Syn/anti lateral protonation

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• Author: ^^^Wim Nerinckx^^^
• Responsible Curator: ^^^Spencer Williams^^^

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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 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 above the page title.

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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1. 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. Article online.

5. Hrmova M, Varghese JN, De Gori R, Smith BJ, Driguez H, and Fincher GB. (2001). Catalytic mechanisms and reaction intermediates along the hydrolytic pathway of a plant beta-D-glucan glucohydrolase. Structure. 2001;9(11):1005-16. DOI:10.1016/s0969-2126(01)00673-6 |
8. Sulzenbacher G, Mackenzie LF, Wilson KS, Withers SG, Dupont C, and Davies GJ. (1999). The crystal structure of a 2-fluorocellotriosyl complex of the Streptomyces lividans endoglucanase CelB2 at 1.2 A resolution. Biochemistry. 1999;38(15):4826-33. DOI:10.1021/bi982648i |
9. Guérin DM, Lascombe MB, Costabel M, Souchon H, Lamzin V, Béguin P, and Alzari PM. (2002). Atomic (0.94 A) resolution structure of an inverting glycosidase in complex with substrate. J Mol Biol. 2002;316(5):1061-9. DOI:10.1006/jmbi.2001.5404 |
13. Sandgren M, Berglund GI, Shaw A, Ståhlberg J, Kenne L, Desmet T, and Mitchinson C. (2004). Crystal complex structures reveal how substrate is bound in the -4 to the +2 binding sites of Humicola grisea Cel12A. J Mol Biol. 2004;342(5):1505-17. DOI:10.1016/j.jmb.2004.07.098 |
14. Uitdehaag JC, Mosi R, Kalk KH, van der Veen BA, Dijkhuizen L, Withers SG, and Dijkstra BW. (1999). X-ray structures along the reaction pathway of cyclodextrin glycosyltransferase elucidate catalysis in the alpha-amylase family. Nat Struct Biol. 1999;6(5):432-6. DOI:10.1038/8235 |
20. Vocadlo DJ, Davies GJ, Laine R, and Withers SG. (2001). Catalysis by hen egg-white lysozyme proceeds via a covalent intermediate. Nature. 2001;412(6849):835-8. DOI:10.1038/35090602 |
23. Ducros VM, Zechel DL, Murshudov GN, Gilbert HJ, Szabó L, Stoll D, Withers SG, and Davies GJ. (2002). Substrate distortion by a beta-mannanase: snapshots of the Michaelis and covalent-intermediate complexes suggest a B(2,5) conformation for the transition state. Angew Chem Int Ed Engl. 2002;41(15):2824-7. DOI:10.1002/1521-3773(20020802)41:15<2824::AID-ANIE2824>3.0.CO;2-G |
30. Amaya MF, Watts AG, Damager I, Wehenkel A, Nguyen T, Buschiazzo A, Paris G, Frasch AC, Withers SG, and Alzari PM. (2004). Structural insights into the catalytic mechanism of Trypanosoma cruzi trans-sialidase. Structure. 2004;12(5):775-84. DOI:10.1016/j.str.2004.02.036 |
31. Varghese JN, McKimm-Breschkin JL, Caldwell JB, Kortt AA, and Colman PM. (1992). The structure of the complex between influenza virus neuraminidase and sialic acid, the viral receptor. Proteins. 1992;14(3):327-32. DOI:10.1002/prot.340140302 |
32. Rojas AL, Nagem RA, Neustroev KN, Arand M, Adamska M, Eneyskaya EV, Kulminskaya AA, Garratt RC, Golubev AM, and Polikarpov I. (2004). Crystal structures of beta-galactosidase from Penicillium sp. and its complex with galactose. J Mol Biol. 2004;343(5):1281-92. DOI:10.1016/j.jmb.2004.09.012 |
33. Gibson RP, Gloster TM, Roberts S, Warren RA, Storch de Gracia I, García A, Chiara JL, and Davies GJ. (2007). Molecular basis for trehalase inhibition revealed by the structure of trehalase in complex with potent inhibitors. Angew Chem Int Ed Engl. 2007;46(22):4115-9. DOI:10.1002/anie.200604825 |
36. Hidaka M, Fushinobu S, Ohtsu N, Motoshima H, Matsuzawa H, Shoun H, and Wakagi T. (2002). Trimeric crystal structure of the glycoside hydrolase family 42 beta-galactosidase from Thermus thermophilus A4 and the structure of its complex with galactose. J Mol Biol. 2002;322(1):79-91. DOI:10.1016/s0022-2836(02)00746-5 |
39. Karaveg K, Siriwardena A, Tempel W, Liu ZJ, Glushka J, Wang BC, and Moremen KW. (2005). Mechanism of class 1 (glycosylhydrolase family 47) {alpha}-mannosidases involved in N-glycan processing and endoplasmic reticulum quality control. J Biol Chem. 2005;280(16):16197-207. DOI:10.1074/jbc.M500119200 |
40. Cantú D, Nerinckx W, and Reilly PJ. (2008). Theory and computation show that Asp463 is the catalytic proton donor in human endoplasmic reticulum alpha-(1-->2)-mannosidase I. Carbohydr Res. 2008;343(13):2235-42. DOI:10.1016/j.carres.2008.05.026 |
41. Hövel K, Shallom D, Niefind K, Belakhov V, Shoham G, Baasov T, Shoham Y, and Schomburg D. (2003). Crystal structure and snapshots along the reaction pathway of a family 51 alpha-L-arabinofuranosidase. EMBO J. 2003;22(19):4922-32. DOI:10.1093/emboj/cdg494 |
42. Miyanaga A, Koseki T, Matsuzawa H, Wakagi T, Shoun H, and Fushinobu S. (2004). Crystal structure of a family 54 alpha-L-arabinofuranosidase reveals a novel carbohydrate-binding module that can bind arabinose. J Biol Chem. 2004;279(43):44907-14. DOI:10.1074/jbc.M405390200 |
43. Ishida T, Fushinobu S, Kawai R, Kitaoka M, Igarashi K, and Samejima M. (2009). Crystal structure of glycoside hydrolase family 55 {beta}-1,3-glucanase from the basidiomycete Phanerochaete chrysosporium. J Biol Chem. 2009;284(15):10100-9. DOI:10.1074/jbc.M808122200 |
45. Imamura H, Fushinobu S, Yamamoto M, Kumasaka T, Jeon BS, Wakagi T, and Matsuzawa H. (2003). Crystal structures of 4-alpha-glucanotransferase from Thermococcus litoralis and its complex with an inhibitor. J Biol Chem. 2003;278(21):19378-86. DOI:10.1074/jbc.M213134200 |
47. Meng G and Fütterer K. (2003). Structural framework of fructosyl transfer in Bacillus subtilis levansucrase. Nat Struct Biol. 2003;10(11):935-41. DOI:10.1038/nsb974 |
50. Przylas I, Terada Y, Fujii K, Takaha T, Saenger W, and Sträter N. (2000). X-ray structure of acarbose bound to amylomaltase from Thermus aquaticus. Implications for the synthesis of large cyclic glucans. Eur J Biochem. 2000;267(23):6903-13. DOI:10.1046/j.1432-1033.2000.01790.x |
51. Dennis RJ, Taylor EJ, Macauley MS, Stubbs KA, Turkenburg JP, Hart SJ, Black GN, Vocadlo DJ, and Davies GJ. (2006). Structure and mechanism of a bacterial beta-glucosaminidase having O-GlcNAcase activity. Nat Struct Mol Biol. 2006;13(4):365-71. DOI:10.1038/nsmb1079 |

54. Zhu et al. (2010) Nature Chemical Biology in the press; DOI: 10.1038/nchembio.278 direct link.

55. Hidaka M, Honda Y, Kitaoka M, Nirasawa S, Hayashi K, Wakagi T, Shoun H, and Fushinobu S. (2004). Chitobiose phosphorylase from Vibrio proteolyticus, a member of glycosyl transferase family 36, has a clan GH-L-like (alpha/alpha)(6) barrel fold. Structure. 2004;12(6):937-47. DOI:10.1016/j.str.2004.03.027 |
56. Nagae M, Tsuchiya A, Katayama T, Yamamoto K, Wakatsuki S, and Kato R. (2007). Structural basis of the catalytic reaction mechanism of novel 1,2-alpha-L-fucosidase from Bifidobacterium bifidum. J Biol Chem. 2007;282(25):18497-18509. DOI:10.1074/jbc.M702246200 |
58. van Straaten KE, Barends TR, Dijkstra BW, and Thunnissen AM. (2007). Structure of Escherichia coli Lytic transglycosylase MltA with bound chitohexaose: implications for peptidoglycan binding and cleavage. J Biol Chem. 2007;282(29):21197-205. DOI:10.1074/jbc.M701818200 |