Syn/anti lateral protonation

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

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

Table

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Family	Clan	Structure fold	Anomeric specificity	Mechanism	General acid	syn/anti	Nucleophile or General base	Ligand	Organism	Enzyme	PDB ID	Primary reference
GH1	A	(β/α)8	beta	retaining	Glu160	anti	Glu375	product	Lactococcus lactis	6-phospho-beta-galactosidase	4pbg	[3]
GH2	A	(β/α)8	beta	retaining	Glu461	anti	Glu537	2-F-galactosyl	Escherechia coli	beta-galactosidase	1jz0	[4]
GH3	none	(β/α)8	beta	retaining	Glu491	anti	Asp285	2-F-glucosyl	Hordeum vulgare	exo-1,3-1,4-glucanase	1iew	[5]
GH5	A	(β/α)8	beta	retaining	Glu129	anti	Glu228	2-F-glucosyl	Bacillus agaradhaerans	endo-1,4-glucanase	1h2j	[6]
GH6	none	(β/α)8	beta	inverting	Asp226	syn	debated	Glc-isofagomine	Humicola insolens	cellobiohydrolase	1ocn	[7]
GH7	B	β-jelly roll	beta	retaining	Glu202	syn	Glu197	thio-Glc5	Fusarium oxysporum	endo-1,4-glucanase	1ovw	[8]
GH8	M	(α/α)6	beta	inverting	Glu95	anti	Asp278	Michaelis	Clostridium thermocellum	endo-1,4-glucanase	1kwf	[9]
GH9	none	(α/α)6	beta	inverting	Glu424	syn	Asp55,Asp58	product	Thermomonospora fusca	cellulase	3tf4,4tf4	[10]
GH10	A	(β/α)8	beta	retaining	Glu127	anti	Glu233	Xyl-2-F-xylosyl	Cellulomonas fimi	xylanase	2xyl	[11]
GH11	C	β-jelly roll	beta	retaining	Glu172	syn	Glu78	Xyl-2-F-xylosyl	Bacillus circulans	xylanase	1bvv	[12]
GH12	C	β-jelly roll	beta	retaining	Glu203	syn	Glu120	Glc2-2-F-glucosyl	Streptomyces lividans	endo-1,4-glucanase	2nlr	[13]
GH13	H	(β/α)8	alpha	retaining	Glu257	anti	Asp229	Michaelis	Bacillus circulans	beta-cyclodextrin glucanotransferase	1ckx	[14]
GH14	none	(β/α)8	alpha	inverting	Glu172	syn	Glu367	product	Bacillus cereus	beta-amylase	1b9z	[15]

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.