Molecular architecture and ligand recognition determinants for T4 RNA ligase

doi:10.1074/jbc.M509658200

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A more recent version of this article appeared on January 20, 2006 Originally published In Press as doi:10.1074/jbc.M509658200 on November 21, 2005

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Papers In Press, published online ahead of print November 1, 2005
J. Biol. Chem, 10.1074/jbc.M509658200
Submitted on September 1, 2005
Revised on October 19, 2005
Accepted on October 31, 2005

Molecular architecture and ligand recognition determinants for T4 RNA ligase

Kamel El Omari, Jingshan Ren, Louise E. Bird, Marion K. Bona, George Klarmann, Stuart F. J. LeGrice, and David K. Stammers

Division of Structural Biology, University of Oxford, The Wellcome Trust Centre for Human Genetics, Oxford, OXON OX3 7BN

Corresponding Author: daves{at}strubi.ox.ac.uk

RNA ligase type-1 from bacteriophage T4 (Rnl1) is involved in countering a host defense mechanism by repairing 5'-PO4 and 3'-OH groups in tRNAlys. Rnl1 is widely used as a reagent in molecular biology. Whilst many structures for DNA ligases are available, only a fragment of an RNA ligase (Rnl2) is known. We report the first crystal structure of a complete RNA ligase, Rnl1, in complex with AMPcPP. The N-terminal domain is related to the equivalent region of DNA ligases & Rnl2 and binds AMPcPP but with further interactions from the additional N-terminal 70 amino acids in Rnl1 (via Y37 and R54) and the C-terminal domain (G269 and D272). The active site contains two metal ions, consistent with the two magnesium ion catalytic mechanism. The C-terminal domain represents a new all a-helical fold, and has a charge distribution and architecture for helix-nucleic acid groove interaction compatible with t-RNA binding.

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