1.65A crystal structure of isocitrate dehydrogenase from Burkholderia pseudomallei

Experimental Data Snapshot

  • Resolution: 1.65 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 

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This is version 1.5 of the entry. See complete history


Structural basis of the substrate specificity of bifunctional isocitrate dehydrogenase kinase/phosphatase.

Yates, S.P.Edwards, T.E.Bryan, C.M.Stein, A.J.Van Voorhis, W.C.Myler, P.J.Stewart, L.J.Zheng, J.Jia, Z.

(2011) Biochemistry 50: 8103-8106

  • DOI: https://doi.org/10.1021/bi200809p
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Isocitrate dehydrogenase kinase/phosphatase (AceK) regulates entry into the glyoxylate bypass by reversibly phosphorylating isocitrate dehydrogenase (ICDH). On the basis of the recently determined structure of the AceK-ICDH complex from Escherichia coli, we have classified the structures of homodimeric NADP(+)-ICDHs to rationalize and predict which organisms likely contain substrates for AceK. One example is Burkholderia pseudomallei (Bp). Here we report a crystal structure of Bp-ICDH that exhibits the necessary structural elements required for AceK recognition. Kinetic analyses provided further confirmation that Bp-ICDH is a substrate for AceK. We conclude that the highly stringent AceK binding sites on ICDH are maintained only in Gram-negative bacteria.

  • Organizational Affiliation

    Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON K7L 3N6, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isocitrate dehydrogenase [NADP]427Burkholderia pseudomalleiMutation(s): 0 
Gene Names: icdBPSL0896
Find proteins for Q3JV82 (Burkholderia pseudomallei (strain 1710b))
Explore Q3JV82 
Go to UniProtKB:  Q3JV82
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3JV82
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.65 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.206 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.993α = 90
b = 62.238β = 118.52
c = 70.998γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-10-05
    Changes: Database references
  • Version 1.3: 2013-10-30
    Changes: Database references
  • Version 1.4: 2017-10-25
    Changes: Refinement description
  • Version 1.5: 2024-02-21
    Changes: Data collection, Database references