2CJA

Crystal structure of Methanosarcina barkeri seryl-tRNA synthetase complexed with ATP

2CJA の概要

• エントリーDOI: 10.2210/pdb2cja/pdb
• 関連するPDBエントリー: 2CIM 2CJ9 2CJB
• 分子名称: SERYL-TRNA SYNTHETASE, ZINC ION, CHLORIDE ION, ... (6 entities in total)
• 機能のキーワード: ligase, zinc ion, trna synthetase
• 由来する生物種: METHANOSARCINA BARKERI
• 細胞内の位置: Cytoplasm (By similarity): Q46AN5
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 122824.50

構造登録者

Bilokapic, S.,Maier, T.,Ahel, D.,Gruic-Sovulj, I.,Soll, D.,Weygand-Durasevic, I.,Ban, N. (登録日: 2006-03-30, 公開日: 2006-06-26, 最終更新日: 2024-11-13)

主引用文献

Bilokapic, S.,Maier, T.,Ahel, D.,Gruic-Sovulj, I.,Soll, D.,Weygand-Durasevic, I.,Ban, N.
Structure of the Unusual Seryl-tRNA Synthetase Reveals a Distinct Zinc-Dependent Mode of Substrate Recognition
Embo J., 25:2498-, 2006

PubMed Abstract: Methanogenic archaea possess unusual seryl-tRNA synthetase (SerRS), evolutionarily distinct from the SerRSs found in other archaea, eucaryotes and bacteria. The two types of SerRSs show only minimal sequence similarity, primarily within class II conserved motifs 1, 2 and 3. Here, we report a 2.5 A resolution crystal structure of the atypical methanogenic Methanosarcina barkeri SerRS and its complexes with ATP, serine and the nonhydrolysable seryl-adenylate analogue 5'-O-(N-serylsulfamoyl)adenosine. The structures reveal two idiosyncratic features of methanogenic SerRSs: a novel N-terminal tRNA-binding domain and an active site zinc ion. The tetra-coordinated Zn2+ ion is bound to three conserved protein ligands (Cys306, Glu355 and Cys461) and binds the amino group of the serine substrate. The absolute requirement of the metal ion for enzymatic activity was confirmed by mutational analysis of the direct zinc ion ligands. This zinc-dependent serine recognition mechanism differs fundamentally from the one employed by the bacterial-type SerRSs. Consequently, SerRS represents the only known aminoacyl-tRNA synthetase system that evolved two distinct mechanisms for the recognition of the same amino-acid substrate.

PubMed: 16675947
DOI: 10.1038/SJ.EMBOJ.7601129

実験手法

X-RAY DIFFRACTION (2.2 Å)