spacer
spacer

PDBsum entry 3eca

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Hydrolase PDB id
3eca
Jmol
Contents
Protein chains
326 a.a. *
Ligands
ASP ×4
Waters ×410
* Residue conservation analysis
PDB id:
3eca
Name: Hydrolase
Title: Crystal structure of escherichia coli l-asparaginase, an enzyme used in cancer therapy
Structure: Asparaginase type ii. Chain: a, b, c, d. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562
Biol. unit: Tetramer (from PQS)
Resolution:
2.40Å     R-factor:   0.149    
Authors: A.L.Swain,M.Jaskolski,D.Housset,J.K.M.Rao,A.Wlodawer
Key ref: A.L.Swain et al. (1993). Crystal structure of Escherichia coli L-asparaginase, an enzyme used in cancer therapy. Proc Natl Acad Sci U S A, 90, 1474-1478. PubMed id: 8434007 DOI: 10.1073/pnas.90.4.1474
Date:
02-Jul-93     Release date:   31-Oct-93    
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

 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
Bound ligand (Het Group name = ASP)
corresponds exactly
+ 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   3 terms 
  Biological process     cellular amino acid metabolic process   2 terms 
  Biochemical function     hydrolase activity     2 terms  

 

 
    Added reference    
 
 
DOI no: 10.1073/pnas.90.4.1474 Proc Natl Acad Sci U S A 90:1474-1478 (1993)
PubMed id: 8434007  
 
 
Crystal structure of Escherichia coli L-asparaginase, an enzyme used in cancer therapy.
A.L.Swain, M.Jaskólski, D.Housset, J.K.Rao, A.Wlodawer.
 
  ABSTRACT  
 
The crystal structure of Escherichia coli asparaginase II (EC 3.5.1.1), a drug (Elspar) used for the treatment of acute lymphoblastic leukemia, has been determined at 2.3 A resolution by using data from a single heavy atom derivative in combination with molecular replacement. The atomic model was refined to an R factor of 0.143. This enzyme, active as a homotetramer with 222 symmetry, belongs to the class of alpha/beta proteins. Each subunit has two domains with unique topological features. On the basis of present structural evidence consistent with previous biochemical studies, we propose locations for the active sites between the N- and C-terminal domains belonging to different subunits and postulate a catalytic role for Thr-89.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21106986 M.N.Offman, M.Krol, N.Patel, S.Krishnan, J.Liu, V.Saha, and P.A.Bates (2011).
Rational engineering of L-asparaginase reveals importance of dual activity for cancer cell toxicity.
  Blood, 117, 1614-1621.  
21085483 C.Scotti, P.Sommi, M.V.Pasquetto, D.Cappelletti, S.Stivala, P.Mignosi, M.Savio, L.R.Chiarelli, G.Valentini, V.M.Bolanos-Garcia, D.S.Merrell, S.Franchini, M.L.Verona, C.Bolis, E.Solcia, R.Manca, D.Franciotta, A.Casasco, P.Filipazzi, E.Zardini, and V.Vannini (2010).
Cell-cycle inhibition by Helicobacter pylori L-asparaginase.
  PLoS One, 5, e13892.  
19543838 R.S.Prakasham, M.Hymavathi, C.h.Subba Rao, S.K.Arepalli, J.Venkateswara Rao, P.K.Kennady, K.Nasaruddin, J.B.Vijayakumar, and P.N.Sarma (2010).
Evaluation of antineoplastic activity of extracellular asparaginase produced by isolated Bacillus circulans.
  Appl Biochem Biotechnol, 160, 72-80.  
  19509471 N.Patel, S.Krishnan, M.N.Offman, M.Krol, C.X.Moss, C.Leighton, F.W.van Delft, M.Holland, J.Liu, S.Alexander, C.Dempsey, H.Ariffin, M.Essink, T.O.Eden, C.Watts, P.A.Bates, and V.Saha (2009).
A dyad of lymphoblastic lysosomal cysteine proteases degrades the antileukemic drug L-asparaginase.
  J Clin Invest, 119, 1964-1973.  
19966411 P.Dhavala, and A.C.Papageorgiou (2009).
Structure of Helicobacter pyloriL-asparaginase at 1.4 A resolution.
  Acta Crystallogr D Biol Crystallogr, 65, 1253-1261.
PDB codes: 2wlt 2wt4
  19707421 R.Masetti, and A.Pession (2009).
First-line treatment of acute lymphoblastic leukemia with pegasparaginase.
  Biologics, 3, 359-368.  
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.  
18441029 M.Chruszcz, A.Wlodawer, and W.Minor (2008).
Determination of protein structures--a series of fortunate events.
  Biophys J, 95, 1-9.
PDB code: 3pzw
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.  
  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.  
17696798 C.H.Fu, and K.M.Sakamoto (2007).
PEG-asparaginase.
  Expert Opin Pharmacother, 8, 1977-1984.  
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.  
16892249 H.Geckil, S.Gencer, B.Ates, U.Ozer, M.Uckun, and I.Yilmaz (2006).
Effect of Vitreoscilla hemoglobin on production of a chemotherapeutic enzyme, L-asparaginase, by Pseudomonas aeruginosa.
  Biotechnol J, 1, 203-208.  
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
16963649 L.H.Lucas, B.A.Ersoy, L.A.Kueltzo, S.B.Joshi, D.T.Brandau, N.Thyagarajapuram, L.J.Peek, and C.R.Middaugh (2006).
Probing protein structure and dynamics by second-derivative ultraviolet absorption analysis of cation-{pi} interactions.
  Protein Sci, 15, 2228-2243.  
16452626 S.Benjwal, S.Verma, K.H.Röhm, and O.Gursky (2006).
Monitoring protein aggregation during thermal unfolding in circular dichroism experiments.
  Protein Sci, 15, 635-639.  
15660216 A.Khushoo, Y.Pal, and K.J.Mukherjee (2005).
Optimization of extracellular production of recombinant asparaginase in Escherichia coli in shake-flask and bioreactor.
  Appl Microbiol Biotechnol, 68, 189-197.  
16006240 A.Werner, K.H.Röhm, and H.J.Müller (2005).
Mapping of B-cell epitopes in E. coli asparaginase II, an enzyme used in leukemia treatment.
  Biol Chem, 386, 535-540.  
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
  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.  
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
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.  
15274089 N.S.Murthy, and J.R.Knox (2004).
Hydration of proteins: SAXS study of native and methoxy polyethyleneglycol (mPEG)-modified L-asparaginase and bovine serum albumin in mPEG solutions.
  Biopolymers, 74, 457-466.  
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
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
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
11705966 G.D.Pullinger, R.Sowdhamini, and A.J.Lax (2001).
Localization of functional domains of the mitogenic toxin of Pasteurella multocida.
  Infect Immun, 69, 7839-7850.  
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.  
11005928 L.Guo, J.Wang, S.Qian, X.Yan, R.Chen, and G.Meng (2000).
Construction and structural modeling of a single-chain Fv-asparaginase fusion protein resistant to proteolysis.
  Biotechnol Bioeng, 70, 456-463.  
  10930734 L.Ortuño-Olea, and S.Durán-Vargas (2000).
The L-asparagine operon of Rhizobium etli contains a gene encoding an atypical asparaginase.
  FEMS Microbiol Lett, 189, 177-182.  
10924740 M.Paetzel, R.E.Dalbey, and N.C.Strynadka (2000).
The structure and mechanism of bacterial type I signal peptidases. A novel antibiotic target.
  Pharmacol Ther, 87, 27-49.  
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.  
9188741 A.V.Efimov (1997).
Structural trees for protein superfamilies.
  Proteins, 28, 241-260.  
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
7925369 C.Derst, A.Wehner, V.Specht, and K.H.Röhm (1994).
States and functions of tyrosine residues in Escherichia coli asparaginase II.
  Eur J Biochem, 224, 533-540.  
7881905 G.E.Norris, T.J.Stillman, B.F.Anderson, and E.N.Baker (1994).
The three-dimensional structure of PNGase F, a glycosylasparaginase from Flavobacterium meningosepticum.
  Structure, 2, 1049-1059.
PDB code: 1pgs
8234268 H.H.Chung, D.R.Benson, V.W.Cornish, and P.G.Schultz (1993).
Probing the role of loop 2 in Ras function with unnatural amino acids.
  Proc Natl Acad Sci U S A, 90, 10145-10149.  
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.