RuvB is the ATP-dependent motor subunit of the Pseudomonas putida RuvAB Holliday-junction branch-migration complex, encoded in the ruvCAB locus. A AAA+ ATPase, it forms two homohexameric rings on opposite arms of a junction held open by RuvA and uses ATP hydrolysis to pump duplex DNA through the complex, moving the crossover so that RuvC can find and cleave its consensus site. Function is inferred from strong family and domain conservation with E. coli RuvB.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000400 four-way junction DNA binding | IEA GO_REF:0000104 | KEEP AS NON CORE | Summary: UniRule transfer of four-way junction DNA binding. Reason: RuvB rings bind the duplex arms of the junction (and E. coli RuvB binds junctions directly), but junction specificity is supplied by RuvA; true but peripheral to the motor function. Supporting Evidence: file:PSEPK/ruvB/ruvB-uniprot.txt RuvB forms 2 homohexamers on either side of HJ DNA bound by 1 or 2 RuvA tetramers file:ECOLI/ruvB/ruvB-uniprot.txt Binds to HJ cruciform DNA; in the presence of RuvA, ATP and Mg(2+) the junction is dissociated |
| GO:0003677 DNA binding | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro2GO DNA binding. Reason: True (four subunits per hexamer contact DNA), but entailed by four-way junction DNA binding (GO:0000400, kept). Supporting Evidence: file:PSEPK/ruvB/ruvB-uniprot.txt 4 subunits per hexamer contact DNA at a time |
| GO:0005524 ATP binding | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: Walker A/B AAA+ ATPase binds ATP. Reason: True and required for the motor, but a component of the motor activity rather than the defining function. Supporting Evidence: PMID:3279394 The amino acid sequence predicted for RuvB contains a region that matches a highly conserved sequence found in several DNA repair and recombination proteins that bind ATP |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: Cytoplasmic soluble protein (HAMAP). Reason: Correct but not function-defining. Supporting Evidence: file:PSEPK/ruvB/ruvB-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm |
| GO:0006281 DNA repair | IEA GO_REF:0000120 | MODIFY | Summary: Broad combined-IEA process term. Reason: Correct but general: the gene acts in the homology-directed late step of recombination and repair, so recombinational repair (GO:0000725), an is_a descendant of both DNA repair and DNA recombination and the process used for the E. coli orthologs, is the supported specific term. Proposed replacements: recombinational repair Supporting Evidence: file:PSEPK/ruvB/ruvB-uniprot.txt The RuvA-RuvB-RuvC complex processes Holliday junction (HJ) DNA during genetic recombination and DNA repair PMID:6374379 the ruv + product is involved in recombinational repair of damaged DNA rather than in cell division |
| GO:0006310 DNA recombination | IEA GO_REF:0000120 | MODIFY | Summary: Broad combined-IEA process term. Reason: Correct but general: the gene acts in the homology-directed late step of recombination and repair, so recombinational repair (GO:0000725), an is_a descendant of both DNA repair and DNA recombination and the process used for the E. coli orthologs, is the supported specific term. Proposed replacements: recombinational repair Supporting Evidence: file:PSEPK/ruvB/ruvB-uniprot.txt The RuvA-RuvB-RuvC complex processes Holliday junction (HJ) DNA during genetic recombination and DNA repair PMID:6374379 the ruv + product is involved in recombinational repair of damaged DNA rather than in cell division |
| GO:0009378 four-way junction helicase activity | IEA GO_REF:0000002 | ACCEPT | Summary: RuvB is the ATP-dependent four-way junction helicase motor. Reason: Core molecular function of RuvB; Q88NJ0 is in the RuvB subfamily PTHR42848:SF1 and carries TIGR00635, and the activity is established for E. coli RuvB and, within the genus, for P. aeruginosa RuvAB. Supporting Evidence: file:PSEPK/ruvB/ruvB-uniprot.txt The RuvB hexamer acts as an ATP-dependent pump, pulling dsDNA into and through the RuvAB complex PMID:1617728 indicating that the RuvB ATPase provides the motor force for branch migration file:PSEPK/ruvB/ruvB-deep-research-falcon.md Crucially, biochemical assays demonstrate **ATP-dependent HJ unwinding/processing** only when **both PaRuvA and PaRuvB** are present PMID:9501105 branch migration is catalysed by the RuvB protein, a hexameric DNA helicase that is loaded onto the junction by RuvA |
| GO:0016887 ATP hydrolysis activity | IEA GO_REF:0000116 | ACCEPT | Summary: Rhea-mapped ATP hydrolysis. Reason: RuvB hydrolyzes ATP to power branch migration (shown for E. coli RuvB). Supporting Evidence: PMID:8433990 together with RuvB (an ATPase), promotes their movement along DNA file:PSEPK/ruvB/ruvB-uniprot.txt The RuvB hexamer acts as an ATP-dependent pump |
| GO:0048476 Holliday junction resolvase complex | IEA GO_REF:0000104 | ACCEPT | Summary: RuvB participates in the RuvABC resolvosome. Reason: Conserved RuvABC assembly (HAMAP subunit text; E. coli co-immunoprecipitation). Supporting Evidence: file:PSEPK/ruvB/ruvB-uniprot.txt In the full resolvosome a probable DNA-RuvA(4)-RuvB(12)-RuvC(2) complex forms which resolves the HJ PMID:9637927 a multisubunit complex containing the junction and RuvA, RuvB and RuvC was detected |
| GO:0009379 Holliday junction helicase complex | ISS PMID:7885479 Structure of a multisubunit complex that promotes DNA branch... | NEW | Summary: RuvB hexamers are the motor component of the RuvAB Holliday junction helicase complex; no GOA row records it for Q88NJ0. Reason: The GO term's type example is the E. coli RuvAB complex, and the HAMAP subunit text for Q88NJ0 describes the same RuvA-RuvB-junction assembly; complex membership transfers with the exact RuvB subfamily. The KT2440 RuvA ortholog already carries this term. Supporting Evidence: file:PSEPK/ruvB/ruvB-uniprot.txt Each RuvB hexamer is contacted by two RuvA subunits (via domain III) on 2 adjacent RuvB subunits; this complex drives branch migration PMID:7885479 We observe the formation of a tripartite protein complex in which RuvA binds the crossover and is sandwiched between two hexameric rings of RuvB |
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