1TGO

THERMOSTABLE B TYPE DNA POLYMERASE FROM THERMOCOCCUS GORGONARIUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a thermostable type B DNA polymerase from Thermococcus gorgonarius.

Hopfner, K.P.Eichinger, A.Engh, R.A.Laue, F.Ankenbauer, W.Huber, R.Angerer, B.

(1999) Proc.Natl.Acad.Sci.USA 96: 3600-3605


  • PubMed Abstract: 
  • Most known archaeal DNA polymerases belong to the type B family, which also includes the DNA replication polymerases of eukaryotes, but maintain high fidelity at extreme conditions. We describe here the 2.5 A resolution crystal structure of a DNA pol ...

    Most known archaeal DNA polymerases belong to the type B family, which also includes the DNA replication polymerases of eukaryotes, but maintain high fidelity at extreme conditions. We describe here the 2.5 A resolution crystal structure of a DNA polymerase from the Archaea Thermococcus gorgonarius and identify structural features of the fold and the active site that are likely responsible for its thermostable function. Comparison with the mesophilic B type DNA polymerase gp43 of the bacteriophage RB69 highlights thermophilic adaptations, which include the presence of two disulfide bonds and an enhanced electrostatic complementarity at the DNA-protein interface. In contrast to gp43, several loops in the exonuclease and thumb domains are more closely packed; this apparently blocks primer binding to the exonuclease active site. A physiological role of this "closed" conformation is unknown but may represent a polymerase mode, in contrast to an editing mode with an open exonuclease site. This archaeal B DNA polymerase structure provides a starting point for structure-based design of polymerases or ligands with applications in biotechnology and the development of antiviral or anticancer agents.


    Organizational Affiliation

    Abteilung Strukturforschung, Max-Planck-Institut für Biochemie, D-82152 Martinsried, Germany. hopfner@scripps.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (THERMOSTABLE B DNA POLYMERASE)
A
773Thermococcus gorgonariusMutation(s): 0 
Gene Names: pol (polA)
EC: 2.7.7.7
Find proteins for P56689 (Thermococcus gorgonarius)
Go to UniProtKB:  P56689
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 58.110α = 90.00
b = 105.220β = 90.00
c = 154.160γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
MOSFLMdata reduction
CNSrefinement
SCALAdata scaling
CCP4phasing
CCP4model building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-03-22
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance