2Z3M

complex structure of LF-transferase and dAF

2Z3M の概要

• エントリーDOI: 10.2210/pdb2z3m/pdb
• 関連するPDBエントリー: 2Z3K 2Z3L 2Z3N 2Z3O 2Z3P
• 分子名称: Leucyl/phenylalanyl-tRNA-protein transferase, (2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol, PHENYLALANINE, ... (5 entities in total)
• 機能のキーワード: lf-transferase, transferase
• 由来する生物種: Escherichia coli
• 細胞内の位置: Cytoplasm: P0A8P1
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 54173.67

構造登録者

Watanabe, K.,Toh, Y.,Tomita, K. (登録日: 2007-06-04, 公開日: 2007-10-23, 最終更新日: 2023-11-01)

主引用文献

Watanabe, K.,Toh, Y.,Suto, K.,Shimizu, Y.,Oka, N.,Wada, T.,Tomita, K.
Protein-based peptide-bond formation by aminoacyl-tRNA protein transferase
Nature, 449:867-871, 2007

PubMed Abstract: Eubacterial leucyl/phenylalanyl-tRNA protein transferase (LF-transferase) catalyses peptide-bond formation by using Leu-tRNA(Leu) (or Phe-tRNA(Phe)) and an amino-terminal Arg (or Lys) of a protein, as donor and acceptor substrates, respectively. However, the catalytic mechanism of peptide-bond formation by LF-transferase remained obscure. Here we determine the structures of complexes of LF-transferase and phenylalanyl adenosine, with and without a short peptide bearing an N-terminal Arg. Combining the two separate structures into one structure as well as mutation studies reveal the mechanism for peptide-bond formation by LF-transferase. The electron relay from Asp 186 to Gln 188 helps Gln 188 to attract a proton from the alpha-amino group of the N-terminal Arg of the acceptor peptide. This generates the attacking nucleophile for the carbonyl carbon of the aminoacyl bond of the aminoacyl-tRNA, thus facilitating peptide-bond formation. The protein-based mechanism for peptide-bond formation by LF-transferase is similar to the reverse reaction of the acylation step observed in the peptide hydrolysis reaction by serine proteases.

PubMed: 17891155
DOI: 10.1038/nature06167

実験手法

X-RAY DIFFRACTION (2.7 Å)