spacer
spacer
Go to PDB code: 
protein ligands Protein-protein interface(s) links
Bacterial amidohydrolase PDB id
4pga
Jmol
Contents
Protein chains
330 a.a. *
Ligands
SO4 ×2
NH4 ×2
Waters ×405
* Residue conservation analysis
PDB id:
4pga
Name: Bacterial amidohydrolase
Title: Glutaminase-asparaginase from pseudomonas 7a
Structure: Glutaminase-asparaginase. Chain: a, b. Engineered: yes. Other_details: amidohydrolase, asparaginase
Source: Pseudomonas sp. 7a. Organism_taxid: 65406
Biol. unit: Tetramer (from PDB file)
Resolution:
1.70Å     R-factor:   0.199     R-free:   0.254
Authors: C.G.Jakob,K.Lewinski,M.W.Lacount,J.Roberts,L.Lebioda
Key ref:
C.G.Jakob et al. (1997). Ion binding induces closed conformation in Pseudomonas 7A glutaminase-asparaginase (PGA): crystal structure of the PGA-SO4(2-)-NH4+ complex at 1.7 A resolution. Biochemistry, 36, 923-931. PubMed id: 9020792 DOI: 10.1021/bi961979x
Date:
14-Jan-97     Release date:   23-Jul-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P10182  (ASPQ_PSES7) -  Glutaminase-asparaginase
Seq:
Struc: 		337 a.a.
330 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 12 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.5.1.38  - Glutamin-(asparagin-)ase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction:
1. L-glutamine + H2O = L-glutamate + NH3
2. L-asparagine + H2O = L-aspartate + NH3
L-glutamine
 + H(2)O
 = L-glutamate
 + NH(3)
L-asparagine
 + H(2)O
 = L-aspartate
 + NH(3)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     periplasmic space   1 term 
  Biological process     cellular amino acid metabolic process   2 terms 
  Biochemical function     hydrolase activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi961979x Biochemistry 36:923-931 (1997)
PubMed id: 9020792  
 
 
Ion binding induces closed conformation in Pseudomonas 7A glutaminase-asparaginase (PGA): crystal structure of the PGA-SO4(2-)-NH4+ complex at 1.7 A resolution.
C.G.Jakob, K.Lewinski, M.W.LaCount, J.Roberts, L.Lebioda.
 
  ABSTRACT  
 
Pseudomonas 7A glutaminase-asparaginase (PGA) catalyzes the hydrolysis of D- and L-isomers of glutamine and asparagine. X-ray quality type-1 crystals of PGA have been obtained from 2.0 M ammonium sulfate. The space group is C222(1) with unit-cell dimensions a = 78.62, b = 135.80, and c = 137.88 A. The tetrameric molecule is located on a crystallographic 2-fold axis, and two subunits form the asymmetric portion of the unit cell. The structure was solved by the molecular replacement method and refined at 1.7 A resolution to an R = 19.9% with a good geometry of the model, G = 0.05. The resultant electron density maps enabled us to resolve individual constituent atoms of most residues and introduce minor revisions to the amino acid sequence. The catalytic loop, Thr20-Gly40, is in the closed conformation with excellent electron density in both subunits. A sulfate ion and an ammonium ion are bound in the substrate binding site and interect with the loop. This interaction appears to be responsible for the observed closed conformation. New arguments supporting Thr20 as the catalytic nucleophile in the asparaginase activity are proposed.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18323619 O.V.Kravchenko, Y.A.Kislitsin, A.N.Popov, S.V.Nikonov, and I.P.Kuranova (2008).
Three-dimensional structures of L-asparaginase from Erwinia carotovora complexed with aspartate and glutamate.
  Acta Crystallogr D Biol Crystallogr, 64, 248-256.  
17451745 M.K.Yun, A.Nourse, S.W.White, C.O.Rock, and R.J.Heath (2007).
Crystal structure and allosteric regulation of the cytoplasmic Escherichia coli L-asparaginase I.
  J Mol Biol, 369, 794-811.
PDB codes: 2him 2p2d 2p2n
17116585 S.Yano, A.Kamemura, K.Yoshimune, M.Moriguchi, S.Yamamoto, T.Tachiki, and M.Wakayama (2006).
Analysis of essential amino acid residues for catalytic activity of glutaminase from Micrococcus luteus K-3.
  J Biosci Bioeng, 102, 362-364.  
16216574 E.Schmitt, M.Panvert, S.Blanquet, and Y.Mechulam (2005).
Structural basis for tRNA-dependent amidotransferase function.
  Structure, 13, 1421-1433.
PDB code: 1zq1
15735339 M.Yao, Y.Yasutake, H.Morita, and I.Tanaka (2005).
Structure of the type I L-asparaginase from the hyperthermophilic archaeon Pyrococcus horikoshii at 2.16 angstroms resolution.
  Acta Crystallogr D Biol Crystallogr, 61, 294-301.
PDB code: 1wls
12499544 J.Lubkowski, M.Dauter, K.Aghaiypour, A.Wlodawer, and Z.Dauter (2003).
Atomic resolution structure of Erwinia chrysanthemi L-asparaginase.
  Acta Crystallogr D Biol Crystallogr, 59, 84-92.
PDB code: 1o7j
12021439 D.Christendat, V.Saridakis, Y.Kim, P.A.Kumar, X.Xu, A.Semesi, A.Joachimiak, C.H.Arrowsmith, and A.M.Edwards (2002).
The crystal structure of hypothetical protein MTH1491 from Methanobacterium thermoautotrophicum.
  Protein Sci, 11, 1409-1414.
PDB code: 1l1s
11223513 M.Jaskólski, M.Kozak, J.Lubkowski, G.Palm, and A.Wlodawer (2001).
Structures of two highly homologous bacterial L-asparaginases: a case of enantiomorphic space groups.
  Acta Crystallogr D Biol Crystallogr, 57, 369-377.
PDB codes: 1hfj 1hfk 1ho3
10684596 E.Ortlund, M.W.Lacount, K.Lewinski, and L.Lebioda (2000).
Reactions of Pseudomonas 7A glutaminase-asparaginase with diazo analogues of glutamine and asparagine result in unexpected covalent inhibitions and suggests an unusual catalytic triad Thr-Tyr-Glu.
  Biochemistry, 39, 1199-1204.
PDB codes: 1djo 1djp
11018727 H.P.Aung, M.Bocola, S.Schleper, and K.H.Röhm (2000).
Dynamics of a mobile loop at the active site of Escherichia coli asparaginase.
  Biochim Biophys Acta, 1481, 349-359.  
10739936 M.Kozak, and M.Jaskólski (2000).
Crystallization and preliminary crystallographic studies of a new crystal form of Escherichia coli L--asparaginase II (Ser58Ala mutant).
  Acta Crystallogr D Biol Crystallogr, 56, 509-511.  
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 codes are shown on the right.