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

• Type of Material: Article
• Authors: 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
• Language: English
• Date: 2023-12-01
• Publisher: Springer Nature Limited
• Publication Version: Final Published Version
• Copyright Statement: © The Author(s) 2023
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1038/s41467-023-39250-6
• Title of Journal or Parent Work: Nature Communications
• Volume: 14
• Issue: 1
• Start Page: 3549
• End Page: 3549
• Keywords: Nucleotides; Bacterial Proteins; Escherichia coli Proteins; DNA Helicases; Catalysis; DNA; Escherichia coli; DNA, Cruciform
• Research Categories: Chemistry, Biochemistry; Health Sciences, Oncology

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.