5F92

Fumarate hydratase of Mycobacterium tuberculosis in complex with formate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.859 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.143 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Selective small molecule inhibitor of the Mycobacterium tuberculosis fumarate hydratase reveals an allosteric regulatory site.

Kasbekar, M.Fischer, G.Mott, B.T.Yasgar, A.Hyvonen, M.Boshoff, H.I.Abell, C.Barry, C.E.Thomas, C.J.

(2016) Proc.Natl.Acad.Sci.USA 113: 7503-7508

  • DOI: 10.1073/pnas.1600630113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Enzymes in essential metabolic pathways are attractive targets for the treatment of bacterial diseases, but in many cases, the presence of homologous human enzymes makes them impractical candidates for drug development. Fumarate hydratase, an essenti ...

    Enzymes in essential metabolic pathways are attractive targets for the treatment of bacterial diseases, but in many cases, the presence of homologous human enzymes makes them impractical candidates for drug development. Fumarate hydratase, an essential enzyme in the tricarboxylic acid (TCA) cycle, has been identified as one such potential therapeutic target in tuberculosis. We report the discovery of the first small molecule inhibitor, to our knowledge, of the Mycobacterium tuberculosis fumarate hydratase. A crystal structure at 2.0-Å resolution of the compound in complex with the protein establishes the existence of a previously unidentified allosteric regulatory site. This allosteric site allows for selective inhibition with respect to the homologous human enzyme. We observe a unique binding mode in which two inhibitor molecules interact within the allosteric site, driving significant conformational changes that preclude simultaneous substrate and inhibitor binding. Our results demonstrate the selective inhibition of a highly conserved metabolic enzyme that contains identical active site residues in both the host and the pathogen.


    Organizational Affiliation

    National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20850; Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fumarate hydratase class II
A, B, C, D
495Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)Mutation(s): 0 
Gene Names: fumC (fum)
EC: 4.2.1.2
Find proteins for P9WN92 (Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh))
Go to UniProtKB:  P9WN92
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMT
Query on FMT

Download SDF File 
Download CCD File 
A, B
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
PG4
Query on PG4

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Download CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.859 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.143 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 180.139α = 90.00
b = 96.993β = 103.38
c = 124.129γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
Aimlessdata scaling
BUCCANEERmodel building
PHENIXrefinement
Cootmodel building
AutoPROCdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-06-22
    Type: Initial release
  • Version 1.1: 2016-07-13
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Advisory, Data collection, Database references, Derived calculations, Refinement description