2QO1

2.6 Angstrom Crystal Structure of the Complex Between 11-(decyldithiocarbonyloxy)-undecanoic acid and Mycobacterium Tuberculosis FabH.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Separate Entrance and Exit Portals for Ligand Traffic in Mycobacterium tuberculosis FabH

Sachdeva, S.Musayev, F.N.Alhamadsheh, M.M.Scarsdale, J.N.Wright, H.T.Reynolds, K.A.

(2008) Chem.Biol. 15: 402-412

  • DOI: 10.1016/j.chembiol.2008.03.007
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Mycobacterium tuberculosis FabH initiates type II fatty acid synthase-catalyzed formation of the long chain (C(16)-C(22)) acyl-coenzyme A (CoA) precursors of mycolic acids, which are major constituents of the bacterial cell envelope. Crystal structur ...

    Mycobacterium tuberculosis FabH initiates type II fatty acid synthase-catalyzed formation of the long chain (C(16)-C(22)) acyl-coenzyme A (CoA) precursors of mycolic acids, which are major constituents of the bacterial cell envelope. Crystal structures of M. tuberculosis FabH (mtFabH) show the substrate binding site to be a buried, extended L-shaped channel with only a single solvent access portal. Entrance of an acyl-CoA substrate through the solvent portal would require energetically unfavorable reptational threading of the substrate to its reactive position. Using a class of FabH inhibitors, we have tested an alternative hypothesis that FabH exists in an "open" form during substrate binding and product release, and a "closed" form in which catalysis and intermediate steps occur. This hypothesis is supported by mass spectrometric analysis of the product profile and crystal structures of complexes of mtFabH with these inhibitors.


    Related Citations: 
    • Crystal Structure of a Substrate Complex of Mycobacterium Tuberculosis Beta-Ketoacyl-Acyl Carrier Protein Sythnase III (FABH) with Lauroyl-Coenzyme A.
      Scarsdale, J.N.,Kazanina, G.,He, X.,Reynolds, K.A.,Wright, H.T.
      (2005) J.Mol.Biol. 346: 1313
    • Crystal Structure of the Mycobacterium Tuberculosis Beta-Ketoacyl-Acy; Carrier Protein Synthase III
      Muysavev, F.,Sachdeva, S.,Scarsdale, J.N.,Reynolds, K.A.,Wright, H.T.
      (2001) J.Biol.Chem. 276: 20516


    Organizational Affiliation

    Department of Chemistry, Portland State University, Portland, OR 97207, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-oxoacyl-[acyl-carrier-protein] synthase 3
A, B
335Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: fabH
EC: 2.3.1.180
Find proteins for P9WNG3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WNG3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D1T
Query on D1T

Download SDF File 
Download CCD File 
A, B
DECANE-1-THIOL
C10 H22 S
VTXVGVNLYGSIAR-UHFFFAOYSA-N
 Ligand Interaction
VZZ
Query on VZZ

Download SDF File 
Download CCD File 
A, B
11-[(MERCAPTOCARBONYL)OXY]UNDECANOIC ACID
C12 H22 O4 S
XSZQJZYGKSSUAF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
VZZIC50: 2700 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.221 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 68.411α = 90.00
b = 89.123β = 90.00
c = 233.290γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
REFMACrefinement
CrystalCleardata collection
AMoREphasing
d*TREKdata scaling
d*TREKdata reduction
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-05-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description
  • Version 1.3: 2019-07-24
    Type: Data collection, Derived calculations, Refinement description