3DMS | pdb_00003dms

1.65A crystal structure of isocitrate dehydrogenase from Burkholderia pseudomallei

• PDB DOI: https://doi.org/10.2210/pdb3DMS/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Burkholderia pseudomallei
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-07-01 Released: 2008-07-15 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.234 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

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

• PubMed: 21870819 
• DOI: https://doi.org/10.1021/bi200809p
• Primary Citation Related Structures: 
  3DMS


• 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.

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 47.23 kDa 
• Atom Count: 3,537 
• Modeled Residue Count: 413 
• Deposited Residue Count: 427 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isocitrate dehydrogenase [NADP]	A	427	Burkholderia pseudomallei	Mutation(s): 0  Gene Names: icd, BPSL0896 EC: 1.1.1.42
UniProt
Find proteins for Q3JV82 (Burkholderia pseudomallei (strain 1710b)) Explore Q3JV82  Go to UniProtKB:  Q3JV82

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.234 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.993	α = 90
b = 62.238	β = 118.52
c = 70.998	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-15 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• 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