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Hydrolase PDB id
4eca
Jmol
Contents
Protein chains
326 a.a. *
Waters ×720
* Residue conservation analysis
PDB id:
4eca
Name: Hydrolase
Title: Asparaginase from e. Coli, mutant t89v with covalently bound
Structure: L-asparagine amidohydrolase. Chain: a, b, c, d. Synonym: asparaginase. Engineered: yes. Mutation: yes. Other_details: thr 12 is acylated by aspartic acid in each
Source: Escherichia coli. Organism_taxid: 83333. Strain: k12. Cellular_location: periplasmatic. Gene: ansb. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PDB file)
Resolution:
2.20Å     R-factor:   0.181    
Authors: G.J.Palm,J.Lubkowski,A.Wlodawer
Key ref: G.J.Palm et al. (1996). A covalently bound catalytic intermediate in Escherichia coli asparaginase: crystal structure of a Thr-89-Val mutant. FEBS Lett, 390, 211-216. PubMed id: 8706862 DOI: 10.1016/0014-5793(96)00660-6
Date:
21-Feb-97     Release date:   16-Jun-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00805  (ASPG2_ECOLI) -  L-asparaginase 2
Seq:
Struc: 		348 a.a.
326 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 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!
  Cellular component     periplasmic space   2 terms 
  Biological process     cellular amino acid metabolic process   2 terms 
  Biochemical function     hydrolase activity     2 terms  

 

 
    Added reference    
 
 
DOI no: 10.1016/0014-5793(96)00660-6 FEBS Lett 390:211-216 (1996)
PubMed id: 8706862  
 
 
A covalently bound catalytic intermediate in Escherichia coli asparaginase: crystal structure of a Thr-89-Val mutant.
G.J.Palm, J.Lubkowski, C.Derst, S.Schleper, K.H.Röhm, A.Wlodawer.
 
  ABSTRACT  
 
Escherichia coli asparaginase II catalyzes the hydrolysis of L-asparagine to L-aspartate via a threonine-bound acyl-enzyme intermediate. A nearly inactive mutant in which one of the active site threonines, Thr-89, was replaced by valine was constructed, expressed, and crystallized. Its structure, solved at 2.2 A resolution, shows high overall similarity to the wild-type enzyme, but an aspartyl moiety is covalently bound to Thr-12, resembling a reaction intermediate. Kinetic analysis confirms the deacylation deficiency, which is also explained on a structural basis. The previously identified oxyanion hole is described in more detail.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18252769 K.Sheppard, J.Yuan, M.J.Hohn, B.Jester, K.M.Devine, and D.Söll (2008).
From one amino acid to another: tRNA-dependent amino acid biosynthesis.
  Nucleic Acids Res, 36, 1813-1825.  
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
17008720 J.Wang, and E.R.Kantrowitz (2006).
Trapping the tetrahedral intermediate in the alkaline phosphatase reaction by substitution of the active site serine with threonine.
  Protein Sci, 15, 2395-2401.
PDB codes: 2g9y 2ga3
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
15611111 L.Feng, K.Sheppard, D.Tumbula-Hansen, and D.Söll (2005).
Gln-tRNAGln formation from Glu-tRNAGln requires cooperation of an asparaginase and a Glu-tRNAGln kinase.
  J Biol Chem, 280, 8150-8155.  
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
15162493 A.Berchanski, B.Shapira, and M.Eisenstein (2004).
Hydrophobic complementarity in protein-protein docking.
  Proteins, 56, 130-142.  
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.  
14635124 A.Berchanski, and M.Eisenstein (2003).
Construction of molecular assemblies via docking: modeling of tetramers with D2 symmetry.
  Proteins, 53, 817-829.  
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
12595697 M.Sanches, J.A.Barbosa, R.T.de Oliveira, J.Abrahão Neto, and I.Polikarpov (2003).
Structural comparison of Escherichia coli L-asparaginase in two monoclinic space groups.
  Acta Crystallogr D Biol Crystallogr, 59, 416-422.
PDB code: 1nns
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
  11106175 C.Derst, J.Henseling, and K.H.Röhm (2000).
Engineering the substrate specificity of Escherichia coli asparaginase. II. Selective reduction of glutaminase activity by amino acid replacements at position 248.
  Protein Sci, 9, 2009-2017.  
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.  
10489465 I.Polikarpov, R.T.de Oliveira, and J.Abrahão-Neto (1999).
Preparation and preliminary X-ray diffraction studies of a new crystal form of L-asparaginase from Escherichia coli.
  Acta Crystallogr D Biol Crystallogr, 55, 1616-1617.  
9020792 C.G.Jakob, K.Lewinski, M.W.LaCount, J.Roberts, and L.Lebioda (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.
PDB code: 4pga
8898907 J.Lubkowski, G.J.Palm, G.L.Gilliland, C.Derst, K.H.Röhm, and A.Wlodawer (1996).
Crystal structure and amino acid sequence of Wolinella succinogenes L-asparaginase.
  Eur J Biochem, 241, 201-207.
PDB code: 1wsa
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.