2VWK

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1016/j.jmb.2008.06.004
  • Primary Citation of Related Structures:  

  • 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 c ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA POLYMERASE
A
773Thermococcus gorgonariusMutation(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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 58.432α = 90.00
b = 104.747β = 90.00
c = 154.408γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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