5J5R

M. thermoresistible GuaB2 delta-CBS in complex with inhibitor VCC234718


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Inosine Monophosphate Dehydrogenase, GuaB2, Is a Vulnerable New Bactericidal Drug Target for Tuberculosis.

Singh, V.Donini, S.Pacitto, A.Sala, C.Hartkoorn, R.C.Dhar, N.Keri, G.Ascher, D.B.Mondesert, G.Vocat, A.Lupien, A.Sommer, R.Vermet, H.Lagrange, S.Buechler, J.Warner, D.F.McKinney, J.D.Pato, J.Cole, S.T.Blundell, T.L.Rizzi, M.Mizrahi, V.

(2017) ACS Infect Dis 3: 5-17

  • DOI: 10.1021/acsinfecdis.6b00102

  • PubMed Abstract: 
  • VCC234718, a molecule with growth inhibitory activity against Mycobacterium tuberculosis (Mtb), was identified by phenotypic screening of a 15344-compound library. Sequencing of a VCC234718-resistant mutant identified a Y487C substitution in the inos ...

    VCC234718, a molecule with growth inhibitory activity against Mycobacterium tuberculosis (Mtb), was identified by phenotypic screening of a 15344-compound library. Sequencing of a VCC234718-resistant mutant identified a Y487C substitution in the inosine monophosphate dehydrogenase, GuaB2, which was subsequently validated to be the primary molecular target of VCC234718 in Mtb. VCC234718 inhibits Mtb GuaB2 with a Ki of 100 nM and is uncompetitive with respect to IMP and NAD+. This compound binds at the NAD+ site, after IMP has bound, and makes direct interactions with IMP; therefore, the inhibitor is by definition uncompetitive. VCC234718 forms strong pi interactions with the Y487 residue side chain from the adjacent protomer in the tetramer, explaining the resistance-conferring mutation. In addition to sensitizing Mtb to VCC234718, depletion of GuaB2 was bactericidal in Mtb in vitro and in macrophages. When supplied at a high concentration (≥125 μM), guanine alleviated the toxicity of VCC234718 treatment or GuaB2 depletion via purine salvage. However, transcriptional silencing of guaB2 prevented Mtb from establishing an infection in mice, confirming that Mtb has limited access to guanine in this animal model. Together, these data provide compelling validation of GuaB2 as a new tuberculosis drug target.


    Organizational Affiliation

    MRC/NHLS/UCT Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine & Department of Pathology, University of Cape Town , Anzio Road, Observatory 7925, South Africa.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
A
389Mycobacterium thermoresistibile (strain ATCC 19527 / DSM 44167 / CIP 105390 / JCM 6362 / NCTC 10409 / 316)Mutation(s): 0 
Gene Names: guaB
EC: 1.1.1.205
Find proteins for G7CNL4 (Mycobacterium thermoresistibile (strain ATCC 19527 / DSM 44167 / CIP 105390 / JCM 6362 / NCTC 10409 / 316))
Go to UniProtKB:  G7CNL4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IMP
Query on IMP

Download SDF File 
Download CCD File 
A
INOSINIC ACID
C10 H13 N4 O8 P
GRSZFWQUAKGDAV-KQYNXXCUSA-N
 Ligand Interaction
6G1
Query on 6G1

Download SDF File 
Download CCD File 
A
cyclohexyl{4-[(isoquinolin-5-yl)sulfonyl]piperazin-1-yl}methanone
C20 H25 N3 O3 S
RQGSIJUNMAAIRB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.168 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 89.360α = 90.00
b = 89.360β = 90.00
c = 84.920γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
PHENIXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European UnionUnited Kingdom260872
Medical Research Council (United Kingdom)United KingdomMR/M026302/1
NHMRCAustraliaAPP1072476

Revision History 

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2017-01-25
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence