2e2k | pdb_00002e2k

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

spinqualitylabelsall models 2e2k, resolution 2.50Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 2e2k is a 6 chain structure with sequence from Campylobacter pylori. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Related: 2dyu, 2dyv, 2e2l Gene: amiF (Campylobacter pylori) Activity: Formamidase, with EC number 3.5.1.49 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum Function [AMIF_HELPY] Is an aliphatic amidase with a restricted substrate specificity, as it only hydrolyzes formamide. Probably involved in the nitrogen metabolism of H.pylori. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMed 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. Crystal structure of Helicobacter pylori formamidase AmiF reveals a cysteine-glutamate-lysine catalytic triad.,Hung CL, Liu JH, Chiu WC, Huang SW, Hwang JK, Wang WC J Biol Chem. 2007 Apr 20;282(16):12220-9. Epub 2007 Feb 16. PMID:17307742 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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