2DYV

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

Summary for 2DYV

• Entry DOI: 10.2210/pdb2dyv/pdb
• Related: 2DYU 2E2K 2E2L
• Descriptor: Formamidase (2 entities in total)
• Functional Keywords: formamidase, amif, cek, catalytic triad, helicobacter pylori, aliphatic amidase, hydrolase
• Biological source: Helicobacter pylori
• Total number of polymer chains: 2
• Total formula weight: 74660.80

Authors

Wang, W.C.,Hung, C.L. (deposition date: 2006-09-18, release date: 2007-02-13, Last modification date: 2023-10-25)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (2 Å)