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Structure paper

TitleStructural characterisation of the complete cycle of sliding clamp loading in Escherichia coli.
Journal, issue, pagesNat Commun, Vol. 15, Issue 1, Page 8372, Year 2024
Publish dateSep 27, 2024
AuthorsZhi-Qiang Xu / Slobodan Jergic / Allen T Y Lo / Alok C Pradhan / Simon H J Brown / James C Bouwer / Harshad Ghodke / Peter J Lewis / Gökhan Tolun / Aaron J Oakley / Nicholas E Dixon /
PubMed AbstractRing-shaped DNA sliding clamps are essential for DNA replication and genome maintenance. Clamps need to be opened and chaperoned onto DNA by clamp loader complexes (CLCs). Detailed understanding of ...Ring-shaped DNA sliding clamps are essential for DNA replication and genome maintenance. Clamps need to be opened and chaperoned onto DNA by clamp loader complexes (CLCs). Detailed understanding of the mechanisms by which CLCs open and place clamps around DNA remains incomplete. Here, we present a series of six structures of the Escherichia coli CLC bound to an open or closed clamp prior to and after binding to a primer-template DNA, representing the most significant intermediates in the clamp loading process. We show that the ATP-bound CLC first binds to a clamp, then constricts to hold onto it. The CLC then expands to open the clamp with a gap large enough for double-stranded DNA to enter. Upon binding to DNA, the CLC constricts slightly, allowing clamp closing around DNA. These structures provide critical high-resolution snapshots of clamp loading by the E. coli CLC, revealing how the molecular machine works.
External linksNat Commun / PubMed:39333521 / PubMed Central
MethodsEM (single particle)
Resolution2.6 - 3.7 Å
Structure data

40079

8giy

EMDB-40079, PDB-8giy:
E. coli clamp loader with closed clamp
Method: EM (single particle) / Resolution: 3.7 Å

40080

8giz

EMDB-40080, PDB-8giz:
E. coli clamp loader with open clamp
Method: EM (single particle) / Resolution: 2.7 Å

40081

8gj0

EMDB-40081, PDB-8gj0:
E. coli clamp loader with open clamp on primed template DNA (form 1)
Method: EM (single particle) / Resolution: 2.9 Å

40082

8gj1

EMDB-40082, PDB-8gj1:
E. coli clamp loader with open clamp on primed template DNA (form 2)
Method: EM (single particle) / Resolution: 3.0 Å

40083

8gj2

EMDB-40083, PDB-8gj2:
E. coli clamp loader with closed clamp on primed template DNA
Method: EM (single particle) / Resolution: 2.6 Å

40084

8gj3

EMDB-40084, PDB-8gj3:
E. coli clamp loader on primed template DNA
Method: EM (single particle) / Resolution: 2.8 Å

Chemicals

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

ChemComp-ALF:
TETRAFLUOROALUMINATE ION

Source
  • escherichia coli (E. coli)
  • escherichia coli k-12 (bacteria)
KeywordsDNA BINDING PROTEIN/DNA / clamp loader / DNA clamp / AAA+ / ATPase / DNA BINDING PROTEIN-DNA complex

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