6ISF

Structure of 9N-I DNA polymerase incorporation with dT in the active site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 

wwPDB Validation 3D Report Full Report



Literature

Thermococcus sp. 9°N DNA polymerase exhibits 3'-esterase activity that can be harnessed for DNA sequencing.

LinWu, S.W.Tu, Y.H.Tsai, T.Y.Maestre-Reyna, M.Liu, M.S.Wu, W.J.Huang, J.Y.Chi, H.W.Chang, W.H.Chiou, C.F.Wang, A.H.Lee, J.Tsai, M.D.

(2019) Commun Biol 2: 224-224

  • DOI: 10.1038/s42003-019-0458-7
  • Primary Citation of Related Structures:  
    6IS7, 6ISI, 6ISH, 6ISG, 6ISF

  • PubMed Abstract: 
  • It was reported in 1995 that T7 and Taq DNA polymerases possess 3'-esterase activity, but without follow-up studies. Here we report that the 3'-esterase activity is intrinsic to the Thermococcus sp . 9°N DNA polymerase, and that it can be dev ...

    It was reported in 1995 that T7 and Taq DNA polymerases possess 3'-esterase activity, but without follow-up studies. Here we report that the 3'-esterase activity is intrinsic to the Thermococcus sp . 9°N DNA polymerase, and that it can be developed into a continuous method for DNA sequencing with dNTP analogs carrying a 3'-ester with a fluorophore. We first show that 3'-esterified dNTP can be incorporated into a template-primer DNA, and solve the crystal structures of the reaction intermediates and products. Then we show that the reaction can occur continuously, modulated by active site residues Tyr409 and Asp542. Finally, we use 5'-FAM-labeled primer and esterified dNTP with a dye to show that the reaction can proceed to ca. 450 base pairs, and that the intermediates of many individual steps can be identified. The results demonstrate the feasibility of a 3'-editing based DNA sequencing method that could find practical applications after further optimization.


    Organizational Affiliation

    3Institute of Biochemical Sciences, National Taiwan University, Taipei, 106 Taiwan.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymeraseA, B783Thermococcus sp. 9oN-7Mutation(s): 3 
Gene Names: polpolA
EC: 2.7.7.7
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 (5'-D(P*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*CP*T)-3')C, E15synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*AP*CP*AP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')D, F18synthetic construct
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      CA
      Query on CA

      Download CCD File 
      A, B
      CALCIUM ION
      Ca
      BHPQYMZQTOCNFJ-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.80 Å
      • R-Value Free: 0.272 
      • R-Value Work: 0.232 
      • R-Value Observed: 0.234 
      • Space Group: P 21 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 92.088α = 90
      b = 107.361β = 90
      c = 255.665γ = 90
      Software Package:
      Software NamePurpose
      REFMACrefinement
      XDSdata reduction
      SCALAdata scaling
      PHASERphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2019-08-28
        Type: Initial release