1JSL

Crystal structure of Erwinia chrysanthemi L-asparaginase complexed with 6-HYDROXY-D-NORLEUCINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.200 

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

  • DOI: 10.1016/s0167-4838(01)00270-9
  • Primary Citation of Related Structures:  
    1JSL, 1JSR

  • 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 distances between the Calpha atoms of the inhibitor molecules and the hydroxyl oxygen atoms of Thr-15 and Tyr-29 (1 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
L-asparaginaseA, B, C, D327Dickeya chrysanthemiMutation(s): 4 
Gene Names: ansBasn
EC: 3.5.1.1
UniProt
Find proteins for P06608 (Dickeya chrysanthemi)
Explore P06608 
Go to UniProtKB:  P06608
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.15α = 90
b = 90.386β = 91.38
c = 127.37γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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