| Topic | Key points | Quantitative data | Organism/strain | Source (with DOI URL and year) |
|---|---|---|---|---|
| Verified identity of target protein | Target is **uvrB / PP_1974 / UniProt Q88LF9** from **Pseudomonas putida KT2440**; UniProt description identifies it as **UvrABC system protein B / Excinuclease ABC subunit B**, belonging to the **UvrB family**. Literature context on bacterial UvrB matches this annotation: UvrB is the damage-verification subunit of the bacterial UvrABC excinuclease in NER and is a helicase-family ATPase acting at damaged DNA. | No strain-specific quantitative value reported in provided contexts for identity itself. | *Pseudomonas putida* KT2440 (target); comparative mechanistic literature from diverse bacteria | Thakur & Muniyappa 2023, DOI: https://doi.org/10.1007/s12038-023-00378-8 (pqac-00000003, pqac-00000005) |
| Core molecular function in bacterial NER | UvrB is the central **damage-verification** factor in bacterial nucleotide excision repair. After lesion sensing by UvrA, UvrB is loaded onto DNA, forms the **pre-incision complex**, and then recruits UvrC for dual incision of the damaged strand; downstream UvrD/Pol I/ligase complete repair. UvrB associates stably with the lesion-containing strand after local duplex opening. | UvrC excises a **12–13 nt** lesion-containing oligonucleotide after UvrB pre-incision complex formation. | General bacterial NER | Seck et al. 2023, DOI: https://doi.org/10.1093/nar/gkad108 (pqac-00000000); Thakur & Muniyappa 2023, DOI: https://doi.org/10.1007/s12038-023-00378-8 (pqac-00000003); Genta 2025 review context (pqac-00000002, pqac-00000004) |
| Key domains and catalytic features | UvrB is described as an **SF2/helicase-family ATPase** with conserved **helicase motifs I–VI**, **RecA-like domains 1a and 3**, and auxiliary **domains 1b, 2, and 4**. It has weak intrinsic ATPase/helicase activity that is stimulated in the NER complex and supports local DNA unwinding/translocation needed for lesion engagement. | ATP hydrolysis is **essential for formation of the UvrB–DNA preincision complex**, though reported as dispensable for UvrA dissociation in one mechanistic summary. | General bacterial NER | Thakur & Muniyappa 2023, DOI: https://doi.org/10.1007/s12038-023-00378-8 (pqac-00000003); Seck et al. 2023, DOI: https://doi.org/10.1093/nar/gkad108 (pqac-00000000); Covizzi 2024 context (pqac-00000001) |
| Mechanistic motifs for damage verification | A conserved **β-hairpin** inserts between DNA strands, helping separate them and flip the damaged base into a **hydrophobic pocket** in UvrB for lesion verification. Structural/biochemical summaries also note that a second UvrB protomer can engage the opposite strand in some models before dissociation. | In one mechanistic review, a second UvrB can dissociate after translocating **~22–27 nt** when no lesion is present. | General bacterial NER | Seck et al. 2023, DOI: https://doi.org/10.1093/nar/gkad108 (pqac-00000000); Thakur & Muniyappa 2023, DOI: https://doi.org/10.1007/s12038-023-00378-8 (pqac-00000003) |
| Transcription-coupled repair (TCR) context | In prokaryotic TCR, UvrAB is recruited to transcription-blocking lesions exposed after RNAP displacement/backtracking. Reviews describe UvrB as the component that is loaded onto the damaged template strand for homing/verification. Recent work further links ppGpp-controlled elongation states of RNAP to assembly of functional TCR complexes containing **UvrA, UvrB, and UvrD**. | No direct UvrB-specific kinetic number in the provided TCR contexts. | General bacterial TCR, especially *E. coli* context | Thakur & Muniyappa 2023, DOI: https://doi.org/10.1007/s12038-023-00378-8 (pqac-00000003, pqac-00000005); Weaver et al. 2023, DOI: https://doi.org/10.1038/s41594-023-00948-2 (from cited paper context in prior tool output) |
| Pseudomonas NER significance | In *Pseudomonas* spp., NER is described as a major contributor to UV survival. Gunasekera & Sundin note that the **UvrABC excision repair complex** in *P. aeruginosa* appears to function similarly to the *E. coli* system, although **uvrA and uvrB are not SOS-regulated** there, which may influence UV sensitivity. | NER characterized as probably providing the **greatest contribution** to UVR survival among *Pseudomonas* DNA-repair systems, but no single numeric estimate for uvrB alone. | *Pseudomonas* spp.; discussion includes *P. aeruginosa* and *P. syringae* | Gunasekera & Sundin 2006, DOI: https://doi.org/10.1111/j.1365-2672.2006.02841.x (pqac-00000009) |
| Pseudomonas UV phenotype relevant to NER | In *P. syringae* pv. *syringae* B728a, an **uvrA** mutant showed markedly higher UVB/solar UVB sensitivity, supporting the importance of UvrABC-mediated NER in pseudomonads. This is relevant background for inferred importance of the homologous UvrB pathway component. | Under solar UVB, the **phr uvrA** double mutant showed a **10-fold survival reduction at 2000 J/m²** and about **10^7-fold reduction at 4000 J/m²**; after artificial UVB, recA induction in the **uvrA** mutant occurred at as little as **18 J/m²**, reaching about **60% greater** than unexposed cultures; wild type recA induction under solar UVB was about **20–40% greater** than unexposed cultures. | *Pseudomonas syringae* pv. *syringae* B728a and derivatives | Gunasekera & Sundin 2006, DOI: https://doi.org/10.1111/j.1365-2672.2006.02841.x (pqac-00000010, pqac-00000009) |
| P. putida KT2440 UV/DNA-damage context | In *P. putida* KT2440, strong UV sensitivity is documented, but Martínez-García et al. attribute much of the hypersensitivity to **prophage induction after SOS activation**, not to a demonstrated defect in the host recombination/DNA repair machinery. This is important context when interpreting DNA-damage phenotypes for KT2440. | At **30 J/m²** UV, *E. coli* remained virtually intact whereas *P. putida* KT2440 survival fell by **>4 orders of magnitude**. Prophage-free Δall-Φ strains were more resistant, especially at **15–30 J m⁻²**. | *Pseudomonas putida* KT2440 and prophage-deletion derivatives | Martínez-García et al. 2015, DOI: https://doi.org/10.1111/1462-2920.12492 (pqac-00000007, pqac-00000008) |
| P. putida KT2440 tolerance to other DNA-damaging agents | Removal of KT2440 prophages improved tolerance to several DNA-damaging conditions, indicating that environmental DNA damage is a major stress axis in this strain; these findings do not isolate uvrB but are relevant physiological context for DNA repair demands. | Increased tolerance observed for **nalidixic acid**, **N-methyl-N'-nitro-N-nitrosoguanidine**, and **4NQO** in the prophage-free strain; no difference reported for **EMS**, **MMS**, **paraquat**, or sublethal **ampicillin** in the cited passages. | *Pseudomonas putida* KT2440 and Δall-Φ derivatives | Martínez-García et al. 2015, DOI: https://doi.org/10.1111/1462-2920.12492 (pqac-00000008) |
| Error-prone DNA damage responses in Pseudomonas | In *Pseudomonas* studies of UV-induced mutagenesis, DNA damage responses can involve **rulAB (Pol V)** and **imuC**, complementing but distinct from NER. These data are useful for distinguishing excision repair from inducible mutagenic bypass pathways in pseudomonads. | In *P. putida* PaW1, MMC induced **rulAB ~14-fold** and **imuC ~8-fold**. In *P. fluorescens* PC20, UV-C at **5 J/m²** increased Rif^r mutant frequency about **60-fold**; in PC24, **~38-fold** at **5 J/m²** and **~4.5-fold** at **100 J/m²**; reference *P. putida* PaW85 showed **4.8-fold** increase at **5 J/m²**. Presence of rulAB in controls increased Rif^r frequency **>10-fold** after UV. | *P. putida* PaW1/PaW85 and *P. fluorescens* PC20/PC24 | Ilmjärv et al. 2017, DOI: https://doi.org/10.1371/journal.pone.0182484 (pqac-00000011, pqac-00000013) |


*Table: This table verifies the identity of the target UvrB protein and summarizes conserved mechanistic roles of UvrB in bacterial nucleotide excision repair alongside Pseudomonas-specific DNA-damage phenotypes and quantitative findings useful for functional annotation.*