5M1S

Cryo-EM structure of the E. coli replicative DNA polymerase-clamp-exonuclase-theta complex bound to DNA in the editing mode


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Self-correcting mismatches during high-fidelity DNA replication.

Fernandez-Leiro, R.Conrad, J.Yang, J.C.Freund, S.M.Scheres, S.H.Lamers, M.H.

(2017) Nat. Struct. Mol. Biol. 24: 140-143

  • DOI: 10.1038/nsmb.3348

  • PubMed Abstract: 
  • Faithful DNA replication is essential to all forms of life and depends on the action of 3'-5' exonucleases that remove misincorporated nucleotides from the newly synthesized strand. However, how the DNA is transferred from the polymerase to the exonu ...

    Faithful DNA replication is essential to all forms of life and depends on the action of 3'-5' exonucleases that remove misincorporated nucleotides from the newly synthesized strand. However, how the DNA is transferred from the polymerase to the exonuclease active site is not known. Here we present the cryo-EM structure of the editing mode of the catalytic core of the Escherichia coli replisome, revealing a dramatic distortion of the DNA whereby the polymerase thumb domain acts as a wedge that separates the two DNA strands. Importantly, NMR analysis of the DNA substrate shows that the presence of a mismatch increases the fraying of the DNA, thus enabling it to reach the exonuclease active site. Therefore the mismatch corrects itself, whereas the exonuclease subunit plays a passive role. Hence, our work provides unique insights into high-fidelity replication and establishes a new paradigm for the correction of misincorporated nucleotides.


    Organizational Affiliation

    MRC laboratory of Molecular Biology, Cambridge, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase III subunit alpha
A
927Escherichia coli (strain K12)Mutation(s): 2 
Gene Names: dnaE (polC)
EC: 2.7.7.7
Find proteins for P10443 (Escherichia coli (strain K12))
Go to UniProtKB:  P10443
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase III subunit beta
B, C
366Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: dnaN
Find proteins for P0A988 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A988
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase III subunit epsilon
D
243Escherichia coli (strain K12)Mutation(s): 4 
Gene Names: dnaQ (mutD)
EC: 2.7.7.7
Find proteins for P03007 (Escherichia coli (strain K12))
Go to UniProtKB:  P03007
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase III subunit theta
F
56Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: holE
EC: 2.7.7.7
Find proteins for P0ABS8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ABS8
Entity ID: 4
MoleculeChainsLengthOrganism
DNA Primer StrandP17synthetic construct
Entity ID: 5
MoleculeChainsLengthOrganism
DNA Template StrandT22synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.7 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-02-15
    Type: Database references
  • Version 1.2: 2017-08-30
    Type: Data collection, Derived calculations, Experimental preparation
  • Version 1.3: 2018-10-24
    Type: Advisory, Data collection, Derived calculations