4AHC

Crystal Structure of an Evolved Replicating DNA Polymerase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 

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This is version 1.1 of the entry. See complete history. 


Literature

Structures of an Apo and a Binary Complex of an Evolved Archeal B Family DNA Polymerase Capable of Synthesising Highly Cy-Dye Labelled DNA.

Wynne, S.A., Pinheiro, V.B., Holliger, P., Leslie, A.G.

(2013) PLoS One 8: 70892

  • DOI: 10.1371/journal.pone.0070892
  • Primary Citation of Related Structures:  
    4AHC, 4AIL

  • PubMed Abstract: 

    • Thermophilic DNA polymerases of the polB family are of great importance in biotechnological applications including high-fidelity PCR. Of particular interest is the relative promiscuity of engineered versions of the exo- form of polymerases from the Thermo- and Pyrococcales families towards non-canonical substrates, which enables key advances in Next-generation sequencing ...

    Thermophilic DNA polymerases of the polB family are of great importance in biotechnological applications including high-fidelity PCR. Of particular interest is the relative promiscuity of engineered versions of the exo- form of polymerases from the Thermo- and Pyrococcales families towards non-canonical substrates, which enables key advances in Next-generation sequencing. Despite this there is a paucity of structural information to guide further engineering of this group of polymerases. Here we report two structures, of the apo form and of a binary complex of a previously described variant (E10) of Pyrococcus furiosus (Pfu) polymerase with an ability to fully replace dCTP with Cyanine dye-labeled dCTP (Cy3-dCTP or Cy5-dCTP) in PCR and synthesise highly fluorescent "CyDNA" densely decorated with cyanine dye heterocycles. The apo form of Pfu-E10 closely matches reported apo form structures of wild-type Pfu. In contrast, the binary complex (in the replicative state with a duplex DNA oligonucleotide) reveals a closing movement of the thumb domain, increasing the contact surface with the nascent DNA duplex strand. Modelling based on the binary complex suggests how bulky fluorophores may be accommodated during processive synthesis and has aided the identification of residues important for the synthesis of unnatural nucleic acid polymers.

    Related Citations: 
    • Cydna: Synthesis and Replication of Highly Cy-Dye Substituted DNA by an Evolved Polymerase.
      Ramsay, N., Jemth, A., Brown, A., Crampton, N., Dear, P., Holliger, P.
      (2010) J Am Chem Soc 132: 5096
    Organizational Affiliation: 

    Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA POLYMERASEA, B775Pyrococcus furiosusMutation(s): 8 
EC: 2.7.7.7
UniProt
Find proteins for P61875 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1))
Explore P61875 
Go to UniProtKB:  P61875
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61875
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.207 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.438α = 90
b = 197.862β = 108.39
c = 78.438γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-07
    Type: Initial release
  • Version 1.1: 2013-08-28
    Changes: Database references