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Structure paper

TitleDNA-binding mechanism and evolution of replication protein A.
Journal, issue, pagesNat Commun, Vol. 14, Issue 1, Page 2326, Year 2023
Publish dateApr 22, 2023
AuthorsClément Madru / Markel Martínez-Carranza / Sébastien Laurent / Alessandra C Alberti / Maelenn Chevreuil / Bertrand Raynal / Ahmed Haouz / Rémy A Le Meur / Marc Delarue / Ghislaine Henneke / Didier Flament / Mart Krupovic / Pierre Legrand / Ludovic Sauguet /
PubMed AbstractReplication Protein A (RPA) is a heterotrimeric single stranded DNA-binding protein with essential roles in DNA replication, recombination and repair. Little is known about the structure of RPA in ...Replication Protein A (RPA) is a heterotrimeric single stranded DNA-binding protein with essential roles in DNA replication, recombination and repair. Little is known about the structure of RPA in Archaea, the third domain of life. By using an integrative structural, biochemical and biophysical approach, we extensively characterize RPA from Pyrococcus abyssi in the presence and absence of DNA. The obtained X-ray and cryo-EM structures reveal that the trimerization core and interactions promoting RPA clustering on ssDNA are shared between archaea and eukaryotes. However, we also identified a helical domain named AROD (Acidic Rpa1 OB-binding Domain), and showed that, in Archaea, RPA forms an unanticipated tetrameric supercomplex in the absence of DNA. The four RPA molecules clustered within the tetramer could efficiently coat and protect stretches of ssDNA created by the advancing replisome. Finally, our results provide insights into the evolution of this primordial replication factor in eukaryotes.
External linksNat Commun / PubMed:37087464 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.8 - 8.24 Å
Structure data

16444

8c5y

EMDB-16444, PDB-8c5y:
RPA tetrameric supercomplex from Pyrococcus abyssi
Method: EM (single particle) / Resolution: 3.35 Å

16445

8c5z

EMDB-16445, PDB-8c5z:
RPA tetrameric supercomplex with AROD-OB-1
Method: EM (single particle) / Resolution: 3.8 Å

EMDB-16448: Replication Protein A bound to DNA
Method: EM (single particle) / Resolution: 3.9 Å

16826

8oej

EMDB-16826, PDB-8oej:
Extended RPA-DNA nucleoprotein filament
Method: EM (single particle) / Resolution: 8.0 Å

16827

8oel

EMDB-16827, PDB-8oel:
Condensed RPA-DNA nucleoprotein filament
Method: EM (single particle) / Resolution: 8.2 Å

PDB-8aa9:
Crystal structure of the Rpa1 AROD-OB-1 domains
Method: X-RAY DIFFRACTION / Resolution: 1.8 Å

PDB-8aaj:
Crystal structure of the Pyrococcus abyssi RPA (apo form)
Method: X-RAY DIFFRACTION / Resolution: 3.7 Å

PDB-8aas:
Crystal structure of the Pyrococcus abyssi RPA trimerization core bound to poly-dT20 ssDNA
Method: X-RAY DIFFRACTION / Resolution: 3.2 Å

Chemicals

ChemComp-PEG:
DI(HYDROXYETHYL)ETHER

ChemComp-CL:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-ZN:
Unknown entry

ChemComp-SO4:
SULFATE ION

ChemComp-CA:
Unknown entry

Source
  • pyrococcus abyssi (archaea)
  • escherichia coli (E. coli)
  • pyrococcus abyssi ge5 (archaea)
  • synthetic construct (others)
KeywordsDNA BINDING PROTEIN / Replication protein A / ssDNA-Binding protein / DNA replication / single strand DNA-binding protein / RPA

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