recD Family assigned · medium auto-curated
H37Rv Rv0629c · MTBC0 mtbc0_000662 ·
575 aa · 723558–725285 (-) ·
RefSeq NP_215143.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | exonuclease V subunit alpha RecD |
|---|---|
| MTBC0 PGAP re-annotation | exodeoxyribonuclease V subunit alpha |
| Revised (this work) | Exodeoxyribonuclease V subunit alpha. Pfam: RecD_N (PF21185.4), AAA_30 (PF13604.13), AAA_11 (PF13086.13), UvrD-helicase (PF00580.28), AAA_19 (PF13245.13), AAA_22 (PF13401.13), NAT10_TcmA_helicase (PF05127.22), Viral_helicase1 (PF01443.25), UvrD_C_2 (PF13538.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHJ1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | RecBCD enzyme subunit RecD |
| EC (curated) |
EC 5.6.2.3
|
| Curated function | A helicase/nuclease that prepares dsDNA breaks (DSB) for recombinational DNA repair. Binds to DSBs and unwinds DNA via a highly rapid and processive ATP-dependent bidirectional helicase activity. Holoenzyme degrades any linearized DNA that is unable to undergo homologous recombination. In the holoenzyme this subunit has ssDNA-dependent ATPase and 5'-3' helicase activity. When added to pre-assembled RecBC greatly stimulates nuclease activity and augments holoenzyme processivity. Unlike the case in E.coli, suppresses RecA-dependent homologous recombination, is instead required for single-strand . |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | recD |
| eggNOG description | A helicase nuclease that prepares dsDNA breaks (DSB) for recombinational DNA repair. Binds to DSBs and unwinds DNA via a highly rapid and processive ATP-dependent bidirectional helicase activity. Unwinds dsDNA until it encounters a Chi (crossover hotspot instigator) sequence from the 3' direction. Cuts ssDNA a few nucleotides 3' to the Chi site. The properties and activities of the enzyme are changed at Chi. The Chi-altered holoenzyme produces a long 3'-ssDNA overhang and facilitates RecA-binding to the ssDNA for homologous DNA recombination and repair. Holoenzyme degrades any linearized DNA that is unable to undergo homologous recombination. In the holoenzyme this subunit has ssDNA-dependent ATPase and 5'-3' helicase activity. When added to pre-assembled RecBC greatly stimulates nuclease activity and augments holoenzyme processivity. Negatively regulates the RecA-loading ability of RecBCD |
| Orthologous group | COG0507 |
| EC number |
EC 3.1.11.5
|
| KEGG orthology |
K03581
|
| KEGG pathways |
map03440
|
| Gene Ontology (13) |
GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0016020, GO:0030312, GO:0044424, GO:0044444, GO:0044464 +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 | 0.302 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 9 synonymous, 7 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 |
|---|---|---|---|---|
RecD_N | PF21185.4 | 2.4e-07 | 21–100 | RecBCD enzyme subunit RecD, N-terminal domain |
AAA_30 | PF13604.13 | 5.5e-32 | 151–360 | AAA domain |
AAA_11 | PF13086.13 | 2.0e-07 | 151–234 | AAA domain |
UvrD-helicase | PF00580.28 | 3.0e-06 | 152–243 | UvrD/REP helicase N-terminal domain |
AAA_19 | PF13245.13 | 6.4e-35 | 153–304 | AAA domain |
AAA_22 | PF13401.13 | 2.8e-08 | 162–298 | AAA domain |
NAT10_TcmA_helicase | PF05127.22 | 3.0e-07 | 167–285 | RNA cytidine acetyltransferase NAT10/TcmA, helicase domain |
Viral_helicase1 | PF01443.25 | 3.8e-05 | 497–544 | Viral superfamily 1 RNA helicase core domain |
UvrD_C_2 | PF13538.13 | 1.9e-14 | 499–545 | UvrD-like helicase C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: recC (exonuclease V subunit gamma RecC), high confidence from genomic context alone (score 996 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0631c recC |
exonuclease V subunit gamma RecC | 999 | 996 ctx | neighborhood:881 cooccurence:774 experimental:737 textmining:813 |
Rv0630c recB |
exonuclease V subunit beta RecB | 998 | 996 ctx | neighborhood:881 cooccurence:773 coexpression:460 experimental:510 database:540 textmining:707 |
Rv2793c truB |
tRNA pseudouridine synthase B | 655 | 656 | database:632 |
Rv1329c dinG |
ATP-dependent helicase DinG | 676 | 606 | database:537 |
Rv0628c hyp |
hypothetical protein | 557 | 558 ctx | neighborhood:554 |
Rv2037c |
transmembrane protein | 514 | 514 ctx | neighborhood:511 |
Rv2116 lppK |
lipoprotein LppK | 550 | 508 | experimental:474 |
Rv0002 dnaN |
DNA polymerase III subunit beta | 549 | 507 | experimental:474 |
Rv3202c adnA |
ATP-dependent DNA helicase | 512 | 445 | |
Rv2529 hyp |
hypothetical protein | 503 | 443 | |
Rv3201c adnB |
ATP-dependent DNA helicase | 497 | 442 | |
Rv0632c echA3 |
enoyl-CoA hydratase EchA3 | 432 | 432 ctx | neighborhood:432 |
Rv0949 uvrD1 |
ATP-dependent DNA helicase UvrD | 579 | 428 | |
Rv1278 hyp |
hypothetical protein | 493 | 427 | |
Rv3198c uvrD2 |
ATP-dependent DNA helicase UvrD | 458 | 424 |
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: exonuclease V subunit alpha RecD
- MTBC0 PGAP product: exodeoxyribonuclease V subunit alpha
- Pfam (hmmscan --cut_ga): RecD_N PF21185.4 (E=2e-07), AAA_30 PF13604.13 (E=6e-32), AAA_11 PF13086.13 (E=2e-07), UvrD-helicase PF00580.28 (E=3e-06), AAA_19 PF13245.13 (E=6e-35), AAA_22 PF13401.13 (E=3e-08), NAT10_TcmA_helicase PF05127.22 (E=3e-07), Viral_helicase1 PF01443.25 (E=4e-05), UvrD_C_2 PF13538.13 (E=2e-14)
- (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_215143.1)
- Domains: Pfam-A via hmmscan --cut_ga — RecD_N (PF21185.4), AAA_30 (PF13604.13), AAA_11 (PF13086.13), UvrD-helicase (PF00580.28), AAA_19 (PF13245.13), AAA_22 (PF13401.13), NAT10_TcmA_helicase (PF05127.22), Viral_helicase1 (PF01443.25), UvrD_C_2 (PF13538.13)
- 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
COG0507 - Curated reference: UniProt P9WHJ1 (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 —
54 functional partner(s); context anchor
recC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000662|Rv0629c|recD MKLTDVDFAVEASGMVRAFNQAGVLDVSDVHVAQRLCALAGESDERVALAVAVAVRALRAGSVCVDLLSIARVAGHDDLPWPDPADWLAAVRASPLLADPPVLHLYDDRLLYLDRYWREEEQVCADLLALLTSRRPAGVPDLRRLFPTGFDEQRRAAEIALSQGVTVLTGGPGTGKTTTVARLLALVAEQAELAGEPRPRIALAAPTGKAAARLAEAVRREMAKLDATDRARLGDLHAVTLHRLLGAKPGARFRQDRQNRLPHNVIVVDETSMVSLTLMARLAEAVRPGARLILVGDADQLASVEAGAVLADLVDGFSVRDDALVAQLRTSHRFGKVIGTLAEAIRAGDGDAVLGLLRSGEERIEFVDDEDPAPRLRAVLVPHALRLREAALLGASDVALATLDEHRLLCAHRDGPTGVLHWNRRVQAWLAEETGQPPWTPWYAGRPLLVTANDYGLRVYNGDTGVVLAGPTGLRAVISGASGPLDVATGRLGDVETMHAMTIHKSQGSQVDEVTVLMPQEDSRLLTRELLYTAVTRAKRKVRVVGSEASVRAAIARRAVRASGLRMRLQSTGCG