Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 64.88 kDa 
• Atom Count: 4399 
• Modelled Residue Count: 535 
• Deposited Residue Count: 587 
• Unique protein chains: 1

4ZDJ

Crystal structure of the M. tuberculosis CTP synthase PyrG in complex with two UTP molecules

• DOI: 10.2210/pdb4ZDJ/pdb

• Classification: LIGASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-04-17 Released: 2015-07-01 
• Deposition Author(s): Bellinzoni, M., Barilone, N., Alzari, P.M.
• Funding Organization(s): European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.189 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 

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

• PubMed: 26097035 
• DOI: 10.1016/j.chembiol.2015.05.016
• Primary Citation of Related Structures:  
  4ZDI, 4ZDJ, 4ZDK


• 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. 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.

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Organizational Affiliation: 

Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CTP synthase	A	587	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: pyrG, Rv1699, MTCI125.21 EC: 6.3.4.2
UniProt
Find proteins for P9WHK7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WHK7  Go to UniProtKB:  P9WHK7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UTP (Subject of Investigation/LOI)	B [auth A], C [auth A]	URIDINE 5'-TRIPHOSPHATE C9 H15 N2 O15 P3 PGAVKCOVUIYSFO-XVFCMESISA-N
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 0.189 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.41	α = 90
b = 132.73	β = 90
c = 157.63	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Ligand Structure Quality Assessment  

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-04-17 
• Released Date: 2015-07-01 
Deposition Author(s): Bellinzoni, M., Barilone, N., Alzari, P.M.

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Funding Organization	Location	Grant Number
European Commission	France	HEALTH-F3-2011-260872

Revision History  

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