- furanosidase Geobacillus stearothermophilus PNP-l-arabino-furanoside Glu175 Glu294 [41]
GH53 A (β/α)8 beta retaining predicted anti by clan see e.g. at GH1
GH54 none β-sandwich alpha retaining anti 1wd4 α-l-arabino- furanosidase B Aspergillus kawachii l-arabinofuranose Asp297 Glu221 [42]
GH55 none β-helix beta inverting anti 3eqo β-1,3-glucanase Phanerochaete chrysosporium K-3 d-gluconolacton Glu633 unknown [43]
GH56 none (β/α)7 beta retaining anti 1fcv hyaluronidase Apis mellifera (hyaluron.)4 Glu113 internal [44]
GH57 none (β/α)7 alpha retaining anti 1kly glucanotransferase Thermococcus litoralis acarbose Asp214 Glu123 [45]
GH59 A (β/α)8 beta retaining predicted anti by clan see e.g. at GH1
GH63 G (α/α)6 alpha inverting predicted anti by clan see at GH37
GH65 L (α/α)6 alpha inverting predicted syn by clan see at GH15
GH67 none (β/α)8 alpha inverting syn 1gql α-glucuronidase Cellvibrio japonicus Ueda107 d-glucuronic acid Glu292 unknown [46]
GH68 J 5-fold β-propeller beta retaining anti 1pt2 levansucrase Bacillus subtilis sucrose Glu342 Asp86 [47]
GH70 H (β/α)8 alpha retaining predicted anti by clan see e.g. at GH13
GH72 A (β/α)8 beta retaining anti 2w62 β-1,3-glucano- transferase Saccharomyces cerevisiae S288C laminaripentaose Glu176 Glu275 [48]
GH74 none 7-fold β-propeller beta inverting syn 2ebs cellobiohydrolase (OXG-RCBH) Geotrichum sp. m128 xyloglucan heptasaccharide Asp465 Asp35 [49]
GH77 H (β/α)8 alpha retaining anti 1esw amylomaltase Thermus aquaticus acarbose Asp395 Asp293 [50]
GH79 A (β/α)8 beta retaining predicted anti by clan see e.g. at GH1
GH80 I α + β beta inverting predicted syn by clan see at GH24
GH83 E 6-fold β-propeller alpha retaining predicted anti by clan see e.g. at GH33
GH84 none (β/α)8 beta retaining anti 2chn β-N-acetyl- glucosaminidase Bacteroides thetaiota- omicron VPI-5482 NAG-thiazoline Glu242 internal [51]
GH85 K (β/α)8 beta retaining anti 2w92 endo-β-N-acetyl- glucosaminidase D Streptococcus pneumoniae TIGR4 NAG-thiazoline Glu337 internal [52]
GH86 A (β/α)8 beta retaining predicted anti by clan see e.g. at GH1
GH89 none (β/α)8 alpha retaining anti 2vcb α-N-acetyl- glucosaminidase Clostridium perfringens PUGNAc Glu483 Glu601 [53]
GH92 none (α/α)6 + β-sandw. alpha inverting anti 2ww1 α-1,2-mannosidase Bacteroides thetaiota- omicron VPI-5482 thiomannobioside Glu533 Asp644 Asp642 [54]
GH93 E 6-fold β-propeller alpha retaining predicted anti by clan see e.g. at GH33
GH94 none (α/α)6 beta inverting syn 1v7x chitobiose phosphorylase Vibrio proteolyticus GlcNAc Asp492 phosphate [55]
GH95 none (α/α)6 alpha inverting anti 2ead α-1,2-l-fucosidase Bifidobacterium bifidum Fuc-α-1,2-Gal Glu566 Asn423 Asp766 [56]
GH97 none (β/α)8 alpha retaining + inverting anti 2zq0 α-glucosidase Bacteroides thetaiota- omicron VPI-5482 acarbose Glu532 Glu508 [57]
GH102 none double-ψ β-barrel beta retaining syn 2pi8 lytic transglycosylase A Escherechia coli chitohexaose Asp308 none [58]
GH113 A (β/α)8 beta retaining predicted anti by clan see e.g. at GH1

References

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All Medline abstracts: PubMed HubMed
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