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 

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, 5VU8, 5VU9, 5VU6

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase
A
774Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)EC: 2.7.7.7
Find proteins for D0VWU9 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Go to UniProtKB:  D0VWU9
Entity ID: 2
MoleculeChainsLengthOrganism
DNA templateT16synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA/TNA hybrid primerP12synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FA2
Query on FA2

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Download 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
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
9O4
Query on 9O4
P
DNA linkingC9 H12 N5 O5 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.214 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 66.550α = 90.00
b = 112.610β = 90.00
c = 145.460γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
Aimlessdata scaling
iMOSFLMdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

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