2E2K

Helicobacter pylori formamidase AmiF contains a fine-tuned cysteine-glutamate-lysine catalytic triad

2E2K の概要

• エントリーDOI: 10.2210/pdb2e2k/pdb
• 関連するPDBエントリー: 2DYU 2DYV 2E2L
• 分子名称: Formamidase (2 entities in total)
• 機能のキーワード: formamidase, amif, cek, catalytic triad, helicobacter pylori, aliphatic amidase, c166s, hydrolase
• 由来する生物種: Helicobacter pylori
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 223885.99

構造登録者

Wang, W.C.,Hung, C.L. (登録日: 2006-11-14, 公開日: 2007-02-13, 最終更新日: 2023-10-25)

主引用文献

Hung, C.-L.,Liu, J.-H.,Chiu, W.-C.,Huang, S.-W.,Hwang, J.-K.,Wang, W.-C.
Crystal structure of Helicobacter pylori formamidase AmiF reveals a cysteine-glutamate-lysine catalytic triad
J.Biol.Chem., 282:12220-12229, 2007

PubMed Abstract: Helicobacter pylori AmiF formamidase that hydrolyzes formamide to produce formic acid and ammonia belongs to a member of the nitrilase superfamily. The crystal structure of AmiF was solved to 1.75A resolution using single-wavelength anomalous dispersion methods. The structure consists of a homohexamer related by 3-fold symmetry in which each subunit has an alpha-beta-beta-alpha four-layer architecture characteristic of the nitrilase superfamily. One exterior alpha layer faces the solvent, whereas the other one associates with that of the neighbor subunit, forming a tight alpha-beta-beta-alpha-alpha-beta-beta-alpha dimer. The apo and liganded crystal structures of an inactive mutant C166S were also determined to 2.50 and 2.30 A, respectively. These structures reveal a small formamide-binding pocket that includes Cys(166), Glu(60), and Lys(133) catalytic residues, in which Cys(166) acts as a nucleophile. Analysis of the liganded AmiF and N-carbamoyl d-amino acid amidohydrolase binding pockets reveals a common Cys-Glu-Lys triad, another conserved glutamate, and different subsets of ligand-binding residues. Molecular dynamic simulations show that the conserved triad has minimal fluctuations, catalyzing the hydrolysis of a specific nitrile or amide in the nitrilase superfamily efficiently.

PubMed: 17307742
DOI: 10.1074/jbc.M609134200

実験手法

X-RAY DIFFRACTION (2.5 Å)