3DMS

1.65A crystal structure of isocitrate dehydrogenase from Burkholderia pseudomallei


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

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: 10.1021/bi200809p

  • 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 c ...

    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.


    Related Citations: 
    • Combining functional and structural genomics to sample the essential Burkholderia structome.
      Baugh, L.,Gallagher, L.A.,Patrapuvich, R.,Clifton, M.C.,Gardberg, A.S.,Edwards, T.E.,Armour, B.,Begley, D.W.,Dieterich, S.H.,Dranow, D.M.,Abendroth, J.,Fairman, J.W.,Fox, D.,Staker, B.L.,Phan, I.,Gillespie, A.,Choi, R.,Nakazawa-Hewitt, S.,Nguyen, M.T.,Napuli, A.,Barrett, L.,Buchko, G.W.,Stacy, R.,Myler, P.J.,Stewart, L.J.,Manoil, C.,Van Voorhis, W.C.
      (2013) Plos One 8: e53851


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Isocitrate dehydrogenase [NADP]
A
427Burkholderia pseudomallei (strain 1710b)Mutation(s): 0 
Gene Names: icd
EC: 1.1.1.42
Find proteins for Q3JV82 (Burkholderia pseudomallei (strain 1710b))
Go to UniProtKB:  Q3JV82
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.205 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 103.993α = 90.00
b = 62.238β = 118.52
c = 70.998γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
DENZOdata reduction
d*TREKdata scaling
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-07-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-10-05
    Type: Database references
  • Version 1.3: 2013-10-30
    Type: Database references
  • Version 1.4: 2017-10-25
    Type: Refinement description