RuvB is the ATP-dependent motor subunit of the bacterial RuvAB Holliday junction branch migration complex, which processes four-way (Holliday) junction DNA intermediates that arise during homologous recombination and DNA repair, and which also drives replication fork reversal to rescue blocked replication forks. RuvB is a ring-forming AAA+ ATPase that assembles into homohexamers binding on opposite duplex arms of a Holliday junction held open by RuvA tetramers. ATP binding and hydrolysis in the tandem large and small ATPase domains power a lever motion that pulls double-stranded DNA through the RuvAB complex (about two nucleotides of DNA per ATP hydrolyzed), translocating the junction crossover point and thereby driving branch migration. The C-terminal head domain contacts DNA. Continuous branch migration allows the RuvC resolvase to scan to its cleavage consensus and resolve the junction, completing recombination. RuvB acts in the cytoplasm on chromosomal DNA. The protein is broadly conserved across bacteria, and the function of the Pseudomonas putida ortholog is inferred from this strong family and domain conservation.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000400 four-way junction DNA binding | IEA GO_REF:0000104 | MARK AS OVER ANNOTATED | Summary: RuvB contacts the duplex arms of RuvA-bound Holliday-junction DNA but does not independently recognize the four-way junction. Reason: The term is valid at RuvAB-complex level, but `enables` overstates RuvB's direct substrate specificity; RuvB contributes DNA contacts while RuvA independently enables four-way-junction recognition. Supporting Evidence: file:PSEPK/ruvB/ruvB-uniprot.txt either side of HJ DNA bound by 1 or 2 RuvA tetramers PMID:9501105 branch migration is catalysed by the RuvB protein, a hexameric DNA helicase that is loaded onto the junction by RuvA |
| GO:0003677 DNA binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: RuvB directly contacts duplex arms as the RuvAB motor, but RuvA supplies independent four-way-junction recognition. Reason: Generic DNA binding accurately captures RuvB's direct contacts but is not the representative core function; GO:0009378 captures the ATP-driven branch-migration motor. Supporting Evidence: file:PSEPK/ruvB/ruvB-uniprot.txt hexamer contact DNA at a time |
| GO:0005524 ATP binding | IEA GO_REF:0000120 | ACCEPT | Summary: RuvB is a AAA+ ATPase with a P-loop/Walker A and B motifs; ATP binding is required for the motor activity that drives branch migration. UniProt annotates multiple ATP-binding residues. This is a well-supported molecular function. Reason: ATP binding is a defining feature of the AAA+ ATPase RuvB-L/RuvB-S domains and is supported by conserved Walker A/B motifs and annotated ATP-binding residues. |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: RuvB acts on chromosomal DNA in the cytoplasm/nucleoid. Cytoplasmic localization is consistent with the function of a soluble DNA-processing enzyme and with UniProt subcellular location. Reason: The localization is plausible but generic and does not define RuvB's branch-migration mechanism. |
| GO:0006281 DNA repair | IEA GO_REF:0000120 | ACCEPT | Summary: RuvAB processes Holliday junctions during recombinational DNA repair and drives replication fork reversal to rescue blocked forks, so involvement in DNA repair is correct and a core biological process for this gene. Reason: RuvB's role in Holliday junction branch migration is central to recombinational DNA repair and replication fork rescue; this is a well-established function of the RuvB family. |
| GO:0006310 DNA recombination | IEA GO_REF:0000120 | ACCEPT | Summary: RuvB drives ATP-dependent branch migration of Holliday junctions, the central intermediate of homologous recombination, so involvement in DNA recombination is a core biological process for this gene. Reason: Holliday junction branch migration by the RuvAB complex is intrinsic to homologous recombination; this is a defining, well-established function of the RuvB family. |
| GO:0009378 four-way junction helicase activity | IEA GO_REF:0000002 | ACCEPT | Summary: RuvB is the ATP-dependent motor that translocates duplex DNA through the RuvAB complex to migrate the crossover point of a four-way (Holliday) junction. This four-way junction helicase/branch-migration activity is the defining molecular function of RuvB and is strongly supported by family conservation and structural studies of RuvB orthologs. Reason: ATP-dependent Holliday junction branch migration (four-way junction helicase activity) is the core molecular function of RuvB within RuvAB, supported by the conserved AAA+ motor architecture and structural/biochemical studies of RuvB. Supporting Evidence: file:PSEPK/ruvB/ruvB-deep-research-falcon.md RuvB is widely established as the **chemomechanical motor** of the bacterial **RuvAB** complex, functioning as an **AAA+ ATPase** that converts ATP hydrolysis into mechanical work to drive branch migration of HJs |
| GO:0016887 ATP hydrolysis activity | IEA GO_REF:0000116 | ACCEPT | Summary: RuvB hydrolyzes ATP (ATP + H2O = ADP + Pi) in its AAA+ ATPase domains; this hydrolysis powers the lever motion that pulls dsDNA through the complex, coupling chemical energy to branch migration. Supported by Rhea reaction mapping and conserved Walker A/B motifs. Reason: ATP hydrolysis is the energy-supplying activity underlying RuvB's motor function and is well supported by the AAA+ ATPase architecture and Rhea mapping. |
| GO:0048476 Holliday junction resolvase complex | IEA GO_REF:0000104 | ACCEPT | Summary: RuvB is a subunit of the RuvAB branch migration complex and of the larger RuvABC resolvosome (a DNA-RuvA4-RuvB12-RuvC2 assembly) that processes and resolves Holliday junctions. GO:0048476 captures this resolvase-associated complex membership, consistent with the UniProt SUBUNIT description. Reason: RuvB is an integral, well-established component of the RuvAB(C) Holliday junction processing/resolvosome complex; complex membership is supported by structural data and UniRule annotation. |
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