Active site of RNase: neutron diffraction study of a complex with uridine vanadate, a transition-state analog.

Abstract

A complex of RNase A with a transition-state analog, uridine vanadate, was studied by a combination of neutron and X-ray diffraction. The vanadium atom occupies the center of a distorted trigonal bipyramid, with the ribose oxygen O2'' at the apical position. Contrary to expectations based on the straightforward interpretation of the known in-line mechanism of action of RNase, nitrogen NE2 of histidine-12 formed a H bond to the equatorial oxygen O8, while nitrogen NZ of lysine-41 makes a clear H bond to the apical oxygen O2''. Nitrogen ND1 of histidine-119 appears to be within a H-bond distance of the other apical oxygen, O7. Two other H-bonds between the vanadate and the protein are made by nitrogen NE2 of glutamine-11 and by the amide nitrogen of phenylalanine-120. The observed geometry of the complex may necessitate reinterpretation of the mechanism of action of RNase.