2C5U
T4 RNA Ligase (Rnl1) Crystal Structure
Summary for 2C5U
| Entry DOI | 10.2210/pdb2c5u/pdb |
| Descriptor | RNA LIGASE, DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER, CALCIUM ION, ... (6 entities in total) |
| Functional Keywords | ligase, rna ligase, nucleotidyl transferase, atp-binding |
| Biological source | BACTERIOPHAGE T4 |
| Total number of polymer chains | 2 |
| Total formula weight | 90031.13 |
| Authors | El Omari, K.,Ren, J.,Bird, L.E.,Bona, M.K.,Klarmann, G.,LeGrice, S.F.J.,Stammers, D.K. (deposition date: 2005-11-01, release date: 2005-11-04, Last modification date: 2024-10-23) |
| Primary citation | El Omari, K.,Ren, J.,Bird, L.E.,Bona, M.K.,Klarmann, G.,Legrice, S.F.J.,Stammers, D.K. Molecular Architecture and Ligand Recognition Determinants for T4 RNA Ligase J.Biol.Chem., 281:1573-, 2006 Cited by PubMed Abstract: 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 tRNA(Lys). Rnl1 is widely used as a reagent in molecular biology. Although many structures for DNA ligases are available, only fragments of RNA ligases such as Rnl2 are known. We report the first crystal structure of a complete RNA ligase, Rnl1, in complex with adenosine 5'-(alpha,beta-methylenetriphosphate) (AMPcPP). The N-terminal domain is related to the equivalent region of DNA ligases and Rnl2 and binds AMPcPP but with further interactions from the additional N-terminal 70 amino acids in Rnl1 (via Tyr37 and Arg54) and the C-terminal domain (Gly269 and Asp272). The active site contains two metal ions, consistent with the two-magnesium ion catalytic mechanism. The C-terminal domain represents a new all alpha-helical fold and has a charge distribution and architecture for helix-nucleic acid groove interaction compatible with tRNA binding. PubMed: 16263720DOI: 10.1074/JBC.M509658200 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.21 Å) |
Structure validation
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