1GAX

CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE

Summary for 1GAX

• Entry DOI: 10.2210/pdb1gax/pdb
• Related: 1ILE 1QU2
• Descriptor: TRNA(VAL), VALYL-TRNA SYNTHETASE, ZINC ION, ... (5 entities in total)
• Functional Keywords: protein-rna complex, rossmann fold, coiled coil, trna, riken structural genomics/proteomics initiative, rsgi, structural genomics, ligase-rna complex, ligase/rna
• Biological source: Thermus thermophilus; More
• Cellular location: Cytoplasm: P96142
• Total number of polymer chains: 4
• Total formula weight: 247328.37

Authors

Fukai, S.,Nureki, O.,Sekine, S.,Shimada, A.,Tao, J.,Vassylyev, D.G.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2000-06-23, release date: 2000-12-06, Last modification date: 2024-10-30)

Primary citation

Fukai, S.,Nureki, O.,Sekine, S.,Shimada, A.,Tao, J.,Vassylyev, D.G.,Yokoyama, S.
Structural basis for double-sieve discrimination of L-valine from L-isoleucine and L-threonine by the complex of tRNA(Val) and valyl-tRNA synthetase.
Cell(Cambridge,Mass.), 103:793-803, 2000

PubMed Abstract: Valyl-tRNA synthetase (ValRS) strictly discriminates the cognate L-valine from the larger L-isoleucine and the isosteric L-threonine by the tRNA-dependent "double sieve" mechanism. In this study, we determined the 2.9 A crystal structure of a complex of Thermus thermophilus ValRS, tRNA(Val), and an analog of the Val-adenylate intermediate. The analog is bound in a pocket, where Pro(41) allows accommodation of the Val and Thr moieties but precludes the Ile moiety (the first sieve), on the aminoacylation domain. The editing domain, which hydrolyzes incorrectly synthesized Thr-tRNA(Val), is bound to the 3' adenosine of tRNA(Val). A contiguous pocket was found to accommodate the Thr moiety, but not the Val moiety (the second sieve). Furthermore, another Thr binding pocket for Thr-adenylate hydrolysis was suggested on the editing domain.

PubMed: 11114335
DOI: 10.1016/S0092-8674(00)00182-3

Experimental method

X-RAY DIFFRACTION (2.9 Å)