1HFW

X-ray structure of the complex between Erwinia chrysanthemi L-asparaginase and L-Glutamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Stuctural Basis for the Activity and Substrate Specificity of Erwinia Chrysanthemi L-Asparaginase

Kolyani, K.A.Wlodawer, A.Lubkowski, J.

(2001) Biochemistry 40: 5655

  • Primary Citation of Related Structures:  1HG0, 1HG1

  • PubMed Abstract: 
  • Bacterial L-asparaginases, enzymes that catalyze the hydrolysis of L-asparagine to aspartic acid, have been used for over 30 years as therapeutic agents in the treatment of acute childhood lymphoblastic leukemia. Other substrates of asparaginases inc ...

    Bacterial L-asparaginases, enzymes that catalyze the hydrolysis of L-asparagine to aspartic acid, have been used for over 30 years as therapeutic agents in the treatment of acute childhood lymphoblastic leukemia. Other substrates of asparaginases include L-glutamine, D-asparagine, and succinic acid monoamide. In this report, we present high-resolution crystal structures of the complexes of Erwinia chrysanthemi L-asparaginase (ErA) with the products of such reactions that also can serve as substrates, namely L-glutamic acid (L-Glu), D-aspartic acid (D-Asp), and succinic acid (Suc). Comparison of the four independent active sites within each complex indicates unique and specific binding of the ligand molecules; the mode of binding is also similar between complexes. The lack of the alpha-NH3(+) group in Suc, compared to L-Asp, does not affect the binding mode. The side chain of L-Glu, larger than that of L-Asp, causes several structural distortions in the ErA active side. The active site flexible loop (residues 15-33) does not exhibit stable conformation, resulting in suboptimal orientation of the nucleophile, Thr15. Additionally, the delta-COO(-) plane of L-Glu is approximately perpendicular to the plane of gamma-COO(-) in L-Asp bound to the asparaginase active site. Binding of D-Asp to the ErA active site is very distinctive compared to the other ligands, suggesting that the low activity of ErA against D-Asp could be mainly attributed to the low k(cat) value. A comparison of the amino acid sequence and the crystal structure of ErA with those of other bacterial L-asparaginases shows that the presence of two active-site residues, Glu63(ErA) and Ser254(ErA), may correlate with significant glutaminase activity, while their substitution by Gln and Asn, respectively, may lead to minimal L-glutaminase activity.


    Related Citations: 
    • Crystal Structure of Escherichia Coli L-Asparaginase, an Enzyme Used in Cancer Therapy
      Swain, A.L.,Jaskolski, M.,Housset, D.,Rao, J.K.M.,Wlodawer, A.
      (1993) Proc.Natl.Acad.Sci.USA 90: 1474
    • A Left-Handed Crossover Involved in Amidohydrolase Catalysis, Crystal Structure of Erwinia Chrysanthemi L-Asparaginase with Bound L-Aspartate
      Miller, M.,Rao, J.K.M.,Wlodawer, A.,Gribskov, M.R.
      (1993) FEBS Lett. 328: 275


    Organizational Affiliation

    Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Frederick, Maryland 21702, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-ASPARAGINASE
A, B, C, D
327Dickeya chrysanthemiGene Names: ansB (asn)
EC: 3.5.1.1
Find proteins for P06608 (Dickeya chrysanthemi)
Go to UniProtKB:  P06608
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLU
Query on GLU

Download SDF File 
Download CCD File 
A, B, C, D
GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.168 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 108.470α = 90.00
b = 91.700β = 91.94
c = 130.620γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-08-07
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance