7PU7

DNA polymerase from M. tuberculosis


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

DNA-Dependent Binding of Nargenicin to DnaE1 Inhibits Replication in Mycobacterium tuberculosis.

Chengalroyen, M.D.Mason, M.K.Borsellini, A.Tassoni, R.Abrahams, G.L.Lynch, S.Ahn, Y.M.Ambler, J.Young, K.Crowley, B.M.Olsen, D.B.Warner, D.F.Barry Iii, C.E.Boshoff, H.I.M.Lamers, M.H.Mizrahi, V.

(2022) ACS Infect Dis 8: 612-625

  • DOI: https://doi.org/10.1021/acsinfecdis.1c00643
  • Primary Citation of Related Structures:  
    7PU7

  • PubMed Abstract: 

    Natural products provide a rich source of potential antimicrobials for treating infectious diseases for which drug resistance has emerged. Foremost among these diseases is tuberculosis. Assessment of the antimycobacterial activity of nargenicin, a natural product that targets the replicative DNA polymerase of Staphylococcus aureus , revealed that it is a bactericidal genotoxin that induces a DNA damage response in Mycobacterium tuberculosis ( Mtb ) and inhibits growth by blocking the replicative DNA polymerase, DnaE1. Cryo-electron microscopy revealed that binding of nargenicin to Mtb DnaE1 requires the DNA substrate such that nargenicin is wedged between the terminal base pair and the polymerase and occupies the position of both the incoming nucleotide and templating base. Comparative analysis across three bacterial species suggests that the activity of nargenicin is partly attributable to the DNA binding affinity of the replicative polymerase. This work has laid the foundation for target-led drug discovery efforts focused on Mtb DnaE1.


  • Organizational Affiliation

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


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase III subunit alpha1,184Mycobacterium tuberculosisMutation(s): 0 
Gene Names: 
EC: 2.7.7.7
UniProt
Find proteins for P9WNT7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WNT7 
Go to UniProtKB:  P9WNT7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WNT7
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
TemplateB [auth T]19synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
primerC [auth P]14synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
82W
Query on 82W

Download Ideal Coordinates CCD File 
G [auth A][(1~{S},3~{R},4~{R},5~{R},6~{R},7~{S},8~{R},11~{S},13~{S},16~{S},17~{R},18~{E})-13-methoxy-5,17,19-trimethyl-6-oxidanyl-16-[(1~{R})-1-oxidanylethyl]-14-oxidanylidene-2,15-dioxatetracyclo[9.8.0.0^{1,7}.0^{3,8}]nonadeca-9,18-dien-4-yl] 1~{H}-pyrrole-2-carboxylate
C28 H37 N O8
YEUSSARNQQYBKH-SIMZXIQRSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTREFMAC1.5

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-23
    Type: Initial release
  • Version 1.1: 2022-03-23
    Changes: Database references
  • Version 1.2: 2022-04-13
    Changes: Source and taxonomy
  • Version 1.3: 2024-07-17
    Changes: Data collection