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PDBsum entry 1k17
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Hydrolase PDB id
1k17

 

 

 

 

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Contents
Protein chain
271 a.a.
Theoretical model
PDB id:
1k17
Name: Hydrolase
Title: Aliphatic amidase (ec 3.5.1.4)
Structure: Aliphatic amidase. Chain: a. Fragment: residues 20-290. Ec: 3.5.1.4
Source: Pseudomonas aeruginosa. Bacteria. Strain: 8602
Authors: C.Novo,S.Farnaud,R.Tata,A.Clemente,P.R.Brown
Key ref: C.Novo et al. (2002). Support for a three-dimensional structure predicting a Cys-Glu-Lys catalytic triad for Pseudomonas aeruginosa amidase comes from site-directed mutagenesis and mutations altering substrate specificity. Biochem J, 365, 731-738. PubMed id: 11955282
Date:
24-Sep-01     Release date:   10-Oct-01    
PROCHECK
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 Headers
 References

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

 

 
Biochem J 365:731-738 (2002)
PubMed id: 11955282  
 
 
Support for a three-dimensional structure predicting a Cys-Glu-Lys catalytic triad for Pseudomonas aeruginosa amidase comes from site-directed mutagenesis and mutations altering substrate specificity.
C.Novo, S.Farnaud, R.Tata, A.Clemente, P.R.Brown.
 
  ABSTRACT  
 
The aliphatic amidase from Pseudomonas aeruginosa belongs to the nitrilase superfamily, and Cys(166) is the nucleophile of the catalytic mechanism. A model of amidase was built by comparative modelling using the crystal structure of the worm nitrilase-fragile histidine triad fusion protein (NitFhit; Protein Data Bank accession number 1EMS) as a template. The amidase model predicted a catalytic triad (Cys-Glu-Lys) situated at the bottom of a pocket and identical with the presumptive catalytic triad of NitFhit. Three-dimensional models for other amidases belonging to the nitrilase superfamily also predicted Cys-Glu-Lys catalytic triads. Support for the structure for the P. aeruginosa amidase came from site-direct mutagenesis and from the locations of amino acid residues that altered substrate specificity or binding when mutated.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21489785 D.Pandey, R.Singh, and D.Chand (2011).
An improved bioprocess for synthesis of acetohydroxamic acid using DTT (dithiothreitol) treated resting cells of Bacillus sp. APB-6.
  Bioresour Technol, 102, 6579-6586.  
20122268 S.Wu, T.Liu, and R.B.Altman (2010).
Identification of recurring protein structure microenvironments and discovery of novel functional sites around CYS residues.
  BMC Struct Biol, 10, 4.  
19053248 K.T.Barglow, K.S.Saikatendu, M.H.Bracey, R.Huey, G.M.Morris, A.J.Olson, R.C.Stevens, and B.F.Cravatt (2008).
Functional proteomic and structural insights into molecular recognition in the nitrilase family enzymes.
  Biochemistry, 47, 13514-13523.
PDB code: 2w1v
17416655 D.Vidal-Ingigliardi, S.Lewenza, and N.Buddelmeijer (2007).
Identification of essential residues in apolipoprotein N-acyl transferase, a member of the CN hydrolase family.
  J Bacteriol, 189, 4456-4464.  
17442671 J.Andrade, A.Karmali, M.A.Carrondo, and C.Frazão (2007).
Structure of amidase from Pseudomonas aeruginosa showing a trapped acyl transfer reaction intermediate state.
  J Biol Chem, 282, 19598-19605.
PDB code: 2uxy
  17329817 J.Andrade, A.Karmali, M.A.Carrondo, and C.Frazão (2007).
Crystallization, diffraction data collection and preliminary crystallographic analysis of hexagonal crystals of Pseudomonas aeruginosa amidase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 214-216.  
17914174 S.Martins, S.Lourenço, A.Karmali, and M.L.Serralheiro (2007).
Monoclonal antibodies recognize conformational epitopes on wild-type and recombinant mutant amidases from pseudomonas aeruginosa.
  Mol Biotechnol, 37, 136-145.  
16911525 I.Müller, and R.Müller (2006).
Biochemical characterization of MelJ and MelK.
  FEBS J, 273, 3768-3778.  
17193242 R.Singh, R.Sharma, N.Tewari, and D.S.Rawat (2006).
Nitrilase and its application as a 'green' catalyst.
  Chem Biodivers, 3, 1279-1287.  
  17142891 V.B.Agarkar, S.W.Kimani, D.A.Cowan, M.F.Sayed, and B.T.Sewell (2006).
The quaternary structure of the amidase from Geobacillus pallidus RAPc8 is revealed by its crystal packing.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 1174-1178.
PDB code: 2plq
16336190 S.I.Pertsovich, D.T.Guranda, D.A.Podchernyaev, A.S.Yanenko, and V.K.Svedas (2005).
Aliphatic amidase from Rhodococcus rhodochrous M8 is related to the nitrilase/cyanide hydratase family.
  Biochemistry (Mosc), 70, 1280-1287.  
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.

 

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