1TYD

STRUCTURE OF TYROSYL-TRNA SYNTHETASE REFINED AT 2.3 ANGSTROMS RESOLUTION. INTERACTION OF THE ENZYME WITH THE TYROSYL ADENYLATE INTERMEDIATE

1TYD の概要

• エントリーDOI: 10.2210/pdb1tyd/pdb
• 関連するPDBエントリー: 2TS1
• 分子名称: TYROSYL-tRNA SYNTHETASE, TYROSINE (3 entities in total)
• 機能のキーワード: aminoacyl-trna synthase
• 由来する生物種: Geobacillus stearothermophilus
• 細胞内の位置: Cytoplasm: P00952
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 36490.34

構造登録者

Brown, K.A.,De Meester, P.,Blow, D.M. (登録日: 1992-07-06, 公開日: 1994-01-31, 最終更新日: 2024-02-14)

主引用文献

Brick, P.,Bhat, T.N.,Blow, D.M.
Structure of tyrosyl-tRNA synthetase refined at 2.3 A resolution. Interaction of the enzyme with the tyrosyl adenylate intermediate.
J.Mol.Biol., 208:83-98, 1989

PubMed Abstract: 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.

PubMed: 2504923
DOI: 10.1016/0022-2836(89)90090-9

実験手法

X-RAY DIFFRACTION (2.5 Å)