A nucleophile activation dyad in ribonucleases. A combined X-ray crystallographic/ab initio quantum chemical study.

TitleA nucleophile activation dyad in ribonucleases. A combined X-ray crystallographic/ab initio quantum chemical study.
Publication TypeJournal Article
Year of Publication2002
AuthorsMignon, P., J. Steyaert, R. Loris, P. Geerlings, and S. Loverix
JournalJ Biol Chem
Volume277
Issue39
Pagination36770-4
Date Published2002 Sep 27
ISSN0021-9258
KeywordsBinding Sites, Crystallography, X-Ray, Hydrogen Bonding, Hydrogen-Ion Concentration, Kinetics, Models, Chemical, Models, Molecular, Oxygen, Protein Binding, Ribonuclease T1, Ribonuclease, Pancreatic, Ribonucleases, Substrate Specificity
Abstract

Ribonucleases (RNases) catalyze the cleavage of the phosphodiester bond in RNA up to 10(15)-fold, as compared with the uncatalyzed reaction. High resolution crystal structures of these enzymes in complex with 3'-mononucleotide substrates demonstrate the accommodation of the nucleophilic 2'-OH group in a binding pocket comprising the catalytic base (glutamate or histidine) and a charged hydrogen bond donor (lysine or histidine). Ab initio quantum chemical calculations performed on such Michaelis complexes of the mammalian RNase A (EC ) and the microbial RNase T(1) (EC ) show negative charge build up on the 2'-oxygen upon substrate binding. The increased nucleophilicity results from stronger hydrogen bonding to the catalytic base, which is mediated by a hydrogen bond from the charged donor. This hitherto unrecognized catalytic dyad in ribonucleases constitutes a general mechanism for nucleophile activation in both enzymic and RNA-catalyzed phosphoryl transfer reactions.

DOI10.1074/jbc.M206461200
Alternate JournalJ. Biol. Chem.
PubMed ID12122018