6THC | pdb_00006thc

Crystal structure of Mycobacterium smegmatis CoaB in complex with CTP and (4-hydroxyphenyl)(2,3,4-trihydroxyphenyl)methanone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 
    0.241 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6THC

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 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.

Macromolecule Content 

  • Total Structure Weight: 102.84 kDa 
  • Atom Count: 6,752 
  • Modeled Residue Count: 874 
  • Deposited Residue Count: 948 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Coenzyme A biosynthesis bifunctional protein CoaBC
A, B, C, D
237Mycolicibacterium smegmatisMutation(s): 0 
Gene Names: coaBCMSMEG_3054
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
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CTP

Query on CTP



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B],
M [auth C],
R [auth D]
CYTIDINE-5'-TRIPHOSPHATE
C9 H16 N3 O14 P3
PCDQPRRSZKQHHS-XVFCMESISA-N
N9N
(Subject of Investigation/LOI)

Query on N9N



Download:Ideal Coordinates CCD File
I [auth B]
J [auth B]
K [auth B]
O [auth C]
T [auth D]
I [auth B],
J [auth B],
K [auth B],
O [auth C],
T [auth D],
U [auth D]
(4-hydroxyphenyl)-[2,3,4-tris(oxidanyl)phenyl]methanone
C13 H10 O5
ZRDYULMDEGRWRC-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
L [auth B],
P [auth C],
Q [auth C]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA

Query on CA



Download:Ideal Coordinates CCD File
F [auth A],
H [auth B],
N [auth C],
S [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free:  0.241 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.01α = 90
b = 77.371β = 90
c = 144.351γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



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: 2024-01-24
    Changes: Data collection, Database references, Refinement description