6SA0

Ternary complex of Prim-PolC from Mycobacterium smegmatis with 2nt gapped DNA and UpNHpp


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.176 

wwPDB Validation   3D Report Full Report



Literature

Molecular basis for DNA repair synthesis on short gaps by mycobacterial Primase-Polymerase C.

Brissett, N.C.Zabrady, K.Plocinski, P.Bianchi, J.Korycka-Machala, M.Brzostek, A.Dziadek, J.Doherty, A.J.

(2020) Nat Commun 11: 4196-4196

  • DOI: 10.1038/s41467-020-18012-8
  • Primary Citation of Related Structures:  
    6SA1, 6SA0

  • PubMed Abstract: 
  • Cells utilise specialized polymerases from the Primase-Polymerase (Prim-Pol) superfamily to maintain genome stability. Prim-Pol's function in genome maintenance pathways including replication, repair and damage tolerance. Mycobacteria contain multipl ...

    Cells utilise specialized polymerases from the Primase-Polymerase (Prim-Pol) superfamily to maintain genome stability. Prim-Pol's function in genome maintenance pathways including replication, repair and damage tolerance. Mycobacteria contain multiple Prim-Pols required for lesion repair, including Prim-PolC that performs short gap repair synthesis during excision repair. To understand the molecular basis of Prim-PolC's gap recognition and synthesis activities, we elucidated crystal structures of pre- and post-catalytic complexes bound to gapped DNA substrates. These intermediates explain its binding preference for short gaps and reveal a distinctive modus operandi called Synthesis-dependent Template Displacement (STD). This mechanism enables Prim-PolC to couple primer extension with template base dislocation, ensuring that the unpaired templating bases in the gap are ushered into the active site in an ordered manner. Insights provided by these structures establishes the molecular basis of Prim-PolC's gap recognition and extension activities, while also illuminating the mechanisms of primer extension utilised by closely related Prim-Pols.


    Organizational Affiliation

    Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, BN1 9RQ, UK. ajd21@sussex.ac.uk.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase LigD, polymerase domainAD350Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: ligDMSMEG_6301
Find proteins for A0R5T1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R5T1 
Go to UniProtKB:  A0R5T1
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*GP*CP*GP*AP*GP*CP*G)-3')B, E7synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*CP*GP*CP*TP*CP*GP*CP*AP*AP*CP*GP*CP*A)-3')C, F15synthetic construct
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 4
        MoleculeChainsLengthOrganismImage
        DNA (5'-D(P*TP*GP*CP*GP)-3')G, H6synthetic construct
        Small Molecules
        Ligands 4 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        2KH
        Query on 2KH

        Download CCD File 
        A, D
        5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine
        C9 H16 N3 O14 P3
        OZIBFYOFLVBDIY-XVFCMESISA-N
         Ligand Interaction
        CAC
        Query on CAC

        Download CCD File 
        A
        CACODYLATE ION
        C2 H6 As O2
        OGGXGZAMXPVRFZ-UHFFFAOYSA-M
         Ligand Interaction
        EDO
        Query on EDO

        Download CCD File 
        A, D
        1,2-ETHANEDIOL
        C2 H6 O2
        LYCAIKOWRPUZTN-UHFFFAOYSA-N
         Ligand Interaction
        MN
        Query on MN

        Download CCD File 
        A, D
        MANGANESE (II) ION
        Mn
        WAEMQWOKJMHJLA-UHFFFAOYSA-N
         Ligand Interaction
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 2.21 Å
        • R-Value Free: 0.206 
        • R-Value Work: 0.174 
        • R-Value Observed: 0.176 
        • Space Group: P 31 2 1
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 136.059α = 90
        b = 136.059β = 90
        c = 133.479γ = 120
        Software Package:
        Software NamePurpose
        DIALSdata reduction
        xia2data scaling
        PHASERphasing
        PHENIXrefinement
        PDB_EXTRACTdata extraction
        Cootmodel building

        Structure Validation

        View Full Validation Report



        Entry History & Funding Information

        Deposition Data


        Funding OrganizationLocationGrant Number
        Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/F013795/1
        Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/J018643/1
        Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/M004236/1

        Revision History 

        • Version 1.0: 2020-11-18
          Type: Initial release