sucC Family assigned · medium auto-curated
H37Rv Rv0951 · MTBC0 mtbc0_001015 ·
387 aa · 1069179–1070342 (+) ·
RefSeq NP_215466.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | succinyl-CoA ligase subunit beta |
|---|---|
| MTBC0 PGAP re-annotation | ADP-forming succinate--CoA ligase subunit beta |
| Revised (this work) | ADP-forming succinate--CoA ligase subunit beta. Pfam: ATP-grasp_2 (PF08442.16), ATP-grasp_5 (PF13549.12), CPSase_L_D2 (PF02786.23), Ligase_CoA (PF00549.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGC5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Succinate--CoA ligase [ADP-forming] subunit beta |
| EC (curated) |
EC 6.2.1.5
|
| Curated function | Succinyl-CoA synthetase functions in the citric acid cycle (TCA), coupling the hydrolysis of succinyl-CoA to the synthesis of either ATP or GTP and thus represents the only step of substrate-level phosphorylation in the TCA. The beta subunit provides nucleotide specificity of the enzyme and binds the substrate succinate, while the binding sites for coenzyme A and phosphate are found in the alpha subunit. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | sucC |
| eggNOG description | Succinyl-CoA synthetase functions in the citric acid cycle (TCA), coupling the hydrolysis of succinyl-CoA to the synthesis of either ATP or GTP and thus represents the only step of substrate-level phosphorylation in the TCA. The beta subunit provides nucleotide specificity of the enzyme and binds the substrate succinate, while the binding sites for coenzyme A and phosphate are found in the alpha subunit |
| Orthologous group | COG0045 |
| EC number |
EC 6.2.1.5
|
| KEGG orthology |
K01903
|
| KEGG pathways |
map00020, map00640, map00660, map00720, map01100, map01110, map01120, map01130, map01200
|
| KEGG modules |
M00009, M00011, M00173, M00374, M00620
|
| Gene Ontology (13) |
GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0008150, GO:0030312, GO:0040007, 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 | 1.321 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
ATP-grasp_2 | PF08442.16 | 5.0e-70 | 3–194 | ATP-grasp domain |
ATP-grasp_5 | PF13549.12 | 1.2e-06 | 3–210 | ATP-grasp domain |
CPSase_L_D2 | PF02786.23 | 1.7e-05 | 7–55 | Carbamoyl-phosphate synthase L chain, ATP binding domain |
Ligase_CoA | PF00549.25 | 1.9e-16 | 256–378 | CoA-ligase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: sucD (succinyl-CoA ligase subunit alpha), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0952 sucD |
succinyl-CoA ligase subunit alpha | 999 | 1000 ctx | neighborhood:869 fusion:899 cooccurence:774 coexpression:968 experimental:928 database:984 textmining:854 |
Rv1248c kgd |
multifunctional 2-oxoglutarate dehydrogenase E1 component /2-oxoglutarate dehydrogenase dihydrolipoyllysine-residue succinyltransferase | 998 | 998 | coexpression:988 database:540 textmining:430 |
Rv3316 sdhC |
succinate dehydrogenase cytochrome B-556 subunit | 986 | 982 | coexpression:811 database:900 |
Rv3319 sdhB |
succinate dehydrogenase iron-sulphur protein subunit | 987 | 979 | coexpression:646 database:900 textmining:428 |
Rv2215 dlaT |
pyruvate dehydrogenase E2 component dihydrolipoamide acyltransferase | 989 | 978 | coexpression:744 database:900 textmining:568 |
Rv3317 sdhD |
succinate dehydrogenase hydrophobic membrane anchor subunit | 981 | 976 | coexpression:756 database:900 |
Rv0247c |
succinate dehydrogenase iron-sulfur subunit | 981 | 975 | coexpression:656 database:900 |
Rv3318 sdhA |
succinate dehydrogenase flavoprotein subunit | 984 | 974 | coexpression:566 database:900 textmining:405 |
Rv0248c |
succinate dehydrogenase flavoprotein subunit | 982 | 970 | coexpression:584 database:900 textmining:452 |
Rv1553 frdB |
fumarate reductase iron-sulfur subunit | 974 | 967 ctx | cooccurence:496 coexpression:645 database:800 |
Rv1552 frdA |
fumarate reductase flavoprotein subunit | 967 | 950 | coexpression:563 database:800 |
Rv2455c korA |
2-oxoglutarate oxidoreductase subunit KorA | 979 | 946 | database:900 textmining:631 |
Rv2495c bkdC |
branched-chain keto acid dehydrogenase E2 component | 955 | 941 | coexpression:662 database:800 |
Rv1493 mutB |
methylmalonyl-CoA mutase large subunit | 941 | 923 | database:900 |
Rv2454c korB |
2-oxoglutarate oxidoreductase subunit KorB | 944 | 912 | database:900 |
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: succinyl-CoA ligase subunit beta
- MTBC0 PGAP product: ADP-forming succinate--CoA ligase subunit beta
- Pfam (hmmscan --cut_ga): ATP-grasp_2 PF08442.16 (E=5e-70), ATP-grasp_5 PF13549.12 (E=1e-06), CPSase_L_D2 PF02786.23 (E=2e-05), Ligase_CoA PF00549.25 (E=2e-16)
- (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_215466.1)
- Domains: Pfam-A via hmmscan --cut_ga — ATP-grasp_2 (PF08442.16), ATP-grasp_5 (PF13549.12), CPSase_L_D2 (PF02786.23), Ligase_CoA (PF00549.25)
- 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
COG0045 - Curated reference: UniProt P9WGC5 (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 —
154 functional partner(s); context anchor
sucD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001015|Rv0951|sucC MDLFEYQAKELFAKHNVPSTPGRVTDTAEGAKAIATEIGRPVMVKAQVKIGGRGKAGGVKYAATPQDAYEHAKNILGLDIKGHIVKKLLVAEASDIAEEYYLSFLLDRANRTYLAMCSVEGGMEIEEVAATKPERLAKVPVNAVKGVDLDFARSIAEQGHLPAEVLDTAAVTIAKLWELFVAEDATLVEVNPLVRTPDHKILALDAKITLDGNADFRQPGHAEFEDRAATDPLELKAKEHDLNYVKLDGQVGIIGNGAGLVMSTLDVVAYAGEKHGGVKPANFLDIGGGASAEVMAAGLDVVLGDQQVKSVFVNVFGGITSCDAVATGIVKALGMLGDEANKPLVVRLDGNNVEEGRRILTEANHPLVTLVATMDEAADKAAELASA