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Structure of PolIIIalpha-Tauc-DNA complex suggests an atomic model of the replisome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.266 

wwPDB Validation 3D Report Full Report


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Literature

Structure of PolIIIalpha-Tauc-DNA complex suggests an atomic model of the replisome

Liu, B.Lin, J.Steitz, T.A.

(2013) Structure 21: 658-664

  • DOI: 10.1016/j.str.2013.02.002
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The C-terminal domain (CTD) of the τ subunit of the clamp loader (τc) binds to both the DnaB helicase and the DNA polymerase III α subunit (PolIIIα), and determines their relative positions and orientations on the leading and lagging strands. Here, w ...

    The C-terminal domain (CTD) of the τ subunit of the clamp loader (τc) binds to both the DnaB helicase and the DNA polymerase III α subunit (PolIIIα), and determines their relative positions and orientations on the leading and lagging strands. Here, we present a 3.2 Å resolution structure of Thermus aquaticus PolIIIα in complex with τc and a DNA substrate. The structure reveals that the CTD of τc interacts with the CTD of PolIIIα through its C-terminal helix and the adjacent loop. Additionally, in this complex PolIIIα displays an open conformation that includes the reorientations of the oligonucleotide-binding fold and the thumb domain, which may be an indirect result of crystal packing due to the presence of the τc. Nevertheless, the position of the τc on PolIIIα allows us to suggest an approximate model for how the PolIIIα is oriented and positioned on the DnaB helicase.


    Related Citations: 
    • The structure of T. aquaticus DNA polymerase III is distinct from eukaryotic replicative DNA polymerases.
      Bailey, S., Wing, R.A., Steitz, T.A.
      (2006) Cell 126: 893
    • Insights into the replisome from the structure of a ternary complex of the DNA polymerase III alpha-subunit.
      Wing, R.A., Bailey, S., Steitz, T.A.
      (2008) J Mol Biol 382: 859

    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase III subunit alpha
A, B, C, D
1220Thermus aquaticusMutation(s): 0 
Gene Names: dnaE
EC: 2.7.7.7
Find proteins for Q9XDH5 (Thermus aquaticus)
Go to UniProtKB:  Q9XDH5

Find similar proteins by: Sequence  |  Structure

Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
C-terminal domain of the DNA polymerase III subunit tau
M, N, O, P
177Thermus aquaticusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(P*CP*GP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*A)-3')E, G,K20synthetic construct

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*GP*TP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP*GP*TP*TP*TP*CP*G)-3')F, H,J,L28synthetic construct

Find similar nucleic acids by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*CP*GP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP*CP*CP*AP*(DOC))-3')I21synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DOC
Query on DOC

Download CCD File 
I
2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE
C9 H14 N3 O6 P
RAJMXAZJKUGYGW-POYBYMJQSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.266 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 188.53α = 90
b = 94.97β = 89.97
c = 204.08γ = 90
Software Package:
Software NamePurpose
BOSdata collection
PHASERphasing
PHENIXmodel building
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-13
    Type: Initial release
  • Version 1.1: 2013-06-19
    Changes: Database references