1VQK

The structure of CCDA-PHE-CAP-BIO bound to the a site of the ribosomal subunit of haloarcula marismortui

1VQK の概要

• エントリーDOI: 10.2210/pdb1vqk/pdb
• 関連するPDBエントリー: 1FFK 1FFZ 1FGO 1JJ2 1KQS 1M90 1Q7Y 1Q81 1Q82 1Q86 1QVF 1QVG 1S72 1VQ4 1VQ5 1VQ6 1VQ7 1VQ8 1VQ9 1VQL 1VQM 1VQN 1VQO 1VQP
• 分子名称: 23S ribosomal rna, ACIDIC RIBOSOMAL PROTEIN P0 HOMOLOG, 50S RIBOSOMAL PROTEIN L10E, ... (39 entities in total)
• 機能のキーワード: ribosome 50s, protein-protein complex, rna-rna complex, protein-rna complex, peptidyl transferase reaction, ribosome
• 由来する生物種: Haloarcula marismortui; 詳細
• タンパク質・核酸の鎖数: 32
• 化学式量合計: 1489963.98

構造登録者

Schmeing, T.M.,Steitz, T.A. (登録日: 2004-12-16, 公開日: 2005-11-29, 最終更新日: 2023-11-15)

主引用文献

Schmeing, T.M.,Huang, K.S.,Kitchen, D.E.,Strobel, S.A.,Steitz, T.A.
Structural Insights into the Roles of Water and the 2' Hydroxyl of the P Site tRNA in the Peptidyl Transferase Reaction.
Mol.Cell, 20:437-448, 2005

PubMed Abstract: Peptide bond formation is catalyzed at the peptidyl transferase center (PTC) of the large ribosomal subunit. Crystal structures of the large ribosomal subunit of Haloarcula marismortui (Hma) complexed with several analogs that represent either the substrates or the transition state intermediate of the peptidyl transferase reaction show that this reaction proceeds through a tetrahedral intermediate with S chirality. The oxyanion of the tetrahedral intermediate interacts with a water molecule that is positioned by nucleotides A2637 (E. coli numbering, 2602) and (methyl)U2619(2584). There are no Mg2+ ions or monovalent metal ions observed in the PTC that could directly promote catalysis. The A76 2' hydroxyl of the peptidyl-tRNA is hydrogen bonded to the alpha-amino group and could facilitate peptide bond formation by substrate positioning and by acting as a proton shuttle between the alpha-amino group and the A76 3' hydroxyl of the peptidyl-tRNA.

PubMed: 16285925
DOI: 10.1016/j.molcel.2005.09.006

実験手法

X-RAY DIFFRACTION (2.3 Å)