Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 89.95 kDa 
• Atom Count: 6667 
• Modelled Residue Count: 773 
• Deposited Residue Count: 773 
• Unique protein chains: 1

1TGO

THERMOSTABLE B TYPE DNA POLYMERASE FROM THERMOCOCCUS GORGONARIUS

• PDB DOI: 10.2210/pdb1TGO/pdb

• Classification: TRANSFERASE
• Organism(s): Thermococcus gorgonarius
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-02-23 Released: 1999-03-22 
• Deposition Author(s): Hopfner, K.-P., Eichinger, A., Engh, R.A., Laue, F., Ankenbauer, W., Huber, R., Angerer, B.

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Experimental Data Snapshot

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

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

• PubMed: 10097083 
• 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. 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.

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Organizational Affiliation: 

Abteilung Strukturforschung, Max-Planck-Institut für Biochemie, D-82152 Martinsried, Germany. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (THERMOSTABLE B DNA POLYMERASE)	A	773	Thermococcus gorgonarius	Mutation(s): 0  Gene Names: pol, polA EC: 2.7.7.7
UniProt
Find proteins for P56689 (Thermococcus gorgonarius) Explore P56689  Go to UniProtKB:  P56689

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 = 58.11	α = 90
b = 105.22	β = 90
c = 154.16	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
CCP4	model building
CNS	refinement
CCP4	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-02-23 
• Released Date: 1999-03-22 
Deposition Author(s): Hopfner, K.-P., Eichinger, A., Engh, R.A., Laue, F., Ankenbauer, W., Huber, R., Angerer, B.

Revision History  

• 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