3RV8

Structure of a M. tuberculosis Salicylate Synthase, MbtI, in Complex with an Inhibitor with Cyclopropyl R-Group


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Implications of binding mode and active site flexibility for inhibitor potency against the salicylate synthase from Mycobacterium tuberculosis

Chi, G.Manos-Turvey, A.O'Connor, P.D.Johnston, J.M.Evans, G.L.Baker, E.N.Payne, R.J.Lott, J.S.Bulloch, E.M.

(2012) Biochemistry 51: 4868-4879

  • DOI: 10.1021/bi3002067
  • Primary Citation of Related Structures:  
    3RV6, 3RV7, 3RV8, 3RV9, 3ST6, 3VEH

  • PubMed Abstract: 
  • MbtI is the salicylate synthase that catalyzes the first committed step in the synthesis of the iron chelating compound mycobactin in Mycobacterium tuberculosis. We previously developed a series of aromatic inhibitors against MbtI based on the reaction intermediate for this enzyme, isochorismate ...

    MbtI is the salicylate synthase that catalyzes the first committed step in the synthesis of the iron chelating compound mycobactin in Mycobacterium tuberculosis. We previously developed a series of aromatic inhibitors against MbtI based on the reaction intermediate for this enzyme, isochorismate. The most potent of these inhibitors had hydrophobic substituents, ranging in size from a methyl to a phenyl group, appended to the terminal alkene of the enolpyruvyl group. These compounds exhibited low micromolar inhibition constants against MbtI and were at least an order of magnitude more potent than the parental compound for the series, which carries a native enolpyruvyl group. In this study, we sought to understand how the substituted enolpyruvyl group confers greater potency, by determining cocrystal structures of MbtI with six inhibitors from the series. A switch in binding mode at the MbtI active site is observed for inhibitors carrying a substituted enolpyruvyl group, relative to the parental compound. Computational studies suggest that the change in binding mode, and higher potency, is due to the effect of the substituents on the conformational landscape of the core inhibitor structure. The crystal structures and fluorescence-based thermal shift assays indicate that substituents larger than a methyl group are accommodated in the MbtI active site through significant but localized flexibility in the peptide backbone. These findings have implications for the design of improved inhibitors of MbtI, as well as other chorismate-utilizing enzymes from this family.


    Organizational Affiliation

    School of Biological Sciences and Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, 3 Symonds Street, Private Bag 92019, Auckland 1142, New Zealand.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Isochorismate synthase/isochorismate-pyruvate lyase mbtIA, B, C, D450Mycobacterium tuberculosisMutation(s): 0 
Gene Names: Rv2386c
EC: 4.1.3 (PDB Primary Data), 5.4.4.2 (PDB Primary Data), 5.4.99.5 (UniProt), 4.2.99.21 (UniProt)
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VCE
Query on VCE

Download Ideal Coordinates CCD File 
H [auth C]3-{[(E)-1-carboxy-2-cyclopropylethenyl]oxy}-2-hydroxybenzoic acid
C13 H12 O6
RBBOJHGNWUPRCK-UXBLZVDNSA-N
 Ligand Interaction
RVC
Query on RVC

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
G [auth C],
I [auth D]
3-{[(Z)-1-carboxy-2-cyclopropylethenyl]oxy}-2-hydroxybenzoic acid
C13 H12 O6
RBBOJHGNWUPRCK-POHAHGRESA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
RVC Binding MOAD:  3RV8 Ki: 1.20e+4 (nM) from 1 assay(s)
VCE Binding MOAD:  3RV8 Ki: 1.20e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.152α = 90
b = 115.939β = 91.44
c = 95.852γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
BUSTERrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-09
    Type: Initial release
  • Version 1.1: 2012-05-30
    Changes: Non-polymer description
  • Version 1.2: 2012-06-13
    Changes: Database references
  • Version 1.3: 2013-06-19
    Changes: Database references