4AUT

Crystal structure of the tuberculosis drug target Decaprenyl- Phosphoryl-beta-D-Ribofuranose-2-oxidoreductase (DprE1) from Mycobacterium smegmatis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Basis for Benzothiazinone-Mediated Killing of Mycobacterium Tuberculosis.

Neres, J.Pojer, F.Molteni, E.Chiarelli, L.R.Dhar, N.Boy-Rottger, S.Buroni, S.Fullam, E.Degiacomi, G.Lucarelli, A.P.Read, R.J.Zanoni, G.Edmondson, D.E.De Rossi, E.Pasca, M.R.Mckinney, J.D.Dyson, P.J.Riccardi, G.Mattevi, A.Cole, S.T.Binda, C.

(2012) Sci. Transl. Med. 4: 121

  • DOI: 10.1126/scitranslmed.3004395
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The benzothiazinone BTZ043 is a tuberculosis drug candidate with nanomolar whole-cell activity. BTZ043 targets the DprE1 catalytic component of the essential enzyme decaprenylphosphoryl-β-D-ribofuranose-2'-epimerase, thus blocking biosynthesis of ara ...

    The benzothiazinone BTZ043 is a tuberculosis drug candidate with nanomolar whole-cell activity. BTZ043 targets the DprE1 catalytic component of the essential enzyme decaprenylphosphoryl-β-D-ribofuranose-2'-epimerase, thus blocking biosynthesis of arabinans, vital components of mycobacterial cell walls. Crystal structures of DprE1, in its native form and in a complex with BTZ043, reveal formation of a semimercaptal adduct between the drug and an active-site cysteine, as well as contacts to a neighboring catalytic lysine residue. Kinetic studies confirm that BTZ043 is a mechanism-based, covalent inhibitor. This explains the exquisite potency of BTZ043, which, when fluorescently labeled, localizes DprE1 at the poles of growing bacteria. Menaquinone can reoxidize the flavin adenine dinucleotide cofactor in DprE1 and may be the natural electron acceptor for this reaction in the mycobacterium. Our structural and kinetic analysis provides both insight into a critical epimerization reaction and a platform for structure-based design of improved inhibitors.


    Organizational Affiliation

    Global Health Institute, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DECAPRENYL-PHOSPHORYL-BETA-D-RIBOFURANOSE-2-OXIDOREDUCTASE
A
468Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)Mutation(s): 0 
Gene Names: dprE1
EC: 1.1.98.3
Find proteins for A0R607 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Go to UniProtKB:  A0R607
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.202 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 64.139α = 90.00
b = 64.139β = 90.00
c = 191.204γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
Rosettaphasing
REFMACrefinement
MOSFLMdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2012-09-05
    Type: Initial release
  • Version 1.1: 2012-09-19
    Type: Database references