Molecular mechanisms of Holliday junction branch migration catalyzed by an asymmetric RuvB hexamer

Anthony D. Rish, Zhangfei Shen, Zhenhang Chen, Nan Zhang, Qingfei Zheng and Tian-Min Fu ()
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Anthony D. Rish: The Ohio State University
Zhangfei Shen: The Ohio State University
Zhenhang Chen: The Ohio State University
Nan Zhang: The Ohio State University Comprehensive Cancer Center
Qingfei Zheng: The Ohio State University
Tian-Min Fu: The Ohio State University

Nature Communications, 2023, vol. 14, issue 1, 1-10

Abstract: Abstract 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.

Date: 2023
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DOI: 10.1038/s41467-023-39250-6

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