1tyd
STRUCTURE OF TYROSYL-TRNA SYNTHETASE REFINED AT 2.3 ANGSTROMS RESOLUTION. INTERACTION OF THE ENZYME WITH THE TYROSYL ADENYLATE INTERMEDIATE
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OverviewOverview
The crystal structure of tyrosyl-tRNA synthetase (EC 6.1.1.1) from, Bacillus stearothermophilus has been refined to a crystallographic, R-factor of 22.6% at 2.3 A resolution using a restrained least-squares, procedure. In the final model the root-mean-square deviation from ideality, for bond distances is 0.018 A and for angle distances is 0.044 A. Each, monomer consists of three domains: an alpha/beta domain (residues 1 to, 220) containing a six-stranded beta-sheet, an alpha-helical domain (248 to, 318) containing five helices, and a disordered C-terminal domain (319 to, 418) for which the electron density is very weak and where it has not been, possible to trace the polypeptide chain. Complexes of the enzyme with the, catalytic intermediate tyrosyl adenylate and the inhibitor tyrosinyl, adenylate have also been refined to R-factors of 23.9% at 2.8 A resolution, and 21.0% at 2.7 A resolution, respectively. Formation of the complexes, results in some crystal cracking, but there is no significant difference, in the conformation of the polypeptide chain of the three structures, described here. The relative orientation of the alpha/beta and, alpha-helical domains is similar to that previously observed for the "A", subunit of a deletion mutant lacking the C-terminal domain. Differences, between these structures are confined to surface loops that are involved, in crystal packing. Tyrosyl adenylate and tyrosinyl adenylate bind in, similar conformations within a deep cleft in the alpha/beta domain. The, tyrosine moiety is in the equivalent position to that occupied by tyrosine, in crystals of the truncated mutant and makes similar strong polar, interactions with the enzyme. The alpha-phosphate group interacts with the, main-chain nitrogen of Asp38. The two hydroxyl groups of the ribose form, strong interactions with the protein. The 2'-hydroxyl group interacts with, the carboxylate of Asp194 and the main-chain nitrogen of Gly192 while the, 3'-hydroxyl interacts with a tightly bound water molecule (Wat326). The, adenine moiety appears to make no significant polar interactions with the, protein. The results of site-directed mutagenesis studies are examined in, the light of these refined structures.
About this StructureAbout this Structure
1TYD is a Single protein structure of sequence from Geobacillus stearothermophilus with TYR as ligand. Active as Tyrosine--tRNA ligase, with EC number 6.1.1.1 Full crystallographic information is available from OCA.
ReferenceReference
Structure of tyrosyl-tRNA synthetase refined at 2.3 A resolution. Interaction of the enzyme with the tyrosyl adenylate intermediate., Brick P, Bhat TN, Blow DM, J Mol Biol. 1989 Jul 5;208(1):83-98. PMID:2504923
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