4DF8

Crystal structure of the large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with aminopentinyl-7-deaza-2-dATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structures of KlenTaq DNA Polymerase Caught While Incorporating C5-Modified Pyrimidine and C7-Modified 7-Deazapurine Nucleoside Triphosphates.

Bergen, K.Steck, A.L.Strutt, S.Baccaro, A.Welte, W.Diederichs, K.Marx, A.

(2012) J.Am.Chem.Soc. 134: 11840-11843

  • DOI: 10.1021/ja3017889
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The capability of DNA polymerases to accept chemically modified nucleotides is of paramount importance for many biotechnological applications. Although these analogues are widely used, the structural basis for the acceptance of the unnatural nucleoti ...

    The capability of DNA polymerases to accept chemically modified nucleotides is of paramount importance for many biotechnological applications. Although these analogues are widely used, the structural basis for the acceptance of the unnatural nucleotide surrogates has been only sparsely explored. Here we present in total six crystal structures of modified 2'-deoxynucleoside-5'-O-triphosphates (dNTPs) carrying modifications at the C5 positions of pyrimidines or C7 positions of 7-deazapurines in complex with a DNA polymerase and a primer/template complex. The modified dNTPs are in positions poised for catalysis leading to incorporation. These structural data provide insight into the mechanism of incorporation and acceptance of modified dNTPs. Our results open the door for rational design of modified nucleotides, which should offer great opportunities for future applications.


    Organizational Affiliation

    Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstr. 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')B12N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*AP*AP*TP*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3')C16N/A
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMT
Query on FMT

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A, C
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
0L4
Query on 0L4

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A
5-(5-aminopent-1-yn-1-yl)-7-{2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-7H-pyrrolo[2,3-d]pyrimidin-4-amine
C16 H24 N5 O12 P3
MCSGHAFVOBYWGE-YNEHKIRRSA-N
 Ligand Interaction
CL
Query on CL

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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
EDO
Query on EDO

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

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A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-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: 2 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.195 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 108.609α = 90.00
b = 108.609β = 90.00
c = 90.516γ = 120.00
Software Package:
Software NamePurpose
XDSdata scaling
PHENIXmodel building
PHENIXphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-16
    Type: Initial release
  • Version 1.1: 2012-08-08
    Type: Database references