5VU7

TNA polymerase, open ternary complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for TNA synthesis by an engineered TNA polymerase.

Chim, N.Shi, C.Sau, S.P.Nikoomanzar, A.Chaput, J.C.

(2017) Nat Commun 8: 1810-1810

  • DOI: 10.1038/s41467-017-02014-0
  • Primary Citation of Related Structures:  
    5VU5, 5VU7, 5VU6, 5VU9, 5VU8

  • PubMed Abstract: 
  • Darwinian evolution experiments carried out on xeno-nucleic acid (XNA) polymers require engineered polymerases that can faithfully and efficiently copy genetic information back and forth between DNA and XNA. However, current XNA polymerases function with inferior activity relative to their natural counterparts ...

    Darwinian evolution experiments carried out on xeno-nucleic acid (XNA) polymers require engineered polymerases that can faithfully and efficiently copy genetic information back and forth between DNA and XNA. However, current XNA polymerases function with inferior activity relative to their natural counterparts. Here, we report five X-ray crystal structures that illustrate the pathway by which α-(L)-threofuranosyl nucleic acid (TNA) triphosphates are selected and extended in a template-dependent manner using a laboratory-evolved polymerase known as Kod-RI. Structural comparison of the apo, binary, open and closed ternary, and translocated product detail an ensemble of interactions and conformational changes required to promote TNA synthesis. Close inspection of the active site in the closed ternary structure reveals a sub-optimal binding geometry that explains the slow rate of catalysis. This key piece of information, which is missing for all naturally occurring archaeal DNA polymerases, provides a framework for engineering new TNA polymerase variants.


    Organizational Affiliation

    Departments of Pharmaceutical Sciences, Chemistry, and Molecular Biology and Biochemistry University of California, Irvine, CA, 92697-3958, USA. jchaput@uci.edu.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase A774Thermococcus kodakarensisMutation(s): 6 
EC: 2.7.7.7
Find proteins for D0VWU9 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore D0VWU9 
Go to UniProtKB:  D0VWU9
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA templateT16synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA/TNA hybrid primerP12synthetic construct
      Small Molecules
      Ligands 3 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      FA2
      Query on FA2

      Download Ideal Coordinates CCD File 
      A
      5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXYTETRAHYDROFURAN-3-YL DIHYDROGEN PHOSPHATE
      C9 H12 N5 O6 P
      IJEJRDCFMFEDGL-AFEQZKEHSA-N
       Ligand Interaction
      SO4
      Query on SO4

      Download Ideal Coordinates CCD File 
      A
      SULFATE ION
      O4 S
      QAOWNCQODCNURD-UHFFFAOYSA-L
       Ligand Interaction
      MG
      Query on MG

      Download Ideal Coordinates CCD File 
      A
      MAGNESIUM ION
      Mg
      JLVVSXFLKOJNIY-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.72 Å
      • R-Value Free: 0.268 
      • R-Value Work: 0.214 
      • R-Value Observed: 0.218 
      • Space Group: P 2 21 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 66.55α = 90
      b = 112.61β = 90
      c = 145.46γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      iMOSFLMdata reduction
      Aimlessdata scaling
      PHASERphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      • Deposited Date: 2017-05-18 
      • Released Date: 2017-12-06 
      • Deposition Author(s): Chim, N., Chaput, J.C.

      Revision History  (Full details and data files)

      • Version 1.0: 2017-12-06
        Type: Initial release
      • Version 1.1: 2017-12-13
        Changes: Database references