5DTW

Crystal structure of M. tuberculosis EchA6 bound to C20-CoA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.439 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

THPP target assignment reveals EchA6 as an essential fatty acid shuttle in mycobacteria.

Cox, J.A.Abrahams, K.A.Alemparte, C.Ghidelli-Disse, S.Rullas, J.Angulo-Barturen, I.Singh, A.Gurcha, S.S.Nataraj, V.Bethell, S.Remuinan, M.J.Encinas, L.Jervis, P.J.Cammack, N.C.Bhatt, A.Kruse, U.Bantscheff, M.Futterer, K.Barros, D.Ballell, L.Drewes, G.Besra, G.S.

(2016) Nat Microbiol 1: 15006-15006

  • DOI: 10.1038/nmicrobiol.2015.6
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Phenotypic screens for bactericidal compounds against drug-resistant tuberculosis are beginning to yield novel inhibitors. However, reliable target identification remains challenging. Here, we show that tetrahydropyrazo[1,5-a]pyrimidine-3-carboxamide ...

    Phenotypic screens for bactericidal compounds against drug-resistant tuberculosis are beginning to yield novel inhibitors. However, reliable target identification remains challenging. Here, we show that tetrahydropyrazo[1,5-a]pyrimidine-3-carboxamide (THPP) selectively pulls down EchA6 in a stereospecific manner, instead of the previously assigned target Mycobacterium tuberculosis MmpL3. While homologous to mammalian enoyl-coenzyme A (CoA) hydratases, EchA6 is non-catalytic yet essential and binds long-chain acyl-CoAs. THPP inhibitors compete with CoA-binding, suppress mycolic acid synthesis, and are bactericidal in a mouse model of chronic tuberculosis infection. A point mutation, W133A, abrogated THPP-binding and increased both the in vitro minimum inhibitory concentration and the in vivo effective dose 99 in mice. Surprisingly, EchA6 interacts with selected enzymes of fatty acid synthase II (FAS-II) in bacterial two-hybrid assays, suggesting essentiality may be linked to feeding long-chain fatty acids to FAS-II. Finally, our data show that spontaneous resistance-conferring mutations can potentially obscure the actual target or alternative targets of small molecule inhibitors.


    Organizational Affiliation

    Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
enoyl-CoA hydratase echA6
A, B, C, D, E, F
263Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: echA6
EC: 4.2.1.17
Find proteins for P9WNP1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WNP1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5F9
Query on 5F9

Download SDF File 
Download CCD File 
A, D
Arachinoyl-CoA
C41 H74 N7 O17 P3 S
JYLSVNBJLYCSSW-DLATUHJOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
5F9Kd: 3500 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.439 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.222 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 113.603α = 90.00
b = 51.275β = 106.80
c = 156.825γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XSCALEdata scaling
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-01-20
    Type: Initial release
  • Version 1.1: 2016-09-14
    Type: Database references