ruvA Resolved · high auto-curated
H37Rv Rv2593c · MTBC0 mtbc0_002760 ·
196 aa · 2947783–2948373 (-) ·
RefSeq NP_217109.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | Holliday junction ATP-dependent DNA helicase RuvA |
|---|---|
| MTBC0 PGAP re-annotation | Holliday junction branch migration protein RuvA |
| Revised (this work) | Holliday junction branch migration protein RuvA. Pfam: RuvA_N (PF01330.28), HHH_5 (PF14520.13), RuvA_C (PF07499.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGW3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Holliday junction branch migration complex subunit RuvA |
| Curated function | The RuvA-RuvB-RuvC complex processes Holliday junction (HJ) DNA during genetic recombination and DNA repair, while the RuvA-RuvB complex plays an important role in the rescue of blocked DNA replication forks via replication fork reversal (RFR). Binds HJ DNA. RuvA specifically binds to HJ cruciform DNA, conferring on it an open structure. The RuvB hexamer acts as an ATP-dependent pump, pulling dsDNA into and through the RuvAB complex. HJ branch migration allows RuvC to scan DNA until it finds its consensus sequence, where it cleaves and resolves the cruciform DNA. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | ruvA |
| eggNOG description | The RuvA-RuvB complex in the presence of ATP renatures cruciform structure in supercoiled DNA with palindromic sequence, indicating that it may promote strand exchange reactions in homologous recombination. RuvAB is a helicase that mediates the Holliday junction migration by localized denaturation and reannealing. RuvA stimulates, in the presence of DNA, the weak ATPase activity of RuvB |
| Orthologous group | COG0632 |
| EC number |
EC 3.6.4.12
|
| KEGG orthology |
K03550
|
| KEGG pathways |
map03440
|
| Gene Ontology (56) |
GO:0000724, GO:0000725, GO:0003674, GO:0003678, GO:0003824, GO:0004386, GO:0005575, GO:0005623, GO:0005886, GO:0006139, GO:0006259, GO:0006281 +44 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.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 0.201 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 2 missense, 0 nonsense, 0 frameshift |
pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
RuvA_N | PF01330.28 | 6.6e-22 | 1–61 | RuvA N terminal domain |
HHH_5 | PF14520.13 | 4.1e-14 | 71–129 | Helix-hairpin-helix domain |
RuvA_C | PF07499.20 | 7.0e-10 | 151–192 | RuvA, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ruvB (Holliday junction ATP-dependent DNA helicase RuvB), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2592c ruvB |
Holliday junction ATP-dependent DNA helicase RuvB | 999 | 1000 ctx | neighborhood:882 cooccurence:765 coexpression:976 experimental:928 textmining:934 |
Rv2594c ruvC |
crossover junction endodeoxyribonuclease RuvC | 999 | 998 ctx | neighborhood:882 coexpression:910 experimental:699 textmining:933 |
Rv2600 |
integral membrane protein | 604 | 603 ctx | neighborhood:601 |
Rv2596 vapC40 |
ribonuclease VapC40 | 572 | 572 ctx | neighborhood:567 |
Rv2595 vapB40 |
antitoxin VapB40 | 554 | 555 ctx | neighborhood:552 |
Rv3433c nnr |
bifunctional ADP-dependent (S)-NAD(P)H-hydrate dehydratase/NAD(P)H-hydrate epimerase | 546 | 546 | |
Rv1901 cinA |
competence damage-inducible protein CinA | 552 | 535 | |
Rv2737c recA |
recombinase A | 925 | 510 | coexpression:471 textmining:854 |
Rv3198c uvrD2 |
ATP-dependent DNA helicase UvrD | 615 | 492 | |
Rv1696 recN |
DNA repair protein RecN | 815 | 486 | textmining:656 |
Rv3202c adnA |
ATP-dependent DNA helicase | 513 | 467 | |
Rv1014c pth |
peptidyl-tRNA hydrolase | 460 | 460 | coexpression:425 |
Rv2152c murC |
UDP-N-acetylmuramate--alanine ligase | 451 | 452 ctx | cooccurence:407 |
Rv1629 polA |
DNA polymerase I | 706 | 440 | textmining:498 |
Rv0949 uvrD1 |
ATP-dependent DNA helicase UvrD | 751 | 429 | textmining:583 |
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: Holliday junction ATP-dependent DNA helicase RuvA
- MTBC0 PGAP product: Holliday junction branch migration protein RuvA
- Pfam (hmmscan --cut_ga): RuvA_N PF01330.28 (E=7e-22), HHH_5 PF14520.13 (E=4e-14), RuvA_C PF07499.20 (E=7e-10)
- (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_217109.1)
- Domains: Pfam-A via hmmscan --cut_ga — RuvA_N (PF01330.28), HHH_5 (PF14520.13), RuvA_C (PF07499.20)
- 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
COG0632 - Curated reference: UniProt P9WGW3 (SwissProt, reviewed; Evidence at protein level)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
74 functional partner(s); context anchor
ruvB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002760|Rv2593c|ruvA MIASVRGEVLEVALDHVVIEAAGVGYRVNATPATLATLRQGTEARLITAMIVREDSMTLYGFPDGETRDLFLTLLSVSGVGPRLAMAALAVHDAPALRQVLADGNVAALTRVPGIGKRGAERMVLELRDKVGVAATGGALSTNGHAVRSPVVEALVGLGFAAKQAEEATDTVLAANHDATTSSALRSALSLLGKAR