7Q2F

mycolic acid methyltransferase Hma (MmaA4) from Mycobac-terium tuberculosis in complex with ZT585


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Fragment-Based Ligand Discovery Applied to the Mycolic Acid Methyltransferase Hma (MmaA4) from Mycobacterium tuberculosis : A Crystallographic and Molecular Modelling Study.

Galy, R.Ballereau, S.Genisson, Y.Mourey, L.Plaquevent, J.C.Maveyraud, L.

(2021) Pharmaceuticals (Basel) 14

  • DOI: https://doi.org/10.3390/ph14121282
  • Primary Citation of Related Structures:  
    7Q2B, 7Q2C, 7Q2D, 7Q2E, 7Q2F, 7Q2G, 7Q2H

  • PubMed Abstract: 

    The mycolic acid biosynthetic pathway represents a promising source of pharmacological targets in the fight against tuberculosis. In Mycobacterium tuberculosis , mycolic acids are subject to specific chemical modifications introduced by a set of eight S-adenosylmethionine dependent methyltransferases. Among these, Hma (MmaA4) is responsible for the introduction of oxygenated modifications. Crystallographic screening of a library of fragments allowed the identification of seven ligands of Hma. Two mutually exclusive binding modes were identified, depending on the conformation of residues 147-154. These residues are disordered in apo -Hma but fold upon binding of the S-adenosylmethionine (SAM) cofactor as well as of analogues, resulting in the formation of the short η1-helix. One of the observed conformations would be incompatible with the presence of the cofactor, suggesting that allosteric inhibitors could be designed against Hma. Chimeric compounds were designed by fusing some of the bound fragments, and the relative binding affinities of initial fragments and evolved compounds were investigated using molecular dynamics simulation and generalised Born and Poisson-Boltzmann calculations coupled to the surface area continuum solvation method. Molecular dynamics simulations were also performed on apo -Hma to assess the structural plasticity of the unliganded protein. Our results indicate a significant improvement in the binding properties of the designed compounds, suggesting that they could be further optimised to inhibit Hma activity.


  • Organizational Affiliation

    Institut de Pharmacologie et de Biologie Structurale, Université Toulouse III-Paul Sabatier, Centre National de la Recherche Scientifique, 31077 Toulouse, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hydroxymycolate synthase MmaA4318Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: mmaA4hmamma4Rv0642c
EC: 2.1.1
UniProt
Find proteins for Q79FX8 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore Q79FX8 
Go to UniProtKB:  Q79FX8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ79FX8
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.11α = 90
b = 57.11β = 90
c = 204.46γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
XSCALEdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Centre National de la Recherche Scientifique (CNRS)France--
Universite de ToulouseFrance--

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-02
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description