Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 90.13 kDa 
• Atom Count: 5738 
• Modelled Residue Count: 707 
• Deposited Residue Count: 774 
• Unique protein chains: 1

5VU5

TNA polymerase, apo

• DOI: 10.2210/pdb5VU5/pdb

• Classification: TRANSFERASE
• Organism(s): Thermococcus kodakarensis
• Expression System: Escherichia coli
• Mutation(s): Yes 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.317 
• R-Value Work: 0.268 
• R-Value Observed: 0.271 

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

• PubMed: 29180809 
• 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. 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.

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Organizational Affiliation: 

Departments of Pharmaceutical Sciences, Chemistry, and Molecular Biology and Biochemistry University of California, Irvine, CA, 92697-3958, USA. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase	A	774	Thermococcus kodakarensis	Mutation(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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.317 
• R-Value Work: 0.268 
• R-Value Observed: 0.271 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.819	α = 90
b = 110.62	β = 90
c = 111.8	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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
  Changes: Database references