Rv2492 Resolved · medium
H37Rv Rv2492 · MTBC0 mtbc0_002654 ·
250 aa · 2830168–2830920 (+) ·
RefSeq NP_217008.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Thymidylate-synthase (TS)-superfamily (hydroxymethyl)transferase acting on a deoxyuridylate-type nucleotide, a distinct non-essential locus separate from the essential thymidylate synthases ThyA/ThyX. RefSeq leaves it 'hypothetical protein'. The model superposes on MilA (a CMP hydroxymethyltransferase, PDB 5b6d) with a complete catalytic constellation at the nucleotide (nucleophile Cys151, phosphate-binding Arg175, base-reading Asp178, ribose-binding His222/Tyr224); HHpred places it 100% in the thymidylate-synthase / dCMP-hydroxymethylase superfamily. The specificity residues reassign the substrate away from the template's cytidylate: Asn186 (vs MilA Asp186) and Ser176 (deoxy-type) point to a (deoxy)uridylate (dUMP-type) substrate with one-carbon chemistry on the pyrimidine C5. Vertically conserved through the human and animal MTBC and M. canettii (an earlier anti-phage-defence hypothesis is rejected). A structural prediction; substrate narrowed, not fixed. |
Curated reference (UniProt)
| UniProt |
I6YDJ7
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Thymidylate synthase |
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 0.705 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 10 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 86.1 (confident). A confident model makes the fold comparison meaningful.
Best matches against the PDB, ranked by Foldseek homology probability. A high probability / TM-score suggests a shared fold; unless flagged sig (E < 0.01) these are fold hypotheses, not assignments.
| Target | Prob | TM | E-value | Description |
|---|---|---|---|---|
5jnh-assembly1_B |
1.00 | 0.73 | 3.7e-11 sig | 5jnh-assembly1_B Crystal Structure of cytidine monophosphate hydroxymethylase MilA |
5b6d-assembly1_A |
1.00 | 0.71 | 4.2e-11 sig | 5b6d-assembly1_A Crystal Structure of cytidine monophosphate hydroxymethylase MilA with CMP |
5jnh-assembly1_A |
1.00 | 0.63 | 2.3e-12 sig | 5jnh-assembly1_A Crystal Structure of cytidine monophosphate hydroxymethylase MilA |
5b6e-assembly1_A |
1.00 | 0.70 | 6.3e-11 sig | 5b6e-assembly1_A Crystal Structure of cytidine monophosphate hydroxymethylase MilA with hmCMP |
5jp9-assembly1_A |
1.00 | 0.65 | 1.0e-10 sig | 5jp9-assembly1_A Crystal Structure of cytidine monophosphate hydroxymethylase MilA with dCMP |
5j7w-assembly2_B |
1.00 | 0.64 | 1.2e-10 sig | 5j7w-assembly2_B Enterococcus faecalis thymidylate synthase complex with methotrexate |
4xsd-assembly1_A |
1.00 | 0.64 | 7.6e-11 sig | 4xsd-assembly1_A Complex structure of thymidylate synthase from varicella zoster virus with a dUMP |
4fog-assembly2_B |
1.00 | 0.68 | 4.0e-10 sig | 4fog-assembly2_B Crystal Structure of Mtb ThyA in Complex with 5-Fluoro-dUMP and 5-methyltetrahydrofolic acid |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapC38 (ribonuclease VapC38), medium confidence from genomic context alone (score 619 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2491 hyp |
hypothetical protein | 967 | 967 ctx | neighborhood:882 coexpression:731 |
Rv3109 moaA1 |
cyclic pyranopterin monophosphate synthase | 778 | 778 | coexpression:778 |
Rv3114 hyp |
hypothetical protein | 754 | 739 | coexpression:730 |
Rv2763c dfrA |
dihydrofolate reductase | 749 | 715 | coexpression:699 |
Rv1407 fmu |
16S rRNA m5C967 methyltransferase | 720 | 708 | coexpression:667 |
Rv2902c rnhB |
ribonuclease HII | 717 | 705 | coexpression:649 |
Rv0570 nrdZ |
vitamin B12-dependent ribonucleoside-diphosphate reductase | 688 | 659 | coexpression:647 |
Rv3051c nrdE |
ribonucleoside-diphosphate reductase subunit alpha | 687 | 658 | coexpression:646 |
Rv2116 lppK |
lipoprotein LppK | 675 | 655 | coexpression:598 |
Rv0002 dnaN |
DNA polymerase III subunit beta | 675 | 654 | coexpression:597 |
Rv2494 vapC38 |
ribonuclease VapC38 | 619 | 619 ctx | neighborhood:619 |
Rv2493 vapB38 |
antitoxin VapB38 | 619 | 619 ctx | neighborhood:619 |
Rv2697c dut |
deoxyuridine 5'-triphosphate nucleotidohydrolase | 587 | 531 | coexpression:443 |
Rv1389 gmk |
guanylate kinase | 536 | 480 | coexpression:479 |
Rv0038 hyp |
hypothetical protein | 494 | 467 | coexpression:467 |
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
- RefSeq: hypothetical protein
- Superposition on MilA+CMP (5b6d); HHpred 100% thymidylate-synthase / dCMP-hydroxymethylase superfamily
- Competent catalytic core: Cys151, Arg175, Asp178, His222, Tyr224 at H-bonding distance of the nucleotide
- Specificity residues Asn186 + Ser176 -> (deoxy)uridylate (dUMP-type), not the template CMP
- Distinct, non-essential locus (25% id); not redundant with ThyA/ThyX
- Curated against the companion dark-enzymes re-annotation (Guyeux 2026)
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_217008.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Curated reference: UniProt I6YDJ7 (TrEMBL, unreviewed; Predicted)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Model confidence: ESMFold per-residue pLDDT (mean 86.1, confident)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
35 functional partner(s); context anchor
vapC38 - Primary literature: Guyeux C (2026). Structure-guided functional hypotheses for uncharacterised enzymes of Mycobacterium tuberculosis in preparation. doi:10.5281/zenodo.20571950
Ancestral MTBC0 protein sequence
>mtbc0_002654|Rv2492| MSRRIINEFGVQIYGATIGDTWAGLVRAVLDLGSQCFDEDRERIALSNVRIKSSVQNYPDLTIEEHCNSDQLKAMLDFMFNTDTMEDIDVVKSFSRGAKSYHRRIKEGRMIEFVIERLSLIPESKKAVVVFPTYEDYAAVMRNHRDDYLPCLVSIQFRLLPDGKDYVFHTTFYSRSMDAWQKGHGNLLSIAKLSDWVRENVSARIGRKIMLGPLDGMICDVHIYKETYAEACKRLANLDLRRTQFDAVRN