Rv3839 Resolved · high
H37Rv Rv3839 · MTBC0 mtbc0_004069 ·
258 aa · 4336876–4337652 (+) ·
RefSeq NP_218356.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF2470 domain-containing protein |
| Revised (this work) | Heme-homeostasis regulator: the principal driver of the Rv3839-Rv3840 operon that down-regulates endogenous heme biosynthesis under nitric-oxide and iron-limitation stress (Quirk 2026). It carries a DUF2470/DRI (Domain Related to Iron) regulatory module - the GluTR-binding-protein domain, also found in HugZ - and lies immediately upstream of bacterioferritin bfrB (Rv3841), in an operon with the transcriptional regulator Rv3840. The fold-paralogue safeguard is passed: it is not a copy of the genuine glutamyl-tRNA reductase HemA/Rv0509 but shares only the regulatory DUF2470 domain. RefSeq left this locus uncharacterised; the structure-guided hypothesis (heme/iron homeostasis) was confirmed experimentally by Quirk 2026 while the companion study was in progress - a RefSeq-behind case and an independent validation of the approach. |
Curated reference (UniProt)
| UniProt |
P96239
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | DUF2470 domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Protein of unknown function (DUF2470) |
| Orthologous group | 2E6J0 |
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 5 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 |
|---|---|---|---|---|
DUF2470 | PF10615.15 | 6.2e-07 | 174–241 | Domain of unknown function (DUF2470) |
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 91.8 (very high). 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 |
|---|---|---|---|---|
5che-assembly1_C |
1.00 | 0.74 | 2.6e-12 sig | 5che-assembly1_C Crystal structure of Arabidopsis glutamyl-tRNA reductase in complex with its regulatory proteins |
5che-assembly1_D |
1.00 | 0.74 | 2.3e-12 sig | 5che-assembly1_D Crystal structure of Arabidopsis glutamyl-tRNA reductase in complex with its regulatory proteins |
6m09-assembly1_B |
1.00 | 0.68 | 4.9e-12 sig | 6m09-assembly1_B The ligand-free structure of the chloroplast protein At3g03890 |
6m0a-assembly2_D |
1.00 | 0.69 | 2.2e-11 sig | 6m0a-assembly2_D The heme-bound structure of the chloroplast protein At3g03890 |
5bnc-assembly1_B |
1.00 | 0.56 | 2.6e-12 sig | 5bnc-assembly1_B Structure of heme binding protein MSMEG_6519 from Mycobacterium smegmatis |
2arz-assembly1_A |
1.00 | 0.42 | 2.4e-10 sig | 2arz-assembly1_A Crystal Structure of Protein of Unknown Function from Pseudomonas aeruginosa |
2arz-assembly1_B |
1.00 | 0.41 | 5.5e-09 sig | 2arz-assembly1_B Crystal Structure of Protein of Unknown Function from Pseudomonas aeruginosa |
8gbk-assembly1_G |
1.00 | 0.69 | 5.1e-04 sig | 8gbk-assembly1_G Dri1 hemoprotein variant H79A-R90A with a zinc-mirror heme site |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pheA (prephenate dehydratase), high confidence from genomic context alone (score 784 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) |
|---|---|---|---|---|
Rv2384 mbtA |
2,3-dihydroxybenzoate-AMP ligase | 864 | 827 | coexpression:827 |
Rv2123 PPE37 |
PPE family protein PPE37 | 886 | 806 | coexpression:806 textmining:440 |
Rv3838c pheA |
prephenate dehydratase | 784 | 784 ctx | neighborhood:781 |
Rv3837c |
phosphoglycerate mutase | 783 | 782 ctx | neighborhood:781 |
Rv0010c |
membrane protein | 764 | 764 ctx | cooccurence:764 |
Rv3840 |
transcriptional regulator | 755 | 755 ctx | neighborhood:747 |
Rv2732c |
transmembrane protein | 747 | 748 ctx | cooccurence:747 |
Rv3212 hyp |
hypothetical protein | 714 | 714 ctx | cooccurence:713 |
Rv3004 cfp6 |
low molecular weight protein antigen 6 | 712 | 712 ctx | cooccurence:712 |
Rv2700 cei hyp |
hypothetical protein | 710 | 710 ctx | cooccurence:710 |
Rv1109c hyp |
hypothetical protein | 702 | 702 ctx | cooccurence:702 |
Rv2138 lppL |
lipoprotein LppL | 700 | 700 ctx | cooccurence:700 |
Rv1083 hyp |
hypothetical protein | 693 | 693 ctx | cooccurence:693 |
Rv2360c hyp |
hypothetical protein | 693 | 693 ctx | cooccurence:693 |
Rv0431 |
tuberculin-like peptide | 689 | 689 ctx | cooccurence:689 |
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 (DUF2470); operon Rv3839-Rv3840 immediately upstream of bfrB (Rv3841)
- DUF2470/DRI + GluTR-binding-protein regulatory module (also in HugZ)
- Fold-paralogue safeguard: not the genuine glutamyl-tRNA reductase HemA/Rv0509
- Literature: Rv3839-Rv3840 down-regulates heme biosynthesis under NO / iron-limitation stress, Rv3839 principal driver (Quirk 2026)
- RefSeq-behind case; independent validation of the structure-guided hypothesis
- 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_218356.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF2470 (PF10615.15)
- 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
2E6J0 - Curated reference: UniProt P96239 (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 91.8, very high)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
86 functional partner(s); context anchor
pheA - Primary literature: Quirk NF, Gregory KN, Morita YS, Tan S (2026). Rv3839-Rv3840 links the endogenous heme biosynthesis pathway with Mycobacterium tuberculosis adaptation to nitric oxide and iron limitation stress bioRxiv (preprint). doi:10.64898/2026.02.17.706279
- 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_004069|Rv3839| MPPLTSLAPTTAERIRSACARAGGALLVVEREDPVPVPIHHLLYDGSFAVAVPVDRGEVSGSQALLELTDYAPLPVREPVRSLVWIRGCLHQIPPAELVETLDLIATDNPNPALLQVETPRSGPADAAETRYTMQRLEIESVVVTDATGAEPVTVADLLAARPDPFCEIESTLLWHLATAHDDVVARLVSRLPAPLRRGQIRPLGLDRYGVRFRIEARDGDRDIRLPFHKPVDDMTGLSQAIRVLMGCPFRNGLRARR