5OMV

Ternary complex of 9N DNA polymerase in the replicative state with two metal ions in the active site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structures of ternary complexes of archaeal B-family DNA polymerases.

Kropp, H.M.Betz, K.Wirth, J.Diederichs, K.Marx, A.

(2017) PLoS One 12: e0188005-e0188005

  • DOI: 10.1371/journal.pone.0188005
  • Primary Citation of Related Structures:  
    5OMF, 5OMQ, 5OMV

  • PubMed Abstract: 
  • Archaeal B-family polymerases drive biotechnology by accepting a wide substrate range of chemically modified nucleotides. By now no structural data for archaeal B-family DNA polymerases in a closed, ternary complex are available, which would be the basis for developing next generation nucleotides ...

    Archaeal B-family polymerases drive biotechnology by accepting a wide substrate range of chemically modified nucleotides. By now no structural data for archaeal B-family DNA polymerases in a closed, ternary complex are available, which would be the basis for developing next generation nucleotides. We present the ternary crystal structures of KOD and 9°N DNA polymerases complexed with DNA and the incoming dATP. The structures reveal a third metal ion in the active site, which was so far only observed for the eukaryotic B-family DNA polymerase δ and no other B-family DNA polymerase. The structures reveal a wide inner channel and numerous interactions with the template strand that provide space for modifications within the enzyme and may account for the high processivity, respectively. The crystal structures provide insights into the superiority over other DNA polymerases concerning the acceptance of modified nucleotides.


    Organizational Affiliation

    Konstanz Research School Chemical Biology, University of Konstanz, Baden-Württemberg, Konstanz, Germany.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymeraseA775Thermococcus sp. 9oN-7Mutation(s): 2 
Gene Names: polpolA
EC: 2.7.7.7
UniProt
Find proteins for Q56366 (Thermococcus sp. (strain 9oN-7))
Explore Q56366 
Go to UniProtKB:  Q56366
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA templateB [auth T]16synthetic construct
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA primerC [auth P]12synthetic construct
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 5 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      DTP (Subject of Investigation/LOI)
      Query on DTP

      Download Ideal Coordinates CCD File 
      I [auth A]2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
      C10 H16 N5 O12 P3
      SUYVUBYJARFZHO-RRKCRQDMSA-N
       Ligand Interaction
      PGE
      Query on PGE

      Download Ideal Coordinates CCD File 
      G [auth A], H [auth A]TRIETHYLENE GLYCOL
      C6 H14 O4
      ZIBGPFATKBEMQZ-UHFFFAOYSA-N
       Ligand Interaction
      GOL
      Query on GOL

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

      Download Ideal Coordinates CCD File 
      D [auth A]MANGANESE (II) ION
      Mn
      WAEMQWOKJMHJLA-UHFFFAOYSA-N
       Ligand Interaction
      MG
      Query on MG

      Download Ideal Coordinates CCD File 
      F [auth A], J [auth T]MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 66.688α = 90
      b = 94.964β = 90
      c = 158.735γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      XDSdata reduction
      XDSdata scaling
      PHASERphasing

      Structure Validation

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      Ligand Structure Quality Assessment  



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2017-12-20
        Type: Initial release
      • Version 1.1: 2018-09-12
        Changes: Data collection, Database references