2VWJ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.227 

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): 1 
Gene Names: pol (polA)
EC: 2.7.7.7
Find proteins for P56689 (Thermococcus gorgonarius)
Go to UniProtKB:  P56689
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*AP*AP*UP*GP*GP*AP*GP*AP*CP*GP *GP*CP*TP*TP*TP*TP*GP*CP*CP*GP*TP*GP*TP*C)-3'B26N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.227 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 100.700α = 90.00
b = 161.910β = 90.00
c = 221.820γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

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