ercc3 Resolved · high auto-curated
H37Rv Rv0861c · MTBC0 - ·
542 aa · 958523–960151 (-) ·
RefSeq NP_215376.3
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | DNA helicase Ercc3 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | DNA helicase Ercc3. Pfam: Helicase_C_3 (PF13625.12), ResIII (PF04851.22), DEAD (PF00270.36), ERCC3_RAD25_C (PF16203.12), Helicase_C (PF00271.38). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
O53873
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | DNA 3'-5' helicase XPB |
| EC (curated) |
EC 5.6.2.4
|
| Curated function | ATP-dependent 3'-5' DNA helicase, unwinds 3'-overhangs, 3'- flaps, and splayed-arm DNA substrates but not 5'-overhangs, 5'-flap substrates, 3-way junctions or Holliday junctions. Not highly efficient in vitro. Requires ATP hydrolysis for helicase activity; the ATPase activity is DNA-dependent and requires a minimum of 4 single-stranded nucleotides (nt) with 6-10 nt providing all necessary interactions for full processive unwinding. The ATPase prefers ATP over CTP or GTP, is almost inactive with TTP. DNA helicase activity requires ATP or dATP and only acts when the 3'-overhang is >20 nt. Capabl. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | ercc3 |
| eggNOG description | Type III restriction enzyme res subunit |
| Orthologous group | COG1061 |
| EC number |
EC 3.6.4.12
|
| KEGG orthology |
K10843
|
| KEGG pathways |
map03022, map03420
|
| KEGG modules |
M00290
|
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 | 0.341 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 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 |
|---|---|---|---|---|
Helicase_C_3 | PF13625.12 | 6.7e-38 | 2–127 | Helicase conserved C-terminal domain |
ResIII | PF04851.22 | 1.2e-17 | 174–320 | Type III restriction enzyme, res subunit |
DEAD | PF00270.36 | 6.1e-06 | 177–321 | DEAD/DEAH box helicase |
ERCC3_RAD25_C | PF16203.12 | 3.8e-40 | 346–530 | ERCC3/RAD25/XPB C-terminal helicase |
Helicase_C | PF00271.38 | 1.7e-12 | 389–492 | Helicase conserved C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0862c hyp |
hypothetical protein | 931 | 932 ctx | neighborhood:738 cooccurence:743 |
Rv1329c dinG |
ATP-dependent helicase DinG | 948 | 882 | experimental:685 database:622 textmining:580 |
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 856 | 853 | experimental:578 database:621 |
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 853 | 853 | experimental:627 database:621 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 847 | 848 | experimental:613 database:621 |
Rv1629 polA |
DNA polymerase I | 834 | 768 | experimental:430 database:580 |
Rv2090 |
5'-3' exonuclease | 765 | 752 | experimental:430 database:580 |
Rv0668 rpoC |
DNA-directed RNA polymerase subunit beta' | 703 | 688 | database:620 |
Rv2529 hyp |
hypothetical protein | 705 | 686 | database:610 |
Rv2101 helZ |
helicase HelZ | 843 | 669 | database:615 textmining:548 |
Rv0863 hyp |
hypothetical protein | 662 | 663 ctx | neighborhood:662 |
Rv1334 mec |
[CysO | 646 | 646 | database:613 |
Rv3812 PE_PGRS62 |
PE-PGRS family protein PE_PGRS62 | 620 | 621 | database:563 |
Rv2328 PE23 |
PE family protein PE23 | 620 | 621 | database:563 |
Rv3036c TB22.2 hyp |
hypothetical protein | 620 | 621 | database:563 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): DNA helicase Ercc3
- Pfam (hmmscan --cut_ga): Helicase_C_3 PF13625.12 (E=7e-38), ResIII PF04851.22 (E=1e-17), DEAD PF00270.36 (E=6e-06), ERCC3_RAD25_C PF16203.12 (E=4e-40), Helicase_C PF00271.38 (E=2e-12)
- (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_215376.3)
- Domains: Pfam-A via hmmscan --cut_ga — Helicase_C_3 (PF13625.12), ResIII (PF04851.22), DEAD (PF00270.36), ERCC3_RAD25_C (PF16203.12), Helicase_C (PF00271.38)
- 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
COG1061 - Curated reference: UniProt O53873 (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 — 51 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0861c|ercc3 MQSDKTVLLEVDHELAGAARAAIAPFAELERAPEHVHTYRITPLALWNARAAGHDAEQVVDALVSYSRYAVPQPLLVDIVDTMARYGRLQLVKNPAHGLTLVSLDRAVLEEVLRNKKIAPMLGARIDDDTVVVHPSERGRVKQLLLKIGWPAEDLAGYVDGEAHPISLHQEGWQLRDYQRLAADSFWAGGSGVVVLPCGAGKTLVGAAAMAKAGATTLILVTNIVAARQWKRELVARTSLTENEIGEFSGERKEIRPVTISTYQMITRRTKGEYRHLELFDSRDWGLIIYDEVHLLPAPVFRMTADLQSKRRLGLTATLIREDGREGDVFSLIGPKRYDAPWKDIEAQGWIAPAECVEVRVTMTDSERMMYATAEPEERYRICSTVHTKIAVVKSILAKHPDEQTLVIGAYLDQLDELGAELGAPVIQGSTRTSEREALFDAFRRGEVATLVVSKVANFSIDLPEAAVAVQVSGTFGSRQEEAQRLGRILRPKADGGGAIFYSVVARDSLDAEYAAHRQRFLAEQGYGYIIRDADDLLGPAI