ubiD (PP_5213) encodes 3-octaprenyl-4-hydroxybenzoate carboxy-lyase (UbiD family, EC 4.1.1.98), a homohexameric decarboxylase that requires prenylated FMN (made by UbiX, PP_0548) and a divalent metal ion (Mn2+). It converts 4-hydroxy-3-polyprenylbenzoate to 2-polyprenylphenol, the third step of ubiquinone biosynthesis, following UbiA prenylation. The enzyme is predicted to associate peripherally with the cytoplasmic face of the inner membrane, where its prenylated substrate resides. Function is inferred from the UbiD family and Escherichia coli genetics; the KT2440 protein has not been assayed.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005737 cytoplasm | IEA GO_REF:0000118 | MODIFY | Summary: TreeGrafter cytoplasm, inherited from the PTHR30108 root IBD at PTN000764648 (seed E. coli UbiD). True but general; the gene also carries the more specific cytosol term. Reason: UbiD is a soluble-fold homohexamer that acts from the cytoplasmic side of the membrane, so cytoplasm is correct but general. The more specific cytosol term (GO:0005829) is carried by this gene from the same TreeGrafter source, and is the refinement. Proposed replacements: cytosol Supporting Evidence: file:PSEPK/ubiD/ubiD-uniprot.txt SUBUNIT: Homohexamer. {ECO:0000255|HAMAP-Rule:MF_01636}. file:PSEPK/ubiD/ubiD-uniprot.txt SUBCELLULAR LOCATION: Cell membrane {ECO:0000255|HAMAP-Rule:MF_01636}; Peripheral membrane protein {ECO:0000255|HAMAP-Rule:MF_01636}. |
| GO:0005829 cytosol | IEA GO_REF:0000118 | ACCEPT | Summary: TreeGrafter cytosol from the bacterial UbiD node PTN000764659 (PAINT IBD seeded by E. coli UbiD, P0AAB4). Accepted as the core location, as for the E. coli exemplar. Reason: The PAINT curator placed cytosol on the bacterial UbiD node from E. coli UbiD data: E. coli UbiD is in the cytosolic proteome and much of its decarboxylase activity is recovered in the soluble fraction. PP_5213 has the same non-transmembrane hexameric UbiD fold and no experimental location of its own, so the inherited cytosol location is the best-supported one. UbiD is not one of the seven proteins of the E. coli Ubi metabolon, so this rests on the UbiD data alone. Supporting Evidence: file:PSEPK/ubiD/ubiD-uniprot.txt SUBUNIT: Homohexamer. {ECO:0000255|HAMAP-Rule:MF_01636}. PMID:782527 It was found that a considerable proportion of the carboxylyase activity could be separated from the membrane fraction in cell extracts prepared using a French press. |
| GO:0005886 plasma membrane | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: HAMAP MF_01636 places UbiD as a peripheral protein of the cell (inner) membrane. Kept as a plausible but untested, non-core location, as for the E. coli exemplar. Reason: The UbiD substrate, 3-polyprenyl-4-hydroxybenzoate, is the first membrane-bound intermediate made by the integral membrane UbiA, so a peripheral, substrate-driven association with the inner membrane is plausible, and the curated rule assigns it; no transmembrane segment is predicted. The rule rests on the E. coli inference of Leppik et al., and the purified E. coli enzyme is soluble. Not tested for PP_5213, so the membrane is kept as non-core and cytosol is the core location. Supporting Evidence: file:PSEPK/ubiD/ubiD-uniprot.txt SUBCELLULAR LOCATION: Cell membrane {ECO:0000255|HAMAP-Rule:MF_01636}; Peripheral membrane protein {ECO:0000255|HAMAP-Rule:MF_01636}. file:PSEPK/ubiA/ubiA-uniprot.txt generating the first membrane-bound Q intermediate 3-octaprenyl-4-hydroxybenzoate. |
| GO:0006744 ubiquinone biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: Core process. UbiD catalyses the decarboxylation step of the pathway. Reason: UbiD performs a pathway step. In E. coli UbiD and UbiX are both required for the decarboxylation of 4-hydroxy-3-octaprenylbenzoate, and the PAINT IBD for GO:0006744 at the bacterial UbiD node PTN000764659 is seeded by E. coli UbiD. Supporting Evidence: file:PSEPK/ubiD/ubiD-uniprot.txt Catalyzes the decarboxylation of 3-octaprenyl-4-hydroxy benzoate to 2-octaprenylphenol, an intermediate step in ubiquinone biosynthesis. PMID:17889824 Our results suggest that both UbiX and UbiD are required for the decarboxylation of 4-hydroxy-3-octaprenyl-benzoate in E. coli coenzyme Q biosynthesis, especially during logarithmic growth. |
| GO:0008694 4-hydroxy-3-polyprenylbenzoate decarboxylase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Core molecular function (RHEA:41680, EC 4.1.1.98), chain-length neutral as defined. Reason: Q88CG8 is a HAMAP MF_01636 / InterPro IPR023677 bacterial UbiD with the conserved prFMN-binding positions and HAMAP active site. The UbiD/UbiX pair forms a two-component prFMN-dependent decarboxylase system. GO:0008694 is defined on a generic all-trans-polyprenyl substrate, matching the nonaprenyl intermediate of KT2440, and is the IBD at PAINT node PTN000764659. Supporting Evidence: file:PSEPK/ubiD/ubiD-uniprot.txt Reaction=a 4-hydroxy-3-(all-trans-polyprenyl)benzoate + H(+) = a 2- (all-trans-polyprenyl)phenol + CO2; PMID:25647642 Our results suggest that UbiX and UbiD constitute a similar two-component decarboxylase system and that the same flavin-based cofactor is necessary for the biosynthesis of ubiquinone. file:PSEPK/ubiD/ubiD-deep-research-openscientist.md The enzyme is catalytically inert as a bare apoprotein. |
| GO:0016831 carboxy-lyase activity | IEA GO_REF:0000120 | MODIFY | Summary: Family-level carboxy-lyase activity (InterPro IPR002830, PAINT IBD at the PTHR30108 root PTN000764648). True but general; refine to the specific decarboxylase. Reason: The PTHR30108 family includes decarboxylases with different substrates (UbiD, Fdc1 ferulic acid decarboxylase), which is why PAINT places only carboxy-lyase activity at the root. Q88CG8 is in the bacterial UbiD clade, where the specific activity GO:0008694 is supported and already carried. Proposed replacements: 4-hydroxy-3-polyprenylbenzoate decarboxylase activity Supporting Evidence: file:PSEPK/ubiD/ubiD-uniprot.txt Catalyzes the decarboxylation of 3-octaprenyl-4-hydroxy benzoate to 2-octaprenylphenol, an intermediate step in ubiquinone biosynthesis. |
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Download this section (compressed HTML)Q: Does Q88CG8 act mainly at the membrane or in a soluble pool, and does it prefer the nonaprenyl substrate of KT2440?
Experiment: Purify Q88CG8 with UbiX-made prFMN and Mn2+, compare decarboxylation of polyprenyl-chain substrate analogues, fractionate KT2440 cells to locate the endogenous protein, and test intermediate accumulation in a PP_5213 deletion.
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