RecB is the catalytic helicase-nuclease subunit of the heterotrimeric bacterial RecBCD complex. Its 3-prime-to-5-prime ATP-dependent motor cooperates with the oppositely directed RecD motor to unwind double-strand DNA ends, while its C-terminal nuclease degrades the unwound strands and generates a recombinogenic 3-prime single-stranded tail for RecA loading. RecC provides the recognition and scaffold functions. Pseudomonas RecBCD does not recognize the Escherichia coli Chi octamer, and the sequence or structural signal controlling the KT2440 switch is unknown.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000166 nucleotide binding | IEA GO_REF:0000104 | MARK AS OVER ANNOTATED | Summary: RecB is an ATP-binding/ATP-hydrolyzing motor protein, so nucleotide binding is correct but it is a broad parent of the more specific ATP binding annotation. Reason: Correct but uninformative; subsumed by the specific GO:0005524 ATP binding annotation, which captures the relevant nucleotide-binding activity. |
| GO:0000287 magnesium ion binding | IEA GO_REF:0000104 | ACCEPT | Summary: The RecB C-terminal nuclease center requires a divalent metal (Mg2+/Mn2+) for exodeoxyribonuclease V activity, consistent with this annotation. Reason: Mg2+ dependence of the RecB PD-(D/E)XK nuclease center is well established for RecBCD/Exonuclease V and supported by the UvrD/AddAB-type nuclease domain. |
| GO:0000724 double-strand break repair via homologous recombination | IEA GO_REF:0000104 | ACCEPT | Summary: RecBCD initiates double-strand break repair by homologous recombination; this is the central biological process for RecB. Reason: Strongly supported by conserved RecBCD biology and by pseudomonad genetics (recB null mutants are UV/mitomycin C sensitive and accumulate fragmented chromosomal DNA); a core function. Supporting Evidence: file:PSEPK/recB/recB-deep-research-falcon.md |
| GO:0000725 recombinational repair | IEA GO_REF:0000118 | KEEP AS NON CORE | Summary: RecB participates in recombinational repair; this is a broader parent of GO:0000724 double-strand break repair via homologous recombination. Reason: Accurate but more general than the specific DSB-via-HR term, which better represents the core process; retain as supporting/non-core. |
| GO:0003677 DNA binding | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: RecB binds duplex and single-stranded DNA as part of its helicase/nuclease activity; a true but general molecular function. Reason: Correct supporting activity, but subsumed by the more informative helicase and exonuclease V molecular-function annotations. |
| GO:0003678 DNA helicase activity | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: RecB has ATP-dependent DNA helicase activity; this is captured more precisely by GO:0043138 (3'-5' DNA helicase activity). Reason: Correct but a parent of the more specific 3'-5' DNA helicase activity term. |
| GO:0004386 helicase activity | IEA GO_REF:0000104 | MARK AS OVER ANNOTATED | Summary: General helicase activity; a broad parent of the DNA-specific and directionally specific helicase terms. Reason: Uninformative high-level term subsumed by GO:0003678 and GO:0043138. |
| GO:0005524 ATP binding | IEA GO_REF:0000120 | ACCEPT | Summary: RecB has a P-loop/Walker A motif and binds ATP to power its motor activity; correct and informative. Reason: ATP binding by the RecB helicase motor is well supported by domain architecture and conserved RecBCD biochemistry. |
| GO:0005829 cytosol | IEA GO_REF:0000118 | KEEP AS NON CORE | Summary: RecBCD acts on chromosomal DNA ends in the cytoplasm/nucleoid; a cytosolic localization is consistent. Reason: Reasonable localization for a DNA-repair enzyme but inferred (TreeGrafter); the functionally relevant compartment is the nucleoid-associated cytoplasm. |
| GO:0006281 DNA repair | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: RecB functions in DNA repair; a broad parent of the more specific DSB repair via HR term. Reason: Correct but general; subsumed by GO:0000724. |
| GO:0008854 exodeoxyribonuclease V activity | IEA GO_REF:0000120 | ACCEPT | Summary: RecB carries the nuclease activity of Exonuclease V (EC 3.1.11.5), the defining enzymatic function of the RecBCD complex. Reason: Core molecular function; supported by the RecB C-terminal PD-(D/E)XK nuclease domain and EC mapping, consistent across RecBCD enzymes. |
| GO:0009338 exodeoxyribonuclease V complex | IEA GO_REF:0000118 | ACCEPT | Summary: RecB is a subunit of the RecBCD (Exonuclease V) complex together with RecC and RecD; correct cellular-component/complex assignment. Reason: RecB is an obligate subunit of the heterotrimeric RecBCD/ExoV complex; a core part_of annotation. |
| GO:0016787 hydrolase activity | IEA GO_REF:0000120 | MARK AS OVER ANNOTATED | Summary: Very general hydrolase parent term; RecB hydrolyzes both ATP and phosphodiester bonds, but this term is uninformative. Reason: Root-level molecular function subsumed by specific nuclease and ATP hydrolysis annotations. |
| GO:0016887 ATP hydrolysis activity | IEA GO_REF:0000116 | ACCEPT | Summary: RecB couples ATP hydrolysis to DNA unwinding/translocation (Rhea:13065); correct and informative for the motor function. Reason: ATPase activity driving the RecB helicase motor is well established and supported by Rhea mapping. |
| GO:0043138 3'-5' DNA helicase activity | IEA GO_REF:0000120 | ACCEPT | Summary: RecB is the 3'-5' helicase motor of RecBCD, translocating along the 3'-ended strand; the most specific and correct helicase term. Reason: Core molecular function; the 3'-5' directionality of the RecB motor is a defining mechanistic feature of RecBCD. |
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Download this section (compressed HTML)Q: Does KT2440 RecBCD respond to a species-specific sequence or DNA-structure signal, given its failure to recognize the E. coli Chi octamer?
Experiment: Construct a P. putida KT2440 recB (PP_4673) deletion and complement with wild-type and motor-dead/nuclease-dead alleles to test sensitivity to UV and mitomycin C and quantify homologous recombination capacity.
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