2HPI

Eubacterial and Eukaryotic Replicative DNA Polymerases are not Homologous: X-ray Structure of DNA Polymerase III


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 893-904

  • DOI: 10.1016/j.cell.2006.07.027
  • Primary Citation of Related Structures:  
  • Also Cited By: 4IQJ

  • PubMed Abstract: 
  • The crystal structure of Thermus aquaticus DNA polymerase III alpha subunit reveals that the structure of the catalytic domain of the eubacterial replicative polymerase is unrelated to that of the eukaryotic replicative polymerase but rather belongs ...

    The crystal structure of Thermus aquaticus DNA polymerase III alpha subunit reveals that the structure of the catalytic domain of the eubacterial replicative polymerase is unrelated to that of the eukaryotic replicative polymerase but rather belongs to the Polbeta-like nucleotidyltransferase superfamily. A model of the polymerase complexed with both DNA and beta-sliding clamp interacting with a reoriented binding domain and internal beta binding site was constructed that is consistent with existing biochemical data. Within the crystal, two C-terminal domains are interacting through a surface that is larger than many dimer interfaces. Since replicative polymerases of eubacteria and eukaryotes/archaea are not homologous, the nature of the replicative polymerase in the last common ancestor is unknown. Although other possibilities have been proposed, the plausibility of a ribozyme DNA polymerase should be considered.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase III alpha subunit
A
1220Thermus aquaticusMutation(s): 0 
Gene Names: dnaE
EC: 2.7.7.7
Find proteins for Q9XDH5 (Thermus aquaticus)
Go to UniProtKB:  Q9XDH5
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.222 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 175.146α = 90.00
b = 186.875β = 90.00
c = 125.834γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
SnBphasing
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-09-19
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Derived calculations, Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description