3B4Y

FGD1 (Rv0407) from Mycobacterium tuberculosis

Summary for 3B4Y

• Entry DOI: 10.2210/pdb3b4y/pdb
• Related: 3C8N
• Descriptor: PROBABLE F420-DEPENDENT GLUCOSE-6-PHOSPHATE DEHYDROGENASE FGD1, COENZYME F420, CITRATE ANION, ... (4 entities in total)
• Functional Keywords: tim-barrel, non-prolyl cis-peptide bulge, f420 binding, oxidoreductase, structural genomics, tb structural genomics consortium, tbsgc
• Biological source: Mycobacterium tuberculosis H37Rv
• Total number of polymer chains: 2
• Total formula weight: 81337.64

Authors

Bashiri, G.,Squire, C.J.,Moreland, N.M.,Baker, E.N.,TB Structural Genomics Consortium (TBSGC) (deposition date: 2007-10-25, release date: 2008-04-22, Last modification date: 2024-04-03)

Primary citation

Bashiri, G.,Squire, C.J.,Moreland, N.J.,Baker, E.N.
Crystal structures of F420-dependent glucose-6-phosphate dehydrogenase FGD1 involved in the activation of the anti-tuberculosis drug candidate PA-824 reveal the basis of coenzyme and substrate binding
J.Biol.Chem., 283:17531-17541, 2008

PubMed Abstract: The modified flavin coenzyme F(420) is found in a restricted number of microorganisms. It is widely distributed in mycobacteria, however, where it is important in energy metabolism, and in Mycobacterium tuberculosis (Mtb) is implicated in redox processes related to non-replicating persistence. In Mtb, the F(420)-dependent glucose-6-phosphate dehydrogenase FGD1 provides reduced F(420) for the in vivo activation of the nitroimidazopyran prodrug PA-824, currently being developed for anti-tuberculosis therapy against both replicating and persistent bacteria. The structure of M. tuberculosis FGD1 has been determined by x-ray crystallography both in its apo state and in complex with F(420) and citrate at resolutions of 1.90 and 1.95 A(,) respectively. The structure reveals a highly specific F(420) binding mode, which is shared with several other F(420)-dependent enzymes. Citrate occupies the substrate binding pocket adjacent to F(420) and is shown to be a competitive inhibitor (IC(50) 43 microm). Modeling of the binding of the glucose 6-phosphate (G6P) substrate identifies a positively charged phosphate binding pocket and shows that G6P, like citrate, packs against the isoalloxazine moiety of F(420) and helps promote a butterfly bend conformation that facilitates F(420) reduction and catalysis.

PubMed: 18434308
DOI: 10.1074/jbc.M801854200

Experimental method

X-RAY DIFFRACTION (1.95 Å)