2IYO

Structural characterization of a bacterial 6PDH reveals aspects of specificity, mechanism and mode of inhibition


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal Structures of a Bacterial 6-Phosphogluconate Dehydrogenase Reveal Aspects of Specificity, Mechanism and Mode of Inhibition by Analogues of High-Energy Reaction Intermediates.

Sundaramoorthy, R.Iulek, J.Barrett, M.P.Bidet, O.Ruda, G.F.Gilbert, I.H.Hunter, W.N.

(2007) FEBS J 274: 275

  • DOI: 10.1111/j.1742-4658.2006.05585.x
  • Primary Citation of Related Structures:  
    2IYP, 2IZ1, 2IYO, 2IZ0

  • PubMed Abstract: 
  • Crystal structures of recombinant Lactococcus lactis 6-phosphogluconate dehydrogenase (LlPDH) in complex with substrate, cofactor, product and inhibitors have been determined. LlPDH shares significant sequence identity with the enzymes from sheep liv ...

    Crystal structures of recombinant Lactococcus lactis 6-phosphogluconate dehydrogenase (LlPDH) in complex with substrate, cofactor, product and inhibitors have been determined. LlPDH shares significant sequence identity with the enzymes from sheep liver and the protozoan parasite Trypanosoma brucei for which structures have been reported. Comparisons indicate that the key residues in the active site are highly conserved, as are the interactions with the cofactor and the product ribulose 5-phosphate. However, there are differences in the conformation of the substrate 6-phosphogluconate which may reflect distinct states relevant to catalysis. Analysis of the complex formed with the potent inhibitor 4-phospho-d-erythronohydroxamic acid, suggests that this molecule does indeed mimic the high-energy intermediate state that it was designed to. The analysis also identified, as a contaminant by-product of the inhibitor synthesis, 4-phospho-d-erythronamide, which binds in similar fashion. LlPDH can now serve as a model system for structure-based inhibitor design targeting the enzyme from Trypanosoma species.


    Organizational Affiliation

    Division of Biological Chemistry and Molecular Microbiology, College of Life Sciences, University of Dundee, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATINGA472Lactococcus lactisMutation(s): 0 
EC: 1.1.1.44
Find proteins for P96789 (Lactococcus lactis subsp. cremoris (strain MG1363))
Explore P96789 
Go to UniProtKB:  P96789
Protein Feature View
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6PG
Query on 6PG

Download CCD File 
A
6-PHOSPHOGLUCONIC ACID
C6 H13 O10 P
BIRSGZKFKXLSJQ-SQOUGZDYSA-N
 Ligand Interaction
CAC
Query on CAC

Download CCD File 
A
CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.162 
  • Space Group: P 32 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.582α = 90
b = 60.582β = 90
c = 243.128γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-01-23
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-05-23
    Changes: Data collection