3B4Y

FGD1 (Rv0407) from Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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

Bashiri, G.Squire, C.J.Moreland, N.J.Baker, E.N.

(2008) J Biol Chem 283: 17531-17541

  • DOI: 10.1074/jbc.M801854200
  • Primary Citation of Related Structures:  
    3C8N, 3B4Y

  • 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 ...

    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.


    Organizational Affiliation

    School of Biological Sciences and Centre of Molecular Biodiscovery, University of Auckland, Private Bag 92019, Auckland, New Zealand.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROBABLE F420-DEPENDENT GLUCOSE-6-PHOSPHATE DEHYDROGENASE FGD1A, B356Mycobacterium tuberculosis H37RvMutation(s): 1 
Gene Names: Rv0407fgd1fgd
EC: 1 (PDB Primary Data), 1.1.98.2 (UniProt)
UniProt
Find proteins for P9WNE1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WNE1 
Go to UniProtKB:  P9WNE1
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F42
Query on F42

Download Ideal Coordinates CCD File 
C [auth A], E [auth B]COENZYME F420
C29 H36 N5 O18 P
GEHSZWRGPHDXJO-NALJQGANSA-N
 Ligand Interaction
FLC
Query on FLC

Download Ideal Coordinates CCD File 
D [auth A], F [auth B]CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A, BL-PEPTIDE LINKINGC3 H7 N O3 SCYS
MSE
Query on MSE
A, BL-PEPTIDE LINKINGC5 H11 N O2 SeMET
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FLCIC50:  43000   nM  Binding MOAD
F42Kd:  4500   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.078α = 90
b = 89.907β = 90
c = 80.146γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance