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: 2.10 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.206 

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:  
    4F4Q, 4AUT

  • 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 arabinans, vital components of mycobacterial cell walls ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DECAPRENYL-PHOSPHORYL-BETA-D-RIBOFURANOSE-2-OXIDOREDUCTASEA468Mycolicibacterium smegmatisMutation(s): 0 
EC: 1.1.98.3
Find proteins for A0R607 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R607 
Go to UniProtKB:  A0R607
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
B [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.206 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.139α = 90
b = 64.139β = 90
c = 191.204γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
Rosettaphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

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