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Hydrolase PDB id
1jsl
Jmol
Contents
Protein chains
324 a.a. *
Ligands
DDO ×4
1PE
GOL ×3
Waters ×1164
* Residue conservation analysis
PDB id:
1jsl
Name: Hydrolase
Title: Crystal structure of erwinia chrysanthemi l-asparaginase com with 6-hydroxy-d-norleucine
Structure: L-asparaginase. Chain: a, b, c, d. Ec: 3.5.1.1
Source: Erwinia chrysanthemi. Organism_taxid: 556
Biol. unit: Tetramer (from PQS)
Resolution:
1.70Å     R-factor:   0.186     R-free:   0.212
Authors: K.Aghaiypour,A.Wlodawer,J.Lubkowski
Key ref: K.Aghaiypour et al. (2001). Do bacterial L-asparaginases utilize a catalytic triad Thr-Tyr-Glu? Biochim Biophys Acta, 1550, 117-128. PubMed id: 11755201 DOI: 10.1016/S0167-4838(01)00270-9
Date:
17-Aug-01     Release date:   09-Jan-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P06608  (ASPG_ERWCH) -  L-asparaginase
Seq:
Struc: 		348 a.a.
324 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
Bound ligand (Het Group name = DDO)
matches with 58.33% similarity 		+ 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: 10.1016/S0167-4838(01)00270-9 Biochim Biophys Acta 1550:117-128 (2001)
PubMed id: 11755201  
 
 
Do bacterial L-asparaginases utilize a catalytic triad Thr-Tyr-Glu?
K.Aghaiypour, A.Wlodawer, J.Lubkowski.
 
  ABSTRACT  
 
The structures of Erwinia chrysanthemi L-asparaginase (ErA) complexed with the L- and D-stereoisomers of the suicide inhibitor, 6-diazo-5-oxy-norleucine, have been solved using X-ray crystallography and refined with data extending to 1.7 A. The distances between the Calpha atoms of the inhibitor molecules and the hydroxyl oxygen atoms of Thr-15 and Tyr-29 (1.20 and 1.60 A, respectively) clearly indicate the presence of covalent bonds between these moieties, confirming the nucleophilic role of Thr-15 during the first stage of enzymatic reactions and also indicating direct involvement of Tyr-29. The factors responsible for activating Tyr-29 remain unclear, although some structural changes around Ser-254', Asp-96, and Glu-63, common to both complexes, suggest that those residues play a function. The role of Glu-289' as the activator of Tyr-29, previously postulated for the closely related Pseudomonas 7A L-glutaminase-asparaginase, is not confirmed in this study, due to the lack of interactions between these residues in these complexes and in holoenzymes. The results reported here are consistent with previous reports that mutants of Escherichia coli L-asparaginase lacking Glu-289 remain catalytically active and prove the catalytic roles of both Thr-15 and Tyr-29, while still leaving open the question of the exact mechanism resulting in the unusual chemical properties of these residues.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20832300 S.Kumar, V.Venkata Dasu, and K.Pakshirajan (2011).
Purification and characterization of glutaminase-free L-asparaginase from Pectobacterium carotovorum MTCC 1428.
  Bioresour Technol, 102, 2077-2082.  
18459799 G.Brown, A.Singer, M.Proudfoot, T.Skarina, Y.Kim, C.Chang, I.Dementieva, E.Kuznetsova, C.F.Gonzalez, A.Joachimiak, A.Savchenko, and A.F.Yakunin (2008).
Functional and structural characterization of four glutaminases from Escherichia coli and Bacillus subtilis.
  Biochemistry, 47, 5724-5735.
PDB codes: 1mki 1u60 3brm
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
17364689 N.Verma, K.Kumar, G.Kaur, and S.Anand (2007).
L-asparaginase: a promising chemotherapeutic agent.
  Crit Rev Biotechnol, 27, 45-62.  
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
12753071 D.C.Dieterich, M.Landwehr, C.Reissner, K.H.Smalla, K.Richter, G.Wolf, T.M.Böckers, E.D.Gundelfinger, and M.R.Kreutz (2003).
Gliap--a novel untypical L-asparaginase localized to rat brain astrocytes.
  J Neurochem, 85, 1117-1125.  
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
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.