Understanding the Structural Basis for Substrate and Inhibitor Recognition in Eukaryotic GH11 Xylanases

Vardakou, M; Dumon, C; Murray, JW; Christakopoulos, P; Weiner, DP; Juge, N; Lewis, RJ; Gilbert, HJ; Flint, JE

dc.contributor.author	Vardakou, M	en
dc.contributor.author	Dumon, C	en
dc.contributor.author	Murray, JW	en
dc.contributor.author	Christakopoulos, P	en
dc.contributor.author	Weiner, DP	en
dc.contributor.author	Juge, N	en
dc.contributor.author	Lewis, RJ	en
dc.contributor.author	Gilbert, HJ	en
dc.contributor.author	Flint, JE	en
dc.date.accessioned	2014-03-01T01:29:26Z
dc.date.available	2014-03-01T01:29:26Z
dc.date.issued	2008	en
dc.identifier.issn	0022-2836	en
dc.identifier.uri	https://dspace.lib.ntua.gr/xmlui/handle/123456789/19262
dc.subject	decoration	en
dc.subject	ferulic acid	en
dc.subject	glycoside hydrolase	en
dc.subject	structure	en
dc.subject	xylanase	en
dc.subject.classification	Biochemistry & Molecular Biology	en
dc.subject.other	4 methyl dextro glucuronic acid	en
dc.subject.other	enzyme gh11	en
dc.subject.other	ferulic acid	en
dc.subject.other	ferulic acid 1,5 arabinofuranose alpha1,3 xylotriose	en
dc.subject.other	furan	en
dc.subject.other	glucuronic acid	en
dc.subject.other	levo arabinofuranose	en
dc.subject.other	protein xip 1	en
dc.subject.other	unclassified drug	en
dc.subject.other	vegetable protein	en
dc.subject.other	xylan endo 1,3 beta xylosidase	en
dc.subject.other	article	en
dc.subject.other	catalysis	en
dc.subject.other	controlled study	en
dc.subject.other	crystal structure	en
dc.subject.other	eukaryote	en
dc.subject.other	gene expression	en
dc.subject.other	molecular cloning	en
dc.subject.other	Neocallimastix	en
dc.subject.other	nonhuman	en
dc.subject.other	priority journal	en
dc.subject.other	Apoenzymes	en
dc.subject.other	Avena sativa	en
dc.subject.other	Binding Sites	en
dc.subject.other	Carrier Proteins	en
dc.subject.other	Catalysis	en
dc.subject.other	Comprehension	en
dc.subject.other	Crystallography, X-Ray	en
dc.subject.other	Endo-1,4-beta Xylanases	en
dc.subject.other	Enzyme Inhibitors	en
dc.subject.other	Eukaryotic Cells	en
dc.subject.other	Fungal Proteins	en
dc.subject.other	Glycoside Hydrolases	en
dc.subject.other	Hydrogen Bonding	en
dc.subject.other	Hydrogen-Ion Concentration	en
dc.subject.other	Hydrolysis	en
dc.subject.other	Kinetics	en
dc.subject.other	Models, Chemical	en
dc.subject.other	Models, Molecular	en
dc.subject.other	Mutation	en
dc.subject.other	Neocallimastix	en
dc.subject.other	Penicillium	en
dc.subject.other	Plant Proteins	en
dc.subject.other	Protein Binding	en
dc.subject.other	Protein Conformation	en
dc.subject.other	Protein Folding	en
dc.subject.other	Protein Structure, Secondary	en
dc.subject.other	Structure-Activity Relationship	en
dc.subject.other	Substrate Specificity	en
dc.subject.other	Triticum	en
dc.subject.other	X-Ray Diffraction	en
dc.subject.other	Eukaryota	en
dc.subject.other	Neocallimastix	en
dc.subject.other	Neocallimastix patriciarum	en
dc.subject.other	Triticum aestivum	en
dc.title	Understanding the Structural Basis for Substrate and Inhibitor Recognition in Eukaryotic GH11 Xylanases	en
heal.type	journalArticle	en
heal.identifier.primary	10.1016/j.jmb.2007.11.007	en
heal.identifier.secondary	http://dx.doi.org/10.1016/j.jmb.2007.11.007	en
heal.language	English	en
heal.publicationDate	2008	en
heal.abstract	Endo-beta 1,4-xylanases (xylanases) hydrolyse the beta 1,4 glycosidic bonds in the backbone of xylan. Although xylanases from glycoside hydrolase family 11 (GH11) have been extensively studied, several issues remain unresolved. Thus, the mechanism by which these enzymes hydrolyse decorated xylans is unclear and the structural basis for the variation in catalytic activity within this family is unknown. Furthermore, the mechanism for the differences in the inhibition of fungal GH11 enzymes by the wheat protein XIP-I remains opaque. To address these issues we report the crystal structure and biochemical properties of the Neocallimastix patriciarum xylanase NpXyn11A, which displays unusually high catalytic activity and is one of the few fungal GH11 proteins not inhibited by XIP-I. Although the structure of NpXyn11A could not be determined in complex with substrates, we have been able to investigate how GH11 enzymes hydrolyse decorated substrates by solving the crystal structure of a second GH11 xylanase, EnXyn11A (encoded by an environmental DNA sample), bound to ferulic acid-1,5-arabinofuranose-alpha 1,3-xylotriose (FAX(3)). The crystal structure of the EnXyn11A-FAX(3) complex shows that solvent exposure of the backbone xylose O2 and O3 groups at subsites -3 and +2 allow accommodation of alpha 1,2-linked 4-methyl-D-glucuronic acid and L-arabinofuranose side chains. Furthermore, the ferulated arabinofuranose side chain makes hydrogen bonds and hydrophobic interactions at the +2 subsite, indicating that the decoration may represent a specificity determinant at this aglycone subsite. The structure of NpXyn11A reveals potential -3 and +3 subsites that are kinetically significant. The extended substrate-binding cleft of NpXyn11A, compared to other GH11 xylanases, may explain why the Neocallimastix enzyme displays unusually high catalytic activity. Finally, the crystal structure of NpXyn11A shows that the resistance of the enzyme to XIP-1 is not due solely to insertions in the loop connecting beta strands 11 and 12, as suggested previously, but is highly complex. (C) 2007 Published by Elsevier Ltd.	en
heal.publisher	ACADEMIC PRESS LTD ELSEVIER SCIENCE LTD	en
heal.journalName	Journal of Molecular Biology	en
dc.identifier.doi	10.1016/j.jmb.2007.11.007	en
dc.identifier.isi	ISI:000253098100011	en
dc.identifier.volume	375	en
dc.identifier.issue	5	en
dc.identifier.spage	1293	en
dc.identifier.epage	1305	en