1VBM

Crystal structure of the Escherichia coli tyrosyl-tRNA synthetase complexed with Tyr-AMS

1VBM の概要

• エントリーDOI: 10.2210/pdb1vbm/pdb
• 関連するPDBエントリー: 1UDF 1UDJ 1VBN
• 分子名称: Tyrosyl-tRNA synthetase, SULFATE ION, 5'-O-[N-(L-TYROSYL)SULFAMOYL]ADENOSINE, ... (4 entities in total)
• 機能のキーワード: ligase, structural genomics, riken structural genomics/proteomics initiative, rsgi
• 由来する生物種: Escherichia coli
• 細胞内の位置: Cytoplasm: P00951
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 72797.94

構造登録者

Kobayashi, T.,Sakamoto, K.,Takimura, T.,Kamata, K.,Sekine, R.,Nishimura, S.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (登録日: 2004-02-27, 公開日: 2005-01-25, 最終更新日: 2023-10-25)

主引用文献

Kobayashi, T.,Takimura, T.,Sekine, R.,Kelly, V.P.,Vincent, K.,Kamata, K.,Sakamoto, K.,Nishimura, S.,Yokoyama, S.
Structural snapshots of the KMSKS loop rearrangement for amino acid activation by bacterial tyrosyl-tRNA synthetase.
J.Mol.Biol., 346:105-117, 2005

PubMed Abstract: Tyrosyl-tRNA synthetase (TyrRS) has been studied extensively by mutational and structural analyses to elucidate its catalytic mechanism. TyrRS has the HIGH and KMSKS motifs that catalyze the amino acid activation with ATP. In the present study, the crystal structures of the Escherichia coli TyrRS catalytic domain, in complexes with l-tyrosine and a l-tyrosyladenylate analogue, Tyr-AMS, were solved at 2.0A and 2.7A resolution, respectively. In the Tyr-AMS-bound structure, the 2'-OH group and adenine ring of the Tyr-AMS are strictly recognized by hydrogen bonds. This manner of hydrogen-bond recognition is conserved among the class I synthetases. Moreover, a comparison between the two structures revealed that the KMSKS loop is rearranged in response to adenine moiety binding and hydrogen-bond formation, and the KMSKS loop adopts the more compact ("semi-open") form, rather than the flexible, open form. The HIGH motif initially recognizes the gamma-phosphate, and then the alpha and gamma-phosphates of ATP, with a slight rearrangement of the residues. The other residues around the substrate also accommodate the Tyr-AMS. This induced-fit form presents a novel "snapshot" of the amino acid activation step in the aminoacylation reaction by TyrRS. The present structures and the T.thermophilus TyrRS ATP-free and bound structures revealed that the extensive induced-fit conformational changes of the KMSKS loop and the local conformational changes within the substrate binding site form the basis for driving the amino acid activation step: the KMSKS loop adopts the open form, transiently shifts to the semi-open conformation according to the adenosyl moiety binding, and finally assumes the rigid ATP-bound, closed form. After the amino acid activation, the KMSKS loop adopts the semi-open form again to accept the CCA end of tRNA for the aminoacyl transfer reaction.

PubMed: 15663931
DOI: 10.1016/j.jmb.2004.11.034

実験手法

X-RAY DIFFRACTION (2.7 Å)