Title | A nucleophile activation dyad in ribonucleases. A combined X-ray crystallographic/ab initio quantum chemical study. |
Publication Type | Journal Article |
Year of Publication | 2002 |
Authors | Mignon, P., J. Steyaert, R. Loris, P. Geerlings, and S. Loverix |
Journal | J Biol Chem |
Volume | 277 |
Issue | 39 |
Pagination | 36770-4 |
Date Published | 2002 Sep 27 |
ISSN | 0021-9258 |
Keywords | Binding 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. |
DOI | 10.1074/jbc.M206461200 |
Alternate Journal | J. Biol. Chem. |
PubMed ID | 12122018 |
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