3cqs

Publication Abstract from PubMed

Reaction-intermediate analogs have been used to understand how phosphoryl transfer enzymes promote catalysis. Herein we report the first structure of a small ribozyme crystallized with a 3'-OH, 2',5'-linkage in lieu of the normal phosphodiester substrate. The new structure shares features of the reaction coordinate exhibited in prior ribozyme structures including a vanadate complex that mimicked the oxyphosphorane transition state. As such, the structure exhibits reaction-intermediate traits that allow direct comparison of stabilizing interactions to the 3'-OH, 2',5'-linkage contributed by the RNA enzyme and its protein counterpart, ribonuclease. Clear similarities are observed between the respective structures including hydrogen bonds to the non-bridging oxygens of the scissile phosphate. Other commonalities include carefully poised water molecules that may alleviate charge build-up in the transition state and placement of a positive charge near the leaving group. The advantages of 2',5'-linkages to investigate phosphoryl-transfer reactions are discussed, and argue for their expanded use in structural studies.

Shared traits on the reaction coordinates of ribonuclease and an RNA enzyme.,Torelli AT, Spitale RC, Krucinska J, Wedekind JE Biochem Biophys Res Commun. 2008 Jun 20;371(1):154-8. Epub 2008 Apr 16. PMID:18423397^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.