5TYY

DNA Polymerase Mu Product Complex, Mn2+ (60 min)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.218 
  • 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

Time-lapse crystallography snapshots of a double-strand break repair polymerase in action.

Jamsen, J.A.Beard, W.A.Pedersen, L.C.Shock, D.D.Moon, A.F.Krahn, J.M.Bebenek, K.Kunkel, T.A.Wilson, S.H.

(2017) Nat Commun 8: 253-253

  • DOI: 10.1038/s41467-017-00271-7
  • Primary Citation of Related Structures:  
    5TXX, 5TXZ, 5TYB, 5TYC, 5TYD, 5TYE, 5TYF, 5TYG, 5TYU, 5TYV, 5TYW, 5TYX, 5TYY, 5TYZ

  • PubMed Abstract: 
  • DNA polymerase (pol) μ is a DNA-dependent polymerase that incorporates nucleotides during gap-filling synthesis in the non-homologous end-joining pathway of double-strand break repair. Here we report time-lapse X-ray crystallography snapshots of catalytic events during gap-filling DNA synthesis by pol μ ...

    DNA polymerase (pol) μ is a DNA-dependent polymerase that incorporates nucleotides during gap-filling synthesis in the non-homologous end-joining pathway of double-strand break repair. Here we report time-lapse X-ray crystallography snapshots of catalytic events during gap-filling DNA synthesis by pol μ. Unique catalytic intermediates and active site conformational changes that underlie catalysis are uncovered, and a transient third (product) metal ion is observed in the product state. The product manganese coordinates phosphate oxygens of the inserted nucleotide and PP i . The product metal is not observed during DNA synthesis in the presence of magnesium. Kinetic analyses indicate that manganese increases the rate constant for deoxynucleoside 5'-triphosphate insertion compared to magnesium. The likely product stabilization role of the manganese product metal in pol μ is discussed. These observations provide insight on structural attributes of this X-family double-strand break repair polymerase that impact its biological function in genome maintenance.DNA polymerase (pol) μ functions in DNA double-strand break repair. Here the authors use time-lapse X-ray crystallography to capture the states of pol µ during the conversion from pre-catalytic to product complex and observe a third transiently bound metal ion in the product state.


    Organizational Affiliation

    Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA. wilson5@niehs.nih.gov.



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
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*GP*GP*CP*AP*TP*AP*CP*G)-3')B [auth T]9unidentified
    Protein Feature View
    Expand
    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*CP*GP*TP*AP*T)-3')C [auth P]5unidentified
      Protein Feature View
      Expand
      • Reference Sequence
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 4
        MoleculeChainsLengthOrganismImage
        DNA (5'-D(P*GP*CP*CP*G)-3')D4unidentified
        Protein Feature View
        Expand
        • Reference Sequence
        Small Molecules
        Ligands 6 Unique
        IDChainsName / Formula / InChI Key2D Diagram3D Interactions
        EPE
        Query on EPE

        Download Ideal Coordinates CCD File 
        M [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
        C8 H18 N2 O4 S
        JKMHFZQWWAIEOD-UHFFFAOYSA-N
         Ligand Interaction
        PPV
        Query on PPV

        Download Ideal Coordinates CCD File 
        K [auth A]PYROPHOSPHATE
        H4 O7 P2
        XPPKVPWEQAFLFU-UHFFFAOYSA-N
         Ligand Interaction
        DTT
        Query on DTT

        Download Ideal Coordinates CCD File 
        L [auth A]2,3-DIHYDROXY-1,4-DITHIOBUTANE
        C4 H10 O2 S2
        VHJLVAABSRFDPM-IMJSIDKUSA-N
         Ligand Interaction
        EDO
        Query on EDO

        Download Ideal Coordinates CCD File 
        P1,2-ETHANEDIOL
        C2 H6 O2
        LYCAIKOWRPUZTN-UHFFFAOYSA-N
         Ligand Interaction
        MN
        Query on MN

        Download Ideal Coordinates CCD File 
        E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], N [auth T], O [auth P]MANGANESE (II) ION
        Mn
        WAEMQWOKJMHJLA-UHFFFAOYSA-N
         Ligand Interaction
        NA
        Query on NA

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

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 1.93 Å
        • R-Value Free: 0.218 
        • R-Value Work: 0.186 
        • R-Value Observed: 0.187 
        • Space Group: P 21 21 21
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 59.985α = 90
        b = 68.67β = 90
        c = 110.181γ = 90
        Software Package:
        Software NamePurpose
        PHENIXrefinement
        HKL-2000data collection
        PDB_EXTRACTdata extraction
        HKL-2000data reduction
        HKL-2000data scaling
        PHENIXphasing

        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 StatesZ01-ES050158

        Revision History  (Full details and data files)

        • Version 1.0: 2017-08-30
          Type: Initial release
        • Version 1.1: 2017-09-27
          Changes: Author supporting evidence
        • Version 1.2: 2019-12-18
          Changes: Advisory, Author supporting evidence