3VEH

Structure of a M. tuberculosis salicylate synthase, MbtI, in complex with an inhibitor methylAMT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 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
  • Structures With Same Primary Citation

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Isochorismate synthase/isochorismate-pyruvate lyase mbtIA, B, C, D451Mycobacterium tuberculosisMutation(s): 0 
Gene Names: mbtItrpE2Rv2386cMT2454
EC: 4.1.3 (PDB Primary Data), 5.4.4.2 (PDB Primary Data), 5.4.99.5 (UniProt), 4.2.99.21 (UniProt)
Find proteins for P9WFX1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WFX1 
Go to UniProtKB:  P9WFX1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0GA
Query on 0GA

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A, B, C, D
3-{[(1Z)-1-carboxyprop-1-en-1-yl]oxy}-2-hydroxybenzoic acid
C11 H10 O6
MPHSNGOSXHODDD-UQCOIBPSSA-N
 Ligand Interaction
PEG
Query on PEG

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C
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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A, B, C
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
SCN
Query on SCN

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A, B, C
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
 Ligand Interaction
K
Query on K

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B, D
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0GAKi:  11000   nM  Binding MOAD
0GAKi :  11000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.674α = 90
b = 115.955β = 91.59
c = 94.715γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-06-13
    Type: Initial release
  • Version 1.1: 2013-01-09
    Changes: Database references
  • Version 1.2: 2014-02-12
    Changes: Non-polymer description