pafA Resolved · high auto-curated
H37Rv Rv2097c · MTBC0 mtbc0_002231 ·
452 aa · 2383943–2385301 (-) ·
RefSeq NP_216613.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | proteasome accessory factor PafA |
|---|---|
| MTBC0 PGAP re-annotation | Pup--protein ligase |
| Revised (this work) | Pup--protein ligase. Pfam: Pup_ligase (PF03136.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WNU7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Pup--protein ligase |
| EC (curated) |
EC 6.3.1.19
|
| Curated function | Catalyzes the covalent attachment of the prokaryotic ubiquitin-like protein modifier Pup to the proteasomal substrate proteins, thereby targeting them for proteasomal degradation. This tagging system is termed pupylation. The ligation reaction involves the side-chain carboxylate of the C-terminal glutamate of Pup and the side-chain amino group of a substrate lysine. PafA is required to confer resistance against the lethal effects of reactive nitrogen intermediates (RNI), antimicrobial molecules produced by activated macrophages and other cell types. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | pafA |
| eggNOG description | Catalyzes the covalent attachment of the prokaryotic ubiquitin-like protein modifier Pup to the proteasomal substrate proteins, thereby targeting them for proteasomal degradation. This tagging system is termed pupylation. The ligation reaction involves the side-chain carboxylate of the C-terminal glutamate of Pup and the side-chain amino group of a substrate lysine |
| Orthologous group | COG0638 |
| EC number |
EC 6.3.1.19
|
| KEGG orthology |
K13571
|
| KEGG modules |
M00342
|
| Gene Ontology (92) |
GO:0000166, GO:0000302, GO:0003674, GO:0003824, GO:0005488, GO:0005524, GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0006464, GO:0006508 +80 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 | 0.139 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 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 |
|---|---|---|---|---|
Pup_ligase | PF03136.21 | 4.2e-171 | 4–423 | Pup-ligase protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: prcA (proteasome subunit alpha), high confidence from genomic context alone (score 934 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2109c prcA |
proteasome subunit alpha | 985 | 934 ctx | neighborhood:539 fusion:473 cooccurence:744 textmining:782 |
Rv2111c pup |
ubiquitin-like protein Pup | 926 | 905 ctx | neighborhood:504 cooccurence:769 |
Rv2096c pafB |
proteasome accessory factor B | 985 | 893 ctx | neighborhood:881 textmining:872 |
Rv2095c pafC |
proteasome accessory factor C | 980 | 886 ctx | neighborhood:881 textmining:839 |
Rv2110c prcB |
proteasome subunit beta | 960 | 875 ctx | neighborhood:539 cooccurence:734 textmining:696 |
Rv2115c mpa |
proteasome-associated ATPase | 984 | 835 ctx | cooccurence:774 textmining:908 |
Rv2094c tatA |
Sec-independent protein translocase membrane-bound protein TatA | 824 | 801 ctx | neighborhood:796 |
Rv3780 bpa hyp |
hypothetical protein | 777 | 713 ctx | cooccurence:709 |
Rv2112c dop |
pup deamidase/depupylase | 718 | 666 | database:500 |
Rv2092c helY |
ATP-dependent DNA helicase HelY | 651 | 651 ctx | neighborhood:561 |
Rv2093c tatC |
Sec-independent protein translocase transmembrane protein TatC | 646 | 646 ctx | neighborhood:641 |
Rv2098c PE_PGRS36 |
PE-PGRS family protein PE_PGRS36; Rv2098c, (MTCY49.38c), len: 434 aa. PE_PGRS36,Member of the Mycobacterium tuberculosis PE family, PGRS sub | 624 | 624 ctx | neighborhood:622 |
Rv2099c PE21 |
Rv2099c, (MTCY49.39c), len: 58 aa. PE21, Member of the Mycobacterium tuberculosis PE family (see Brennan and Delogu, 2002); 5'-end of Rv2098 | 622 | 622 ctx | neighborhood:622 |
Rv2239c hyp |
hypothetical protein | 609 | 610 ctx | cooccurence:604 |
Rv3626c hyp |
hypothetical protein | 508 | 508 ctx | cooccurence:501 |
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: proteasome accessory factor PafA
- MTBC0 PGAP product: Pup--protein ligase
- Pfam (hmmscan --cut_ga): Pup_ligase PF03136.21 (E=4e-171)
- (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_216613.1)
- Domains: Pfam-A via hmmscan --cut_ga — Pup_ligase (PF03136.21)
- 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
COG0638 - Curated reference: UniProt P9WNU7 (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); context anchor
prcA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002231|Rv2097c|pafA MQRRIMGIETEFGVTCTFHGHRRLSPDEVARYLFRRVVSWGRSSNVFLRNGARLYLDVGSHPEYATAECDSLVQLVTHDRAGEWVLEDLLVDAEQRLADEGIGGDIYLFKNNTDSAGNSYGCHENYLIVRAGEFSRISDVLLPFLVTRQLICGAGKVLQTPKAATYCLSQRAEHIWEGVSSATTRSRPIINTRDEPHADAEKYRRLHVIVGDSNMSETTTMLKVGTAALVLEMIESGVAFRDFSLDNPIRAIREVSHDVTGRRPVRLAGGRQASALDIQREYYTRAVEHLQTREPNAQIEQVVDLWGRQLDAVESQDFAKVDTEIDWVIKRKLFQRYQDRYDMELSHPKIAQLDLAYHDIKRGRGIFDLLQRKGLAARVTTDEEIAEAVDQPPQTTRARLRGEFISAAQEAGRDFTVDWVHLKLNDQAQRTVLCKDPFRAVDERVKRLIASM