6FBC

KlenTaq DNA polymerase processing a modified primer - bearing the modification at the 3'-terminus of the primer.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


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: 10.1073/pnas.1811518115
  • Primary Citation of Related Structures:  

  • 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 nucleo ...

    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.,Department of Chemistry, Universität Konstanz, 78464 Konstanz, Germany.,Konstanz Research School Chemical Biology, Universität Konstanz, 78464 Konstanz, Germany.,Department of Chemistry, Universität Konstanz, 78464 Konstanz, Germany; andreas.marx@uni-konstanz.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase I, thermostable
A
541Thermus aquaticusMutation(s): 0 
Gene Names: polA (pol1)
EC: 2.7.7.7
Find proteins for P19821 (Thermus aquaticus)
Go to UniProtKB:  P19821
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*CP*AP*(OH3))-3')B12synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*AP*AP*CP*GP*TP*GP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')C16synthetic construct
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
XG4
Query on XG4

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Download CCD File 
A
2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine
C10 H17 N6 O12 P3
DWGAAFQEGIMTIA-KVQBGUIXSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A, C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
D4B
Query on D4B
B
DNA LINKINGC19 H18 N3 O7 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.186 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 109.230α = 90.00
b = 109.230β = 90.00
c = 90.700γ = 120.00
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
PHENIXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermany--

Revision History 

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