ruvB Resolved · high auto-curated
H37Rv Rv2592c · MTBC0 mtbc0_002759 ·
344 aa · 2946752–2947786 (-) ·
RefSeq NP_217108.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | Holliday junction ATP-dependent DNA helicase RuvB |
|---|---|
| MTBC0 PGAP re-annotation | Holliday junction branch migration DNA helicase RuvB |
| Revised (this work) | Holliday junction branch migration DNA helicase RuvB. Pfam: RuvB_N (PF05496.19), TIP49 (PF06068.20), AAA (PF00004.36), AAA_lid_4 (PF17864.8), WHD_RuvB (PF05491.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGW1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Holliday junction branch migration complex subunit RuvB |
| EC (curated) |
EC 3.6.4.-
|
| 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). RuvB binds Holliday junction (HJ) DNA in the presence of RuvA. 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. RuvB forms 2 homohexamers on either side of HJ DNA bound by 1 or 2 RuvA tetramers; 4 subunits per hexamer contact. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | ruvB |
| 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 |
| Orthologous group | COG2255 |
| EC number |
EC 3.6.4.12
|
| KEGG orthology |
K03551
|
| KEGG pathways |
map03440
|
| Gene Ontology (13) |
GO:0006950, GO:0006974, GO:0007154, GO:0008150, GO:0009432, GO:0009605, GO:0009987, GO:0009991, GO:0031668, GO:0033554, GO:0050896, GO:0051716 +1 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 | 0.513 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 4 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 |
|---|---|---|---|---|
RuvB_N | PF05496.19 | 1.1e-73 | 24–182 | Holliday junction DNA helicase RuvB P-loop domain |
TIP49 | PF06068.20 | 1.5e-05 | 31–85 | TIP49 P-loop domain |
AAA | PF00004.36 | 3.3e-18 | 59–180 | ATPase family associated with various cellular activities (AAA) |
AAA_lid_4 | PF17864.8 | 1.6e-30 | 185–258 | RuvB AAA lid domain |
WHD_RuvB | PF05491.20 | 2.7e-21 | 259–329 | RuvB C-terminal winged helix domain |
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 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2593c ruvA |
Holliday junction ATP-dependent DNA helicase RuvA | 999 | 1000 ctx | neighborhood:882 cooccurence:765 coexpression:976 experimental:928 textmining:934 |
Rv2594c ruvC |
crossover junction endodeoxyribonuclease RuvC | 999 | 994 ctx | neighborhood:882 cooccurence:529 coexpression:878 textmining:922 |
Rv3014c ligA |
DNA ligase A | 823 | 612 ctx | cooccurence:612 textmining:564 |
Rv0384c clpB |
chaperone protein ClpB | 630 | 607 ctx | cooccurence:531 |
Rv2596 vapC40 |
ribonuclease VapC40 | 572 | 572 ctx | neighborhood:567 |
Rv1629 polA |
DNA polymerase I | 811 | 563 ctx | cooccurence:458 textmining:587 |
Rv2595 vapB40 |
antitoxin VapB40 | 553 | 554 ctx | neighborhood:552 |
Rv0198c zmp1 |
zinc metalloprotease | 527 | 527 | coexpression:527 |
Rv3596c clpC1 |
ATP-dependent protease ATP-binding subunit ClpC | 541 | 512 ctx | cooccurence:411 |
Rv1638 uvrA |
excinuclease ABC subunit UvrA | 887 | 502 ctx | cooccurence:457 textmining:783 |
Rv2603c |
transcriptional regulator | 512 | 469 | |
Rv0668 rpoC |
DNA-directed RNA polymerase subunit beta' | 481 | 458 | coexpression:440 |
Rv2748c ftsK |
DNA translocase FtsK | 483 | 455 | |
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 481 | 452 | coexpression:435 |
Rv3919c gid |
16S rRNA (guanine(527)-N(7))-methyltransferase RsmG | 450 | 451 | coexpression:419 |
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 RuvB
- MTBC0 PGAP product: Holliday junction branch migration DNA helicase RuvB
- Pfam (hmmscan --cut_ga): RuvB_N PF05496.19 (E=1e-73), TIP49 PF06068.20 (E=2e-05), AAA PF00004.36 (E=3e-18), AAA_lid_4 PF17864.8 (E=2e-30), WHD_RuvB PF05491.20 (E=3e-21)
- (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_217108.1)
- Domains: Pfam-A via hmmscan --cut_ga — RuvB_N (PF05496.19), TIP49 (PF06068.20), AAA (PF00004.36), AAA_lid_4 (PF17864.8), WHD_RuvB (PF05491.20)
- 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
COG2255 - Curated reference: UniProt P9WGW1 (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 —
68 functional partner(s); context anchor
ruvA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002759|Rv2592c|ruvB MTERSDRDVSPALTVGEGDIDVSLRPRSLREFIGQPRVREQLQLVIEGAKNRGGTPDHILLSGPPGLGKTSLAMIIAAELGSSLRVTSGPALERAGDLAAMLSNLVEHDVLFIDEIHRIARPAEEMLYLAMEDFRVDVVVGKGPGATSIPLEVAPFTLVGATTRSGALTGPLRDRFGFTAHMDFYEPAELERVLARSAGILGIELGADAGAEIARRSRGTPRIANRLLRRVRDFAEVRADGVITRDVAKAALEVYDVDELGLDRLDRAVLSALTRSFGGGPVGVSTLAVAVGEEAATVEEVCEPFLVRAGMVARTPRGRVATALAWTHLGMTPPVGASQPGLFE