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Hydrolase PDB id
1o7j
Jmol
Contents
Protein chains
325 a.a. *
Ligands
SO4 ×8
GOL ×2
EDO-EDO-EDO-EDO-
EDO
EDO-EDO-EDO
EDO-EDO-EDO-EDO
Waters ×1360
* Residue conservation analysis
PDB id:
1o7j
Name: Hydrolase
Title: Atomic resolution structure of erwinia chrysanthemi l-asparaginase
Structure: L-asparaginase. Chain: a, b, c, d. Synonym: l-asparagine amidohydrolase, l-asnase. Ec: 3.5.1.1
Source: Erwinia chrysanthemi. Organism_taxid: 556
Biol. unit: Tetramer (from PDB file)
Resolution:
1.0Å     R-factor:   0.109     R-free:   0.128
Authors: J.Lubkowski,M.Dauter,K.Aghaiypour,A.Wlodawer,Z.Dauter
Key ref:
J.Lubkowski et al. (2003). Atomic resolution structure of Erwinia chrysanthemi L-asparaginase. Acta Crystallogr D Biol Crystallogr, 59, 84-92. PubMed id: 12499544 DOI: 10.1107/S0907444902019443
Date:
07-Nov-02     Release date:   04-Dec-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P06608  (ASPG_ERWCH) -  L-asparaginase
Seq:
Struc: 		348 a.a.
325 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.5.1.1  - Asparaginase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-asparagine + H2O = L-aspartate + NH3
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!
  Biological process     cellular amino acid metabolic process   2 terms 
  Biochemical function     hydrolase activity     2 terms  

 

 
    Added reference    
 
 
DOI no: 10.1107/S0907444902019443 Acta Crystallogr D Biol Crystallogr 59:84-92 (2003)
PubMed id: 12499544  
 
 
Atomic resolution structure of Erwinia chrysanthemi L-asparaginase.
J.Lubkowski, M.Dauter, K.Aghaiypour, A.Wlodawer, Z.Dauter.
 
  ABSTRACT  
 
An X-ray structure of L-asparaginase from Erwinia chrysanthemi (ErA) has been refined at 1 A resolution to an R factor of below 0.1, using data collected on a synchrotron source. With four molecules of the enzyme consisting of 327 amino acids each, this crystal contains one of the largest asymmetric units of a protein refined to date at atomic resolution. Previously, structures of ErA and of related enzymes from other bacterial sources have been refined at resolutions not exceeding 1.7 A; thus, the present structure represents a very significant improvement in the quality of the available models of these proteins and should provide a good basis for future studies of the conformational variability of proteins, identification of subtle conformational features and corroboration of the stereochemical libraries, amongst other things. L-Asparaginases, which are enzymes that catalyze the hydrolysis of L-asparagine to aspartic acid, have been used for over 30 y as therapeutic agents in the treatment of acute childhood lymphoblastic leukemia, although the details of the enzymatic reaction and substrate specificity have not yet been completely elucidated. This atomic resolution structure is a step in that direction.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20516624 L.Gabison, M.Chiadmi, M.El Hajji, B.Castro, N.Colloc'h, and T.Prangé (2010).
Near-atomic resolution structures of urate oxidase complexed with its substrate and analogues: the protonation state of the ligand.
  Acta Crystallogr D Biol Crystallogr, 66, 714-724.
PDB codes: 3lbg 3ld4
  18678946 P.Dhavala, J.Krasotkina, C.Dubreuil, and A.C.Papageorgiou (2008).
Expression, purification and crystallization of Helicobacter pylori L-asparaginase.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 740-742.  
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
16214343 A.Gutteridge, and J.M.Thornton (2005).
Understanding nature's catalytic toolkit.
  Trends Biochem Sci, 30, 622-629.  
  16511054 L.E.Wikman, J.Krasotkina, A.Kuchumova, N.N.Sokolov, and A.C.Papageorgiou (2005).
Crystallization and preliminary crystallographic analysis of L-asparaginase from Erwinia carotovora.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 407-409.  
15265041 D.Borek, K.Michalska, K.Brzezinski, A.Kisiel, J.Podkowinski, D.T.Bonthron, D.Krowarsch, J.Otlewski, and M.Jaskolski (2004).
Expression, purification and catalytic activity of Lupinus luteus asparagine beta-amidohydrolase and its Escherichia coli homolog.
  Eur J Biochem, 271, 3215-3226.  
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.