Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 90.66 kDa 
• Atom Count: 6176 
• Residue Count: 773 
• Unique protein chains: 1

2VWK

Uracil Recognition in Archaeal DNA Polymerases Captured by X-ray Crystallography. V93Q polymerase variant

• DOI: 10.2210/pdb2VWK/pdb

• Classification: DNA REPLICATION
• Organism(s): Thermococcus gorgonarius
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2008-06-26 Released: 2008-07-22 
• Deposition Author(s): Firbank, S.J., Wardle, J., Heslop, P., Lewis, R.J., Connolly, B.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.275 
• R-Value Work: 0.217 
• R-Value Observed: 0.220 

Literature

Uracil Recognition in Archaeal DNA Polymerases Captured by X-Ray Crystallography.

Firbank, S.J., Wardle, J., Heslop, P., Lewis, R.J., Connolly, B.A.

(2008) J Mol Biol 381: 529

• PubMed: 18614176 
• DOI: 10.1016/j.jmb.2008.06.004
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Archaeal family B DNA polymerases bind tightly to template-strand uracil and stall replication on encountering the pro-mutagenic base. This article describes an X-ray crystal structure, at 2.8 A resolution, of Thermococcus gorgonarius polymerase in complex with a DNA primer-template containing uracil in the single-stranded region. The DNA backbone is distorted to position the uracil deeply within a pocket, located in the amino-terminal domain of the polymerase. Specificity arises from a combination of hydrogen bonds between the protein backbone and uracil, with the pocket shaped to prevent the stable binding of the four standard DNA bases. Strong interactions are seen with the two phosphates that flank the uracil and the structure gives clues concerning the coupling of uracil binding to the halting of replication. The importance of key amino acids, identified by the analysis of the structure and their conservation between archaeal polymerases, was confirmed by site-directed mutagenesis. The crystal structure of V93Q, a polymerase variant that no longer recognises uracil, is also reported, explaining the V93Q phenotype by the steric exclusion of uracil from the pocket.

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Organizational Affiliation: 

Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DNA POLYMERASE	A	773	Thermococcus gorgonarius	Mutation(s): 2  Gene Names: pol, polA EC: 2.7.7.7
Find proteins for P56689 (Thermococcus gorgonarius) Go to UniProtKB:  P56689

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.275 
• R-Value Work: 0.217 
• R-Value Observed: 0.220 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.432	α = 90
b = 104.747	β = 90
c = 154.408	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-06-26 
• Released Date: 2008-07-22 
Deposition Author(s): Firbank, S.J., Wardle, J., Heslop, P., Lewis, R.J., Connolly, B.A.

Revision History 

• Version 1.0: 2008-07-22
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance