標題: Crystal structure of Helicobacter pylori formamidase AmiF reveals a cysteine-glutamate-lysine catalytic triad
作者: Hung, Chiu-Lien
Liu, Jia-Hsin
Chiu, Wei-Chun
Huang, Shao-Wei
Hwang, Jenn-Kang
Wang, Wen-Ching
生物資訊及系統生物研究所
Institude of Bioinformatics and Systems Biology
公開日期: 20-Apr-2007
摘要: 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 1.75 angstrom 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 angstrom, respectively. These structures reveal a small formamide-binding pocket that includes Cys(166), Glu(60), and Lys(133) catalytic residues, in which Cys166 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.
URI: http://dx.doi.org/10.1074/jbc.M609134200
http://hdl.handle.net/11536/10890
ISSN: 0021-9258
DOI: 10.1074/jbc.M609134200
期刊: JOURNAL OF BIOLOGICAL CHEMISTRY
Volume: 282
Issue: 16
起始頁: 12220
結束頁: 12229
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