| Claim/annotation item | Evidence summary (1 sentence) | Organism/context | Key quantitative data | Top citation IDs | Publication (year, journal) + URL |
|---|---|---|---|---|---|
| Molecular function / EC | RuvB is a bacterial AAA+ ATPase motor/helicase that powers Holliday junction branch migration in the RuvAB complex, matching the UniProt description of a Holliday junction branch migration complex subunit RuvB (EC 3.6.4.-). | Canonical bacterial RuvB; strong mechanistic evidence from *Thermotoga maritima*, *Thermus thermophilus*, and *E. coli* models | Hexameric motor; ATP hydrolysis coupled to branch migration | (pqac-00000001, pqac-00000007) | Putnam et al. 2001, *J. Mol. Biol.* https://doi.org/10.1006/jmbi.2001.4852; Iwasaki et al. 2000, *Mol. Microbiol.* https://doi.org/10.1046/j.1365-2958.2000.01842.x |
| Complex partners | RuvB acts with Holliday-junction-binding RuvA, and the branch-migrated junction is then processed in concert with the resolvase RuvC. | Bacterial homologous recombination / stalled-fork repair pathway | RuvA recruits RuvB to opposite HJ arms; RuvC is dimeric resolvase | (pqac-00000001, pqac-00000008) | Putnam et al. 2001, *J. Mol. Biol.* https://doi.org/10.1006/jmbi.2001.4852; Zhang et al. 2023, *Front. Plant Sci.* https://doi.org/10.3389/fpls.2023.1139106 |
| Substrate specificity | The relevant substrate is branched Holliday junction DNA, with RuvB acting on duplex arms after loading by RuvA rather than as a general ssDNA helicase. | Reconstituted HJ substrates in structural/biochemical studies | *P. aeruginosa* assay used a synthetic HJ assembled from four 55-bp strands | (pqac-00000008, pqac-00000001) | Zhang et al. 2023, *Front. Plant Sci.* https://doi.org/10.3389/fpls.2023.1139106; Putnam et al. 2001, *J. Mol. Biol.* https://doi.org/10.1006/jmbi.2001.4852 |
| Mechanism / step size | Recent cryo-EM supports an asymmetric, sequential ATPase cycle in which DNA-engaged RuvB protomers pull/revolve dsDNA and advance branch migration by about 2 nt per ATP hydrolyzed. | Modern mechanistic model for bacterial RuvB motors | ~2 nt per ATP; ~12 nt per six-ATP revolution; DNA-binding contacts repeat every ~2 nt (~7 Å) | (pqac-00000000, pqac-00000002, pqac-00000005) | Fu et al. 2022, preprint https://doi.org/10.21203/rs.3.rs-2091230/v1; Rish et al. 2023, *bioRxiv* https://doi.org/10.1101/2022.09.22.509074 |
| Structural organization (hexamer / open rings) | RuvB forms homohexameric AAA+ rings in canonical models, while the *Pseudomonas aeruginosa* RuvAB-HJ intermediate captured by cryo-EM shows two RuvA tetramers and eight RuvB subunits arranged as two open rings on opposite HJ arms. | Canonical bacterial RuvB and *P. aeruginosa* intermediate complex | Central pore ~3–3.4 nm in RuvB hexamer; *P. aeruginosa* intermediate contains 8 RuvB subunits; FRET plateau at 1000 nM PaRuvB with 400 nM PaRuvA | (pqac-00000003, pqac-00000008) | Rish et al. 2023, *bioRxiv* https://doi.org/10.1101/2022.09.22.509074; Zhang et al. 2023, *Front. Plant Sci.* https://doi.org/10.3389/fpls.2023.1139106 |
| Regulation (SOS inducible where supported) | In *Pseudomonas aeruginosa*, RuvA and RuvB are reported as SOS-inducible proteins, while *P. putida* KT2440 has a comparatively weak SOS response overall, so direct strong induction of chromosomal ruvB in KT2440 should be inferred cautiously unless shown explicitly. | *Pseudomonas* DNA-damage response | *P. putida* SOS promoters show only moderate induction by norfloxacin in the cited study | (pqac-00000008, pqac-00000009) | Zhang et al. 2023, *Front. Plant Sci.* https://doi.org/10.3389/fpls.2023.1139106; Akkaya et al. 2021, *Environ. Microbiol.* https://doi.org/10.1111/1462-2920.15384 |
| Pseudomonas-specific note: *P. aeruginosa* cryo-EM | The 2023 *P. aeruginosa* study directly reconstituted PaRuvA/PaRuvB on HJ DNA, showed ATP-dependent HJ unwinding only when both proteins were present, and visualized an assembly intermediate for motor loading. | *Pseudomonas aeruginosa* structural/biochemical evidence | Synthetic HJ of 4 × 55-bp strands; activity increased with PaRuvB concentration and plateaued at 1000 nM PaRuvB with 400 nM PaRuvA | (pqac-00000008) | Zhang et al. 2023, *Front. Plant Sci.* https://doi.org/10.3389/fpls.2023.1139106 |
| Pseudomonas-specific note: *P. putida* plasmid rulAB vs chromosomal ruvAB | In *P. putida* work on TOL plasmid pWW0, plasmid-borne ruvAB-like genes were renamed rulAB to avoid confusion with chromosomal ruvAB; the paper explicitly states that chromosomal ruvAB encode the Holliday junction helicase complex required for branch migration along DNA. | *P. putida* PaW85 / pWW0 context, informative but not direct KT2440 gene-specific biochemistry | UV-C at 100 J/m² gave ~10-fold increase in Rif^r mutants for pWW0-carrying cells; mitomycin C at 2 µg/mL increased mutation frequency by 2–3 orders of magnitude | (pqac-00000009) | Tark et al. 2005, *J. Bacteriol.* https://doi.org/10.1128/jb.187.15.5203-5213.2005 |
| Organism-specific annotation confidence for UniProt Q88NJ0 / PP_1217 | Direct experimental literature on Q88NJ0/PP_1217 in *P. putida* KT2440 appears limited, but the assignment to bacterial RuvB is strongly supported by the conserved AAA+ RuvB family/domain architecture and by concordant function of chromosomal ruvAB described in *Pseudomonas* and other bacteria. | *P. putida* KT2440 functional annotation by homology plus genus-level support | Domain-level agreement: AAA+ ATPase / P-loop NTPase / RuvB-like N-terminal features (per target description) | (pqac-00000001, pqac-00000007, pqac-00000009) | Putnam et al. 2001, *J. Mol. Biol.* https://doi.org/10.1006/jmbi.2001.4852; Iwasaki et al. 2000, *Mol. Microbiol.* https://doi.org/10.1046/j.1365-2958.2000.01842.x; Tark et al. 2005, *J. Bacteriol.* https://doi.org/10.1128/jb.187.15.5203-5213.2005 |


*Table: This table maps core functional-annotation claims for bacterial RuvB to the strongest available evidence, emphasizing Pseudomonas findings and clearly separating direct organism-specific evidence from broader high-confidence homology-based inference.*