UvrC (UvrABC system protein C, excinuclease ABC subunit C; PP_4098) is the nuclease subunit of the UvrABC nucleotide excision repair system of Pseudomonas putida KT2440, which removes bulky, helix-distorting DNA lesions. After UvrA and UvrB recognize damage and leave UvrB bound at the lesion, UvrC is recruited through its UVR domain and makes two incisions in the damaged strand: the N-terminal GIY-YIG nuclease domain cleaves 3' of the lesion and the C-terminal RNase H-like domain cleaves 5' of it, releasing a short lesion-containing oligonucleotide; repair synthesis and ligation then restore the strand. A C-terminal helix-hairpin-helix module binds DNA. The 607-residue protein conserves every catalytic residue identified in Escherichia coli UvrC and acts on the chromosome in the cytoplasm.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003677 DNA binding | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: UvrC contacts DNA in the incision complex through its C-terminal helix-hairpin-helix module, positioning the damaged strand for the two incisions. Reason: As for E. coli UvrC: DNA contact is real and the generic term is as precise as the evidence allows (UvrC is not the damage-recognition subunit). It serves the incision chemistry captured by GO:0009381 and GO:0004520, so it is non-core. Supporting Evidence: PMID:33477956 The other structural feature of UvrC is the DNA-binding domain comprising two helix-hairpin-helix motifs (HhH)2 that is located at the C-terminus of UvrC [71] (Figure 2C). file:PSEPK/uvrC/uvrC-uniprot.txt UvrC both incises the 5' and 3' sides of the lesion. The N-terminal half is responsible for the 3' incision and the C-terminal half is responsible for the 5' incision. |
| GO:0005737 cytoplasm | IEA GO_REF:0000120 | ACCEPT | Summary: UvrC acts on the chromosome inside the cell; the HAMAP rule assigns cytoplasm. Reason: Soluble chromosomal repair enzyme without signal peptide or membrane segment; consistent with the reviewed E. coli ortholog. Supporting Evidence: file:PSEPK/uvrC/uvrC-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm file:PSEPK/uvrC/uvrC-deep-research-falcon.md UvrC functions on chromosomal DNA in the bacterial cytoplasm/nucleoid as part of the DNA repair machinery. |
| GO:0006281 DNA repair | IEA GO_REF:0000120 | MODIFY | Summary: UvrC acts in DNA repair; the specific pathway is nucleotide-excision repair. Reason: True but general; the supported specific child is GO:0006289 nucleotide-excision repair, already carried by this gene, so the row is refined to it (same action as E. coli uvrC). Proposed replacements: nucleotide-excision repair Supporting Evidence: file:PSEPK/uvrC/uvrC-uniprot.txt UvrC both incises the 5' and 3' sides of the lesion. The N-terminal half is responsible for the 3' incision and the C-terminal half is responsible for the 5' incision. PMID:33477956 UvrC is a dual endonuclease recruited to the UvrB•DNA pre-incision complex to introduce incisions on either side of the lesion [23]. |
| GO:0006289 nucleotide-excision repair | IEA GO_REF:0000120 | ACCEPT | Summary: UvrC performs the dual incision step of bacterial nucleotide-excision repair. Reason: Core process. Q88FJ7 is a full-length UvrC-family protein (HAMAP MF_00203) whose 3' and 5' incision catalytic residues are all conserved relative to E. coli UvrC, where they are experimentally required for the NER incisions. Supporting Evidence: file:PSEPK/uvrC/uvrC-uniprot.txt UvrC both incises the 5' and 3' sides of the lesion. The N-terminal half is responsible for the 3' incision and the C-terminal half is responsible for the 5' incision. file:PSEPK/uvrC/uvrC-bioinformatics/RESULTS.md 3' incision (GIY-YIG domain) catalytic residue E. coli R42 aligns to Q88FJ7 R42 (conserved). file:PSEPK/uvrC/uvrC-bioinformatics/RESULTS.md 5' incision (RNase H-like domain) catalytic residues E. coli D399, D438, D466, H538 align to Q88FJ7 D398, D437, D466, H534 (all conserved). PMID:10671556 Here we show that the catalytic site for incision on the 3' side is in this protein as well, because substitution R42A abolishes 3' incision, whereas formation of the UvrBC-DNA complex and the 5' incision reaction are unaffected. file:PSEPK/uvrC/uvrC-deep-research-falcon.md Direct biochemical characterization of **the specific KT2440 UvrC protein (Q88FJ7)** was not found in the retrieved corpus |
| GO:0006974 DNA damage response | IEA GO_REF:0000120 | MODIFY | Summary: Broad DNA damage response assignment. Reason: True but general (DNA repair is_a DNA damage response); refined to the supported specific process GO:0006289 nucleotide-excision repair, as for E. coli uvrC. Proposed replacements: nucleotide-excision repair Supporting Evidence: file:PSEPK/uvrC/uvrC-uniprot.txt UvrC both incises the 5' and 3' sides of the lesion. The N-terminal half is responsible for the 3' incision and the C-terminal half is responsible for the 5' incision. PMID:33477956 UvrC is a dual endonuclease recruited to the UvrB•DNA pre-incision complex to introduce incisions on either side of the lesion [23]. |
| GO:0009380 excinuclease repair complex | IEA GO_REF:0000120 | ACCEPT | Summary: UvrC joins UvrB at the lesion to form the UvrB-UvrC incision complex of the UvrABC system. Reason: Complex membership is established for E. coli UvrC and the UvrB-interacting UVR domain is present in Q88FJ7 (HAMAP rule SUBUNIT statement). Supporting Evidence: file:PSEPK/uvrC/uvrC-uniprot.txt Interacts with UvrB in an incision complex. PMID:33477956 UvrC is a dual endonuclease recruited to the UvrB•DNA pre-incision complex to introduce incisions on either side of the lesion [23]. |
| GO:0009381 excinuclease ABC activity | IEA GO_REF:0000120 | ACCEPT | Summary: UvrC is the catalytic subunit of the UvrABC excinuclease; both incision active sites lie in UvrC. Reason: Changed from the earlier draft's MARK_AS_OVER_ANNOTATED. GO:0009381 (is_a GO:0004520) names the hydrolysis of DNA ester bonds flanking damage bound by the Uvr ABC complexes, and both of those cleavages are catalysed by UvrC itself (R42 for 3'; D399, D438, D466, H538 for 5' in E. coli). All of these residues are conserved in Q88FJ7, so UvrC is the subunit that executes the activity, with UvrB positioning the lesion. Kept consistent with E. coli uvrC. Supporting Evidence: file:PSEPK/uvrC/uvrC-uniprot.txt UvrC both incises the 5' and 3' sides of the lesion. The N-terminal half is responsible for the 3' incision and the C-terminal half is responsible for the 5' incision. file:PSEPK/uvrC/uvrC-bioinformatics/RESULTS.md 3' incision (GIY-YIG domain) catalytic residue E. coli R42 aligns to Q88FJ7 R42 (conserved). file:PSEPK/uvrC/uvrC-bioinformatics/RESULTS.md 5' incision (RNase H-like domain) catalytic residues E. coli D399, D438, D466, H538 align to Q88FJ7 D398, D437, D466, H534 (all conserved). PMID:1387639 Enzyme reconstituted with these mutant proteins carried out normal 3' incision but was completely defective in 5' incision activity. |
| GO:0009432 SOS response | IEA GO_REF:0000104 | MARK AS OVER ANNOTATED | Summary: UniRule transfer of SOS response from UvrC-family annotation. Reason: Changed from the earlier draft's KEEP_AS_NON_CORE, for consistency with E. coli uvrC. GO:0009432 is defined as an error-prone repair process; UvrC performs error-free excision repair. In E. coli, the source of the rule, uvrC transcription is not UV-inducible (the SOS-inducible paralog is Cho). No KT2440 evidence places uvrC under LexA control. Supporting Evidence: PMID:3295776 We show that transcription from both promoters on the chromosome is not inducible by UV damage. PMID:11818552 The genome of E. coli contains an SOS-inducible gene (ydjQ) encoding a protein that is homologous to the N-terminal half of UvrC. |
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Download this section (compressed HTML)Q: Is uvrC in P. putida KT2440 transcriptionally induced as part of the LexA/SOS regulon upon DNA damage, and is it co-regulated within the predicted pp4100-gacA-uvrC-pgsA operon context?
Experiment: Construct a P. putida KT2440 uvrC deletion mutant and measure UV and bulky-adduct (e.g., mitomycin C, formaldehyde) sensitivity to confirm the NER incision role in this organism.
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