4ZDI

Crystal structure of the M. tuberculosis CTP synthase PyrG (apo form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.52 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Thiophenecarboxamide Derivatives Activated by EthA Kill Mycobacterium tuberculosis by Inhibiting the CTP Synthetase PyrG.

Mori, G.Chiarelli, L.R.Esposito, M.Makarov, V.Bellinzoni, M.Hartkoorn, R.C.Degiacomi, G.Boldrin, F.Ekins, S.de Jesus Lopes Ribeiro, A.L.Marino, L.B.Centarova, I.Svetlikova, Z.Blasko, J.Kazakova, E.Lepioshkin, A.Barilone, N.Zanoni, G.Porta, A.Fondi, M.Fani, R.Baulard, A.R.Mikusova, K.Alzari, P.M.Manganelli, R.de Carvalho, L.P.Riccardi, G.Cole, S.T.Pasca, M.R.

(2015) Chem.Biol. 22: 917-927

  • DOI: 10.1016/j.chembiol.2015.05.016
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • To combat the emergence of drug-resistant strains of Mycobacterium tuberculosis, new antitubercular agents and novel drug targets are needed. Phenotypic screening of a library of 594 hit compounds uncovered two leads that were active against M. tuber ...

    To combat the emergence of drug-resistant strains of Mycobacterium tuberculosis, new antitubercular agents and novel drug targets are needed. Phenotypic screening of a library of 594 hit compounds uncovered two leads that were active against M. tuberculosis in its replicating, non-replicating, and intracellular states: compounds 7947882 (5-methyl-N-(4-nitrophenyl)thiophene-2-carboxamide) and 7904688 (3-phenyl-N-[(4-piperidin-1-ylphenyl)carbamothioyl]propanamide). Mutants resistant to both compounds harbored mutations in ethA (rv3854c), the gene encoding the monooxygenase EthA, and/or in pyrG (rv1699) coding for the CTP synthetase, PyrG. Biochemical investigations demonstrated that EthA is responsible for the activation of the compounds, and by mass spectrometry we identified the active metabolite of 7947882, which directly inhibits PyrG activity. Metabolomic studies revealed that pharmacological inhibition of PyrG strongly perturbs DNA and RNA biosynthesis, and other metabolic processes requiring nucleotides. Finally, the crystal structure of PyrG was solved, paving the way for rational drug design with this newly validated drug target.


    Organizational Affiliation

    Collaborative Drug Discovery, 1633 Bayshore Highway, Suite 342, Burlingame, CA 94010, USA.,Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK.,Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy. Electronic address: mariarosalia.pasca@unipv.it.,Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Station 19, 1015 Lausanne, Switzerland.,Institute of Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina, 84215 Bratislava, Slovak Republic.,Institut Pasteur, Unité de Microbiologie Structurale, CNRS-UMR3528, Université Paris Diderot, Sorbonne Paris Cité, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France.,Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK; Faculty of Pharmaceutical Sciences, UNESP - Univ Estadual Paulista, Araraquara, São Paulo 14801-902, Brazil.,Institut Pasteur de Lille, Center for Infection and Immunity, 59019 Lille, France.,Department of Biology, University of Florence, Sesto Fiorentino, Florence 50019, Italy.,A. N. Bakh Institute of Biochemistry, Russian Academy of Science, 119071 Moscow, Russia.,Department of Molecular Medicine, University of Padova, 35128 Padua, Italy.,Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina, 84215 Bratislava, Slovakia.,Department of Chemistry, University of Pavia, 27100 Pavia, Italy.,Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Station 19, 1015 Lausanne, Switzerland. Electronic address: stewart.cole@epfl.ch.,Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CTP synthase
A, B, C, D, E, F, G, H
587Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: pyrG
EC: 6.3.4.2
Find proteins for P9WHK7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WHK7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.52 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.213 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 196.826α = 90.00
b = 196.826β = 90.00
c = 184.047γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
BUSTERrefinement
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European CommissionFranceHEALTH-F3-2011-260872

Revision History 

  • Version 1.0: 2015-07-01
    Type: Initial release
  • Version 1.1: 2015-08-05
    Type: Database references