5OP0

Structure of Prim-PolC from Mycobacterium smegmatis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

DNA Ligase C and Prim-PolC participate in base excision repair in mycobacteria.

Pocinski, P.Brissett, N.C.Bianchi, J.Brzostek, A.Korycka-Machaa, M.Dziembowski, A.Dziadek, J.Doherty, A.J.

(2017) Nat Commun 8: 1251-1251

  • DOI: https://doi.org/10.1038/s41467-017-01365-y
  • Primary Citation of Related Structures:  
    5OP0

  • PubMed Abstract: 

    Prokaryotic Ligase D is a conserved DNA repair apparatus processing DNA double-strand breaks in stationary phase. An orthologous Ligase C (LigC) complex also co-exists in many bacterial species but its function is unknown. Here we show that the LigC complex interacts with core BER enzymes in vivo and demonstrate that together these factors constitute an excision repair apparatus capable of repairing damaged bases and abasic sites. The polymerase component, which contains a conserved C-terminal structural loop, preferentially binds to and fills-in short gapped DNA intermediates with RNA and LigC ligates the resulting nicks to complete repair. Components of the LigC complex, like LigD, are expressed upon entry into stationary phase and cells lacking either of these pathways exhibit increased sensitivity to oxidising genotoxins. Together, these findings establish that the LigC complex is directly involved in an excision repair pathway(s) that repairs DNA damage with ribonucleotides during stationary phase.


  • Organizational Affiliation

    Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, BN1 9RQ, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase LigD, polymerase domainA [auth B],
B [auth A]
331Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: ligDMSMEG_6301
UniProt
Find proteins for A0R5T1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R5T1 
Go to UniProtKB:  A0R5T1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R5T1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.55α = 97.17
b = 56.43β = 100.2
c = 64.45γ = 90.64
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
xia2data reduction
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/J018643/1
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/M004236/1

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-15
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Source and taxonomy
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description