6ISH

Structure of 9N-I DNA polymerase incorporation with 3'-AL in the active site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.219 

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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:  
    6IS7, 6ISF, 6ISG, 6ISH, 6ISI

  • 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 developed into a continuous method for DNA sequencing with dNTP analogs carrying a 3'-ester with a fluorophore ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymeraseA783Thermococcus sp. 9oN-7Mutation(s): 3 
Gene Names: polpolA
EC: 2.7.7.7
UniProt
Find proteins for Q56366 (Thermococcus sp. (strain 9oN-7))
Explore Q56366 
Go to UniProtKB:  Q56366
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ56366
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*CP*CP*(DAL))-3')B [auth C]14synthetic construct
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(*AP*CP*TP*GP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*C)-3')C [auth D]17synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B9X
Query on B9X

Download Ideal Coordinates CCD File 
G [auth C][(2R,3S,5R)-5-(6-aminopurin-9-yl)-2-(phosphonooxymethyl)oxolan-3-yl] 3-(2-ethoxyethoxy)propanoate
C17 H26 N5 O9 P
YOZZSXDAZQISJN-YNEHKIRRSA-N
 Ligand Interaction
PPV
Query on PPV

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

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.219 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 207.654α = 90
b = 207.654β = 90
c = 207.654γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata 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: 2019-08-28
    Type: Initial release