kshA Family assigned · medium auto-curated
H37Rv Rv3526 · MTBC0 mtbc0_003742 ·
386 aa · 3986116–3987276 (+) ·
RefSeq NP_218043.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 3-ketosteroid-9-alpha-monooxygenase oxygenase subunit |
|---|---|
| MTBC0 PGAP re-annotation | 3-ketosteroid-9-alpha-hydroxylase subunit KshA |
| Revised (this work) | 3-ketosteroid-9-alpha-hydroxylase subunit KshA. Pfam: Rieske (PF00355.33), KshA_C (PF19298.6). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71875
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | 3-ketosteroid-9-alpha-monooxygenase, oxygenase component |
| EC (curated) |
EC 1.14.15.30
|
| Curated function | Involved in the degradation of cholesterol. Catalyzes the introduction of a 9a-hydroxyl moiety into 1,4-androstadiene-3,17-dione (ADD) to yield the 9alpha-hydroxy-1,4-androstadiene-3,17-dione (9OHADD) intermediate which spontaneously form 3-hydroxy-9,10-seconandrost-1,3,5(10)-triene-9,17-dione (HSA) via the meta-cleavage of ring B with concomitant aromatization of ring A. KSH is also able to use 4-androstene-3,17-dione (AD), 3-oxo-23,24-bisnorcholesta-4-en-22-oate (4-BNC), 3-oxo-23,24-bisnorcholesta-1,4-dien-22-oate (1,4-BNC), 3-oxo-23,24-bisnorcholesta-4-en-22-oyl-coenzyme A thioester (4-BNC-. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | kshA |
| eggNOG description | Rieske 2Fe-2S |
| Orthologous group | COG4638 |
| EC number |
EC 1.14.13.142
|
| KEGG orthology |
K15982
|
| KEGG pathways |
map00984, map01100, map01120
|
| Gene Ontology (71) |
GO:0003674, GO:0003824, GO:0004497, GO:0005488, GO:0005506, GO:0006066, GO:0006629, GO:0006694, GO:0006706, GO:0006707, GO:0008150, GO:0008152 +59 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 | 0.213 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 3 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 |
|---|---|---|---|---|
Rieske | PF00355.33 | 6.2e-22 | 26–109 | Rieske [2Fe-2S] domain |
KshA_C | PF19298.6 | 1.8e-87 | 128–337 | 3-Ketosteroid 9alpha-hydroxylase C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: kstD (3-oxosteroid 1-dehydrogenase), high confidence from genomic context alone (score 978 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3537 kstD |
3-oxosteroid 1-dehydrogenase | 998 | 978 ctx | cooccurence:753 database:900 textmining:932 |
Rv3527 hyp |
hypothetical protein | 979 | 977 ctx | neighborhood:882 cooccurence:692 coexpression:409 |
Rv3571 kshB |
3-ketosteroid-9-alpha-hydroxylase reductase subunit | 998 | 959 ctx | cooccurence:450 database:900 textmining:964 |
Rv3531c hyp |
hypothetical protein | 817 | 817 ctx | cooccurence:766 |
Rv3568c hsaC |
extradiol dioxygenase | 974 | 802 ctx | cooccurence:774 textmining:878 |
Rv3570c hsaA |
flavin-dependent monooxygenase oxygenase subunit HsaA | 959 | 801 ctx | cooccurence:772 textmining:806 |
Rv3529c hyp |
hypothetical protein | 797 | 798 ctx | cooccurence:765 |
Rv3525c |
siderophore-binding protein | 780 | 779 ctx | neighborhood:778 |
Rv3542c chsH2 hyp |
hypothetical protein | 778 | 778 ctx | cooccurence:766 |
Rv3521 hyp |
hypothetical protein | 774 | 775 ctx | cooccurence:760 |
Rv3541c chsH1 hyp |
hypothetical protein | 776 | 768 ctx | cooccurence:760 |
Rv3552 |
CoA-transferase subunit beta | 800 | 755 ctx | cooccurence:745 |
Rv3551 |
CoA-transferase subunit alpha | 766 | 751 ctx | cooccurence:741 |
Rv3522 ltp4 |
lipid transfer protein | 748 | 738 ctx | cooccurence:719 |
Rv0760c hyp |
hypothetical protein | 736 | 736 ctx | cooccurence:728 |
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: 3-ketosteroid-9-alpha-monooxygenase oxygenase subunit
- MTBC0 PGAP product: 3-ketosteroid-9-alpha-hydroxylase subunit KshA
- Pfam (hmmscan --cut_ga): Rieske PF00355.33 (E=6e-22), KshA_C PF19298.6 (E=2e-87)
- (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_218043.1)
- Domains: Pfam-A via hmmscan --cut_ga — Rieske (PF00355.33), KshA_C (PF19298.6)
- 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
COG4638 - Curated reference: UniProt P71875 (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 —
56 functional partner(s); context anchor
kstD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003742|Rv3526|kshA MSTDTSGVGVREIDAGALPTRYARGWHCLGVAKDYLEGKPHGVEAFGTKLVVFADSHGDLKVLDGYCRHMGGDLSEGTVKGDEVACPFHDWRWGGDGRCKLVPYARRTPRMARTRSWTTDVRSGLLFVWHDHEGNPPDPAVRIPEIPEAASDEWTDWRWNRILIEGSNCRDIIDNVTDMAHFFYIHFGLPTYFKNVFEGHIASQYLHNVGRPDVDDLGTSYGEAHLDSEASYFGPSFMINWLHNRYGNYKSESILINCHYPVTQNSFVLQWGVIVEKPKGMSEEMTDKLSRVFTEGVSKGFLQDVEIWKHKTRIDNPLLVEEDGAVYQLRRWYEQFYVDVADIKPEMVERFEIEVDTKRANEFWNAEVEKNLKSREVSDDVPAEQH