ppnK Resolved · high auto-curated
H37Rv Rv1695 · MTBC0 mtbc0_001803 ·
307 aa ·
1930761–1931684 MTBC0
(+) ·
RefSeq NP_216211.1
Genomic neighbourhood (genome browser)
Open in full genome browser →This gene (outlined) in its genomic context; arrows are neighbouring genes coloured by verdict. Click any gene to navigate. Pan and zoom in the full browser.
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | inorganic polyphosphate/ATP-NAD kinase |
|---|---|
| MTBC0 PGAP re-annotation | NAD kinase |
| Revised (this work) | NAD kinase. Pfam: NAD_kinase (PF01513.27), NAD_kinase_C (PF20143.5). |
| Functional category (TubercuList) | intermediary metabolism and respiration |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
In the literature (TB corpus sweep) 7 publications
7 TB publications mention this gene. 7 publication(s) discuss this gene (7 in a M. tuberculosis context, 1 in other mycobacteria — M. smegmatis (1)).
| Publication | Date |
|---|---|
| Metabolically distinct roles of NAD synthetase and NAD kinase define the essentiality of NAD and NADP in Mycobacterium tuberculosis. doi:10.1128/mbio.00340-23 | 2023 |
| Characterization of a novel mutation in the overlap of tlyA and ppnK involved in capreomycin resistance in Mycobacterium. doi:10.1002/iub.1277 | 2014 |
| Mycobacterial RNase E-associated proteins. doi:10.1111/j.1348-0421.2005.tb03697.x | 2005 |
| Crystallographic studies of Mycobacterium tuberculosis polyphosphate/ATP-NAD kinase complexed with NAD. doi:10.1016/S1389-1723(04)00302-0 | 2004 |
| Establishment of a mass-production system for NADP using bacterial inorganic polyphosphate/ATP-NAD kinase. doi:10.1263/jbb.92.447 | 2001 |
This layer CITES the literature and adds context; it does not change the verdict or the function stated elsewhere in this fiche. This distinguishes a gene that is dark because nobody has looked from one that is dark despite having been studied. Source: PubMed (whole): H37Rv locus tag + GENE NAME + ortholog identifiers (Mb…, MMAR_…, MSMEG_…, ML…, MAB_…), under a mycobacterial context filter; hits verified against the abstract text. Species-context counts distinguish M. tuberculosis literature from literature on other mycobacteria. phase76/phase77, 2026-07-13.
Genomic-neighbour overlap (structural caveat) co-directional · 0 % of gene
| Neighbour | tlyA (Rv1694, + strand) |
|---|---|
| Overlap | 1 bp, 0 % of this gene's length |
co-directional overlap: ordinary (e.g. shared stop/start codons in an operon), not the Rv2438A-type artefact P20.1, derived from GFF3 gene coordinates, 2026-08-03.
CRISPRi vulnerability
Vulnerability index -6.01 (95% CI -7.12 to -4.85). A more negative index = more vulnerable to knockdown (better drug-target quality); indicative threshold VI ≤ -6 = highly vulnerable.
Quantitative CRISPRi knockdown, graded (finer than binary Tn-seq essentiality). Source: CRISPRi vulnerability index (Bosch 2021, pebble.rockefeller.edu).
Legacy record & comparison (Mycobrowser)
| Mycobrowser function | Catalyzes the phosphorylation of NAD to NADP. Utilizes ATP and other nucleoside triphosphates as well as inorganic polyphosphate as a source of phosphorus [catalytic activity: ATP + NAD+ = ADP + NADP+]. |
|---|---|
| Mycobrowser EC |
2.7.1.23
· agrees with the atlas
|
The legacy Mycobrowser record is shown for verification. Mycobrowser is no longer maintained; its EC numbers predate recent nomenclature revisions, so a class change usually reflects re-numbering, not a conflict.
Orthologues (reciprocal best hits across mycobacteria)
| M. bovis |
Mb1721
· 99.7% identity |
|---|---|
| M. leprae |
ML1359
· 87.9% identity |
| M. marinum |
MMAR_2500
· 91.5% identity |
| M. smegmatis |
MSMEG_3750
· 83.4% identity |
| M. orygis |
RJtmp_001772
· 99.7% identity |
| M. abscessus |
MAB_2360
· 77.2% identity |
Reciprocal-best-hit orthologues (DIAMOND) against the Mycobrowser reference proteomes. A missing species is informative: e.g. a gene absent from M. leprae was likely lost in its reductive genome evolution. Locus tags link to Mycobrowser.
Curated reference (UniProt)
| UniProt |
P9WHV7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | NAD kinase |
| EC (curated) |
EC 2.7.1.23
|
| Curated function | Involved in the regulation of the intracellular balance of NAD and NADP, and is a key enzyme in the biosynthesis of NADP. Catalyzes specifically the phosphorylation on 2'-hydroxyl of the adenosine moiety of NAD to yield NADP. It can use ATP and other nucleoside triphosphates as well as inorganic polyphosphate (poly(P)) as a source of phosphorus. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| Preferred name | nadK |
| eggNOG description | Involved in the regulation of the intracellular balance of NAD and NADP, and is a key enzyme in the biosynthesis of NADP. Catalyzes specifically the phosphorylation on 2'-hydroxyl of the adenosine moiety of NAD to yield NADP |
| Orthologous group | COG0061 |
| EC number |
EC 2.7.1.23
|
| KEGG orthology |
K00858
|
| KEGG pathways |
map00760, map01100
|
| Gene Ontology (77) |
GO:0000166, GO:0003674, GO:0003824, GO:0003951, GO:0005488, GO:0005524, GO:0006082, GO:0006139, GO:0006725, GO:0006732, GO:0006733, GO:0006739 +65 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 | 0.142 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 2 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.
Outgroup conservation (beyond the MTBC) Bacteria
| M. canettii dN/dS (deep-divergence selection) |
0.0 (low power)
· 2 consensus substitution(s) low power (2 canettii-consensus substitution(s)); present in M. canettii but dN/dS not reliable |
|---|---|
| Genus-wide presence (~53 non-MTBC Mycobacterium) |
present in 53/53 (100%) · mean identity 88.7%
· 4/4 closest MTBAP relatives conserved across the genus (present in 53/53 non-MTBC Mycobacterium genomes, incl. distant relatives) — an ancient core gene predating the genus radiation |
| Phylostratum (deepest detected homolog) |
MTBC-specific → Mycobacterium → Mycobacteriaceae → Corynebacteriales → Actinomycetia → Bacteria detected in 12/13 non-Mycobacterium reference genomes (down to Bacteria) · mean identity 53.4% detected down to outside the phylum (Proteobacteria/Firmicutes controls) — a universally conserved, ancient bacterial gene |
Two orthogonal outgroup signals. M. canettii (the immediate outgroup) gives a deep-divergence dN/dS (a low value confirms a constrained, real gene; shown as confident only at ≥8 substitutions, else flagged low-power). Genus-wide presence/absence (tblastn vs assembled non-MTBC genomes) places the gene on the ancient-core ↔ MTBC-specific axis: a gene absent even from the closest MTBAP relatives is a candidate MTBC-specific innovation (possible host-adaptation factor, to confirm by synteny). The phylostratum extends that axis outside the genus (tblastn vs 13 reference genomes spanning Mycobacteriaceae → Corynebacteriales → Actinomycetia → outside the phylum): it is the deepest clade in which a homolog is still detected, i.e. a proxy for gene age. Read it with the null model in mind: a shallow (young) stratum can also reflect homology-detection failure for short or fast-evolving ORFs, so it is a descriptive axis, not a proof of novelty.
Essentiality (transposon mutagenesis) essential
| DeJesus 2017 call | ES · essential |
|---|---|
| What the call means | essential: insertions absent across the whole ORF |
| TA sites (Himar1) | 8 in the ORF — 7 in the essential state, 0 growth-defect, 1 non-essential, 0 growth-advantage. Saturation 0.125, mean read count 15. A region of the protein devoid of TA sites is invisible to this assay: nothing can be inferred about it, in either direction. |
| Caveat | Read with some caution: only 8 TA (Himar1) sites in the whole ORF (atlas median 13). The DeJesus 2017 call rests on fewer independent observations than for a longer gene. If this gene overlaps a neighbour (see Genomic-neighbour overlap section below), some of these 8 sites may fall inside the neighbour's ORF rather than its own, leaving even fewer truly informative sites than the raw count suggests. (P20.3) |
Genome-wide Himar1 transposon essentiality in H37Rv (DeJesus 2017). An essential call (ES/ESD/GD) is strong, independent evidence that a "hypothetical" locus encodes a functional, selectively required gene — orthogonal to intra-species conservation.
Chemical-genetic target & druggability (PROSPECT) hypomorph tool strain
This gene is part of the PROSPECT collection of TetON transcriptional-knockdown (hypomorph) strains of essential M. tuberculosis genes, built as a sensitised background for chemical-genetic mechanism-of-action deconvolution. Being in the panel means the gene is an essential / vulnerable target for which a validated knockdown tool strain exists.
| Hypomorph strain | Rv1695-ppnK-TetOn6.1 (TetON promoter 6) |
|---|---|
| Baseline knockdown fitness | 4.796 median doublings (across 6 screen pool(s)) — fewer doublings = stronger growth defect on knockdown |
| Used in target deconvolution | yes (informs phenotypic-cluster / MOA assignment) |
Panel membership reflects essentiality/vulnerability and the availability of a genetic tool, not a specific molecular function; it never changes the verdict here. Source: Bond AN et al., Nat Commun 2025;16:9673 (doi:10.1038/s41467-025-64662-x); PROSPECT chemical-genetic platform.
Proteomics (mass spectrometry) detected
| MS detection | detected in 11 of 16 independent MS datasets |
|---|---|
| Integrated abundance | 77.9 ppm · rank 1471/3519 (58.2th percentile) |
Detection by mass spectrometry is direct, experimental evidence that the protein product exists — orthogonal to sequence conservation and to Tn-seq essentiality, and especially decisive for a "hypothetical" locus. Reproducible detection across several independent datasets (PaxDb) makes the existence claim robust; the integrated abundance places the protein in the proteome's dynamic range.
Physico-chemical properties (computed, ProtParam)
| Length | 307 aa |
|---|---|
| Molecular weight | 32.9 kDa |
| Theoretical pI | 5.26 |
| GRAVY | 0.136 (hydrophobic) |
| Aliphatic index | 106.7 |
| Aromaticity | 0.046 |
| Instability index | 31.5 (stable) |
Computed from the ancestral MTBC0 sequence with the ExPASy ProtParam method (Biopython). Descriptive biophysical context: a positive GRAVY flags a hydrophobic (often membrane) protein, a high instability index (>40) predicts a short in-vitro half-life, an extreme pI hints at compartment or binding partner.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
NAD_kinase | PF01513.27 | 4.4e-31 | 7–133 | ATP-NAD kinase N-terminal domain |
NAD_kinase_C | PF20143.5 | 1.0e-38 | 158–283 | ATP-NAD kinase C-terminal domain |
Experimental structures (Protein Data Bank) 4 solved
| PDB | Method | Resolution | Coverage |
|---|---|---|---|
1u0t |
X-ray diffraction | 2.3 Å | 100% |
1y3i |
X-ray diffraction | 2.6 Å | 100% |
1u0r |
X-ray diffraction | 2.8 Å | 100% |
1y3h |
X-ray diffraction | 2.8 Å | 100% |
Experimentally solved structures mapped from the UniProt accession via PDBe/SIFTS (4 total; up to 8 shown, ranked by sequence coverage then resolution). An experimental structure is direct proof of the folded product and the strongest structural evidence — superseding the predicted ESMFold/AlphaFold models below for any covered region.
Structural search (AlphaFold DB model, Foldseek vs PDB — genome-wide) pLDDT 88.0
| PDB hit | prob | TM-score | E-value | Description |
|---|---|---|---|---|
1u0r-assembly1_A |
1.00 | 0.96 | 8.5e-57 sig | 1u0r-assembly1_A Crystal structure of Mycobacterium tuberculosis NAD kinase |
1u0r-assembly1_D |
1.00 | 0.94 | 1.2e-57 sig | 1u0r-assembly1_D Crystal structure of Mycobacterium tuberculosis NAD kinase |
1u0t-assembly1_B-2 |
1.00 | 0.96 | 2.0e-55 sig | 1u0t-assembly1_B-2 Crystal structure of Mycobacterium tuberculosis NAD kinase |
1u0r-assembly1_C |
1.00 | 0.95 | 9.5e-55 sig | 1u0r-assembly1_C Crystal structure of Mycobacterium tuberculosis NAD kinase |
1y3h-assembly1_A-2 |
1.00 | 0.96 | 3.3e-53 sig | 1y3h-assembly1_A-2 Crystal Structure of Inorganic Polyphosphate/ATP-NAD kinase from Mycobacterium tuberculosis |
Foldseek search of the AlphaFold DB model (mean pLDDT 88.0, gated at 70) against the PDB — a genome-wide extension of the ESMFold dark-gene search that also covers proteins beyond the single-sequence length limit. Confident structural neighbours (E < 0.01) shown.
Genomic context (neighbours & predicted operon) operon of 7
| Upstream (5' on genome) | tlyA (+ strand, -1 bp gap) |
|---|---|
| Downstream (3' on genome) | recN (+ strand, 13 bp gap) |
| Predicted operon |
lprJ · Rv1691 · Rv1692 · Rv1693 · tlyA · ppnK · recN
|
Neighbours from the H37Rv annotation (+ strand). The operon is predicted by co-directional intergenic distance (same strand, gaps ≤50 bp) — a transcription-unit hypothesis, not a mapped TSS. For a "hypothetical", co-transcription with a characterised operon is a concrete functional lead (complements the STRING neighborhood channel below).
Functional interaction network (STRING v12, guilt-by-association)
Explore full network →Node colour = verdict, dashed = hypothetical; edge colour = evidence (green experimental, orange genomic-context, grey co-expression), width ∝ score. Click a partner to open its page; "Explore full network" to walk the graph.
Closest characterised functional partner: tlyA (16S/23S rRNA (cytidine-2'-O)-methyltransferase TlyA), high confidence from genomic context alone (score 938 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1694 tlyA |
16S/23S rRNA (cytidine-2'-O)-methyltransferase TlyA | 986 | 938 ctx | neighborhood:882 coexpression:494 textmining:790 |
Rv2421c nadD exp |
nicotinate-nucleotide adenylyltransferase | 948 | 932 | database:900 |
Rv2438c nadE exp |
glutamine-dependent NAD(+) synthetase | 959 | 924 | database:900 textmining:498 |
Rv0212c nadR exp |
transcriptional regulator NadR | 941 | 919 | database:900 |
Rv1151c cobB exp |
NAD-dependent protein deacylase | 923 | 906 | database:900 |
Rv0157 pntB exp |
NAD(P) transhydrogenase subunit beta PntB | 910 | 903 | database:900 |
Rv0156 pntAb exp |
NAD(P) transhydrogenase subunit alpha PntAb | 916 | 901 | database:900 |
Rv0155 pntAa exp |
NAD(P) transhydrogenase subunit alpha PntAa | 913 | 901 | database:900 |
Rv2713 sthA exp |
pyridine nucleotide transhydrogenase | 907 | 901 | database:900 |
Rv3199c nudC exp |
NADH pyrophosphatase | 905 | 901 | database:900 |
Rv1691 hyp |
hypothetical protein | 986 | 900 ctx | neighborhood:882 textmining:870 |
Rv1693 hyp |
hypothetical protein | 984 | 884 ctx | neighborhood:882 textmining:870 |
Rv1692 |
phosphatase | 984 | 882 ctx | neighborhood:882 textmining:870 |
Rv1696 recN |
DNA repair protein RecN | 978 | 882 ctx | neighborhood:867 textmining:821 |
Rv1697 steA hyp |
hypothetical protein | 769 | 769 ctx | neighborhood:766 |
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 exp badge marks an experimentally-supported partner (measured interaction, experimental/database channel ≥400) as opposed to a purely predicted one — but note that the M. tuberculosis experimental interactome is dominated by a noisy bacterial-two-hybrid screen, so a strong measured link that contradicts the operon/localisation context is likely a false positive. 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: inorganic polyphosphate/ATP-NAD kinase
- MTBC0 PGAP product: NAD kinase
- Pfam (hmmscan --cut_ga): NAD_kinase PF01513.27 (E=4e-31), NAD_kinase_C PF20143.5 (E=1e-38)
- (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_216211.1)
- Domains: Pfam-A via hmmscan --cut_ga — NAD_kinase (PF01513.27), NAD_kinase_C (PF20143.5)
- 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
COG0061 - Curated reference: UniProt P9WHV7 (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)
- Genome-wide structure: AlphaFold DB model (Jumper et al. 2021, doi:10.1038/s41586-021-03819-2; Varadi et al. 2024, doi:10.1093/nar/gkad1011) searched vs PDB with Foldseek (mean pLDDT 88.0)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
65 functional partner(s); context anchor
tlyA - Essentiality: genome-wide transposon mutagenesis in H37Rv — DeJesus et al. 2017 (mBio, doi:10.1128/mBio.02133-16, CC BY)
- Proteomics: integrated mass-spectrometry abundance from PaxDb 5.0 (Huang et al. 2023, doi:10.1016/j.mcpro.2023.100640), taxon 83332 — weighted average of 16 datasets, incl. Schubert et al. 2013 (doi:10.1016/j.chom.2013.04.008) and Albrethsen et al. 2013 (doi:10.1074/mcp.M112.018846)
- Functional category: TubercuList scheme (Cole et al. 1998, doi:10.1038/31159), via Mycobrowser (Kapopoulou et al. 2011, doi:10.1016/j.tube.2010.09.006)
- Orthologues: reciprocal best hits (DIAMOND, Buchfink et al. 2021, doi:10.1038/s41592-021-01101-x) against Mycobrowser release 5 reference proteomes
- Experimental structures: PDBe/SIFTS UniProt→PDB mapping (Dana et al. 2019, doi:10.1093/nar/gky1114)
- Genomic context / operon: H37Rv annotation; operon predicted by co-directional intergenic distance (Salgado et al. 2000, doi:10.1073/pnas.030539397)
- Physico-chemical properties: ExPASy ProtParam method via Biopython (Gasteiger et al. 2005), computed from the MTBC0 sequence
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001803|Rv1695|ppnK MTAHRSVLLVVHTGRDEATETARRVEKVLGDNKIALRVLSAEAVDRGSLHLAPDDMRAMGVEIEVVDADQHAADGCELVLVLGGDGTFLRAAELARNASIPVLGVNLGRIGFLAEAEAEAIDAVLEHVVAQDYRVEDRLTLDVVVRQGGRIVNRGWALNEVSLEKGPRLGVLGVVVEIDGRPVSAFGCDGVLVSTPTGSTAYAFSAGGPVLWPDLEAILVVPNNAHALFGRPMVTSPEATIAIEIEADGHDALVFCDGRREMLIPAGSRLEVTRCVTSVKWARLDSAPFTDRLVRKFRLPVTGWRGK
Spot an error? Suggest an improvement
Found a mistake, a missing reference, or have a better functional hypothesis for ppnK? Email the maintainer — the message is pre-filled with this gene's details.