Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Differences between bacteria and eukaryotes in clamp loader mechanism, a conserved process underlying DNA replication.
Journal, issue, pages	J Biol Chem, Vol. 300, Issue 4, Page 107166, Year 2024
Publish date	Mar 13, 2024
Authors	Jacob T Landeck / Joshua Pajak / Emily K Norman / Emma L Sedivy / Brian A Kelch /
PubMed Abstract	Clamp loaders are pentameric ATPases that place circular sliding clamps onto DNA, where they function in DNA replication and genome integrity. The central activity of a clamp loader is the opening of ...Clamp loaders are pentameric ATPases that place circular sliding clamps onto DNA, where they function in DNA replication and genome integrity. The central activity of a clamp loader is the opening of the ring-shaped sliding clamp and the subsequent binding to primer-template (p/t)-junctions. The general architecture of clamp loaders is conserved across all life, suggesting that their mechanism is retained. Recent structural studies of the eukaryotic clamp loader replication factor C (RFC) revealed that it functions using a crab-claw mechanism, where clamp opening is coupled to a massive conformational change in the loader. Here we investigate the clamp loading mechanism of the Escherichia coli clamp loader at high resolution using cryo-electron microscopy. We find that the E. coli clamp loader opens the clamp using a crab-claw motion at a single pivot point, whereas the eukaryotic RFC loader uses motions distributed across the complex. Furthermore, we find clamp opening occurs in multiple steps, starting with a partly open state with a spiral conformation, and proceeding to a wide open clamp in a surprising planar geometry. Finally, our structures in the presence of p/t-junctions illustrate how the clamp closes around p/t-junctions and how the clamp loader initiates release from the loaded clamp. Our results reveal mechanistic distinctions in a macromolecular machine that is conserved across all domains of life.
External links	J Biol Chem / PubMed:38490435
Methods	EM (single particle)
Resolution	3.0 - 7.7 Å
Structure data	43094 8val EMDB-43094, PDB-8val: Structure of the E. coli clamp loader bound to the beta clamp in a Open-DNAp/t conformation Method: EM (single particle) / Resolution: 3.7 Å 43095 8vam EMDB-43095, PDB-8vam: Structure of the E. coli clamp loader bound to the beta clamp in a Semi-Open conformation Method: EM (single particle) / Resolution: 3.9 Å 43096 8van EMDB-43096, PDB-8van: Structure of the E. coli clamp loader bound to the beta clamp in an Initial-Binding conformation Method: EM (single particle) / Resolution: 7.7 Å 43098 8vap EMDB-43098, PDB-8vap: Structure of the E. coli clamp loader bound to the beta clamp in a Fully-Open conformation Method: EM (single particle) / Resolution: 3.0 Å 43099 8vaq EMDB-43099, PDB-8vaq: Structure of the E. coli clamp loader bound to the beta clamp in a Closed-DNA1 conformation Method: EM (single particle) / Resolution: 3.8 Å 43100 8var EMDB-43100, PDB-8var: Structure of the E. coli clamp loader bound to the beta clamp in a Closed-DNA2 conformation Method: EM (single particle) / Resolution: 3.9 Å 43101 8vas EMDB-43101, PDB-8vas: Structure of the E. coli clamp loader bound to the beta clamp in an Altered-Collar conformation Method: EM (single particle) / Resolution: 3.8 Å 43102 8vat EMDB-43102, PDB-8vat: Structure of the E. coli clamp loader bound to the beta clamp in a Open-RNAp/t conformation Method: EM (single particle) / Resolution: 3.2 Å
Chemicals	ChemComp-ZN: Unknown entry ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM / Adenosine diphosphate ChemComp-BEF: BERYLLIUM TRIFLUORIDE ION ChemComp-MG*: Unknown entry
Source	escherichia coli (E. coli) synthetic construct (others)
Keywords	REPLICATION / TRANSFERASE/DNA / Bacterial Clamp Loader Complex / TRANSFERASE-DNA complex / TRANSFERASE / REPLICATION/DNA / REPLICATION-DNA complex