dtd Resolved · high auto-curated
H37Rv Rv1897c · MTBC0 mtbc0_002011 ·
143 aa · 2162516–2162947 (-) ·
RefSeq NP_216413.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | D-tyrosyl-tRNA(Tyr) deacylase |
|---|---|
| MTBC0 PGAP re-annotation | D-aminoacyl-tRNA deacylase |
| Revised (this work) | D-aminoacyl-tRNA deacylase. Pfam: Tyr_Deacylase (PF02580.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WNS9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | D-aminoacyl-tRNA deacylase |
| EC (curated) |
EC 3.1.1.96
|
| Curated function | An aminoacyl-tRNA editing enzyme that deacylates mischarged D-aminoacyl-tRNAs. Also deacylates mischarged glycyl-tRNA(Ala), protecting cells against glycine mischarging by AlaRS. Acts via tRNA-based rather than protein-based catalysis; rejects L-amino acids rather than detecting D-amino acids in the active site. By recycling D-aminoacyl-tRNA to D-amino acids and free tRNA molecules, this enzyme counteracts the toxicity associated with the formation of D-aminoacyl-tRNA entities in vivo and helps enforce protein L-homochirality. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | dtd |
| eggNOG description | rejects L-amino acids rather than detecting D-amino acids in the active site. By recycling D-aminoacyl-tRNA to D-amino acids and free tRNA molecules, this enzyme counteracts the toxicity associated with the formation of D-aminoacyl-tRNA entities in vivo and helps enforce protein L-homochirality |
| Orthologous group | COG1490 |
| KEGG orthology |
K07560
|
| Gene Ontology (37) |
GO:0002161, GO:0003674, GO:0003824, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0006139, GO:0006399, GO:0006450, GO:0006725, GO:0006807 +25 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 | 1.468 · 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 |
|---|---|---|---|---|
Tyr_Deacylase | PF02580.22 | 1.2e-47 | 2–142 | D-Tyr-tRNA(Tyr) deacylase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1896c (S-adenosyl-L-methionine-dependent methyltransferase), high confidence from genomic context alone (score 883 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1896c |
S-adenosyl-L-methionine-dependent methyltransferase | 883 | 883 ctx | neighborhood:882 |
Rv1898 hyp |
hypothetical protein | 786 | 787 ctx | neighborhood:787 |
Rv1364c |
sigma factor regulatory protein | 544 | 544 ctx | neighborhood:544 |
Rv2583c relA |
bifunctional (p)ppGpp synthase/hydrolase RelA | 478 | 479 | coexpression:436 |
Rv3013 hyp |
hypothetical protein | 461 | 461 | coexpression:430 |
Rv0702 rplD |
50S ribosomal protein L4 | 615 | 149 | textmining:567 |
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: D-tyrosyl-tRNA(Tyr) deacylase
- MTBC0 PGAP product: D-aminoacyl-tRNA deacylase
- Pfam (hmmscan --cut_ga): Tyr_Deacylase PF02580.22 (E=1e-47)
- (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_216413.1)
- Domains: Pfam-A via hmmscan --cut_ga — Tyr_Deacylase (PF02580.22)
- 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
COG1490 - Curated reference: UniProt P9WNS9 (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 —
6 functional partner(s); context anchor
Rv1896c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002011|Rv1897c|dtd MRVLVQRVSSAAVRVDGRVVGAIRPDGQGLVAFVGVTHGDDLDKARRLAEKLWNLRVLADEKSASDMHAPILVISQFTLYADTAKGRRPSWNAAAPGAVAQPLIAAFAAALRQLGAHVEAGVFGAHMQVELVNDGPVTVMLEG