3CQS

A 3'-OH, 2',5'-phosphodiester substitution in the hairpin ribozyme active site reveals similarities with protein ribonucleases

Summary for 3CQS

• Entry DOI: 10.2210/pdb3cqs/pdb
• Related: 11BA 2P7E 2P7F
• Descriptor: 13-mer substrate strand with 3'-OH, 2',5'-phosphodiester covalently linking 5th and 6th nucleotides, 29-mer ribozyme strand with S9L synthetic linker at 13th position, 19-mer ribozyme strand, ... (5 entities in total)
• Functional Keywords: 2', 5' phosphodiester; hairpin ribozyme; reaction-intermediate; transition-state stabilization; ribonuclease; phosphoryl-transfer, rna
• Total number of polymer chains: 3
• Total formula weight: 19968.14

Authors

Torelli, A.T.,Spitale, R.C.,Krucinska, J.,Wedekind, J.E. (deposition date: 2008-04-03, release date: 2008-05-20, Last modification date: 2023-08-30)

Primary citation

Torelli, A.T.,Spitale, R.C.,Krucinska, J.,Wedekind, J.E.
Shared traits on the reaction coordinates of ribonuclease and an RNA enzyme
Biochem.Biophys.Res.Commun., 371:154-158, 2008

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.

PubMed: 18423397
DOI: 10.1016/j.bbrc.2008.04.036

Experimental method

X-RAY DIFFRACTION (2.8 Å)