6ZA5

M. tuberculosis salicylate synthase MbtI in complex with salicylate and Mg2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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: https://doi.org/10.1021/acs.jmedchem.0c00373
  • Primary Citation of Related Structures:  
    6ZA4, 6ZA5, 6ZA6

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Salicylate synthase
A, B, C, D
452Mycobacterium 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)
UniProt
Find proteins for P9WFX1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WFX1 
Go to UniProtKB:  P9WFX1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WFX1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAL (Subject of Investigation/LOI)
Query on SAL

Download Ideal Coordinates CCD File 
KA [auth D],
Z [auth B]
2-HYDROXYBENZOIC ACID
C7 H6 O3
YGSDEFSMJLZEOE-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
E [auth A]
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
E [auth A],
EA [auth B],
F [auth A],
FA [auth C],
G [auth A],
GA [auth C],
H [auth A],
HA [auth C],
I [auth A],
IA [auth C],
J [auth A],
K [auth A],
L [auth A],
LA [auth D],
M [auth A],
MA [auth D],
N [auth A],
NA [auth D],
O [auth A],
OA [auth D],
P [auth A],
PA [auth D],
Q [auth A],
QA [auth D],
R [auth A],
RA [auth D],
S [auth A],
SA [auth D],
T [auth A],
U [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
ACT
Query on ACT

Download Ideal Coordinates CCD File 
X [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
JA [auth D],
V [auth A],
W [auth A],
Y [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.196 
  • Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 193.973α = 90
b = 193.973β = 90
c = 257.034γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-15
    Type: Initial release
  • Version 1.1: 2020-07-22
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Derived calculations, Refinement description