1XEM

High Resolution Crystal Structure of Escherichia coli Zinc- Peptide Deformylase bound to formate

1XEM の概要

• エントリーDOI: 10.2210/pdb1xem/pdb
• 関連するPDBエントリー: 1BSK 1DFF
• 分子名称: Peptide deformylase, ZINC ION, FORMIC ACID, ... (4 entities in total)
• 機能のキーワード: zinc deformylase, formate, hydrolase
• 由来する生物種: Escherichia coli
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 19751.91

構造登録者

Jain, R.,Hao, B.,Liu, R.-P.,Chan, M.K. (登録日: 2004-09-10, 公開日: 2005-03-29, 最終更新日: 2024-02-14)

主引用文献

Jain, R.,Hao, B.,Liu, R.-P.,Chan, M.K.
Structures of E. coli peptide deformylase bound to formate: insight into the preference for Fe2+ over Zn2+ as the active site metal
J.Am.Chem.Soc., 127:4558-4559, 2005

PubMed Abstract: E. coli peptide deformylase (PDF) catalyzes the deformylation of nascent polypeptides generated during protein synthesis. While PDF was originally thought to be a zinc enzyme, subsequent studies revealed that the active site metal is iron. In an attempt to understand this unusual metal preference, high-resolution structures of Fe-, Co-, and Zn-PDF were determined in complex with its deformylation product, formate. In all three structures, the formate ion binds the metal and forms hydrogen-bonding interactions with the backbone nitrogen of Leu91, the amide side chain of Gln50, and the carboxylate side chain of Glu133. One key difference, however, is how the formate binds the metal. In Fe-PDF and Co-PDF, formate binds in a bidentate fashion, while in Zn-PDF, it binds in a monodentate fashion. Importantly, these structural results provide the first clues into the origins of PDF's metal-dependent activity differences. On the basis of these structures, we propose that the basis for the higher activity of Fe-PDF stems from the better ability of iron to bind and activate the tetrahedral transition state required for cleavage of the N-terminal formyl group.

PubMed: 15796505
DOI: 10.1021/ja0503074

実験手法

X-RAY DIFFRACTION (1.76 Å)