ubiE (PP_5011) encodes the ubiquinone/menaquinone biosynthesis C-methyltransferase UbiE (MenG/UbiE family of class I SAM-dependent methyltransferases). It transfers a methyl group from S-adenosyl-L-methionine to C-2 of 2-methoxy-6-polyprenyl-1,4-benzoquinol, the ring C-methylation of ubiquinone biosynthesis, between the UbiH and Coq7 hydroxylations. ubiE is the first gene of a ubiE-ubiJ-ubiB cluster (PP_5011-PP_5013). In Escherichia coli UbiE also methylates demethylmenaquinol, but Pseudomonas putida KT2440 has no menaquinone pathway and uses ubiquinone-9 as its sole respiratory quinone. Function is inferred from the family and E. coli UbiE; the KT2440 protein has not been assayed.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0006744 ubiquinone biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: Core process. UbiE catalyses the ring C-methylation step. Reason: UbiE performs a pathway step. E. coli ubiE mutants cannot carry out the C-methylation and accumulate 2-octaprenyl-6-methoxy-1,4-benzoquinone. PAINT places GO:0006744 at the proteobacterial UbiE/COQ5 node PTN001297884 (seeds include E. coli UbiE). Supporting Evidence: file:PSEPK/ubiE/ubiE-uniprot.txt Methyltransferase required for the conversion of demethylmenaquinol (DMKH2) to menaquinol (MKH2) and the conversion of 2-polyprenyl-6-methoxy-1,4-benzoquinol (DDMQH2) to 2-polyprenyl-3-methyl-6-methoxy-1,4-benzoquinol (DMQH2). PMID:9045837 E. coli strains containing either the disruption or the point mutation in ubiE accumulated 2-octaprenyl-6-methoxy-1,4-benzoquinone and demethylmenaquinone as predominant intermediates. |
| GO:0008168 methyltransferase activity | IEA GO_REF:0000120 | MODIFY | Summary: Family-level methyltransferase activity. True but general; refine to the specific C-methyltransferase activity carried by this gene. Reason: Correct but less specific than the evidence supports. The ubiquinone C-methylation (GO:0008425) is the physiological activity in KT2440 and is already carried. Proposed replacements: 2-methoxy-6-polyprenyl-1,4-benzoquinol methyltransferase activity Supporting Evidence: file:PSEPK/ubiE/ubiE-uniprot.txt Reaction=a 2-methoxy-6-(all-trans-polyprenyl)benzene-1,4-diol + S- adenosyl-L-methionine = a 5-methoxy-2-methyl-3-(all-trans- polyprenyl)benzene-1,4-diol + S-adenosyl-L-homocysteine + H(+); |
| GO:0008425 2-methoxy-6-polyprenyl-1,4-benzoquinol methyltransferase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Core molecular function (RHEA:28286, EC 2.1.1.201). Reason: Q88D17 is a HAMAP MF_01813 / TIGR01934 UbiE with the conserved SAM-binding positions; E. coli UbiE is required for the C-methylation; and the PAINT IBD for GO:0008425 at PTN001297884 is seeded by E. coli UbiE. In KT2440 the substrate is made by UbiH (PP_5199). Supporting Evidence: file:PSEPK/ubiE/ubiE-uniprot.txt Reaction=a 2-methoxy-6-(all-trans-polyprenyl)benzene-1,4-diol + S- adenosyl-L-methionine = a 5-methoxy-2-methyl-3-(all-trans- polyprenyl)benzene-1,4-diol + S-adenosyl-L-homocysteine + H(+); PMID:9045837 The data presented identify the E. coli UbiE polypeptide and provide evidence that it is required for the C methylation reactions in both ubiquinone and menaquinone biosynthesis. |
| GO:0009060 aerobic respiration | IEA GO_REF:0000104 | MARK AS OVER ANNOTATED | Summary: UniRule process term. UbiE makes the respiratory quinone but does not itself take part in respiratory electron transfer. Reason: Ubiquinone is needed for aerobic respiration, and E. coli ubiE mutants grow poorly on succinate, but that is a downstream requirement for the product. UbiE performs no step of respiration itself; its process is ubiquinone biosynthesis (accepted). Supporting Evidence: PMID:9045837 Disruption of o251 in a wild-type parental strain produced a mutant with defects in growth on succinate and in both ubiquinone and menaquinone synthesis. |
| GO:0009234 menaquinone biosynthetic process | IEA GO_REF:0000120 | REMOVE | Summary: HAMAP rule transfer of the E. coli dual role. Wrong for KT2440, which has no menaquinone pathway. Reason: The HAMAP rule MF_01813 is unconditional and transfers menaquinone biosynthesis to every MenG/UbiE member. KT2440 lacks the upstream menaquinone genes (menA and menD searches return no hits) and makes no menaquinone, so PP_5011 cannot take part in the process in this organism. This is an over-propagated rule annotation, not a statement about the protein's chemistry (see the GO:0043770 row). Supporting Evidence: file:projects/P_PUTIDA/deep-research/PSEPK__ubiquinone_biosynthesis__ppu00130-deep-research-openscientist.md not present in KT2440 (proteome searches for *menA* and *menD* return zero hits) |
| GO:0042181 ketone biosynthetic process | IEA GO_REF:0000117 | MODIFY | Summary: ARBA ketone biosynthetic process, an ancestor of ubiquinone biosynthesis. True but uninformative. Reason: GO:0042181 is an is_a ancestor of GO:0006744 ubiquinone biosynthetic process, which is supported and accepted for this gene. Refine to that term. Proposed replacements: ubiquinone biosynthetic process Supporting Evidence: PMID:9045837 The data presented identify the E. coli UbiE polypeptide and provide evidence that it is required for the C methylation reactions in both ubiquinone and menaquinone biosynthesis. |
| GO:0043770 demethylmenaquinone methyltransferase activity | IEA GO_REF:0000120 | MARK AS OVER ANNOTATED | Summary: The E. coli ortholog has this activity, but KT2440 makes no demethylmenaquinol, so the activity has no physiological substrate in this organism. Reason: E. coli UbiE methylates both quinones, and PP_5011 may well retain the chemistry, so the activity is not contradicted. But KT2440 lacks the menaquinone pathway that would supply demethylmenaquinol. The capacity is plausible yet untested and without a substrate in vivo, so it is not a function of the protein in this organism. Supporting Evidence: PMID:9045837 The data presented identify the E. coli UbiE polypeptide and provide evidence that it is required for the C methylation reactions in both ubiquinone and menaquinone biosynthesis. file:projects/P_PUTIDA/deep-research/PSEPK__ubiquinone_biosynthesis__ppu00130-deep-research-openscientist.md not present in KT2440 (proteome searches for *menA* and *menD* return zero hits) |
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Experiment: Delete PP_5011 in KT2440 and look for accumulation of 2-nonaprenyl-6-methoxy-1,4-benzoquinol; assay purified PP_5011 with SAM on both the ubiquinone and demethylmenaquinone substrates.
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