nrnA Resolved · high auto-curated
H37Rv Rv2837c · MTBC0 mtbc0_003016 ·
336 aa · 3164301–3165311 (-) ·
RefSeq NP_217353.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | bifunctional oligoribonuclease/PAP phosphatase NrnA |
|---|---|
| MTBC0 PGAP re-annotation | bifunctional oligoribonuclease/PAP phosphatase NrnA |
| Revised (this work) | Bifunctional oligoribonuclease/PAP phosphatase NrnA. Pfam: DHH (PF01368.28), DHHA1 (PF02272.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71615
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Bifunctional oligoribonuclease and PAP phosphatase NrnA |
| EC (curated) |
EC 3.1.-.-, EC 3.1.3.7
|
| Curated function | Bifunctional enzyme which has both oligoribonuclease and pAp-phosphatase activities. Degrades RNA oligonucleotides with a length of 5 nucleotides and shorter, with a preference for 2-mers. Also degrades 24-mers. Converts 3'(2')-phosphoadenosine 5'-phosphate (PAP) to AMP. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | nrnA |
| eggNOG description | Phosphoesterase |
| Orthologous group | COG0618 |
| EC number |
EC 3.1.13.3, EC 3.1.3.7
|
| KEGG orthology |
K06881
|
| KEGG pathways |
map00920, map01100, map01120
|
| Gene Ontology (2) |
GO:0008150, GO:0040007
|
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 | 0.369 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
DHH | PF01368.28 | 1.0e-14 | 36–177 | DHH family, N-terminal domain |
DHHA1 | PF02272.25 | 2.3e-08 | 258–334 | DHHA1 domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rbfA (ribosome-binding factor RbfA), high confidence from genomic context alone (score 982 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2838c rbfA |
ribosome-binding factor RbfA | 983 | 982 ctx | neighborhood:882 coexpression:853 |
Rv2839c infB |
translation initiation factor IF-2 | 965 | 963 ctx | neighborhood:882 coexpression:703 |
Rv1286 cysC |
adenylyl-sulfate kinase | 911 | 911 | database:900 |
Rv2392 cysH |
phosphoadenosine phosphosulfate reductase | 903 | 903 | database:900 |
Rv1285 cysD |
sulfate adenylyltransferase subunit 2 | 902 | 903 | database:900 |
Rv2131c cysQ |
3'(2'),5'-bisphosphate nucleotidase CysQ | 963 | 901 | database:900 textmining:644 |
Rv2836c dinF |
DNA-damage-inducible protein DinF | 927 | 881 ctx | neighborhood:881 textmining:414 |
Rv2840c hyp |
hypothetical protein | 805 | 805 ctx | neighborhood:782 |
Rv2835c ugpA |
sn-glycerol-3-phosphate ABC transporter permease UgpA | 784 | 785 ctx | neighborhood:782 |
Rv2834c ugpE |
sn-glycerol-3-phosphate ABC transporter permease UgpE | 744 | 744 ctx | neighborhood:743 |
Rv2833c ugpB |
sn-glycerol-3-phosphate ABC transporter substrate-binding lipoprotein UgpB | 743 | 744 ctx | neighborhood:743 |
Rv2832c ugpC |
sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC | 572 | 573 ctx | neighborhood:572 |
Rv2841c nusA |
transcription termination/antitermination protein NusA | 535 | 535 ctx | neighborhood:528 |
Rv3605c hyp |
hypothetical protein | 526 | 526 ctx | cooccurence:526 |
Rv2844 hyp |
hypothetical protein | 516 | 516 |
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: bifunctional oligoribonuclease/PAP phosphatase NrnA
- MTBC0 PGAP product: bifunctional oligoribonuclease/PAP phosphatase NrnA
- Pfam (hmmscan --cut_ga): DHH PF01368.28 (E=1e-14), DHHA1 PF02272.25 (E=2e-08)
- (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_217353.1)
- Domains: Pfam-A via hmmscan --cut_ga — DHH (PF01368.28), DHHA1 (PF02272.25)
- 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
COG0618 - Curated reference: UniProt P71615 (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 —
37 functional partner(s); context anchor
rbfA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003016|Rv2837c|nrnA MTTIDPRSELVDGRRRAGARVDAVGAAALLSAAARVGVVCHVHPDADTIGAGLALALVLDGCGKRVEVSFAAPATLPESLRSLPGCHLLVRPEVMRRDVDLVVTVDIPSVDRLGALGDLTDSGRELLVIDHHASNDLFGTANFIDPSADSTTTMVAEILDAWGKPIDPRVAHCIYAGLATDTGSFRWASVRGYRLAARLVEIGVDNATVSRTLMDSHPFTWLPLLSRVLGSAQLVSEAVGGRGLVYVVVDNREWVAARSEEVESIVDIVRTTQQAEVAAVFKEVEPHRWSVSMRAKTVNLAAVASGFGGGGHRLAAGYTTTGSIDDAVASLRAALG