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PDBsum entry 2plq

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protein links
Hydrolase PDB id
2plq
Jmol
Contents
Protein chain
340 a.a. *
Waters ×305
* Residue conservation analysis
PDB id:
2plq
Name: Hydrolase
Title: Crystal structure of the amidase from geobacillus pallidus r
Structure: Aliphatic amidase. Chain: a. Synonym: acylamide amidohydrolase. Engineered: yes
Source: Geobacillus pallidus. Organism_taxid: 33936. Strain: rapc8. Gene: amie, ami. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
1.90Å     R-factor:   0.147     R-free:   0.177
Authors: S.W.Kimani,B.T.Sewell,V.B.Agarkar,M.F.Sayed,D.A.Cowan
Key ref:
V.B.Agarkar et al. (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. PubMed id: 17142891 DOI: 10.1107/S1744309106043855
Date:
20-Apr-07     Release date:   01-May-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9L543  (AMIE_BACSP) -  Aliphatic amidase
Seq:
Struc:
348 a.a.
340 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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   1 term 
  Biochemical function     hydrolase activity     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1107/S1744309106043855 Acta Crystallogr Sect F Struct Biol Cryst Commun 62:1174-1178 (2006)
PubMed id: 17142891  
 
 
The quaternary structure of the amidase from Geobacillus pallidus RAPc8 is revealed by its crystal packing.
V.B.Agarkar, S.W.Kimani, D.A.Cowan, M.F.Sayed, B.T.Sewell.
 
  ABSTRACT  
 
The amidase from Geobacillus pallidus RAPc8, a moderate thermophile, is a member of the nitrilase enzyme superfamily. It converts amides to the corresponding acids and ammonia and has application as an industrial catalyst. RAPc8 amidase has been cloned and functionally expressed in Escherichia coli and has been purified by heat treatment and a number of chromatographic steps. The enzyme was crystallized using the hanging-drop vapour-diffusion method. Crystals produced in the presence of 1.2 M sodium citrate, 400 mM NaCl, 100 mM sodium acetate pH 5.6 were selected for X-ray diffraction studies. A data set having acceptable statistics to 1.96 A resolution was collected under cryoconditions using an in-house X-ray source. The space group was determined to be primitive cubic P4(2)32, with unit-cell parameter a = 130.49 (+/-0.05) A. The structure was solved by molecular replacement using the backbone of the hypothetical protein PH0642 from Pyrococcus horikoshii (PDB code 1j31) with all non-identical side chains substituted with alanine as a probe. There is one subunit per asymmetric unit. The subunits are packed as trimers of dimers with D3 point-group symmetry around the threefold axis in such a way that the dimer interface seen in the homologues is preserved.
 
  Selected figure(s)  
 
Figure 2.
A crystal of the amidase from G. pallidus RAPc8. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 December 1; 62(Pt 12): 1174–1178. Published online 2006 November 4. doi: 10.1107/S1744309106043855. Copyright [copyright] International Union of Crystallography 2006
Figure 4.
Stereoviews of the suggested solution hexamer viewed down one of the twofold axes from both directions. The preserved dimer surface is centred in (a). The interacting surfaces depicted in the foreground of (b) are based on the model of the putative CN hydrolase from yeast (PDB code 1f89). 66 C-terminal amino acids for each subunit are not depicted in this model. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 December 1; 62(Pt 12): 1174–1178. Published online 2006 November 4. doi: 10.1107/S1744309106043855. Copyright [copyright] International Union of Crystallography 2006
 
  The above figures are reprinted from an Open Access publication published by the IUCr: Acta Crystallogr Sect F Struct Biol Cryst Commun (2006, 62, 1174-1178) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  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.  
17371547 R.N.Thuku, B.W.Weber, A.Varsani, and B.T.Sewell (2007).
Post-translational cleavage of recombinantly expressed nitrilase from Rhodococcus rhodochrous J1 yields a stable, active helical form.
  FEBS J, 274, 2099-2108.  
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