1WK9

Structural basis for non-cognate amino acid discrimination by the valyl-tRNA synthetase editing domain

Summary for 1WK9

• Entry DOI: 10.2210/pdb1wk9/pdb
• Related: 1WKA
• Descriptor: Valyl-tRNA synthetase, 5'-O-(N-(L-THREONYL)-SULFAMOYL)ADENOSINE (3 entities in total)
• Functional Keywords: editing, cp1, valyl-trna synthetase, fidelity, thermus thrmophilus, translation, amino acid, thr-ams, structural genomics, riken structural genomics/proteomics initiative, rsgi, ligase
• Biological source: Thermus thermophilus
• Cellular location: Cytoplasm: P96142
• Total number of polymer chains: 1
• Total formula weight: 16988.26

Authors

Fukunaga, R.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2004-05-30, release date: 2005-06-28, Last modification date: 2023-10-25)

Primary citation

Fukunaga, R.,Yokoyama, S.
Structural Basis for Non-cognate Amino Acid Discrimination by the Valyl-tRNA Synthetase Editing Domain
J.Biol.Chem., 280:29937-29945, 2005

PubMed Abstract: The editing domain of valyl-tRNA synthetase (ValRS) is known to deacylate, or edit, misformed Thr-tRNA(Val) (post-transfer editing). Here, we determined the 1.7-Angstroms resolution crystal structure of the Thermus thermophilus ValRS editing domain. A comparison of the structure with the previously reported tRNA complex structure revealed conformational changes of the editing domain upon accommodation of the terminal A76; the "GTG loop" moves to expand the pocket, and the side chain of Phe-264 on the GTG loop rotates to interact with the A76 adenine ring. If these conformational changes did not occur, then C75 and A76 of the tRNA would clash with Phe-264. To elucidate the mechanism of the threonine side-chain recognition, we determined the crystal structure of the editing domain bound with [N-(L-threonyl)-sulfamoyl]adenosine at 1.7-Angstroms resolution. The gamma-OH of the threonyl moiety is recognized by the Lys-270, Thr-272, and Asp-279 side chains, which may reject the cognate valyl moiety. Accordingly, ValRS mutants with an Ala substitution for Lys-270 or Asp-279 synthesized significant amounts of Thr-tRNA(Val). The misproduced Thr-tRNA(Val) was hydrolyzed efficiently by the wild-type ValRS, but this post-transfer editing activity was drastically impaired by the Ala substitutions for Lys-270 and Asp-279 and was also decreased by those for Arg-216, Phe-264, and Thr-272. These results indicate that the threonyl moiety and A76 of Thr-tRNA(Val) are recognized by the Lys-270, Thr-272, and Asp-279 side chains and by the Phe-264 side chain, respectively, of the ValRS editing domain.

PubMed: 15970591
DOI: 10.1074/jbc.M502668200

Experimental method

X-RAY DIFFRACTION (1.75 Å)