5VNS

M.tb Antigen 85C Acyl-Enzyme Intermediate with Tetrahydrolipstatin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 ?
  • R-Value Free: 0.174 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.161 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Mycolyltransferase fromMycobacterium tuberculosisin covalent complex with tetrahydrolipstatin provides insights into antigen 85 catalysis.

Goins, C.M.Dajnowicz, S.Smith, M.D.Parks, J.M.Ronning, D.R.

(2018) J Biol Chem 293: 3651-3662

  • DOI: https://doi.org/10.1074/jbc.RA117.001681
  • Primary Citation of Related Structures:  
    5VNS

  • PubMed Abstract: 

    Mycobacterium tuberculosis antigen 85 (Ag85) enzymes catalyze the transfer of mycolic acid (MA) from trehalose monomycolate to produce the mycolyl arabinogalactan (mAG) or trehalose dimycolate (TDM). These lipids define the protective mycomembrane of mycobacteria. The current model of substrate binding within the active sites of Ag85s for the production of TDM is not sterically and geometrically feasible; additionally, this model does not account for the production of mAG. Furthermore, this model does not address how Ag85s limit the hydrolysis of the acyl-enzyme intermediate while catalyzing acyl transfer. To inform an updated model, we obtained an Ag85 acyl-enzyme intermediate structure that resembles the mycolated form. Here, we present a 1.45-? X-ray crystal structure of M. tuberculosis Ag85C covalently modified by tetrahydrolipstatin (THL), an esterase inhibitor that suppresses M. tuberculosis growth and mimics structural attributes of MAs. The mode of covalent inhibition differs from that observed in the reversible inhibition of the human fatty-acid synthase by THL. Similarities between the Ag85-THL structure and previously determined Ag85C structures suggest that the enzyme undergoes structural changes upon acylation, and positioning of the peptidyl arm of THL limits hydrolysis of the acyl-enzyme adduct. Molecular dynamics simulations of the modeled mycolated-enzyme form corroborate the structural analysis. From these findings, we propose an alternative arrangement of substrates that rectifies issues with the previous model and suggest a direct role for the ¦Â-hydroxy of MA in the second half-reaction of Ag85 catalysis. This information affords the visualization of a complete mycolyltransferase catalytic cycle.


  • Organizational Affiliation

    From the Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio 43606-3390.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Diacylglycerol acyltransferase/mycolyltransferase Ag85C303Mycobacterium tuberculosisMutation(s): 0 
Gene Names: fbpCmpt45MT0137
EC: 2.3.1.122 (PDB Primary Data), 2.3.1.20 (PDB Primary Data)
Membrane Entity: Yes 
UniProt
Find proteins for P9WQN9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WQN9 
Go to UniProtKB:  P9WQN9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WQN9
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 ?
  • R-Value Free: 0.174 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.161 
  • Space Group: P 21 21 2
Unit Cell:
Length ( ? )Angle ( ? )
a = 68.379¦Á = 90
b = 122.784¦Â = 90
c = 40.256¦Ă = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI105084

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-24
    Type: Initial release
  • Version 1.1: 2018-05-02
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.3: 2024-11-06
    Changes: Data collection, Database references, Structure summary
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