6ZA4

M. tuberculosis salicylate synthase MbtI in complex with 5-(3-cyanophenyl)furan-2-carboxylate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Shedding X-ray Light on the Role of Magnesium in the Activity ofMycobacterium tuberculosisSalicylate Synthase (MbtI) for Drug Design.

Mori, M.Stelitano, G.Gelain, A.Pini, E.Chiarelli, L.R.Sammartino, J.C.Poli, G.Tuccinardi, T.Beretta, G.Porta, A.Bellinzoni, M.Villa, S.Meneghetti, F.

(2020) J Med Chem 63: 7066-7080

  • DOI: 10.1021/acs.jmedchem.0c00373
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The Mg 2+ -dependent Mycobacterium tuberculosis salicylate synthase (MbtI) is a key enzyme involved in the biosynthesis of siderophores. Because iron is essential for the survival and pathogenicity of the microorganism, this prote ...

    The Mg 2+ -dependent Mycobacterium tuberculosis salicylate synthase (MbtI) is a key enzyme involved in the biosynthesis of siderophores. Because iron is essential for the survival and pathogenicity of the microorganism, this protein constitutes an attractive target for antitubercular therapy, also considering the absence of homologous enzymes in mammals. An extension of the structure-activity relationships of our furan-based candidates allowed us to disclose the most potent competitive inhibitor known to date ( 10 , K i = 4 μM), which also proved effective on mycobacterial cultures. By structural studies, we characterized its unexpected Mg 2+ -independent binding mode. We also investigated the role of the Mg 2+ cofactor in catalysis, analyzing the first crystal structure of the MbtI-Mg 2+ -salicylate ternary complex. Overall, these results pave the way for the development of novel antituberculars through the rational design of improved MbtI inhibitors.


    Organizational Affiliation

    Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano,Italy.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Salicylate synthaseA, B, C, D452Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: mbtItrpE2Rv2386c
EC: 5.4.99.5 (PDB Primary Data), 4.2.99.21 (PDB Primary Data), 5.4.4.2 (PDB Primary Data)
Find proteins for P9WFX1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WFX1 
Go to UniProtKB:  P9WFX1
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
M83
Query on M83

Download CCD File 
A, B, C, D
5-(3-cyanophenyl)furan-2-carboxylic acid
C12 H7 N O3
ZBBYBWMLIOUQRN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.336α = 90
b = 111.687β = 92.67
c = 94.998γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-07-01
    Type: Initial release
  • Version 1.1: 2020-07-08
    Changes: Database references
  • Version 1.2: 2020-07-22
    Changes: Database references, Refinement description