1LOW

X-ray structure of the H40A mutant of Ribonuclease T1 complexed with 3'-guanosine monophosphate

Summary for 1LOW

• Entry DOI: 10.2210/pdb1low/pdb
• Related: 1LOV 1LOY 1RGA 1RLS
• Descriptor: Guanyl-specific ribonuclease T1, CALCIUM ION, GUANOSINE-3'-MONOPHOSPHATE, ... (4 entities in total)
• Functional Keywords: rnase, catalytic dyad, nucleophile activation, ab initio calculations, hydrolase
• Biological source: Aspergillus oryzae
• Total number of polymer chains: 1
• Total formula weight: 11430.92

Authors

Mignon, P.,Steyaert, J.,Loris, R.,Geerlings, P.,Loverix, S. (deposition date: 2002-05-07, release date: 2002-08-21, Last modification date: 2024-10-30)

Primary citation

Mignon, P.,Steyaert, J.,Loris, R.,Geerlings, P.,Loverix, S.
A nucleophile activation dyad in ribonucleases. A combined X-ray crystallographic/ab initio quantum chemical study
J.Biol.Chem., 277:36770-36774, 2002

PubMed 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.

PubMed: 12122018
DOI: 10.1074/jbc.M206461200

Experimental method

X-RAY DIFFRACTION (1.9 Å)