ubiB encodes an inner-membrane-anchored member of the UbiB/ABC1 atypical protein-kinase-like family that is required for aerobic ubiquinone biosynthesis. Characterized UbiB-family homologs lack canonical protein kinase activity in trans and instead hydrolyze ATP and interact with lipid ubiquinone intermediates. For PP_5013, this ATP-dependent accessory role is inferred from conserved family architecture, orthology, and pathway context; the Pseudomonas putida protein itself has not been assayed.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004672 protein kinase activity | IEA GO_REF:0000104 | MODIFY | Summary: The UbiB protein-kinase-like fold does not establish canonical protein kinase activity. Characterized COQ8/Coq8 homologs lack trans protein kinase activity and instead show ATP hydrolysis activity. Reason: ATP hydrolysis is the experimentally supported family activity, whereas PP_5013 has no direct enzymatic characterization. The replacement is therefore a strong family-level inference rather than a target-specific assay result. Proposed replacements: ATP hydrolysis activity Supporting Evidence: PMID:27499294 Although COQ8 was predicted to be a protein kinase, we demonstrate that it lacks canonical protein kinase activity in trans. PMID:27499294 Instead, COQ8 has ATPase activity and interacts with lipid CoQ intermediates, functions that are likely conserved across all domains of life. |
| GO:0005886 plasma membrane | IEA GO_REF:0000120 | ACCEPT | Summary: Plasma-membrane localization is consistent with the predicted single-pass inner-membrane topology of PP_5013. Reason: UniProt/HAMAP places UbiB in the bacterial inner membrane and predicts a C-terminal transmembrane helix; this topology has not been measured in P. putida. Supporting Evidence: file:PSEPK/ubiB/ubiB-uniprot.txt Cell inner membrane file:PSEPK/ubiB/ubiB-uniprot.txt Single-pass membrane protein |
| GO:0006744 ubiquinone biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: Ubiquinone biosynthesis is the conserved core process of bacterial UbiB proteins. Reason: E. coli ubiB disruption abolishes CoQ accumulation, and PP_5013 is a conserved UbiB-family ortholog in the P. putida ubiquinone pathway. This supports pathway requirement, not assignment of the blocked hydroxylase reaction to UbiB itself. Supporting Evidence: PMID:10960098 Both the P. stuartii aarF and E. coli ubiB (yigR) disruption mutant strains lack CoQ and accumulate octaprenylphenol. file:PSEPK/ubiB/ubiB-deep-research-openscientist.md There is no published enzymatic assay, structure, knockout phenotype, or CoQ-profiling study specific to PP_5013/A0A140FWS4. |
| GO:0010795 regulation of ubiquinone biosynthetic process | IEA GO_REF:0000104 | MARK AS OVER ANNOTATED | Summary: A specific regulatory role, especially regulation of UbiI activity, is more precise than the available evidence supports. Reason: UbiB is a required ATP-dependent pathway accessory factor, but neither a direct UbiI target nor the coupling between nucleotide turnover and pathway assembly has been established for PP_5013. GO:0006744 captures the defensible pathway role without asserting a regulatory mechanism. Supporting Evidence: file:PSEPK/ubiB/ubiB-uniprot.txt Is probably a protein kinase regulator of UbiI activity file:PSEPK/ubiB/ubiB-deep-research-openscientist.md The precise molecular "output" of UbiB remains debated even in model organisms. |
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Download this section (compressed HTML)Q: Does PP_5013 primarily couple ATP hydrolysis to lipid-intermediate handling, pathway-complex assembly, or an unresolved small-molecule phosphotransfer reaction?
Experiment: Delete and complement PP_5013 in P. putida, profile ubiquinone and pathway intermediates, and assay purified UbiB for membrane- or intermediate-stimulated ATP hydrolysis.
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