4LZG

Binary complex of human DNA Polymerase Mu with DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Sustained active site rigidity during synthesis by human DNA polymerase mu.

Moon, A.F.Pryor, J.M.Ramsden, D.A.Kunkel, T.A.Bebenek, K.Pedersen, L.C.

(2014) Nat Struct Mol Biol 21: 253-260

  • DOI: 10.1038/nsmb.2766
  • Primary Citation of Related Structures:  
    4LZD, 4LZG, 4M04, 4M0A

  • PubMed Abstract: 
  • DNA polymerase μ (Pol μ) is the only template-dependent human DNA polymerase capable of repairing double-strand DNA breaks (DSBs) with unpaired 3' ends in nonhomologous end joining (NHEJ). To probe this function, we structurally characterized Pol μ's catalytic cycle for single-nucleotide incorporation ...

    DNA polymerase μ (Pol μ) is the only template-dependent human DNA polymerase capable of repairing double-strand DNA breaks (DSBs) with unpaired 3' ends in nonhomologous end joining (NHEJ). To probe this function, we structurally characterized Pol μ's catalytic cycle for single-nucleotide incorporation. These structures indicate that, unlike other template-dependent DNA polymerases, Pol μ shows no large-scale conformational changes in protein subdomains, amino acid side chains or DNA upon dNTP binding or catalysis. Instead, the only major conformational change is seen earlier in the catalytic cycle, when the flexible loop 1 region repositions upon DNA binding. Pol μ variants with changes in loop 1 have altered catalytic properties and are partially defective in NHEJ. The results indicate that specific loop 1 residues contribute to Pol μ's unique ability to catalyze template-dependent NHEJ of DSBs with unpaired 3' ends.


    Organizational Affiliation

    Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed DNA/RNA polymerase muA356Homo sapiensMutation(s): 0 
Gene Names: POLMpolmu
EC: 2.7.7.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NP87 (Homo sapiens)
Explore Q9NP87 
Go to UniProtKB:  Q9NP87
PHAROS:  Q9NP87
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    template strandB [auth T]9N/A
    Protein Feature View
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    • Reference Sequence
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    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      upstream primer strandC [auth P]4N/A
      Protein Feature View
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      • Reference Sequence
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      • Entity ID: 4
        MoleculeChainsLengthOrganismImage
        downstream primer strandD4N/A
        Protein Feature View
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        • Reference Sequence
        Small Molecules
        Ligands 3 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        GOL
        Query on GOL

        Download Ideal Coordinates CCD File 
        E [auth A]GLYCEROL
        C3 H8 O3
        PEDCQBHIVMGVHV-UHFFFAOYSA-N
         Ligand Interaction
        CL
        Query on CL

        Download Ideal Coordinates CCD File 
        F [auth A], I [auth A]CHLORIDE ION
        Cl
        VEXZGXHMUGYJMC-UHFFFAOYSA-M
         Ligand Interaction
        NA
        Query on NA

        Download Ideal Coordinates CCD File 
        G [auth A], H [auth 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: 0.205 
        • R-Value Work: 0.174 
        • R-Value Observed: 0.175 
        • Space Group: P 21 21 21
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 60.003α = 90
        b = 68.514β = 90
        c = 110.307γ = 90
        Software Package:
        Software NamePurpose
        SCALEPACKdata scaling
        PHASERphasing
        PHENIXrefinement
        PDB_EXTRACTdata extraction
        StructureStudiodata collection
        HKL-2000data reduction

        Structure Validation

        View Full Validation Report




        Entry History 

        Deposition Data

        Revision History  (Full details and data files)

        • Version 1.0: 2014-02-05
          Type: Initial release
        • Version 1.1: 2014-03-05
          Changes: Database references
        • Version 1.2: 2014-03-19
          Changes: Database references