1JSR

CRYSTAL STRUCTURE OF ERWINIA CHRYSANTHEMI L-ASPARAGINASE COMPLEXED WITH 6-HYDROXY-L-NORLEUCINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Do bacterial L-asparaginases utilize a catalytic triad Thr-Tyr-Glu?

Aghaiypour, K.Wlodawer, A.Lubkowski, J.

(2001) Biochim.Biophys.Acta 1550: 117-128

  • Primary Citation of Related Structures:  1JSL

  • PubMed 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 dista ...

    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.


    Related Citations: 
    • Structural Basis for the Activity and Substrate Specificity of Erwinia chrysanthemi L-Asparaginase
      Aghaiypour, K.,Wlodawer, A.,Lubkowski, J.
      (2001) Biochemistry 40: 5655
    • A Left-Handed Crossover Involved in Amidohydrolase Catalysis. Crystal Structure of Erwinia Chrysanthemi L-Asparaginase with Bound L-Aspartate
      Miller, M.,Rao, J.K.,Wlodawer, A.,Gribskov, M.R.
      (1993) FEBS Lett. 328: 275


    Organizational Affiliation

    Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Frederick, MD 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
LDO
Query on LDO

Download SDF File 
Download CCD File 
A, B, C, D
6-HYDROXY-L-NORLEUCINE
C6 H13 N O3
OLUWXTFAPJJWPL-YFKPBYRVSA-N
 Ligand Interaction
1PE
Query on 1PE

Download SDF File 
Download CCD File 
A
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.182 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 106.065α = 90.00
b = 90.361β = 91.35
c = 127.406γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CNSphasing
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-01-09
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance