| Topic | Key points | Best supporting citations | Key sources |
|---|---|---|---|
| Function | • UvrC is the endonuclease component of the bacterial UvrABC excinuclease in nucleotide excision repair (NER).<br>• It performs dual incision on the damaged DNA strand to release a short lesion-containing oligonucleotide.<br>• The excised fragment is typically ~12–13 nt long in bacterial NER. | (pqac-00000000, pqac-00000002, pqac-00000005) | Seck et al. 2023 — https://doi.org/10.1093/nar/gkad108; Kraithong et al. 2021 — https://doi.org/10.3390/ijms22020952; Taylor 2011 — source in context |
| Pathway step | • In global-genome NER, UvrA/UvrB detect damage and load UvrB at the lesion; UvrC is then recruited to the pre-incision complex.<br>• After UvrC cuts 3′ and 5′ to the lesion, UvrD removes the damaged oligonucleotide and downstream gap filling/ligation complete repair.<br>• UvrB interaction is important for proper incision activity and specificity. | (pqac-00000000, pqac-00000002, pqac-00000005) | Seck et al. 2023 — https://doi.org/10.1093/nar/gkad108; Kraithong et al. 2021 — https://doi.org/10.3390/ijms22020952 |
| Catalytic activities/incision positions | • UvrC carries two nuclease activities that cut on both sides of the lesion.<br>• The 3′ cut occurs at about the 4th or 5th phosphodiester bond from the lesion.<br>• The 5′ cut occurs at about the 8th phosphodiester bond from the lesion.<br>• In the 2023 mechanistic study, dual incision could occur in either order in the tested homolog, indicating flexibility in activation. | (pqac-00000002, pqac-00000003, pqac-00000004) | Kraithong et al. 2021 — https://doi.org/10.3390/ijms22020952; Seck et al. 2023 — https://doi.org/10.1093/nar/gkad108 |
| Domains/motifs | • The N-terminus contains a GIY-YIG endonuclease domain associated with the 3′ incision activity.<br>• UvrC also contains a C-terminal RNase H-like nuclease region linked to 5′ incision activity.<br>• An (HhH)2 DNA-binding motif helps bind DNA/ssDNA-dsDNA junctions.<br>• A Cys-rich region is proposed to coordinate an Fe-S cluster; the provided UniProt domain set (GIY-YIG, HHH/SAM-like, Hlx-hairpin-Hlx DNA-binding motif) is consistent with literature-derived architecture. | (pqac-00000000, pqac-00000002, pqac-00000003, pqac-00000015) | Seck et al. 2023 — https://doi.org/10.1093/nar/gkad108; Kraithong et al. 2021 — https://doi.org/10.3390/ijms22020952 |
| Interaction partners | • UvrC acts with UvrA and UvrB in the UvrABC excinuclease pathway.<br>• UvrB directly recruits/positions UvrC at the lesion-containing pre-incision complex.<br>• After incision, UvrD helicase removes the cut fragment and helps disassemble the complex. | (pqac-00000000, pqac-00000002, pqac-00000005) | Seck et al. 2023 — https://doi.org/10.1093/nar/gkad108; Kraithong et al. 2021 — https://doi.org/10.3390/ijms22020952 |
| Cellular localization | • UvrC functions on chromosomal DNA in the bacterial cytoplasm/nucleoid as part of the DNA repair machinery.<br>• No evidence in the retrieved context supports secretion, membrane localization, or extracellular function.<br>• For Q88FJ7 in P. putida KT2440, localization is therefore inferred as intracellular DNA repair-associated. | (pqac-00000000, pqac-00000002) | Seck et al. 2023 — https://doi.org/10.1093/nar/gkad108; Kraithong et al. 2021 — https://doi.org/10.3390/ijms22020952 |
| P. putida-specific evidence | • Direct: retrieved context did not provide a KT2440-specific uvrC knockout/biochemical study for Q88FJ7 itself.<br>• Direct: a P. putida promoter-library study notes a predicted pp4100-gacA-uvrC-pgsA operon context, supporting genomic linkage/regulatory context in this species.<br>• Direct: in P. putida KT2440, other NER components are functionally important under genotoxic stress; a uvrB mutant was hypersensitive to 10 mM formaldehyde, with killing 3–4 orders of magnitude above wild type, supporting pathway relevance in this organism.<br>• Inferred: Q88FJ7/PP_4098 likely performs canonical UvrC dual-incision repair in KT2440 because its annotation and domain architecture match conserved UvrC family proteins. | (pqac-00000008, pqac-00000012, pqac-00000000) | Jiménez-Fernández et al. 2016 — https://doi.org/10.1371/journal.pone.0163142; Roca et al. 2008 — https://doi.org/10.1111/j.1751-7915.2007.00014.x; Seck et al. 2023 — https://doi.org/10.1093/nar/gkad108 |
| Recent advances 2023-2024 | • A 2023 NAR study produced the first complete model of full-length UvrC and proposed a closed inactive state that must rearrange into an open active state for dual incision.<br>• That work identified a central inactive RNase H-like platform and clarified how surrounding catalytic/DNA-binding modules may be coordinated.<br>• A 2023 review of prokaryotic NER highlighted updated understanding of global-genome and transcription-coupled NER steps involving UvrC. | (pqac-00000000, pqac-00000003) | Seck et al. 2023 — https://doi.org/10.1093/nar/gkad108; Thakur & Muniyappa 2023 — https://doi.org/10.1007/s12038-023-00378-8 |


*Table: This table summarizes the supported functional annotation for UvrC Q88FJ7 in Pseudomonas putida KT2440, separating direct organism-specific evidence from broader mechanistic inference. It is useful as a concise evidence map linking domain architecture, catalytic role, pathway placement, and recent structural advances.*