Biological Assembly 1  

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

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

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: 158.76 kDa 
• Atom Count: 10741 
• Modelled Residue Count: 1337 
• Deposited Residue Count: 1424 
• Unique protein chains: 1

3C8N

Crystal structure of apo-FGD1 from Mycobacterium tuberculosis

• PDB DOI: 10.2210/pdb3C8N/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Mycolicibacterium smegmatis
• Mutation(s): Yes 


• Deposited: 2008-02-12 Released: 2008-04-22 
• Deposition Author(s): Bashiri, G., Squire, C.J., Moreland, N.J., Baker, E.N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.255 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 

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

• PubMed: 18434308 
• DOI: 10.1074/jbc.M801854200
• Primary Citation of Related Structures:  
  3B4Y, 3C8N


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable F420-dependent glucose-6-phosphate dehydrogenase FGD1	A, B, C, D	356	Mycobacterium tuberculosis H37Rv	Mutation(s): 1  Gene Names: fgd1, fgd, MT0420, Rv0407 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

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.255 
• R-Value Work: 0.212 
• R-Value Observed: 0.214 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.954	α = 90
b = 89.133	β = 91.64
c = 90.859	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
MOSFLM	data reduction
SCALA	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-02-12 
• Released Date: 2008-04-22 
Deposition Author(s): Bashiri, G., Squire, C.J., Moreland, N.J., Baker, E.N.

Revision History  

• Version 1.0: 2008-04-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Source and taxonomy, Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations