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Syn/anti lateral protonation

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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]
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 [11]
GH6 none (β/α)8 beta-d inverting syn 1qjw cellobiohydrolase 2 Hypocrea jecorina (Glc)2-S-(Glc)2 Asp221 debated [12]
GH7 B β-jelly roll beta-d retaining syn 1ovw endo-1,4-glucanase Fusarium oxysporum thio-(Glc)5 Glu202 Glu197 [13]
GH8 M (α/α)6 beta-d inverting anti 1kwf endo-1,4-glucanase Clostridium thermocellum cellopentaose Glu95 Asp278 [14]
GH9 none (α/α)6 beta-d inverting syn 1rq5 cellobiohydrolase Clostridium thermocellum cellotetraose Glu795 Asp383 [15]
GH10 A (β/α)8 beta-d retaining anti 2d24 β-1,4-xylanase Streptomyces olivaceoviridis E-86 xylopentaose Glu128 Glu236 [16]
GH11 C β-jelly roll beta-d retaining syn 4hk8 endo-β-1,4-xylanase Hypocrea jecorina xylohexaose Glu177 Glu86 [17]
GH12 C β-jelly roll beta-d retaining syn 1w2u endoglucanase Humicola grisea thiocellotetraose Glu205 Glu120 [18]
GH13 H (β/α)8 alpha-d retaining anti 1cxk β-cyclodextrin glucanotransferase Bacillus circulans maltononaose Glu257 Asp229 [19]
GH14 none (β/α)8 alpha-d inverting syn 1itc β-amylase Bacillus cereus maltopentaose Glu172 Glu367 [20]
GH15 L (α/α)6 alpha-d inverting anti 1dog glucoamylase Aspergillus awamori 1-deoxynojirimycin Glu179 Glu400 [21]
GH16 B β-jelly roll beta-d retaining syn 1urx β-agarase A Zobellia galactanivorans oligoagarose Glu152 Glu147 [22]
GH17 A (β/α)8 beta-d retaining predicted anti by clan see e.g. at GH1
GH18 K (β/α)8 beta-d retaining anti 1ffr chitinase A Serratia marcescens (NAG)6 Glu315 internal [23]
GH19 none lysozyme type beta-d inverting syn 3wh1 chitinase Bryum coronatum (GlcNAc)4 Glu61 Glu70 [24]
GH20 K (β/α)8 beta-d retaining anti 1c7s chitobiase Serratia marcescens chitobiose Glu540 internal [25]
GH22 none lysozyme type beta-d retaining syn 1h6m lysozyme C Gallus gallus Chit-2-F-chitosyl Glu35 Asp52 [26]
GH23 none lysozyme type beta-d inverting syn 1lsp lysozyme G Cygnus atratus Bulgecin A Glu73 internal [27]
GH24 I α + β beta-d inverting syn 148l lysozyme E Bacteriophage T4 chitobiosyl Glu11 Glu26 [28]
GH26 A (β/α)8 beta-d retaining anti 2vx6 exo-β-mannanase Cellvibrio japonicus Ueda107 Gal1Man4 Glu221 Glu338 [29]
GH27 D (β/α)8 alpha-d / beta-l retaining anti 3lrm α-galactosidase Saccharomyces cerevisiae raffinose Asp209 Asp141 [30]
GH28 N β-helix alpha-d (and α-l-rham) inverting anti 2uvf exo-polygalacturonosidase Yersinia enterocolitica ATCC9610D digalacturonic acid Asp402 Asp381 Asp403 [31]
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 [32]
GH30 A (β/α)8 beta-d retaining anti 2y24 glucurono-xylanase Dickea chrysanthemi D1 glucuronoxylan tetrasaccharide Glu163 Glu253 [33]
GH31 D (β/α)8 alpha-d retaining anti 2qmj maltase-glucoamylase Homo sapiens acarbose Asp542 Asp443 [34]
GH32 J 5-fold β-propeller beta-d retaining anti 2add fructan β-(2,1)-fructosidase Cichorium intybus sucrose Glu201 Asp22 [35]
GH33 E 6-fold β-propeller alpha-d retaining anti 1s0i transsialidase Trypanosoma cruzi sialyllactose Asp59 Tyr342 [36]
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 [37]
GH35 A (β/α)8 beta-d retaining anti 3ogv β-galactosidase Hypocrea jecorina 2-phenylethyl 1-thio-β-d-galactopyranoside Glu200 Glu298 [38]
GH36 D (β/α)8 alpha-d retaining anti 4fns β-galactosidase Geobacillus stearothermophilus 1-deoxy galactonojirimycin Asp584 Asp478 [39]
GH37 G (α/α)6 alpha-d inverting anti 2jf4 trehalase Escherichia coli validoxylamine Asp312 Glu496 [40]
GH38 none (β/α)7 alpha-d retaining anti 3czn Golgi α-mannosidase II Drosophila melanogaster GlcNAcMan(5)GlcNAc(2) Asp341 Asp204 [41]
GH39 A (β/α)8 beta-d / alpha-l retaining anti 2bfg β-xylosidase Geobacillus stearothermophilus 2,5-dinitrophenyl-β-d-xyloside Glu160 Glu278 [42]
GH42 A (β/α)8 beta-d / alpha-l retaining anti 4ucf β-galactosidase Bifidobacterium bifidum d-galactose Glu161 Glu320 [43]
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 [44]
GH44 none (β/α)8 beta-d retaining anti 2eqd endoglucanase Clostridium thermocellum cellooctaose Glu186 Glu359 [45]
GH45 none 6-stranded β-barrel beta-d inverting syn 4eng endo-1,4-glucanase Humicola insolens cellohexaose Asp121 Asp10 [46]
GH46 I lysozyme type beta-d inverting syn 4olt chitosanase Microbacterium sp. OU01 hexa-glucosamine Glu25 Asp43 [47]
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 [48], [49]
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 [50]
GH51 A (β/α)8 beta-d / alpha-l retaining anti 1qw9 α-l-arabinofuranosidase Geobacillus stearothermophilus PNP-l-arabinofuranoside Glu175 Glu294 [51]
GH52 O (α/α)6 beta-d retaining anti 4c1p β-xylosidase Geobacillus thermoglucosidasius xylobiose Asp517 Glu537 [52]
GH53 A (β/α)8 beta-d retaining anti 2ccr β-1,4-galactanase Bacillus licheniformis galactotriose Glu165 Glu263 [53]
GH54 none β-sandwich beta-d / alpha-l retaining anti 1wd4 α-l-arabinofuranosidase B Aspergillus kawachii l-arabinofuranose Asp297 Glu221 [54]
GH55 none β-helix beta-d inverting syn 4tz5 exo-β-1,3-glucanase Streptomyces sp. SirexAA-E laminarihexaose Glu502 unknown [55]
GH56 none (β/α)7 beta-d retaining anti 1fcv hyaluronidase Apis mellifera (hyaluron.)4 Glu113 internal [56]
GH57 none (β/α)7 alpha-d retaining anti 1k1y glucanotransferase Thermococcus litoralis acarbose Asp214 Glu123 [57]
GH59 A (β/α)8 beta-d retaining anti 4ccc β-galactocerebrosidase Mus musculus PNP-β-d-galactoside Glu182 Glu258 [58]
GH62 F 5-fold β-propeller alpha-l inverting predicted anti by clan see at GH43
GH63 G (α/α)6 alpha-d inverting anti 5ca3 α-glucosidase Escherichia coli glucose and lactose Asp501 Glu727 [59]
GH65 L (α/α)6 alpha-d (and α-l-rham) inverting anti 4ktr 2-O-α-glucosylglycerol phosphorylase Bacillus selenitireducens isofagomine Glu475 phosphate [60]
GH66 none (β/α)8 alpha-d retaining anti 5axh dextranase Thermoanaerobacter pseudethanolicus isomaltohexaose Glu374 Asp312 [61]
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 [62]
GH68 J 5-fold β-propeller beta-d retaining anti 1pt2 levansucrase Bacillus subtilis sucrose Glu342 Asp86 [63]
GH70 H (β/α)8 alpha-d retaining anti 3aic glucansucrase Streptococcus mutans α-acarbose Glu515 Asp477 [64]
GH72 A (β/α)8 beta-d retaining anti 2w62 β-1,3-glucanotransferase Saccharomyces cerevisiae S288C laminaripentaose Glu176 Glu275 [65]
GH74 none 7-fold β-propeller beta-d inverting syn 2ebs cellobiohydrolase (OXG-RCBH) Geotrichum sp. m128 xyloglucan heptasaccharide Asp465 Asp35 [66]
GH76 none (α/α)6 alpha-d retaining anti 5agd endo-α-1,6-mannanase Bacillus circulans α-1,6-mannopentaose Asp125 Asp124 [67]
GH77 H (β/α)8 alpha-d retaining anti 2oww 4-α-glucanotransferase Thermus thermofilus acarbose + 4-deoxy-α-d-glucose Glu340 Asp293 [68]
GH78 H (α/α)6 alpha-l inverting anti 3w5n α-l-rhamnosidase Streptomyces avermitilis l-rhamnose Glu636 Glu895 [69]
GH79 A (β/α)8 beta-d retaining anti 5e9c heparanase Homo sapiens heparin tetrasaccharide Glu225 Glu343 [70]
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 [71]
GH83 E 6-fold β-propeller alpha-d retaining predicted anti by clan see e.g. at GH33
GH84 none (β/α)8 beta-d retaining anti 2chn β-N-acetyl-glucosaminidase Bacteroides thetaiotaomicron VPI-5482 NAG-thiazoline Glu242 internal [72]
GH85 K (β/α)8 beta-d retaining anti 2w92 endo-β-N-acetyl-glucosaminidase D Streptococcus pneumoniae TIGR4 NAG-thiazoline Glu337 internal [73]
GH86 A (β/α)8 beta-d retaining anti 4aw7 β-porphyranase Bacteroides plebeius porphyran fragment Glu152 Glu279 [74]
GH89 none (β/α)8 alpha-d retaining anti 2vcb α-N-acetyl-glucosaminidase Clostridium perfringens PUGNAc Glu483 Glu601 [75]
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 [76]
GH93 E 6-fold β-propeller alpha-l retaining anti 3a72 exo-arabinanase Penicillium chrysogenum arabinobiose Glu246 Glu174 [77]
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 [78]
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 [79]
GH97 none (β/α)8 alpha-d retaining + inverting anti 2zq0 α-glucosidase Bacteroides thetaiotaomicron VPI-5482 acarbose Glu532 Glu508 [80]
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 [81]
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 [82]
GH100 none (α/α)6 core beta-d inverting anti 5gop invertase Anabaena (Nostoc) sp. pcc7120 sucrose Asp188 Glu414 [83]
GH102 none double-ψ β-barrel beta-d retaining syn 2pi8 lytic transglycosylase A Escherichia coli chitohexaose Asp308 none [84]
GH103 none lysozyme type beta-d retaining syn 1d0k lytic transglycosylase SLT35 Escherichia coli murodipeptides Glu162 internal [85]
GH106 none (β/α)8 alpha-l inverting anti 5mwk α-l-rhamnosidase BT_0986 Bacteroides thetaiotaomicron pectin heptasaccharide Glu461 Glu593 or Glu561 [86]
GH107 R (β/α)8 alpha-l retaining predicted syn by clan see at GH29
GH113 A (β/α)8 beta-d retaining anti 4cd8 β-mannanase Alicyclobacillus acidocaldarius mannobioimidazole Glu151 Glu231 [87]
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 Asp90 [88]
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 [89]
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 [90]
GH125 L (α/α)6 alpha-d inverting anti 5m7y exo-α-1,6-mannosidase Clostridium perfringens 1,6-α-mannotriose Asp220 Glu393 [91]
GH127 P (α/α)6 and β-sandwich beta-l retaining anti 3wrg β-l-arabinofuranosidase Bifidobacterium longum l-arabinose Glu322 Cys417 [92]
GH128 A (β/α)8 beta-d retaining predicted anti by clan see e.g. at GH1
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 [93]
GH134 none β + α beta-d inverting syn 5jug β-mannanase Streptomyces sp. mannopentaose Glu45 Asp57 [94]
GH136 none β-helix beta-d retaining syn 5gqf lacto-N-biosidase Bifidobacterium longum lacto-N-biose Asp411 Asp418 [95]
GH137 none 5-fold β-propeller beta-l unknown anti 5mui β-l-arabinofuranosidase BT_0996 Bacteroides thetaiotaomicron pectin oligosaccharide Glu240 Glu159 [86]
GH146 P (α/α)6 beta-l retaining predicted anti by clan see at GH127
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
n.c.* none parallel β-helix alpha-d inverting anti 2vjj endo-α-N-acetylglucosaminidase Bacteriophage HK620 O18A1 O-antigen hexasaccharide Asp339 Glu372 [96]

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

References

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