5SZT

Crystal structure of the large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with 7-(N-(10-hydroxydecanoyl)-aminopentenyl)-7-deaza-2'-dATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Basis for the KlenTaq DNA Polymerase Catalysed Incorporation of Alkene- versus Alkyne-Modified Nucleotides.

Hottin, A.Betz, K.Diederichs, K.Marx, A.

(2017) Chemistry 23: 2109-2118

  • DOI: 10.1002/chem.201604515
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Efficient incorporation of modified nucleotides by DNA polymerases is essential for many cutting-edge biomolecular technologies. The present study compares the acceptance of either alkene- or alkyne-modified nucleotides by KlenTaq DNA polymerase and ...

    Efficient incorporation of modified nucleotides by DNA polymerases is essential for many cutting-edge biomolecular technologies. The present study compares the acceptance of either alkene- or alkyne-modified nucleotides by KlenTaq DNA polymerase and provides structural insights into how 7-deaza-adenosine and deoxyuridine with attached alkene-modifications are incorporated into the growing DNA strand. Thereby, we identified modified nucleotides that prove to be superior substrates for KlenTaq DNA polymerase compared with their natural analogues. The knowledge can be used to guide future design of functionalized nucleotide building blocks.


    Organizational Affiliation

    Department of Chemistry and Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase I, thermostable
A
540Thermus 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*GP*CP*(DOC))-3')B12synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*AP*AP*TP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')C16synthetic construct
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

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A, C
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
72J
Query on 72J

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A
7-(N-(10-hydroxydecanoyl)-aminopentenyl)-7-deaza-2'-dATP
C26 H44 N5 O14 P3
KGSINQKQGHRQNT-MNMHHJAXSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
DOC
Query on DOC
B
DNA LINKINGC9 H14 N3 O6 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.194 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 108.425α = 90.00
b = 108.425β = 90.00
c = 90.615γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-12-14
    Type: Initial release
  • Version 1.1: 2017-02-22
    Type: Database references