RecC is the largest, non-motor subunit of the RecBCD helicase-nuclease that processes double-strand DNA ends in Pseudomonas putida. It has helicase-like folds but no ATPase motor or nuclease active site; within the holoenzyme it binds the DNA end, splits the duplex, channels the 3' strand towards RecB and stimulates RecB helicase processivity, contributing to end resection and RecA loading for double-strand break repair by homologous recombination. Pseudomonas RecBCD enzymes do not respond to the Escherichia coli Chi octamer, and the sequence that regulates the KT2440 enzyme is unknown.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000724 double-strand break repair via homologous recombination | IEA GO_REF:0000104 | ACCEPT | Summary: RecC is an obligate subunit of RecBCD, which initiates repair of double-strand breaks by homologous recombination. Reason: KT2440 RecC is the RecC subunit of the recD-recB-recC operon. Pseudomonad recBCD genes restore recombination and ATP-dependent nuclease activity to an E. coli recBCD deletion, and deletion of recC in P. syringae causes severe repair defects (UV and mitomycin C sensitivity). RecC does part of the end-processing work (duplex splitting, channelling of the 3' strand) rather than merely being required. Supporting Evidence: PMID:20195537 essential for DNA repair and growth of P. syringae at low temperatures PMID:2559208 Three clones from Pseudomonas aeruginosa and Ps. putida conferred recombination proficiency and ATP-dependent nuclease activity, but neither Chi hotspot activity nor Chi-dependent DNA cleavage file:PSEPK/recC/recC-uniprot.txt The Chi-altered holoenzyme produces a long 3'-ssDNA overhang and facilitates RecA-binding to the ssDNA for homologous DNA recombination and repair |
| GO:0003677 DNA binding | IEA GO_REF:0000104 | MODIFY | Summary: RecC binds DNA within RecBCD, specifically engaging the double-strand DNA end. Reason: DNA binding is correct but general. RecBCD binds DSB ends; in the E. coli enzyme RecBC binds blunt duplex ends and melts out six base pairs without ATP, and the duplex is split across RecC itself. KT2440 RecC is the orthologous subunit (same family, HAMAP MF_01486), so the informative term is DNA end binding (GO:0045027, is_a DNA binding), as in the E. coli RecC review. Proposed replacements: DNA end binding Supporting Evidence: file:PSEPK/recC/recC-uniprot.txt Heterotrimer of RecB, RecC and RecD. All subunits contribute to DNA-binding. file:PSEPK/recC/recC-uniprot.txt Binds to DSBs and unwinds DNA via a highly rapid and processive ATP-dependent bidirectional helicase activity PMID:15538360 In this initiation complex, the DNA duplex has been split across the RecC subunit to create a fork with the separated strands each heading towards different helicase motor subunits PMID:16126227 These data suggest that both RecBC and RecBCD helicases can destabilize or "melt out" six base-pairs upon binding to a blunt DNA duplex end in the absence of ATP |
| GO:0003678 DNA helicase activity | IEA GO_REF:0000104 | MARK AS OVER ANNOTATED | Summary: UniRule transfers DNA helicase activity to RecC, but the helicase motors of RecBCD are RecB and RecD. Reason: RecC contributes to holoenzyme unwinding by stimulating RecB processivity and splitting the duplex, but it is not itself a helicase: it lacks the Walker A motif present in KT2440 RecB and RecD, and in the E. coli enzyme isolated RecC has no holoenzyme activity. The enables qualifier attributes a motor activity to the non-motor subunit; at most contributes_to would be correct. Previously REMOVE in the draft; changed because the holoenzyme helicase claim is real and RecC participates in it, so the problem is overstatement, not falsity. Supporting Evidence: file:PSEPK/recC/recC-uniprot.txt while RecC stimulates the ATPase and processivity of the RecB helicase and contributes to recognition of the Chi site file:analysis/module_audits/bacterial_recbcd_end_resection/WALKER_A_RESULTS.md Neither RecC sequence contains a Walker A motif, under the strict or the relaxed pattern, whereas every RecB and RecD control has one near its N-terminal motor domain PMID:1618858 none of the individual RecB, RecC, or RecD subunits have readily detectable activities of the holoenzyme, except RecB protein which had previously been shown to exhibit DNA-dependent ATPase activity |
| GO:0005524 ATP binding | IEA GO_REF:0000104 | REMOVE | Summary: UniRule transfers ATP binding to RecC; RecC has no ATP-binding site. Reason: KT2440 RecC has no Walker A motif (strict or relaxed), whereas KT2440 RecB and RecD each have one, and the record annotates no nucleotide-binding site. RecC stimulates the ATPase of RecB rather than hydrolysing ATP, and in the E. coli enzyme isolated RecC has no ATPase activity. There is no positive evidence of ATP binding, and the sequence argues against a helicase-type site. Supporting Evidence: file:analysis/module_audits/bacterial_recbcd_end_resection/WALKER_A_RESULTS.md Neither RecC sequence contains a Walker A motif, under the strict or the relaxed pattern, whereas every RecB and RecD control has one near its N-terminal motor domain file:PSEPK/recC/recC-uniprot.txt while RecC stimulates the ATPase and processivity of the RecB helicase and contributes to recognition of the Chi site PMID:1618858 none of the individual RecB, RecC, or RecD subunits have readily detectable activities of the holoenzyme, except RecB protein which had previously been shown to exhibit DNA-dependent ATPase activity |
| GO:0006310 DNA recombination | IEA GO_REF:0000118 | MODIFY | Summary: TreeGrafter propagates DNA recombination to RecC. Reason: Correct but general. Pseudomonad recBCD genes confer recombination proficiency on an E. coli recBCD deletion, and the enzyme acts in RecA-dependent homologous recombination and in DSB repair by homologous recombination (GO:0000724, already carried by this gene). MODIFY to GO:0000724 and GO:0035825 homologous recombination, matching the E. coli RecC review. GO:0035825 is a sibling of GO:0000724 under GO:0006310, not its ancestor, and covers conjugational and transductional recombination that is not break repair. Previously ACCEPT in the draft. Proposed replacements: double-strand break repair via homologous recombination homologous recombination Supporting Evidence: PMID:2559208 Three clones from Pseudomonas aeruginosa and Ps. putida conferred recombination proficiency and ATP-dependent nuclease activity, but neither Chi hotspot activity nor Chi-dependent DNA cleavage file:PSEPK/recC/recC-uniprot.txt The Chi-altered holoenzyme produces a long 3'-ssDNA overhang and facilitates RecA-binding to the ssDNA for homologous DNA recombination and repair |
| GO:0008854 exodeoxyribonuclease V activity | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO (IPR006697 RecC) maps exonuclease V activity to RecC; RecC contributes to but does not catalyse it. Reason: The term names the defining activity of the RecBCD holoenzyme. RecC is required for it (pseudomonad recBCD clones restore ATP-dependent nuclease activity, and in E. coli the activity requires all three subunits) but has no nuclease active site, which is in RecB. The claim is correct as a contribution, as in core_functions (contributes_to_molecular_function). Relation-only correction following projects/SDH_GP2TERM_CONTRIBUTES_TO.md (SDHB precedent); the GOA enables row is MODIFY with the same term, and the intended contributes_to assertion is the paired NEW row below. Changed from the draft's MARK_AS_OVER_ANNOTATED, which judged the qualifier rather than the term; this matches the E. coli RecC review. Proposed replacements: exodeoxyribonuclease V activity Supporting Evidence: PMID:2559208 Three clones from Pseudomonas aeruginosa and Ps. putida conferred recombination proficiency and ATP-dependent nuclease activity, but neither Chi hotspot activity nor Chi-dependent DNA cleavage PMID:1618858 The RecB, RecC, and RecD subunits can associate in vitro to give nuclease, helicase, ATPase, and Chi-specific endonuclease activities which are indistinguishable from those of the RecBCD holoenzyme file:PSEPK/recC/recC-uniprot.txt while RecC stimulates the ATPase and processivity of the RecB helicase and contributes to recognition of the Chi site |
| GO:0009338 exodeoxyribonuclease V complex | IEA GO_REF:0000002 | ACCEPT | Summary: RecC is a subunit of the RecBCD (exonuclease V) complex. Reason: The family assignment and the pseudomonad genetics both place RecC in the RecB-RecC-RecD heterotrimer; P. syringae requires all three cognate subunits for a functional complex. Supporting Evidence: file:PSEPK/recC/recC-uniprot.txt Heterotrimer of RecB, RecC and RecD. All subunits contribute to DNA-binding. PMID:20195537 The RecD requirement is only a function of the RecBCD complex in the bacterium. |
| GO:0140097 catalytic activity, acting on DNA | IEA GO_REF:0000117 | MARK AS OVER ANNOTATED | Summary: ARBA predicts catalytic activity acting on DNA for RecC. Reason: RecC has no nuclease active site and no ATPase motor; the catalytic activities of RecBCD reside in RecB (nuclease, 3'-5' helicase) and RecD (5'-3' helicase). RecC contributes to the holoenzyme's activities, recorded as contributes_to exodeoxyribonuclease V activity, but enables on a generic catalytic term overstates its own function. Changed from the draft's REMOVE to keep it consistent with accepting the descendant exodeoxyribonuclease V term as a contribution. Supporting Evidence: file:PSEPK/recC/recC-uniprot.txt while RecC stimulates the ATPase and processivity of the RecB helicase and contributes to recognition of the Chi site file:analysis/module_audits/bacterial_recbcd_end_resection/WALKER_A_RESULTS.md Neither RecC sequence contains a Walker A motif, under the strict or the relaxed pattern, whereas every RecB and RecD control has one near its N-terminal motor domain |
| GO:0008854 exodeoxyribonuclease V activity | IDA PMID:2559208 Activation of Chi recombinational hotspots by RecBCD-like en... | NEW | Summary: Intended replacement for the GOA enables GO:0008854 IEA row, recording that KT2440 RecC contributes_to RecBCD exodeoxyribonuclease V activity. Reason: Cloned P. putida RecBCD-like genes restore ATP-dependent nuclease activity to an E. coli recBCD deletion. In the characterized E. coli enzyme the activity needs all three subunits, and the nuclease site is in RecB. RecC therefore contributes_to, and does not enable, the activity. This follows projects/SDH_GP2TERM_CONTRIBUTES_TO.md and is recorded here pending an upstream qualifier change. The IDA code reflects the direct nuclease assay of the cloned P. putida enzyme (heterologous complementation in E. coli). The subunit-level contributes_to relation is inferred from E. coli reconstitution (PMID:1618858). Supporting Evidence: PMID:2559208 Three clones from Pseudomonas aeruginosa and Ps. putida conferred recombination proficiency and ATP-dependent nuclease activity PMID:1618858 none of the individual RecB, RecC, or RecD subunits have readily detectable activities of the holoenzyme |
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Download this section (compressed HTML)Q: Which DNA sequence or DNA-structure feature is recognized by KT2440 RecC to switch RecBCD from degradative processing toward recombinogenic tail production?
Experiment: Test a clean recC deletion for double-strand-break repair, homologous recombination, and RecA loading, then complement with wild-type protein.
Type: genetic pathway validation
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