Download MendeleyShared traits on the reaction coordinates of ribonuclease and an RNA enzyme
Torelli, A.T., Spitale, R.C., Krucinska, J., Wedekind, J.E.(2008) Biochem Biophys Res Commun 371: 154-158
- PubMed: 18423397
- DOI: https://doi.org/10.1016/j.bbrc.2008.04.036
- Primary Citation of Related Structures:
3CQS - PubMed Abstract:
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.
Organizational Affiliation:
Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue Box 712, Rochester, New York 14642, USA.
