Crystal structure of archaeal family B DNA polymerase mutant

Experimental Data Snapshot

  • Resolution: 2.75 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 

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Structural Mechanism for Coordination of Proofreading and Polymerase Activities in Archaeal DNA Polymerases

Kuroita, T.Matsumura, H.Yokota, N.Kitabayashi, M.Hashimoto, H.Inoue, T.Imanaka, T.Kai, Y.

(2005) J Mol Biol 351: 291-298

  • DOI: https://doi.org/10.1016/j.jmb.2005.06.015
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    A novel mechanism for controlling the proofreading and polymerase activities of archaeal DNA polymerases was studied. The 3'-5'exonuclease (proofreading) activity and PCR performance of the family B DNA polymerase from Thermococcus kodakaraensis KOD1 (previously Pyrococcus kodakaraensis KOD1) were altered efficiently by mutation of a "unique loop" in the exonuclease domain. Interestingly, eight different H147 mutants showed considerable variations in respect to their 3'-5'exonuclease activity, from 9% to 276%, as against that of the wild-type (WT) enzyme. We determined the 2.75A crystal structure of the H147E mutant of KOD DNA polymerase that shows 30% of the 3'-5'exonuclease activity, excellent PCR performance and WT-like fidelity. The structural data indicate that the properties of the H147E mutant were altered by a conformational change of the Editing-cleft caused by an interaction between the unique loop and the Thumb domain. Our data suggest that electrostatic and hydrophobic interactions between the unique loop of the exonuclease domain and the tip of the Thumb domain are essential for determining the properties of these DNA polymerases.

  • Organizational Affiliation

    Tsuruga Institute of Biotechnology, Toyobo Co., Ltd., 10-24 Toyo-cho, Tsuruga, Fukui 914-0047, Japan. toshihiro_kuroita@bio.toyobo.co.jp

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Family B DNA Polymerase774Thermococcus kodakarensis KOD1Mutation(s): 0 
Find proteins for D0VWU9 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore D0VWU9 
Go to UniProtKB:  D0VWU9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0VWU9
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 2.75 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.226 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.344α = 90
b = 111.131β = 90
c = 111.559γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-08-02
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description