ruvC Resolved · high auto-curated
H37Rv Rv2594c · MTBC0 mtbc0_002761 ·
188 aa · 2948370–2948936 (-) ·
RefSeq NP_217110.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | crossover junction endodeoxyribonuclease RuvC |
|---|---|
| MTBC0 PGAP re-annotation | crossover junction endodeoxyribonuclease RuvC |
| Revised (this work) | Crossover junction endodeoxyribonuclease RuvC. Pfam: RuvC (PF02075.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGV9
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Crossover junction endodeoxyribonuclease RuvC |
| EC (curated) |
EC 3.1.21.10
|
| Curated function | The RuvA-RuvB-RuvC complex processes Holliday junction (HJ) DNA during genetic recombination and DNA repair. Endonuclease that resolves HJ intermediates. Cleaves cruciform DNA by making single-stranded nicks across the HJ at symmetrical positions within the homologous arms, yielding a 5'-phosphate and a 3'-hydroxyl group; requires a central core of homology in the junction. The consensus cleavage sequence is 5'-(A/T)TT(C/G)-3'. Cleavage occurs on the 3'-side of the TT dinucleotide at the point of strand exchange. HJ branch migration catalyzed by RuvA-RuvB allows RuvC to scan DNA until it finds. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | ruvC |
| eggNOG description | Nuclease that resolves Holliday junction intermediates in genetic recombination. Cleaves the cruciform structure in supercoiled DNA by nicking to strands with the same polarity at sites symmetrically opposed at the junction in the homologous arms and leaves a 5'-terminal phosphate and a 3'-terminal hydroxyl group |
| Orthologous group | COG0817 |
| EC number |
EC 3.1.22.4
|
| KEGG orthology |
K01159
|
| KEGG pathways |
map03440
|
| Gene Ontology (54) |
GO:0000725, GO:0003674, GO:0003824, GO:0004518, GO:0004519, GO:0004520, GO:0004536, GO:0005575, GO:0005622, GO:0005623, GO:0006139, GO:0006259 +42 more
|
Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
RuvC | PF02075.24 | 1.1e-61 | 3–152 | Crossover junction endodeoxyribonuclease RuvC |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ruvA (Holliday junction ATP-dependent DNA helicase RuvA), high confidence from genomic context alone (score 998 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2593c ruvA |
Holliday junction ATP-dependent DNA helicase RuvA | 999 | 998 ctx | neighborhood:882 coexpression:910 experimental:699 textmining:933 |
Rv2592c ruvB |
Holliday junction ATP-dependent DNA helicase RuvB | 999 | 994 ctx | neighborhood:882 cooccurence:529 coexpression:878 textmining:922 |
Rv2897c hyp |
hypothetical protein | 719 | 689 ctx | cooccurence:683 |
Rv2736c recX |
regulatory protein RecX | 859 | 674 | coexpression:663 textmining:588 |
Rv2898c hyp |
hypothetical protein | 606 | 606 ctx | cooccurence:592 |
Rv2600 |
integral membrane protein | 602 | 602 ctx | neighborhood:601 |
Rv2596 vapC40 |
ribonuclease VapC40 | 570 | 571 ctx | neighborhood:567 |
Rv0429c def |
polypeptide deformylase | 621 | 559 ctx | cooccurence:478 |
Rv2595 vapB40 |
antitoxin VapB40 | 554 | 555 ctx | neighborhood:552 |
Rv2926c hyp |
hypothetical protein | 489 | 490 ctx | cooccurence:452 |
Rv2603c |
transcriptional regulator | 496 | 419 | |
Rv2586c secF |
protein translocase subunit SecF | 410 | 411 | |
Rv2597 |
membrane protein | 408 | 409 ctx | neighborhood:408 |
Rv2152c murC |
UDP-N-acetylmuramate--alanine ligase | 405 | 406 | |
Rv2965c kdtB |
phosphopantetheine adenylyltransferase | 405 | 405 |
STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.
Evidence
- Legacy H37Rv annotation: crossover junction endodeoxyribonuclease RuvC
- MTBC0 PGAP product: crossover junction endodeoxyribonuclease RuvC
- Pfam (hmmscan --cut_ga): RuvC PF02075.24 (E=1e-61)
- (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_217110.1)
- Domains: Pfam-A via hmmscan --cut_ga — RuvC (PF02075.24)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
COG0817 - Curated reference: UniProt P9WGV9 (SwissProt, reviewed; Inferred from homology)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
55 functional partner(s); context anchor
ruvA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002761|Rv2594c|ruvC MRVMGVDPGLTRCGLSLIESGRGRQLTALDVDVVRTPSDAALAQRLLAISDAVEHWLDTHHPEVVAIERVFSQLNVTTVMGTAQAGGVIALAAAKRGVDVHFHTPSEVKAAVTGNGSADKAQVTAMVTKILALQAKPTPADAADALALAICHCWRAPTIARMAEATSRAEARAAQQRHAYLAKLKAAR