4CVY

Crystal structure of the M. tuberculosis sulfate ester dioxygenase Rv3406 in complex with iron.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

2-Carboxyquinoxalines Kill Mycobacterium Tuberculosis Through Noncovalent Inhibition of Dpre1.

Neres, J.Hartkoorn, R.C.Chiarelli, L.R.Gadupudi, R.Pasca, M.R.Mori, G.Venturelli, A.Savina, S.Makarov, V.Kolly, G.S.Molteni, E.Binda, C.Dhar, N.Ferrari, S.Brodin, P.Delorme, V.Landry, V.De Jesus Lopes Ribeiro, A.L.Farina, D.Saxena, P.Pojer, F.Carta, A.Luciani, R.Porta, A.Zanoni, G.De Rossi, E.Costi, M.P.Riccardi, G.Cole, S.T.

(2015) ACS Chem Biol 10: 705

  • DOI: 10.1021/cb5007163
  • Primary Citation of Related Structures:  
    4CVY, 4P8C, 4P8K, 4P8L, 4P8M, 4P8N, 4P8P, 4P8T, 4P8Y

  • PubMed Abstract: 
  • Phenotypic screening of a quinoxaline library against replicating Mycobacterium tuberculosis led to the identification of lead compound Ty38c (3-((4-methoxybenzyl)amino)-6-(trifluoromethyl)quinoxaline-2-carboxylic acid). With an MIC99 and MBC of 3.1 μM, Ty38c is bactericidal and active against intracellular bacteria ...

    Phenotypic screening of a quinoxaline library against replicating Mycobacterium tuberculosis led to the identification of lead compound Ty38c (3-((4-methoxybenzyl)amino)-6-(trifluoromethyl)quinoxaline-2-carboxylic acid). With an MIC99 and MBC of 3.1 μM, Ty38c is bactericidal and active against intracellular bacteria. To investigate its mechanism of action, we isolated mutants resistant to Ty38c and sequenced their genomes. Mutations were found in rv3405c, coding for the transcriptional repressor of the divergently expressed rv3406 gene. Biochemical studies clearly showed that Rv3406 decarboxylates Ty38c into its inactive keto metabolite. The actual target was then identified by isolating Ty38c-resistant mutants of an M. tuberculosis strain lacking rv3406. Here, mutations were found in dprE1, encoding the decaprenylphosphoryl-d-ribose oxidase DprE1, essential for biogenesis of the mycobacterial cell wall. Genetics, biochemical validation, and X-ray crystallography revealed Ty38c to be a noncovalent, noncompetitive DprE1 inhibitor. Structure-activity relationship studies generated a family of DprE1 inhibitors with a range of IC50's and bactericidal activity. Co-crystal structures of DprE1 in complex with eight different quinoxaline analogs provided a high-resolution interaction map of the active site of this extremely vulnerable target in M. tuberculosis.


    Organizational Affiliation

    ‡Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DIOXYGENASE RV3406/MT3514A, B, C, D295Mycobacterium tuberculosisMutation(s): 0 
EC: 1 (PDB Primary Data), 1.14.11 (UniProt)
UniProt
Find proteins for P9WKZ1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WKZ1 
Go to UniProtKB:  P9WKZ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WKZ1
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.97α = 90
b = 128.15β = 90
c = 138.42γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
BALBESphasing

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-10
    Type: Initial release
  • Version 1.1: 2015-04-15
    Changes: Database references