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	Example PDB ID	General acid	syn/anti	Nucleophile or General base	Ligand	Organism	Enzyme	Primary reference
GH1	A	(β/α)8	beta	retaining	4pbg	Glu160	anti	Glu375	product	Lactococcus lactis	6-phospho-beta-galactosidase	[3]
GH2	A	(β/α)8	beta	retaining	1jz0	Glu461	anti	Glu537	2-F-galactosyl	Escherechia coli	beta-galactosidase	[4]
GH3	none	(β/α)8	beta	retaining	1iew	Glu491	anti	Asp285	2-F-glucosyl	Hordeum vulgare	exo-1,3-1,4-glucanase	[5]
GH5	A	(β/α)8	beta	retaining	1h2j	Glu129	anti	Glu228	2-F-glucosyl	Bacillus agaradhaerans	endo-1,4-glucanase	[6]
GH6	none	(β/α)8	beta	inverting	1ocn	Asp226	syn	debated	Glc-isofagomine	Humicola insolens	cellobiohydrolase	[7]
GH7	B	β-jelly roll	beta	retaining	1ovw	Glu202	syn	Glu197	thio-Glc5	Fusarium oxysporum	endo-1,4-glucanase	[8]
GH8	M	(α/α)6	beta	inverting	1kwf	Glu95	anti	Asp278	Michaelis	Clostridium thermocellum	endo-1,4-glucanase	[9]
GH9	none	(α/α)6	beta	inverting	3tf4,4tf4	Glu424	syn	Asp55,Asp58	product	Thermomonospora fusca	cellulase	[10]
GH10	A	(β/α)8	beta	retaining	2xyl	Glu127	anti	Glu233	Xyl-2-F-xylosyl	Cellulomonas fimi	xylanase B (Cex)	[11]
GH11	C	β-jelly roll	beta	retaining	1bvv	Glu172	syn	Glu78	Xyl-2-F-xylosyl	Bacillus circulans	xylanase	[12]
GH12	C	β-jelly roll	beta	retaining	2nlr	Glu203	syn	Glu120	Glc2-2-F-glucosyl	Streptomyces lividans	endo-1,4-glucanase	[13]
GH13	H	(β/α)8	alpha	retaining	1ckx	Glu257	anti	Asp229	Michaelis	Bacillus circulans	beta-cyclodextrin glucanotransferase	[14]
GH14	none	(β/α)8	alpha	inverting	1b9z	Glu172	syn	Glu367	product	Bacillus cereus	beta-amylase	[15]
GH15	L	(α/α)6	alpha	inverting	1gah	Glu179	syn	Glu400	acarbose	Aspergillus awamori	glucoamylase	[16]
GH16	B	β-jelly roll	beta	retaining	1urx	Glu152	syn	Glu147	product	Zobellia galactanivorans	beta-agarase A	[17]

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.