1TGO

THERMOSTABLE B TYPE DNA POLYMERASE FROM THERMOCOCCUS GORGONARIUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.209 

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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 U S A 96: 3600-3605

  • DOI: 10.1073/pnas.96.7.3600
  • Primary Citation of Related Structures:  
    1TGO

  • 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 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 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (THERMOSTABLE B DNA POLYMERASE)A773Thermococcus gorgonariusMutation(s): 0 
Gene Names: polpolA
EC: 2.7.7.7
UniProt
Find proteins for P56689 (Thermococcus gorgonarius)
Explore P56689 
Go to UniProtKB:  P56689
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP56689
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.11α = 90
b = 105.22β = 90
c = 154.16γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CCP4model building
CNSrefinement
CCP4data scaling
CCP4phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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