4C8K

Crystal structure of the large fragment of DNA polymerase I from Thermus Aquaticus in a partially closed complex with the artificial base pair d5SICS-dNaMTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Structural Insights Into DNA Replication without Hydrogen Bonds.

Betz, K.Malyshev, D.A.Lavergne, T.Welte, W.Diederichs, K.Romesberg, F.E.Marx, A.

(2013) J.Am.Chem.Soc. 135: 18637

  • DOI: 10.1021/ja409609j
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The genetic alphabet is composed of two base pairs, and the development of a third, unnatural base pair would increase the genetic and chemical potential of DNA. d5SICS-dNaM is one of the most efficiently replicated unnatural base pairs identified to ...

    The genetic alphabet is composed of two base pairs, and the development of a third, unnatural base pair would increase the genetic and chemical potential of DNA. d5SICS-dNaM is one of the most efficiently replicated unnatural base pairs identified to date, but its pairing is mediated by only hydrophobic and packing forces, and in free duplex DNA it forms a cross-strand intercalated structure that makes its efficient replication difficult to understand. Recent studies of the KlenTaq DNA polymerase revealed that the insertion of d5SICSTP opposite dNaM proceeds via a mutually induced-fit mechanism, where the presence of the triphosphate induces the polymerase to form the catalytically competent closed structure, which in turn induces the pairing nucleotides of the developing unnatural base pair to adopt a planar Watson-Crick-like structure. To understand the remaining steps of replication, we now report the characterization of the prechemistry complexes corresponding to the insertion of dNaMTP opposite d5SICS, as well as multiple postchemistry complexes in which the already formed unnatural base pair is positioned at the postinsertion site. Unlike with the insertion of d5SICSTP opposite dNaM, addition of dNaMTP does not fully induce the formation of the catalytically competent closed state. The data also reveal that once synthesized and translocated to the postinsertion position, the unnatural nucleobases again intercalate. Two modes of intercalation are observed, depending on the nature of the flanking nucleotides, and are each stabilized by different interactions with the polymerase, and each appear to reduce the affinity with which the next correct triphosphate binds. Thus, continued primer extension is limited by deintercalation and rearrangements with the polymerase active site that are required to populate the catalytically active, triphosphate bound conformation.


    Organizational Affiliation

    Departments of Chemistry and Biology, Konstanz Research School Chemical Biology, Universität Konstanz , Universitätsstrasse 10, D-78464 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
5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*C*DOC)-3'B12synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*AP*AP*C*LHOP*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
BMR
Query on BMR

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Download CCD File 
A
((2R,3S,5R)-3-hydroxy-5-(3-methoxynaphthalen-2-yl)methyl-tetrahydrogen-triphosphate
dNaM-Triphosphate
C16 H21 O13 P3
OYLYLYUMXXAEFZ-NUEKZKHPSA-J
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
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
TRS
Query on TRS

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Download CCD File 
C
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
DOC
Query on DOC
B
DNA LINKINGC9 H14 N3 O6 PDC
LHO
Query on LHO
C
DNA LINKINGC15 H18 N O6 P S

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.181 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 115.039α = 90.00
b = 115.039β = 90.00
c = 91.106γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXphasing
XDSdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-11
    Type: Initial release
  • Version 1.1: 2013-12-25
    Type: Atomic model, Database references
  • Version 2.0: 2017-08-23
    Type: Atomic model, Data collection, Refinement description