dprE1 Resolved · high auto-curated
H37Rv Rv3790 · MTBC0 mtbc0_004018 ·
461 aa · 4259900–4261285 (+) ·
RefSeq NP_218307.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | decaprenylphosphoryl-beta-D-ribose oxidase |
|---|---|
| MTBC0 PGAP re-annotation | decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase DprE1 |
| Revised (this work) | Decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase DprE1. Pfam: FAD_binding_4 (PF01565.29), ALO (PF04030.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJF1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Decaprenylphosphoryl-beta-D-ribose oxidase |
| EC (curated) |
EC 1.1.98.3
|
| Curated function | Component of the DprE1-DprE2 complex that catalyzes the 2-step epimerization of decaprenyl-phospho-ribose (DPR) to decaprenyl-phospho-arabinose (DPA), a key precursor that serves as the arabinose donor required for the synthesis of cell-wall arabinans. DprE1 catalyzes the first step of epimerization, namely FAD-dependent oxidation of the C2' hydroxyl of DPR to yield the keto intermediate decaprenyl-phospho-2'-keto-D-arabinose (DPX). The intermediate DPX is then transferred to DprE2 subunit of the epimerase complex, most probably through a 'substrate channel' at the interface of DprE1-DprE2 com. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | dprE1 |
| eggNOG description | FAD linked oxidase |
| Orthologous group | COG0277 |
| EC number |
EC 1.1.98.3
|
| KEGG orthology |
K16653
|
| Gene Ontology (39) |
GO:0000271, GO:0005575, GO:0005623, GO:0005886, GO:0005975, GO:0005976, GO:0008150, GO:0008152, GO:0009058, GO:0009059, GO:0009987, GO:0010383 +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 | 0.443 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 4 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 |
|---|---|---|---|---|
FAD_binding_4 | PF01565.29 | 1.9e-24 | 30–161 | FAD binding domain |
ALO | PF04030.20 | 3.8e-07 | 399–457 | D-arabinono-1,4-lactone oxidase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: dprE2 (decaprenylphosphoryl-D-2-keto erythropentose reductase), high confidence from genomic context alone (score 988 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3791 dprE2 |
decaprenylphosphoryl-D-2-keto erythropentose reductase | 999 | 988 ctx | neighborhood:881 cooccurence:774 database:500 textmining:947 |
Rv3789 |
GtrA family protein | 965 | 958 ctx | neighborhood:823 cooccurence:762 |
Rv3793 embC |
arabinosyltransferase C | 972 | 941 ctx | neighborhood:881 cooccurence:486 textmining:542 |
Rv3792 aftA |
arabinofuranosyltransferase | 933 | 904 ctx | neighborhood:881 |
Rv3806c ubiA |
decaprenyl-phosphate phosphoribosyltransferase | 965 | 899 ctx | cooccurence:774 database:552 textmining:675 |
Rv3794 embA |
arabinosyltransferase A | 872 | 791 ctx | neighborhood:601 cooccurence:455 textmining:413 |
Rv3795 embB |
arabinosyltransferase B | 852 | 788 ctx | neighborhood:580 cooccurence:493 |
Rv2073c |
oxidoreductase | 787 | 786 ctx | cooccurence:774 |
Rv3788 hyp |
hypothetical protein | 744 | 745 ctx | neighborhood:732 |
Rv3807c |
decaprenylphosphoryl-5-phosphoribose phosphatase | 879 | 650 | database:500 textmining:670 |
Rv2482c plsB2 |
glycerol-3-phosphate acyltransferase | 644 | 603 | database:549 |
Rv1551 plsB1 |
acyltransferase PlsB | 619 | 602 | database:549 |
Rv1501 hyp |
hypothetical protein | 600 | 586 | database:463 |
Rv2036 hyp |
hypothetical protein | 577 | 578 ctx | neighborhood:500 |
Rv1310 atpD |
ATP synthase subunit beta | 573 | 558 | database:538 |
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: decaprenylphosphoryl-beta-D-ribose oxidase
- MTBC0 PGAP product: decaprenylphospho-beta-D-ribofuranose 2-dehydrogenase DprE1
- Pfam (hmmscan --cut_ga): FAD_binding_4 PF01565.29 (E=2e-24), ALO PF04030.20 (E=4e-07)
- (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_218307.1)
- Domains: Pfam-A via hmmscan --cut_ga — FAD_binding_4 (PF01565.29), ALO (PF04030.20)
- 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
COG0277 - Curated reference: UniProt P9WJF1 (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 —
47 functional partner(s); context anchor
dprE2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004018|Rv3790|dprE1 MLSVGATTTATRLTGWGRTAPSVANVLRTPDAEMIVKAVARVAESGGGRGAIARGLGRSYGDNAQNGGGLVIDMTPLNTIHSIDADTKLVDIDAGVNLDQLMKAALPFGLWVPVLPGTRQVTVGGAIACDIHGKNHHSAGSFGNHVRSMDLLTADGEIRHLTPTGEDAELFWATVGGNGLTGIIMRATIEMTPTSTAYFIADGDVTASLDETIALHSDGSEARYTYSSAWFDAISAPPKLGRAAVSRGRLATVEQLPAKLRSEPLKFDAPQLLTLPDVFPNGLANKYTFGPIGELWYRKSGTYRGKVQNLTQFYHPLDMFGEWNRAYGPAGFLQYQFVIPTEAVDEFKKIIGVIQASGHYSFLNVFKLFGPRNQAPLSFPIPGWNICVDFPIKDGLGKFVSELDRRVLEFGGRLYTAKDSRTTAETFHAMYPRVDEWISVRRKVDPLRVFASDMARRLELL