5OCJ

Crystal structure of Ag85C bound to cyclophostin 8beta inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cyclipostins and cyclophostin analogs inhibit the antigen 85C from

Viljoen, A.Richard, M.Nguyen, P.C.Fourquet, P.Camoin, L.Paudal, R.R.Gnawali, G.R.Spilling, C.D.Cavalier, J.F.Canaan, S.Blaise, M.Kremer, L.

(2018) J Biol Chem 293: 2755-2769

  • DOI: 10.1074/jbc.RA117.000760
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • An increasing prevalence of cases of drug-resistant tuberculosis requires the development of more efficacious chemotherapies. We previously reported the discovery of a new class of cyclipostins and cyclophostin (CyC) analogs exhibiting potent activit ...

    An increasing prevalence of cases of drug-resistant tuberculosis requires the development of more efficacious chemotherapies. We previously reported the discovery of a new class of cyclipostins and cyclophostin (CyC) analogs exhibiting potent activity against Mycobacterium tuberculosis both in vitro and in infected macrophages. Competitive labeling/enrichment assays combined with MS have identified several serine or cysteine enzymes in lipid and cell wall metabolism as putative targets of these CyC compounds. These targets included members of the antigen 85 (Ag85) complex ( i.e. Ag85A, Ag85B, and Ag85C), responsible for biosynthesis of trehalose dimycolate and mycolylation of arabinogalactan. Herein, we used biochemical and structural approaches to validate the Ag85 complex as a pharmacological target of the CyC analogs. We found that CyC , CyC , and CyC 17 bind covalently to the catalytic Ser 124 residue in Ag85C; inhibit mycolyltransferase activity ( i.e. the transfer of a fatty acid molecule onto trehalose); and reduce triacylglycerol synthase activity, a property previously attributed to Ag85A. Supporting these results, an X-ray structure of Ag85C in complex with CyC disclosed that this inhibitor occupies Ag85C's substrate-binding pocket. Importantly, metabolic labeling of M. tuberculosis cultures revealed that the CyC compounds impair both trehalose dimycolate synthesis and mycolylation of arabinogalactan. Overall, our study provides compelling evidence that CyC analogs can inhibit the activity of the Ag85 complex in vitro and in mycobacteria, opening the door to a new strategy for inhibiting Ag85. The high-resolution crystal structure obtained will further guide the rational optimization of new CyC scaffolds with greater specificity and potency against M. tuberculosis .


    Organizational Affiliation

    INSERM, IRIM, 34293 Montpellier, France.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Diacylglycerol acyltransferase/mycolyltransferase Ag85CA, B303Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: fbpCmpt45Rv0129cMTCI5.03c
EC: 2.3.1.122 (PDB Primary Data), 2.3.1.20 (PDB Primary Data)
Find proteins for P9WQN9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WQN9 
Go to UniProtKB:  P9WQN9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9SW
Query on 9SW

Download CCD File 
A, B
methoxy-[(3~{R})-3-[(2~{R})-1-methoxy-1,3-bis(oxidanylidene)butan-2-yl]pentadecyl]phosphinic acid
C21 H41 O6 P
VBHWHUMRWJDMHN-UXHICEINSA-N
 Ligand Interaction
DMS
Query on DMS

Download CCD File 
A, B
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.151 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.39α = 90
b = 75.77β = 90
c = 137.32γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-01-24
    Type: Initial release
  • Version 1.1: 2018-02-21
    Changes: Database references
  • Version 1.2: 2018-03-07
    Changes: Database references