3E7F

Crystal structure of 6-phosphogluconolactonase from Trypanosoma brucei complexed with 6-phosphogluconic acid

Summary for 3E7F

• Entry DOI: 10.2210/pdb3e7f/pdb
• Related: 2J0E
• Descriptor: 6-phosphogluconolactonase, ZINC ION, 6-PHOSPHOGLUCONIC ACID, ... (4 entities in total)
• Functional Keywords: catalytic mechanism, pentose phosphate pathway, 6-phosphogluconolactonase, trypanosoma brucei, hydrolase, zinc binding site
• Biological source: Trypanosoma brucei
• Total number of polymer chains: 2
• Total formula weight: 57780.47

Authors

Poggi, L.,Delarue, M.,Duclert-Savatier, N.,Stoven, V. (deposition date: 2008-08-18, release date: 2009-05-26, Last modification date: 2024-02-21)

Primary citation

Duclert-Savatier, N.,Poggi, L.,Miclet, E.,Lopes, P.,Ouazzani, J.,Chevalier, N.,Nilges, M.,Delarue, M.,Stoven, V.
Insights into the enzymatic mechanism of 6-phosphogluconolactonase from Trypanosoma brucei using structural data and molecular dynamics simulation.
J.Mol.Biol., 388:1009-1021, 2009

PubMed Abstract: Trypanosoma brucei is the causative agent of African sleeping sickness. Current work for the development of new drugs against this pathology includes evaluation of enzymes of the pentose phosphate pathway (PPP), which first requires a clear understanding of their function and mechanism of action. In this context, we focused on T. brucei 6-phosphogluconolactonase (Tb6PGL), which converts delta-6-phosphogluconolactone into 6-phosphogluconic acid in the second step of the PPP. We have determined the crystal structure of Tb6PGL in complex with two ligands, 6-phosphogluconic acid and citrate, at 2.2 A and 2.0 A resolution, respectively. We have performed molecular dynamics (MD) simulations on Tb6PGL in its empty form and in complex with delta-6-phosphogluconolactone, its natural ligand. Analysis of the structural data and MD simulations allowed us to propose a detailed enzymatic mechanism for 6PGL enzymes.

PubMed: 19345229
DOI: 10.1016/j.jmb.2009.03.063

Experimental method

X-RAY DIFFRACTION (2.2 Å)