PMID: 12122018 , Related PDB ids: 1LOV, 1LOW, 1LOY

Authors:

Mignon P, Steyaert J, Loris R, Geerlings P, Loverix S

Title:

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

Journal:

J Biol Chem. 2002 Sep 27;277(39):36770-4. Epub 2002 Jul 16.

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.