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Mechanism of Processivity Clamp Opening by the Delta Subunit Wrench of the Clamp Loader Complex of E. coli DNA Polymerase III: Structure of the beta-delta complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.266 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history. 

Literature

Mechanism of processivity clamp opening by the delta subunit wrench of the clamp loader complex of E. coli DNA polymerase III.

Jeruzalmi, D., Yurieva, O., Zhao, Y., Young, M., Stewart, J., Hingorani, M., O'Donnell, M., Kuriyan, J.

(2001) Cell 106: 417-428

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The dimeric ring-shaped sliding clamp of E. coli DNA polymerase III (beta subunit, homolog of eukaryotic PCNA) is loaded onto DNA by the clamp loader gamma complex (homolog of eukaryotic Replication Factor C, RFC). The delta subunit of the gamma comp ...

    The dimeric ring-shaped sliding clamp of E. coli DNA polymerase III (beta subunit, homolog of eukaryotic PCNA) is loaded onto DNA by the clamp loader gamma complex (homolog of eukaryotic Replication Factor C, RFC). The delta subunit of the gamma complex binds to the beta ring and opens it. The crystal structure of a beta:delta complex shows that delta, which is structurally related to the delta' and gamma subunits of the gamma complex, is a molecular wrench that induces or traps a conformational change in beta such that one of its dimer interfaces is destabilized. Structural comparisons and molecular dynamics simulations suggest a spring-loaded mechanism in which the beta ring opens spontaneously once a dimer interface is perturbed by the delta wrench.

    Organizational Affiliation: 

    Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase III, beta chain
A, B
366Escherichia coli (strain K12)Mutation(s): 2 
Gene Names: dnaN
Find proteins for P0A988 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A988
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase III, delta subunit
C, D
343Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: holA
EC: 2.7.7.7
Find proteins for P28630 (Escherichia coli (strain K12))
Go to UniProtKB:  P28630
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.266 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 198.836α = 90.00
b = 99.293β = 119.17
c = 113.023γ = 90.00
Software Package:
Software NamePurpose
MLPHAREphasing
SCALEPACKdata scaling
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-11-07
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description
  • Version 1.4: 2018-01-31
    Type: Experimental preparation