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PDBsum entry 2dyu

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protein Protein-protein interface(s) links
Hydrolase PDB id
2dyu
Jmol
Contents
Protein chains
322 a.a. *
Waters ×713
* Residue conservation analysis
PDB id:
2dyu
Name: Hydrolase
Title: Helicobacter pylori formamidase amif contains a fine-tuned c glutamate-lysine catalytic triad
Structure: Formamidase. Chain: a, b. Synonym: formamide amidohydrolase. Engineered: yes
Source: Helicobacter pylori. Organism_taxid: 85962. Strain: 26695. Gene: amif. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.75Å     R-factor:   0.176     R-free:   0.215
Authors: W.C.Wang,C.L.Hung
Key ref:
C.L.Hung et al. (2007). Crystal structure of Helicobacter pylori formamidase AmiF reveals a cysteine-glutamate-lysine catalytic triad. J Biol Chem, 282, 12220-12229. PubMed id: 17307742 DOI: 10.1074/jbc.M609134200
Date:
18-Sep-06     Release date:   13-Feb-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O25836  (AMIF_HELPY) -  Formamidase
Seq:
Struc:
334 a.a.
322 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.5.1.49  - Formamidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Formamide + H2O = formate + NH3
Formamide
+ H(2)O
= formate
+ NH(3)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     nitrogen compound metabolic process   1 term 
  Biochemical function     hydrolase activity     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1074/jbc.M609134200 J Biol Chem 282:12220-12229 (2007)
PubMed id: 17307742  
 
 
Crystal structure of Helicobacter pylori formamidase AmiF reveals a cysteine-glutamate-lysine catalytic triad.
C.L.Hung, J.H.Liu, W.C.Chiu, S.W.Huang, J.K.Hwang, W.C.Wang.
 
  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.
 
  Selected figure(s)  
 
Figure 3.
FIGURE 3. The 2F[o] - F[c] electron density map of the inactive mutant C166S in its apo form (A) and model 1 (B) and model 2 (C) of the liganded C166S complex around C166S, Glu^60, and Lys^133, contoured at the 1.0- level. The bound formamide (FRA) is drawn as ball-and-stick models. The carbon, oxygen, and nitrogen atoms are colored in white, red, and blue, respectively.
Figure 7.
FIGURE 7. Proposed acylation-deacylation catalytic mechanism of AmiF. The carbon atom of formamide is attacked by a nucleophilic catalyst (Cys^166). An acyl intermediate is formed, and an ammonia molecule is released via the collaboration by Glu^60 and Lys^133. The subsequent nucleophilic attack is presumed by a water molecule to begin the deacylation reaction.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 12220-12229) copyright 2007.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20960531 G.Zanotti, and L.Cendron (2010).
Functional and structural aspects of Helicobacter pylori acidic stress response factors.
  IUBMB Life, 62, 715-723.  
19830420 S.Martínez-Rodríguez, A.I.Martínez-Gómez, F.Rodríguez-Vico, J.M.Clemente-Jiménez, and F.J.Las Heras-Vázquez (2010).
Carbamoylases: characteristics and applications in biotechnological processes.
  Appl Microbiol Biotechnol, 85, 441-458.  
19153727 J.S.Kim, M.K.Tiwari, H.J.Moon, M.Jeya, T.Ramu, D.K.Oh, I.W.Kim, and J.K.Lee (2009).
Identification and characterization of a novel nitrilase from Pseudomonas fluorescens Pf-5.
  Appl Microbiol Biotechnol, 83, 273-283.  
18946669 K.C.Dent, B.W.Weber, M.J.Benedik, and B.T.Sewell (2009).
The cyanide hydratase from Neurospora crassa forms a helix which has a dimeric repeat.
  Appl Microbiol Biotechnol, 82, 271-278.  
19270703 N.LaRonde-LeBlanc, M.Resto, and B.Gerratana (2009).
Regulation of active site coupling in glutamine-dependent NAD(+) synthetase.
  Nat Struct Mol Biol, 16, 421-429.
PDB code: 3dla
17881822 S.W.Kimani, V.B.Agarkar, D.A.Cowan, M.F.Sayed, and B.T.Sewell (2007).
Structure of an aliphatic amidase from Geobacillus pallidus RAPc8.
  Acta Crystallogr D Biol Crystallogr, 63, 1048-1058.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.