New insights into the mechanism of nucleoside hydrolases from the crystal structure of the Escherichia coli YbeK protein bound to the reaction product.

TitleNew insights into the mechanism of nucleoside hydrolases from the crystal structure of the Escherichia coli YbeK protein bound to the reaction product.
Publication TypeJournal Article
Year of Publication2006
AuthorsMuzzolini, L., W. Versées, P. Tornaghi, E. Van Holsbeke, J. Steyaert, and M. Degano
JournalBiochemistry
Volume45
Issue3
Pagination773-82
Date Published2006 Jan 24
ISSN0006-2960
KeywordsCrystallography, X-Ray, Escherichia coli, Escherichia coli Proteins, Models, Molecular, N-Glycosyl Hydrolases, Protein Structure, Tertiary, Ribose
Abstract

Nucleoside hydrolases (NHs) are enzymes that catalyze the excision of the N-glycosidic bond in nucleosides to allow recycling of the nitrogenous bases. The fine details of the catalytic mechanism and the structural features imposing the substrate specificity of the various members of the NH family are still debated. Here we present the functional characterization of the Escherichia coli YbeK (RihA) protein as a pyrimidine nucleoside-preferring NH and its first crystal structure to 1.8 A resolution. The enzyme active site is occupied by either the alpha or beta anomer of ribose and provides the first structural description of the binding of the NH reaction product. While the amino acid residues involved in ribosyl binding are strictly conserved in pyrimidine-specific NHs, the residues involved in specific interactions with the nitrogenous bases differ considerably. Further comparison of the active site architecture of YbeK with the related NHs establishes structural determinants involved in triggering the conformational transition between the open and closed structures and suggests a mechanism for product release.

DOI10.1021/bi0511991
Alternate JournalBiochemistry
PubMed ID16411753