prsA Resolved · high auto-curated
H37Rv Rv1017c · MTBC0 mtbc0_001092 ·
326 aa · 1142838–1143818 (-) ·
RefSeq NP_215533.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ribose-phosphate pyrophosphokinase |
|---|---|
| MTBC0 PGAP re-annotation | ribose-phosphate diphosphokinase |
| Revised (this work) | Ribose-phosphate diphosphokinase. Pfam: Pribosyltran_N (PF13793.13), Pribosyltran (PF00156.34), Pribosyl_synth (PF14572.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKE3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Ribose-phosphate pyrophosphokinase |
| EC (curated) |
EC 2.7.6.1
|
| Curated function | Involved in the biosynthesis of the central metabolite phospho-alpha-D-ribosyl-1-pyrophosphate (PRPP) and of the decaprenylphosphoryl-arabinose (DPA), an essential precursor for the mycobacterial cell wall biosynthesis. Catalyzes the transfer of pyrophosphoryl group from ATP to 1-hydroxyl of ribose-5-phosphate (Rib-5-P) to yield phosphoribosyl diphosphate (PRPP) and AMP. It can also use GTP, CTP and UTP as diphosphoryl donors. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | prs |
| eggNOG description | Involved in the biosynthesis of the central metabolite phospho-alpha-D-ribosyl-1-pyrophosphate (PRPP) via the transfer of pyrophosphoryl group from ATP to 1-hydroxyl of ribose-5-phosphate (Rib-5-P) |
| Orthologous group | COG0462 |
| EC number |
EC 2.7.6.1
|
| KEGG orthology |
K00948
|
| KEGG pathways |
map00030, map00230, map01100, map01110, map01120, map01130, map01200, map01230
|
| KEGG modules |
M00005
|
| Gene Ontology (39) |
GO:0000287, GO:0003674, GO:0003824, GO:0004749, GO:0005488, GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0006015, GO:0006793, GO:0006796 +27 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 | 0.25 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 3 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 |
|---|---|---|---|---|
Pribosyltran_N | PF13793.13 | 3.9e-49 | 12–128 | N-terminal domain of ribose phosphate pyrophosphokinase |
Pribosyltran | PF00156.34 | 2.9e-17 | 161–263 | Phosphoribosyl transferase domain |
Pribosyl_synth | PF14572.13 | 1.8e-20 | 216–322 | Phosphoribosyl synthetase-associated domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: glmU (bifunctional UDP-N-acetylglucosamine pyrophosphorylase/glucosamine-1-phosphate N-acetyltransferase), high confidence from genomic context alone (score 960 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2496c bkdB |
3-methyl-2-oxobutanoate dehydrogenase subunit beta | 989 | 987 | coexpression:407 experimental:869 database:844 |
Rv1248c kgd |
multifunctional 2-oxoglutarate dehydrogenase E1 component /2-oxoglutarate dehydrogenase dihydrolipoyllysine-residue succinyltransferase | 987 | 980 | experimental:831 database:844 textmining:429 |
Rv1018c glmU |
bifunctional UDP-N-acetylglucosamine pyrophosphorylase/glucosamine-1-phosphate N-acetyltransferase | 969 | 960 ctx | neighborhood:778 cooccurence:442 coexpression:700 |
Rv1449c tkt |
transketolase | 964 | 944 | coexpression:463 database:900 |
Rv2436 rbsK |
ribokinase RbsK | 934 | 925 | database:900 |
Rv0808 purF |
amidophosphoribosyltransferase | 959 | 918 | database:900 textmining:519 |
Rv2465c rpiB |
ribose-5-phosphate isomerase B | 928 | 906 | database:900 |
Rv3068c pgmA |
phosphoglucomutase PgmA | 910 | 901 | database:900 |
Rv1015c rplY |
50S ribosomal protein L25/general stress protein Ctc | 873 | 852 ctx | neighborhood:503 coexpression:714 |
Rv1826 gcvH |
glycine cleavage system protein H | 855 | 849 | database:844 |
Rv1016c lpqT |
lipoprotein LpqT | 833 | 834 ctx | neighborhood:832 |
Rv2215 dlaT |
pyruvate dehydrogenase E2 component dihydrolipoamide acyltransferase | 845 | 831 | experimental:434 database:623 |
Rv2121c hisG |
ATP phosphoribosyltransferase | 863 | 827 | database:800 |
Rv2495c bkdC |
branched-chain keto acid dehydrogenase E2 component | 839 | 825 | experimental:434 database:623 |
Rv1734c hyp |
hypothetical protein | 838 | 824 | experimental:434 database:623 |
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: ribose-phosphate pyrophosphokinase
- MTBC0 PGAP product: ribose-phosphate diphosphokinase
- Pfam (hmmscan --cut_ga): Pribosyltran_N PF13793.13 (E=4e-49), Pribosyltran PF00156.34 (E=3e-17), Pribosyl_synth PF14572.13 (E=2e-20)
- (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_215533.1)
- Domains: Pfam-A via hmmscan --cut_ga — Pribosyltran_N (PF13793.13), Pribosyltran (PF00156.34), Pribosyl_synth (PF14572.13)
- 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
COG0462 - Curated reference: UniProt P9WKE3 (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 —
204 functional partner(s); context anchor
glmU - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001092|Rv1017c|prsA MSHDWTDNRKNLMLFAGRAHPELAEQVAKELDVHVTSQDAREFANGEIFVRFHESVRGCDAFVLQSCPAPVNRWLMEQLIMIDALKRGSAKRITAVMPFYPYARQDKKHRGREPISARLIADLLKTAGADRIVTVDLHTDQIQGFFDGPVDHMRGQNLLTGYIRDNYPDGNMVVVSPDSGRVRIAEKWADALGGVPLAFIHKTRDPRVPNQVVSNRVVGDVAGRTCVLIDDMIDTGGTIAGAVALLHNDGAGDVIIAATHGVLSDPAAQRLASCGAREVIVTNTLPIGEDKRFPQLTVLSIAPLLASTIRAVFENGSVTGLFDGDA