3E0D

Insights into the Replisome from the Crystral Structure of the Ternary Complex of the Eubacterial DNA Polymerase III alpha-subunit


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.6 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.287 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 859-869

  • DOI: 10.1016/j.jmb.2008.07.058
  • Also Cited By: 4IQJ

  • PubMed Abstract: 
  • The crystal structure of the catalytic alpha-subunit of the DNA polymerase III (Pol IIIalpha) holoenzyme bound to primer-template DNA and an incoming deoxy-nucleoside 5'-triphosphate has been determined at 4.6-A resolution. The polymerase interacts w ...

    The crystal structure of the catalytic alpha-subunit of the DNA polymerase III (Pol IIIalpha) holoenzyme bound to primer-template DNA and an incoming deoxy-nucleoside 5'-triphosphate has been determined at 4.6-A resolution. The polymerase interacts with the sugar-phosphate backbone of the DNA across its minor groove, which is made possible by significant movements of the thumb, finger, and beta-binding domains relative to their orientations in the unliganded polymerase structure. Additionally, the DNA and incoming nucleotide are bound to the active site of Pol IIIalpha nearly identically as they are in their complex with DNA polymerase beta, thereby proving that the eubacterial replicating polymerase, but not the eukaryotic replicating polymerase, is homologous to DNA polymerase beta. Finally, superimposing a recent structure of the clamp bound to DNA on this Pol IIIalpha complex with DNA places a loop of the beta-binding domain into the appropriate clamp cleft and supports a mechanism of polymerase switching.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase III subunit alpha
A, B
1220Thermus aquaticusMutation(s): 6 
Gene Names: dnaE
EC: 2.7.7.7
Find proteins for Q9XDH5 (Thermus aquaticus)
Go to UniProtKB:  Q9XDH5
Entity ID: 1
MoleculeChainsLengthOrganism
DNA substrate template strandC,E27N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA substrate primer strandD,F21N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DTP
Query on DTP

Download SDF File 
Download CCD File 
A, B
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
SUYVUBYJARFZHO-RRKCRQDMSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
DOC
Query on DOC
D, F
DNA LINKINGC9 H14 N3 O6 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.6 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.287 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 149.546α = 90.00
b = 149.546β = 90.00
c = 163.338γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance