6P1N

Pre-catalytic ternary complex of human DNA Polymerase Mu with 1-nt gapped substrate containing template 8OG and bound incoming dAMPNPP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Unexpected behavior of DNA polymerase Mu opposite template 8-oxo-7,8-dihydro-2'-guanosine.

Kaminski, A.M.Chiruvella, K.K.Ramsden, D.A.Kunkel, T.A.Bebenek, K.Pedersen, L.C.

(2019) Nucleic Acids Res 47: 9410-9422

  • DOI: 10.1093/nar/gkz680
  • Primary Citation of Related Structures:  
    6P1P, 6P1O, 6P1R, 6P1Q, 6P1T, 6P1S, 6P1V, 6P1U, 6P1N, 6P1M

  • PubMed Abstract: 
  • DNA double-strand breaks (DSBs) resulting from reactive oxygen species generated by exposure to UV and ionizing radiation are characterized by clusters of lesions near break sites. Such complex DSBs are repaired slowly, and their persistence can have ...

    DNA double-strand breaks (DSBs) resulting from reactive oxygen species generated by exposure to UV and ionizing radiation are characterized by clusters of lesions near break sites. Such complex DSBs are repaired slowly, and their persistence can have severe consequences for human health. We have therefore probed DNA break repair containing a template 8-oxo-7,8-dihydro-2'-guanosine (8OG) by Family X Polymerase μ (Pol μ) in steady-state kinetics and cell-based assays. Pol μ tolerates 8OG-containing template DNA substrates, and the filled products can be subsequently ligated by DNA Ligase IV during Nonhomologous end-joining. Furthermore, Pol μ exhibits a strong preference for mutagenic bypass of 8OG by insertion of adenine. Crystal structures reveal that the template 8OG is accommodated in the Pol μ active site with none of the DNA substrate distortions observed for Family X siblings Pols β or λ. Kinetic characterization of template 8OG bypass indicates that Pol μ inserts adenosine nucleotides with weak sugar selectivity and, given the high cellular concentration of ATP, likely performs its role in repair of complex 8OG-containing DSBs using ribonucleotides.


    Organizational Affiliation

    Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed DNA/RNA polymerase muA354Homo sapiensMutation(s): 0 
Gene Names: POLMpolmu
EC: 2.7.7.7
Find proteins for Q9NP87 (Homo sapiens)
Explore Q9NP87 
Go to UniProtKB:  Q9NP87
NIH Common Fund Data Resources
PHAROS  Q9NP87
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*GP*GP*CP*(8OG)P*TP*AP*CP*G)-3')T9Homo sapiens
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*CP*GP*TP*A)-3')P4Homo sapiens
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 4
        MoleculeChainsLengthOrganismImage
        DNA (5'-D(P*GP*CP*CP*G)-3')D4Homo sapiens
        Small Molecules
        Ligands 6 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        DZ4
        Query on DZ4

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        A
        2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine
        C10 H17 N6 O11 P3
        WKIPJDSLGCBQCU-RRKCRQDMSA-N
         Ligand Interaction
        EPE
        Query on EPE

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        A
        4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
        C8 H18 N2 O4 S
        JKMHFZQWWAIEOD-UHFFFAOYSA-N
         Ligand Interaction
        EDO
        Query on EDO

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        A
        1,2-ETHANEDIOL
        C2 H6 O2
        LYCAIKOWRPUZTN-UHFFFAOYSA-N
         Ligand Interaction
        CL
        Query on CL

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        A
        CHLORIDE ION
        Cl
        VEXZGXHMUGYJMC-UHFFFAOYSA-M
         Ligand Interaction
        MG
        Query on MG

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        A
        MAGNESIUM ION
        Mg
        JLVVSXFLKOJNIY-UHFFFAOYSA-N
         Ligand Interaction
        NA
        Query on NA

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        A
        SODIUM ION
        Na
        FKNQFGJONOIPTF-UHFFFAOYSA-N
         Ligand Interaction
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 1.60 Å
        • R-Value Free: 0.187 
        • R-Value Work: 0.165 
        • R-Value Observed: 0.166 
        • Space Group: P 21 21 21
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 59.926α = 90
        b = 68.772β = 90
        c = 110.609γ = 90
        Software Package:
        Software NamePurpose
        PHENIXrefinement
        HKL-3000data reduction
        HKL-3000data scaling
        PHASERphasing

        Structure Validation

        View Full Validation Report



        Entry History & Funding Information

        Deposition Data


        Funding OrganizationLocationGrant Number
        National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United States1ZIA ES 102645

        Revision History 

        • Version 1.0: 2019-09-04
          Type: Initial release
        • Version 1.1: 2019-10-09
          Changes: Data collection, Database references
        • Version 1.2: 2019-12-18
          Changes: Author supporting evidence