UvrB (UvrABC system protein B, PP_1974) is the DNA damage-verification subunit of the nucleotide excision repair system of Pseudomonas putida KT2440, which removes bulky, helix-distorting DNA lesions such as UV photoproducts. It is a superfamily 2 helicase-like ATPase with two RecA-like domains, a P-loop ATP-binding site, a damage-sensing beta-hairpin and a C-terminal UVR domain that contacts UvrC. By analogy with the closely related and well-studied E. coli protein, two UvrB subunits join a UvrA dimer to scan DNA; at a putative lesion the DNA wraps around one UvrB, the beta-hairpin inserts between the strands, and ATP hydrolysis by UvrB drives formation of a stable UvrB-DNA preincision complex. UvrA then leaves and UvrB recruits the UvrC endonuclease, which incises the damaged strand on both sides of the lesion. UvrB acts on the chromosome in the cytoplasm.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003677 DNA binding | IEA GO_REF:0000120 | MODIFY | Summary: UvrB binds DNA as part of damage scanning and pre-incision complex formation; its beta-hairpin motif inserts between DNA strands for lesion probing. Reason: DNA binding is correct but general. UvrB's beta-hairpin makes lesion-specific contacts (shown by mutagenesis in E. coli UvrB, with all those residues conserved here), so the specific supported term is damaged DNA binding (GO:0003684), as in the E. coli UvrB review. Proposed replacements: damaged DNA binding Supporting Evidence: file:PSEPK/uvrB/uvrB-uniprot.txt The beta-hairpin motif is involved in DNA binding. file:PSEPK/uvrB/uvrB-uniprot.txt Then UvrB probes one DNA strand for the presence of a lesion. PMID:11689453 Residues Y95 and Y96 at the base of the hairpin have a direct role in damage recognition and are positioned close to the damage in the UvrB-DNA complex. file:PSEPK/uvrB/uvrB-bioinformatics/RESULTS.md The Walker A segment (GVTGSGKT) and all six beta-hairpin residues characterised by mutagenesis in E. coli UvrB (Y92, Y93, Y95, Y96, Y101, F108) are conserved in P. putida UvrB |
| GO:0005524 ATP binding | IEA GO_REF:0000120 | ACCEPT | Summary: UvrB has a conserved Walker A ATP-binding site; ATP binding drives DNA wrapping and, separately from hydrolysis, is needed for 3' incision. Reason: ATP binding is intrinsic to UvrB function; the HAMAP-annotated ATP-binding motif is conserved and ATP binding is a distinct, experimentally characterised step in E. coli UvrB. Consistent with the E. coli review. Supporting Evidence: file:PSEPK/uvrB/uvrB-uniprot.txt DNA wrap is dependent on ATP binding by UvrB and probably causes local melting of the DNA helix PMID:10713125 The subsequent induction of 3' incision does require ATP binding by UvrB but not hydrolysis. file:PSEPK/uvrB/uvrB-bioinformatics/RESULTS.md The Walker A segment (GVTGSGKT) and all six beta-hairpin residues characterised by mutagenesis in E. coli UvrB (Y92, Y93, Y95, Y96, Y101, F108) are conserved in P. putida UvrB |
| GO:0005737 cytoplasm | IEA GO_REF:0000120 | ACCEPT | Summary: UvrB acts on chromosomal DNA in the bacterial cytoplasm/nucleoid. Reason: Bacterial NER acts on the nucleoid in the cytoplasm; consistent with the UniRule location and with the E. coli review. Supporting Evidence: file:PSEPK/uvrB/uvrB-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm |
| GO:0006281 DNA repair | IEA GO_REF:0000104 | MODIFY | Summary: UvrB is a core DNA repair protein acting in nucleotide excision repair. Reason: Correct but general; the specific process, nucleotide-excision repair (GO:0006289, an is_a descendant), is already carried by this gene. Revised from the earlier draft's KEEP_AS_NON_CORE, which argued the same over-generality. Proposed replacements: nucleotide-excision repair Supporting Evidence: file:PSEPK/uvrB/uvrB-uniprot.txt If a lesion is found the UvrA subunits dissociate and the UvrB-DNA preincision complex is formed. PMID:10671556 The two incision reactions take place in a complex of damaged DNA with UvrB and UvrC. |
| GO:0006289 nucleotide-excision repair | IEA GO_REF:0000120 | ACCEPT | Summary: UvrB is the damage-verification subunit of the UvrABC excinuclease, central to bacterial nucleotide excision repair. Reason: Core process. Q88LF9 is a full-length UvrB family member (HAMAP MF_00204, TIGR00631) with the catalytic and damage-sensing residues of E. coli UvrB conserved; no KT2440-specific experiments exist. Supporting Evidence: file:PSEPK/uvrB/uvrB-uniprot.txt HAMAP; MF_00204; UvrB; 1. file:PSEPK/uvrB/uvrB-uniprot.txt If a lesion is found the UvrA subunits dissociate and the UvrB-DNA preincision complex is formed. file:PSEPK/uvrB/uvrB-bioinformatics/RESULTS.md The Walker A segment (GVTGSGKT) and all six beta-hairpin residues characterised by mutagenesis in E. coli UvrB (Y92, Y93, Y95, Y96, Y101, F108) are conserved in P. putida UvrB |
| GO:0009380 excinuclease repair complex | IEA GO_REF:0000002 | ACCEPT | Summary: UvrB forms a heterotetramer (UvrA2B2) with UvrA during lesion scanning and interacts with UvrC in the incision complex. Reason: UvrB is a subunit of the UvrA2B2 scanning complex and the UvrBC incision complex; family-conserved and consistent with the E. coli review. Supporting Evidence: file:PSEPK/uvrB/uvrB-uniprot.txt Forms a heterotetramer with UvrA during the search for lesions. Interacts with UvrC in an incision complex. |
| GO:0009381 excinuclease ABC activity | IEA GO_REF:0000104 | MARK AS OVER ANNOTATED | Summary: GO:0009381 describes the dual-incision chemistry of the assembled UvrABC system; UvrB verifies the lesion and forms the preincision complex rather than independently catalyzing incision. Reason: GO:0009381 is catalysis of hydrolysis of DNA ester linkages flanking the lesion. Both incision catalytic sites are in UvrC (E. coli), so 'enables' overstates UvrB, which verifies the lesion and positions UvrC. Same verdict as the E. coli review. Supporting Evidence: PMID:10671556 Here we show that the catalytic site for incision on the 3' side is in this protein as well PMID:10671556 The two incision reactions take place in a complex of damaged DNA with UvrB and UvrC. file:PSEPK/uvrB/uvrB-uniprot.txt Forms a heterotetramer with UvrA during the search for lesions. Interacts with UvrC in an incision complex. |
| GO:0009432 SOS response | IEA GO_REF:0000104 | MARK AS OVER ANNOTATED | Summary: UniRule-propagated SOS response, transferred from E. coli where uvrB is a LexA-repressed SOS gene. Reason: UvrB's repair function is SOS-independent, so this term rests on regulatory membership of the LexA regulon. That membership is not conserved in Pseudomonas: the P. aeruginosa uvrB lacks a LexA box and is not DNA-damage inducible, and no KT2440 study shows uvrB under LexA control. The E. coli review keeps this term as non-core because E. coli uvrB is LexA-regulated; that regulatory fact does not transfer here. Supporting Evidence: PMID:8808952 contrary to what happens with the homologous gene of E. coli, the P. aeruginosa uvrB gene is not DNA damage inducible PMID:8808952 A P. aeruginosa SOS consensus region, which functions as a binding site for the LexA repressor molecule, is not present in the upstream region of the uvrB gene isolated. file:PSEPK/uvrB/uvrB-deep-research-falcon.md While direct *P. putida* KT2440 uvrB knock-out phenotypes were not retrieved in the available corpus |
| GO:0016787 hydrolase activity | IEA GO_REF:0000002 | MODIFY | Summary: Very general hydrolase parent term; UvrB's relevant hydrolase activity is ATP hydrolysis. Reason: Correct but uninformative; UvrB's hydrolase activity is ATP hydrolysis (GO:0016887), a descendant already carried by this gene. Revised from the draft's MARK_AS_OVER_ANNOTATED, which argued generality rather than an incorrect claim. Proposed replacements: ATP hydrolysis activity Supporting Evidence: PMID:2974538 the stimulation in DNA dependent ATPase activity following formation of the UvrAB complex results from the activation of the normally sequestered UvrB associated ATPase PMID:10713125 To initiate the formation of an active UvrBC-DNA incision complex, however, UvrB first needs to hydrolyze ATP, and subsequently a new ATP molecule must be bound. |
| GO:0016887 ATP hydrolysis activity | IEA GO_REF:0000002 | ACCEPT | Summary: UvrB hydrolyzes ATP via its SF2 helicase ATPase machinery; ATP hydrolysis is essential for forming the UvrB-DNA pre-incision complex. Reason: Core function. In E. coli the UvrAB ATPase is UvrB's own activated ATPase and its hydrolysis is required for an incision-competent complex; the Walker A and helicase motifs are conserved in Q88LF9. Consistent with the E. coli review. Supporting Evidence: PMID:2974538 the stimulation in DNA dependent ATPase activity following formation of the UvrAB complex results from the activation of the normally sequestered UvrB associated ATPase PMID:10713125 To initiate the formation of an active UvrBC-DNA incision complex, however, UvrB first needs to hydrolyze ATP, and subsequently a new ATP molecule must be bound. PMID:8035457 the helicase motifs V and VI are involved in the induction of ATP hydrolysis in the presence of (damaged) DNA and in the strand-displacement activity of the UvrA2B complex file:PSEPK/uvrB/uvrB-uniprot.txt PROSITE; PS51192; HELICASE_ATP_BIND_1; 1. |
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Download this section (compressed HTML)Q: Is uvrB (PP_1974) DNA-damage inducible or LexA1-regulated in P. putida KT2440, as in E. coli, or constitutive as in P. aeruginosa?
Experiment: Measure PP_1974 transcript levels after UV or mitomycin C in wild-type and lexA1 mutant KT2440, and test UV sensitivity of a uvrB deletion, to settle SOS regulation and confirm the NER role in this strain.
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