2IYO

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

Summary for 2IYO

• Entry DOI: 10.2210/pdb2iyo/pdb
• Related: 2IYP 2IZ0 2IZ1
• Descriptor: 6-PHOSPHOGLUCONATE DEHYDROGENASE, DECARBOXYLATING, 6-PHOSPHOGLUCONIC ACID, CACODYLATE ION, ... (4 entities in total)
• Functional Keywords: oxidoreductase, 6-phosphogluconate dehydrogenase, nadp, pentose shunt, gluconate utilization
• Biological source: LACTOCOCCUS LACTIS
• Total number of polymer chains: 1
• Total formula weight: 52914.34

Authors

Sundaramoorthy, R.,Iulek, J.,Hunter, W.N. (deposition date: 2006-07-21, release date: 2007-01-23, Last modification date: 2023-12-13)

Primary citation

Sundaramoorthy, R.,Iulek, J.,Barrett, M.P.,Bidet, O.,Ruda, G.F.,Gilbert, I.H.,Hunter, W.N.
Crystal Structures of a Bacterial 6-Phosphogluconate Dehydrogenase Reveal Aspects of Specificity, Mechanism and Mode of Inhibition by Analogues of High-Energy Reaction Intermediates.
FEBS J., 274:275-, 2007

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.

PubMed: 17222187
DOI: 10.1111/J.1742-4658.2006.05585.X

Experimental method

X-RAY DIFFRACTION (2.4 Å)