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PDBsum entry 2uxy

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Hydrolase PDB id
2uxy
Jmol
Contents
Protein chain
341 a.a. *
Ligands
SO4
Waters ×305
* Residue conservation analysis
PDB id:
2uxy
Name: Hydrolase
Title: Aliphatic amidase
Structure: Aliphatic amidase. Chain: a. Fragment: residues 1-341. Synonym: acylamide amidohydrolase. Other_details: an acyl reaction intermediate was found bount to sg of cys166
Source: Pseudomonas aeruginosa. Organism_taxid: 287
Resolution:
1.25Å     R-factor:   0.110     R-free:   0.135
Authors: J.Andrade,A.Karmali,M.A.Carrondo,C.Frazao
Key ref:
J.Andrade et al. (2007). Structure of amidase from Pseudomonas aeruginosa showing a trapped acyl transfer reaction intermediate state. J Biol Chem, 282, 19598-19605. PubMed id: 17442671 DOI: 10.1074/jbc.M701039200
Date:
02-Apr-07     Release date:   17-Apr-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P11436  (AMIE_PSEAE) -  Aliphatic amidase
Seq:
Struc:
346 a.a.
341 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.5.1.4  - Amidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: A monocarboxylic acid amide + H2O = a monocarboxylate + NH3
monocarboxylic acid amide
+ H(2)O
= monocarboxylate
+ 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   2 terms 
  Biochemical function     hydrolase activity     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1074/jbc.M701039200 J Biol Chem 282:19598-19605 (2007)
PubMed id: 17442671  
 
 
Structure of amidase from Pseudomonas aeruginosa showing a trapped acyl transfer reaction intermediate state.
J.Andrade, A.Karmali, M.A.Carrondo, C.Frazão.
 
  ABSTRACT  
 
Microbial amidases belong to the thiol nitrilases family and have potential biotechnological applications in chemical and pharmaceutical industries as well as in bioremediation. The amidase from Pseudomonas aeruginosa isa6 x 38-kDa enzyme that catalyzes the hydrolysis of a small range of short aliphatic amides. The hereby reported high resolution crystallographic structure shows that each amidase monomer is formed by a globular four-layer alphabetabetaalpha sandwich domain with an additional 81-residue long C-terminal segment. This wraps arm-in-arm with a homologous C-terminal chain of another monomer, producing a strongly packed dimer. In the crystal, the biological active homo-hexameric amidase is built grouping three such dimers around a crystallographic 3-fold axis. The structure also elucidates the structural basis for the enzyme activity, with the nitrilases catalytic triad at the bottom of a 13-A deep, funnel-shaped pocket, accessible from the solvent through a narrow neck with 3-A diameter. An acyl transfer intermediate, resulting from the purification protocol, was found bound to the amidase nucleophilic agent, Cys(166). These results suggest that some pocket defining residues should undergo conformational shifts to allow substrates and products to access and leave the catalytic pocket, for turnover to occur.
 
  Selected figure(s)  
 
Figure 2.
FIGURE 2. Amidase homo-hexamer. A, schematic of the biological active amidase hexamer, showing the strong dimeric association involving the wrapping of C-terminal chains. B, representation of the hexamer solvent accessible surface, in the same orientation and with monomers colored similarly. C, view of the amidase hexamer down the crystallographic 3-fold axis. D, schematic representation of the hexamer, in the same orientation, highlighting the packing relationships with 2- (arrows) and 3-fold (triangle) crystallographic rotation axes.
Figure 4.
FIGURE 4. Reaction scheme. Usually accepted reaction scheme for acyl transfer reaction (63–65) on hydroxylamine and undesirable hydrolysis (65). Enz. stands for enzyme. The tetrahedral intermediate found in the present structural study is marked with an asterisk.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 19598-19605) copyright 2007.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20607233 D.S.Williamson, K.C.Dent, B.W.Weber, A.Varsani, J.Frederick, R.N.Thuku, R.A.Cameron, J.H.van Heerden, D.A.Cowan, and B.T.Sewell (2010).
Structural and biochemical characterization of a nitrilase from the thermophilic bacterium, Geobacillus pallidus RAPc8.
  Appl Microbiol Biotechnol, 88, 143-153.  
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.  
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.  
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.