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Structure paper

TitleCommunication between DNA polymerases and Replication Protein A within the archaeal replisome.
Journal, issue, pagesNat Commun, Vol. 15, Issue 1, Page 10926, Year 2024
Publish dateDec 30, 2024
AuthorsMarkel Martínez-Carranza / Léa Vialle / Clément Madru / Florence Cordier / Ayten Dizkirici Tekpinar / Ahmed Haouz / Pierre Legrand / Rémy A Le Meur / Patrick England / Rémi Dulermo / J Iñaki Guijarro / Ghislaine Henneke / Ludovic Sauguet /
PubMed AbstractReplication Protein A (RPA) plays a pivotal role in DNA replication by coating and protecting exposed single-stranded DNA, and acting as a molecular hub that recruits additional replication factors. ...Replication Protein A (RPA) plays a pivotal role in DNA replication by coating and protecting exposed single-stranded DNA, and acting as a molecular hub that recruits additional replication factors. We demonstrate that archaeal RPA hosts a winged-helix domain (WH) that interacts with two key actors of the replisome: the DNA primase (PriSL) and the replicative DNA polymerase (PolD). Using an integrative structural biology approach, combining nuclear magnetic resonance, X-ray crystallography and cryo-electron microscopy, we unveil how RPA interacts with PriSL and PolD through two distinct surfaces of the WH domain: an evolutionarily conserved interface and a novel binding site. Finally, RPA is shown to stimulate the activity of PriSL in a WH-dependent manner. This study provides a molecular understanding of the WH-mediated regulatory activity in central replication factors such as RPA, which regulate genome maintenance in Archaea and Eukaryotes.
External linksNat Commun / PubMed:39738083 / PubMed Central
MethodsEM (single particle) / X-ray diffraction / NMR (solution)
Resolution1.85 - 3.501 Å
Structure data

50140

9f29

EMDB-50140, PDB-9f29:
Pyrococcus abyssi PolD in complex with Rpa2 winged-helix domain class 1 (composite map)
Method: EM (single particle) / Resolution: 2.94 Å

EMDB-50141: Pyrococcus abyssi PolD-Rpa2 winged helix domain complex class 1 main component map
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-50142: Pyrococcus abyssi PolD-Rpa2 winged helix domain complex class 1 DP1 subunit local refinement
Method: EM (single particle) / Resolution: 3.0 Å

50143

9f2a

EMDB-50143, PDB-9f2a:
Pyrococcus abyssi PolD in complex with Rpa2 winged-helix domain class 2 (composite map)
Method: EM (single particle) / Resolution: 2.91 Å

EMDB-50144: Pyrococcus abyssi PolD-Rpa2 winged helix domain complex class 2 main component map
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-50145: Pyrococcus abyssi PolD-Rpa2 winged helix domain complex class 2 DP1 subunit local refinement
Method: EM (single particle) / Resolution: 3.0 Å

PDB-9f26:
Crystal structure of the PriS_PriL-Rpa2WH ternary complex from P. abyssi
Method: X-RAY DIFFRACTION / Resolution: 3.501 Å

PDB-9f27:
Solution structure of the Pyrococcus abyssi Rpa2 winged-helix domain
Method: SOLUTION NMR

PDB-9f28:
Crystal structure of the heterodimeric primase from pyrococcus abyssi (deletion of the PriL-CTD domain)
Method: X-RAY DIFFRACTION / Resolution: 1.85 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-MG:
Unknown entry

ChemComp-FMT:
FORMIC ACID

ChemComp-HOH:
WATER

ChemComp-FE:
Unknown entry

Source
  • pyrococcus abyssi ge5 (archaea)
  • pyrococcus abyssi (archaea)
KeywordsDNA BINDING PROTEIN / Replication protein A / ssDNA-Binding protein / REPLICATION / Winged-helix domain / Polymerase PolD interaction / Primase PriSL interaction / Disordered linker / DNA primase / PriS / PriL / DNA Polymerase / Archaea / RPA

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