2IHM

Polymerase mu in ternary complex with gapped 11mer DNA duplex and bound incoming nucleotide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural insight into the substrate specificity of DNA Polymerase mu.

Moon, A.F.Garcia-Diaz, M.Bebenek, K.Davis, B.J.Zhong, X.Ramsden, D.A.Kunkel, T.A.Pedersen, L.C.

(2007) Nat Struct Mol Biol 14: 45-53

  • DOI: 10.1038/nsmb1180
  • Primary Citation of Related Structures:  
    2IHM

  • PubMed Abstract: 
  • DNA polymerase mu (Pol mu) is a family X enzyme with unique substrate specificity that contributes to its specialized role in nonhomologous DNA end joining (NHEJ). To investigate Pol mu's unusual substrate specificity, we describe the 2.4 A crystal structure of the polymerase domain of murine Pol mu bound to gapped DNA with a correct dNTP at the active site ...

    DNA polymerase mu (Pol mu) is a family X enzyme with unique substrate specificity that contributes to its specialized role in nonhomologous DNA end joining (NHEJ). To investigate Pol mu's unusual substrate specificity, we describe the 2.4 A crystal structure of the polymerase domain of murine Pol mu bound to gapped DNA with a correct dNTP at the active site. This structure reveals substrate interactions with side chains in Pol mu that differ from other family X members. For example, a single amino acid substitution, H329A, has little effect on template-dependent synthesis by Pol mu from a paired primer terminus, but it reduces both template-independent and template-dependent synthesis during NHEJ of intermediates whose 3' ends lack complementary template strand nucleotides. These results provide insight into the substrate specificity and differing functions of four closely related mammalian family X DNA polymerases.


    Organizational Affiliation

    Laboratory of Structural Biology, National Institute of Environmental Health Sciences (National Institutes of Health, US Department of Health and Human Services), 111 T.W. Alexander Drive, MD F3-09, Research Triangle Park, North Carolina 27709, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase muG [auth A], H [auth B]360Mus musculusMutation(s): 0 
Gene Names: Polmpolmu
EC: 2.7.7.7
Find proteins for Q9JIW4 (Mus musculus)
Explore Q9JIW4 
Go to UniProtKB:  Q9JIW4
NIH Common Fund Data Resources
IMPC:  MGI:1860191
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*CP*GP*GP*CP*AP*AP*TP*AP*CP*TP*G)-3'A [auth T], D [auth U]11N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*CP*AP*GP*TP*AP*T)-3'B [auth P], E [auth Q]6N/A
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
        MoleculeChainsLengthOrganismImage
        5'-D(P*GP*CP*CP*G)-3'C [auth D], F [auth E]4N/A
        Small Molecules
        Ligands 3 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        D3T
        Query on D3T

        Download Ideal Coordinates CCD File 
        L [auth A], M [auth A]2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE
        C10 H17 N2 O13 P3
        URGJWIFLBWJRMF-JGVFFNPUSA-N
         Ligand Interaction
        MG
        Query on MG

        Download Ideal Coordinates CCD File 
        I [auth A], N [auth B]MAGNESIUM ION
        Mg
        JLVVSXFLKOJNIY-UHFFFAOYSA-N
         Ligand Interaction
        NA
        Query on NA

        Download Ideal Coordinates CCD File 
        J [auth A], K [auth A], O [auth B]SODIUM ION
        Na
        FKNQFGJONOIPTF-UHFFFAOYSA-N
         Ligand Interaction
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 2.40 Å
        • R-Value Free: 0.277 
        • R-Value Work: 0.230 
        • R-Value Observed: 0.232 
        • Space Group: P 1 21 1
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 71.028α = 90
        b = 96.085β = 106.55
        c = 73.09γ = 90
        Software Package:
        Software NamePurpose
        MAR345dtbdata collection
        MOLREPphasing
        CNSrefinement
        MAR345data collection
        HKL-2000data reduction
        SCALEPACKdata scaling

        Structure Validation

        View Full Validation Report



        Entry History 

        Deposition Data

        Revision History  (Full details and data files)

        • Version 1.0: 2006-12-12
          Type: Initial release
        • Version 1.1: 2008-05-01
          Changes: Version format compliance
        • Version 1.2: 2011-07-13
          Changes: Version format compliance
        • Version 1.3: 2017-10-18
          Changes: Refinement description
        • Version 1.4: 2018-01-24
          Changes: Structure summary