6ISG

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.401 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.252 

wwPDB Validation 3D Report Full Report


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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:  

  • 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 <i>Thermococcus sp </i>. 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

    2Institute of Biological Chemistry, Academia Sinica, 128 Academia Road Sec. 2, Nankang, Taipei, 115 Taiwan.,Personal Genomics, Inc., Zhubei, Hsinchu 30261 Taiwan.,3Institute of Biochemical Sciences, National Taiwan University, Taipei, 106 Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase
A
783Thermococcus sp. (strain 9oN-7)Mutation(s): 3 
Gene Names: pol (polA)
EC: 2.7.7.7
Find proteins for Q56366 (Thermococcus sp. (strain 9oN-7))
Go to UniProtKB:  Q56366
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*CP*G)-3')C15synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*AP*CP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*G)-3')D18synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
PPV
Query on PPV

Download SDF File 
Download CCD File 
A
PYROPHOSPHATE
H4 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.401 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.252 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 208.078α = 90.00
b = 208.078β = 90.00
c = 208.078γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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