6TGV

Crystal structure of Mycobacterium smegmatis CoaBC in complex with CTP and FMN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Inhibiting Mycobacterium tuberculosis CoaBC by targeting an allosteric site.

Mendes, V.Green, S.R.Evans, J.C.Hess, J.Blaszczyk, M.Spry, C.Bryant, O.Cory-Wright, J.Chan, D.S.Torres, P.H.M.Wang, Z.Nahiyaan, N.O'Neill, S.Damerow, S.Post, J.Bayliss, T.Lynch, S.L.Coyne, A.G.Ray, P.C.Abell, C.Rhee, K.Y.Boshoff, H.I.M.Barry, C.E.Mizrahi, V.Wyatt, P.G.Blundell, T.L.

(2021) Nat Commun 12: 143-143

  • DOI: https://doi.org/10.1038/s41467-020-20224-x
  • Primary Citation of Related Structures:  
    6TGV, 6TH2, 6THC

  • PubMed Abstract: 

    Coenzyme A (CoA) is a fundamental co-factor for all life, involved in numerous metabolic pathways and cellular processes, and its biosynthetic pathway has raised substantial interest as a drug target against multiple pathogens including Mycobacterium tuberculosis. The biosynthesis of CoA is performed in five steps, with the second and third steps being catalysed in the vast majority of prokaryotes, including M. tuberculosis, by a single bifunctional protein, CoaBC. Depletion of CoaBC was found to be bactericidal in M. tuberculosis. Here we report the first structure of a full-length CoaBC, from the model organism Mycobacterium smegmatis, describe how it is organised as a dodecamer and regulated by CoA thioesters. A high-throughput biochemical screen focusing on CoaB identified two inhibitors with different chemical scaffolds. Hit expansion led to the discovery of potent and selective inhibitors of M. tuberculosis CoaB, which we show to bind to a cryptic allosteric site within CoaB.


  • Organizational Affiliation

    Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK. vgm23@cam.ac.uk.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Coenzyme A biosynthesis bifunctional protein CoaBC
A, B, C, D
415Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: coaBCMSMEG_3054MSMEI_2978
EC: 4.1.1.36 (PDB Primary Data), 6.3.2.5 (PDB Primary Data)
UniProt
Find proteins for A0QWT2 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QWT2 
Go to UniProtKB:  A0QWT2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0QWT2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CTP (Subject of Investigation/LOI)
Query on CTP

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B],
O [auth C],
R [auth D]
CYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O14 P3
PCDQPRRSZKQHHS-XVFCMESISA-N
FMN (Subject of Investigation/LOI)
Query on FMN

Download Ideal Coordinates CCD File 
J [auth A],
N [auth B],
Q [auth C],
T [auth D]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
L [auth B]
M [auth B]
F [auth A],
G [auth A],
H [auth A],
L [auth B],
M [auth B],
P [auth C],
S [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
I [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 195.132α = 90
b = 195.132β = 90
c = 373.725γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
DIALSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates Foundation--

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-25
    Type: Initial release
  • Version 1.1: 2021-01-20
    Changes: Database references
  • Version 1.2: 2021-06-30
    Changes: Database references, Source and taxonomy, Structure summary