2E2L

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.253 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of Helicobacter pylori formamidase AmiF reveals a cysteine-glutamate-lysine catalytic triad

Hung, C.-L.Liu, J.-H.Chiu, W.-C.Huang, S.-W.Hwang, J.-K.Wang, W.-C.

(2007) J.Biol.Chem. 282: 12220-12229

  • DOI: 10.1074/jbc.M609134200
  • Primary Citation of Related Structures:  2DYU, 2DYV, 2E2K

  • 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 dispers ...

    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.


    Organizational Affiliation

    Institute of Molecular and Cellular Biology and Department of Life Science, National Tsing Hua University, Hsinchu 300, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Formamidase
A, B, C, D, E, F
334Helicobacter pylori (strain ATCC 700392 / 26695)Gene Names: amiF
EC: 3.5.1.49
Find proteins for O25836 (Helicobacter pylori (strain ATCC 700392 / 26695))
Go to UniProtKB:  O25836
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ARF
Query on ARF

Download SDF File 
Download CCD File 
A, C, F
FORMAMIDE
C H3 N O
ZHNUHDYFZUAESO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.253 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 83.089α = 90.00
b = 151.795β = 114.99
c = 89.083γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
HKL-2000data collection
HKL-2000data scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-11-14 
  • Released Date: 2007-02-13 
  • Deposition Author(s): Wang, W.C., Hung, C.L.

Revision History 

  • Version 1.0: 2007-02-13
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Source and taxonomy, Version format compliance