Rv0535 Resolved · high auto-curated
H37Rv Rv0535 · MTBC0 - ·
264 aa · 626457–627251 (+) ·
RefSeq NP_215049.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 5'-methylthioadenosine phosphorylase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | 5'-methylthioadenosine phosphorylase. Pfam: PNP_UDP_1 (PF01048.27). |
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 |
O06401
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | S-methyl-5'-thioadenosine phosphorylase |
| EC (curated) |
EC 2.4.2.28
|
| Curated function | Catalyzes the reversible phosphorylation of S-methyl-5'-thioadenosine (MTA) to adenine and 5-methylthioribose-1-phosphate. Involved in the breakdown of MTA, a major by-product of polyamine biosynthesis. Responsible for the first step in the methionine salvage pathway after MTA has been generated from S-adenosylmethionine. Prefers MTA, with 2% activity on adenosine, 0.8% activity on S-adenosyl-L-homocysteine and no activity on other tested nucleosides. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | mtnP |
| eggNOG description | Catalyzes the reversible phosphorylation of S-methyl-5'- thioadenosine (MTA) to adenine and 5-methylthioribose-1-phosphate. Involved in the breakdown of MTA, a major by-product of polyamine biosynthesis. Responsible for the first step in the methionine salvage pathway after MTA has been generated from S- adenosylmethionine. Has broad substrate specificity with 6- aminopurine nucleosides as preferred substrates |
| Orthologous group | COG0005 |
| EC number |
EC 2.4.2.28
|
| KEGG orthology |
K00772
|
| KEGG pathways |
map00270, map01100
|
| KEGG modules |
M00034
|
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 | 0.115 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 1 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 |
|---|---|---|---|---|
PNP_UDP_1 | PF01048.27 | 2.4e-35 | 9–239 | Phosphorylase superfamily |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: galE3 (UDP-glucose 4-epimerase GalE), high confidence from genomic context alone (score 934 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0536 galE3 |
UDP-glucose 4-epimerase GalE | 991 | 934 ctx | neighborhood:882 cooccurence:441 textmining:875 |
Rv0091 mtn |
5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase | 992 | 903 | database:900 textmining:929 |
Rv2601 speE |
spermidine synthase | 986 | 901 | database:900 textmining:870 |
Rv2584c apt |
adenine phosphoribosyltransferase | 913 | 900 ctx | fusion:766 database:408 |
Rv0534c menA |
1,4-dihydroxy-2-naphthoate octaprenyltransferase | 792 | 792 ctx | neighborhood:791 |
Rv0533c fabH |
3-oxoacyl-ACP synthase III | 558 | 558 ctx | neighborhood:558 |
Rv0539 |
dolichyl-phosphate sugar synthase | 936 | 533 ctx | cooccurence:416 textmining:870 |
Rv0435c |
ATPase | 463 | 463 | |
Rv0512 hemB |
delta-aminolevulinic acid dehydratase | 454 | 455 | |
Rv3396c guaA |
GMP synthase | 588 | 437 | |
Rv0489 gpm1 |
2,3-bisphosphoglycerate-dependent phosphoglycerate mutase | 431 | 432 | database:400 |
Rv0540 hyp |
hypothetical protein | 920 | 410 | textmining:870 |
Rv0478 deoC |
2-deoxyribose-5-phosphate aldolase | 441 | 405 | |
Rv3308 pmmB |
phosphomannomutase PmmB | 428 | 387 | |
Rv3441c mrsA |
phosphoglucosamine mutase | 411 | 387 |
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): 5'-methylthioadenosine phosphorylase
- Pfam (hmmscan --cut_ga): PNP_UDP_1 PF01048.27 (E=2e-35)
- (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_215049.1)
- Domains: Pfam-A via hmmscan --cut_ga — PNP_UDP_1 (PF01048.27)
- 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
COG0005 - Curated reference: UniProt O06401 (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 —
24 functional partner(s); context anchor
galE3 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0535| MHNNGRMLGVIGGSGFYTFFGSDTRTVNSDTPYGQPSAPITIGTIGVHDVAFLPRHGAHHQYSAHAVPYRANMWALRALGVRRVFGPCAVGSLDPELEPGAVVVPDQLVDRTSGRADTYFDFGGVHAAFADPYCPTLRAAVTGLPGVVDGGTMVVIQGPRFSTRAESQWFAAAGCNLVNMTGYPEAVLARELELCYAAIALVTDVDAGVAAGDGVKAADVFAAFGENIELLKRLVRAAIDRVADERTCTHCQHHAGVPLPFELP