Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 160.99 kDa 
• Atom Count: 13480 
• Modelled Residue Count: 1411 
• Deposited Residue Count: 1422 
• Unique protein chains: 1

2IZ1

6PDH complexed with PEX inhibitor synchrotron data

• PDB DOI: 10.2210/pdb2IZ1/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Lactococcus lactis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-07-23 Released: 2007-01-23 
• Deposition Author(s): Sundaramoorthy, R., Iulek, J., Hunter, W.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.198 
• R-Value Work: 0.137 
• R-Value Observed: 0.140 

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

• PubMed: 17222187 
• DOI: 10.1111/j.1742-4658.2006.05585.x
• Primary Citation of Related Structures:  
  2IYO, 2IYP, 2IZ0, 2IZ1


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING	A, B, C	474	Lactococcus lactis	Mutation(s): 0  EC: 1.1.1.44
UniProt
Find proteins for P96789 (Lactococcus lactis subsp. cremoris (strain MG1363)) Explore P96789  Go to UniProtKB:  P96789

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATR	D [auth A], H [auth B], K [auth C]	2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE C10 H16 N5 O13 P3 YPTPYQSAVGGMFN-KQYNXXCUSA-N
P33	F [auth A], N [auth C]	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL C14 H30 O8 XPJRQAIZZQMSCM-UHFFFAOYSA-N
RES	E [auth A]	4-PHOSPHO-D-ERYTHRONOHYDROXAMIC ACID C4 H10 N O8 P JJQQOJRGUHNREK-PWNYCUMCSA-N
PEG	G [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
CL	I [auth B], J [auth B], L [auth C], M [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.198 
• R-Value Work: 0.137 
• R-Value Observed: 0.140 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.069	α = 90
b = 104.879	β = 98.31
c = 240.542	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-07-23 
• Released Date: 2007-01-23 
Deposition Author(s): Sundaramoorthy, R., Iulek, J., Hunter, W.N.

Revision History  

• Version 1.0: 2007-01-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance