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TitleMolecular mechanisms of Holliday junction branch migration catalyzed by an asymmetric RuvB hexamer.
Journal, issue, pagesNat Commun, Vol. 14, Issue 1, Page 3549, Year 2023
Publish dateJun 15, 2023
AuthorsAnthony D Rish / Zhangfei Shen / Zhenhang Chen / Nan Zhang / Qingfei Zheng / Tian-Min Fu /
PubMed AbstractThe Holliday junction (HJ) is a DNA intermediate of homologous recombination, involved in many fundamental physiological processes. RuvB, an ATPase motor protein, drives branch migration of the ...The Holliday junction (HJ) is a DNA intermediate of homologous recombination, involved in many fundamental physiological processes. RuvB, an ATPase motor protein, drives branch migration of the Holliday junction with a mechanism that had yet to be elucidated. Here we report two cryo-EM structures of RuvB, providing a comprehensive understanding of HJ branch migration. RuvB assembles into a spiral staircase, ring-like hexamer, encircling dsDNA. Four protomers of RuvB contact the DNA backbone with a translocation step size of 2 nucleotides. The variation of nucleotide-binding states in RuvB supports a sequential model for ATP hydrolysis and nucleotide recycling, which occur at separate, singular positions. RuvB's asymmetric assembly also explains the 6:4 stoichiometry between the RuvB/RuvA complex, which coordinates HJ migration in bacteria. Taken together, we provide a mechanistic understanding of HJ branch migration facilitated by RuvB, which may be universally shared by prokaryotic and eukaryotic organisms.
External linksNat Commun / PubMed:37322069 / PubMed Central
MethodsEM (single particle)
Resolution2.97 - 4.3 Å
Structure data

28101

8efv

EMDB-28101, PDB-8efv:
Structure of single homo-hexameric Holliday junction ATP-dependent DNA helicase RuvB motor
Method: EM (single particle) / Resolution: 2.97 Å

28107

8efy

EMDB-28107, PDB-8efy:
Structure of double homo-hexameric AAA+ ATPase RuvB motors
Method: EM (single particle) / Resolution: 3.16 Å

40036

8gh8

EMDB-40036, PDB-8gh8:
RuvA Holliday junction DNA complex
Method: EM (single particle) / Resolution: 4.3 Å

Chemicals

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

ChemComp-MG:
Unknown entry

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

Source
  • thermus thermophilus hb8 (bacteria)
  • Punavirus P1
  • synthetic construct (others)
KeywordsSTRUCTURAL PROTEIN / Holliday Junction / AAA+ ATPase / RuvB / Homo-hexamer / DNA recombination / DNA BINDING PROTEIN/DNA / tetramer / RuvA / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex

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