6FBI

KlenTaq DNA polymerase in a closed, ternary complex with dGpNHpp bound in the active site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

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This is version 1.2 of the entry. See complete history


Literature

Snapshots of a modified nucleotide moving through the confines of a DNA polymerase.

Kropp, H.M.Durr, S.L.Peter, C.Diederichs, K.Marx, A.

(2018) Proc Natl Acad Sci U S A 115: 9992-9997

  • DOI: https://doi.org/10.1073/pnas.1811518115
  • Primary Citation of Related Structures:  
    6FBC, 6FBD, 6FBE, 6FBF, 6FBG, 6FBH, 6FBI

  • PubMed Abstract: 

    DNA polymerases have evolved to process the four canonical nucleotides accurately. Nevertheless, these enzymes are also known to process modified nucleotides, which is the key to numerous core biotechnology applications. Processing of modified nucleotides includes incorporation of the modified nucleotide and postincorporation elongation to proceed with the synthesis of the nascent DNA strand. The structural basis for postincorporation elongation is currently unknown. We addressed this issue and successfully crystallized KlenTaq DNA polymerase in six closed ternary complexes containing the enzyme, the modified DNA substrate, and the incoming nucleotide. Each structure shows a high-resolution snapshot of the elongation of a modified primer, where the modification "moves" from the 3'-primer terminus upstream to the sixth nucleotide in the primer strand. Combining these data with quantum mechanics/molecular mechanics calculations and biochemical studies elucidates how the enzyme and the modified substrate mutually modulate their conformations without compromising the enzyme's activity significantly. The study highlights the plasticity of the system as origin of the broad substrate properties of DNA polymerases and facilitates the design of improved systems.


  • Organizational Affiliation

    Department of Biology, Universität Konstanz, 78464 Konstanz, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase I, thermostable541Thermus aquaticusMutation(s): 0 
Gene Names: polApol1
EC: 2.7.7.7
UniProt
Find proteins for P19821 (Thermus aquaticus)
Explore P19821 
Go to UniProtKB:  P19821
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19821
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*CP*AP*C)-3')12synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*AP*AP*CP*GP*TP*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')16synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.77α = 90
b = 109.77β = 90
c = 91.46γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-26
    Type: Initial release
  • Version 1.1: 2018-10-10
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2019-08-14
    Changes: Data collection, Structure summary