Fjoh_1584 encodes the homodimeric geranylgeranylglyceryl phosphate synthase of Flavobacterium johnsoniae UW101. This group II TIM-barrel enzyme transfers a C20 geranylgeranyl group to sn-glycerol-1-phosphate to form an ether-linked glycerophosphate. The Ile90 side chain helps restrict donor-chain length; replacing it with alanine permits heptaprenyl substrate use. The physiological role and downstream fate of the native C20 product remain unresolved.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000107 imidazoleglycerol-phosphate synthase activity | IEA GO_REF:0000118 | REMOVE | Summary: The TreeGrafter HisF reaction is inappropriate for this characterized GGGPS. Reason: GO:0000107 catalyzes the glutamine-dependent histidine-biosynthetic reaction, whereas the characterized target transfers geranylgeranyl to glycerol phosphate. PMID:24684232 identifies HisF through structural similarity, not shared catalysis; curated target FUNCTION evidence specifies GGGPS chemistry. The PTN001846602 TreeGrafter transfer across divergent TIM-barrel activities is inappropriate. This does not assert that a negative HisF assay was performed. Supporting Evidence: file:FLAJ1/Fjoh_1584/Fjoh_1584-uniprot.txt Prenyltransferase that catalyzes the transfer of the geranylgeranyl moiety of geranylgeranyl diphosphate (GGPP) to the C3 hydroxyl of sn-glycerol-1-phosphate (G1P). file:analysis/module_audits/bacterial_heptaprenylglyceryl_ether_lipid/comparative-members/PMID24684232-fulltext-scope.md The article identifies HisF as a structural relative, not an equivalent catalytic activity. |
| GO:0000287 magnesium ion binding | IEA GO_REF:0000120 | ACCEPT | Summary: Magnesium supports the catalytic prenyl-transfer mechanism. Reason: The curated HAMAP cofactor assignment and conserved Mg-binding features support magnesium as the catalytic metal. This is a mechanistic family inference, not a claim that magnesium occupancy was directly measured in this target crystal. The full 2014 study reports no magnesium density in the groupII structures and treats its position as modeled; the accepted binding function rests on catalytic-family inference, not crystal occupancy. Supporting Evidence: file:FLAJ1/Fjoh_1584/Fjoh_1584-uniprot.txt Name=Mg(2+); Xref=ChEBI:CHEBI:18420; |
| GO:0005737 cytoplasm | IEA GO_REF:0000002 | UNDECIDED | Summary: The target cellular location is not independently established by the available sources. Reason: Cytoplasm is compatible with the soluble TIM-barrel enzyme, but neither the publisher full text of PMID:24684232 nor the curated target record establishes native localization. Recombinant purification and structure do not locate the protein in UW101, and absence of a transmembrane segment does not settle its cellular site. Unlike B. subtilis PcrB, this target lacks an explicit cytosolic-pathway placement. UNDECIDED records unresolved localization, not failed full-text access. Supporting Evidence: file:FLAJ1/Fjoh_1584/Fjoh_1584-uniprot.txt Belongs to the GGGP/HepGP synthase family. Group II subfamily. |
| GO:0006650 glycerophospholipid metabolic process | IEA GO_REF:0000002 | MODIFY | Summary: The supported glycerophospholipid reaction is biosynthetic. Reason: The characterized transfer of geranylgeranyl to glycerol phosphate directly synthesizes an O-alkyl glycerophosphate. GO:0046474 includes that monoether product and is the supported biosynthetic descendant already carried by this gene. This refinement concerns the enzyme reaction, without inferring downstream native product processing. Proposed replacements: glycerophospholipid biosynthetic process Supporting Evidence: file:FLAJ1/Fjoh_1584/Fjoh_1584-uniprot.txt Prenyltransferase that catalyzes the transfer of the geranylgeranyl moiety of geranylgeranyl diphosphate (GGPP) to the C3 hydroxyl of sn-glycerol-1-phosphate (G1P). PMID:24684232 family enzymes catalyse the formation of an ether bond between glycerol-1-phosphate and polyprenyl diphosphates |
| GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups | IEA GO_REF:0000002 | MODIFY | Summary: The prenyl-transfer activity is known at substrate-resolved specificity. Reason: The curated experimental FUNCTION statement specifies transfer of geranylgeranyl from GGPP to sn-glycerol-1-phosphate. Refine the correct broad alkyl-transfer activity to the already annotated substrate-resolved descendant GO:0047294. The wild-type C20 specificity is distinguished from engineered I90A acceptance of HepPP. Proposed replacements: phosphoglycerol geranylgeranyltransferase activity Supporting Evidence: file:FLAJ1/Fjoh_1584/Fjoh_1584-uniprot.txt Prenyltransferase that catalyzes the transfer of the geranylgeranyl moiety of geranylgeranyl diphosphate (GGPP) to the C3 hydroxyl of sn-glycerol-1-phosphate (G1P). PMID:24684232 family enzymes catalyse the formation of an ether bond between glycerol-1-phosphate and polyprenyl diphosphates |
| GO:0046474 glycerophospholipid biosynthetic process | IEA GO_REF:0000104 | ACCEPT | Summary: Ether formation directly synthesizes an O-alkyl glycerophosphate lipid. Reason: GO:0046474 includes glycerophosphate derivatives bearing at least one O-alkyl group. The characterized GGGPS reaction directly forms that ether-linked product and therefore performs the biosynthetic step. Native downstream processing and the physiological role of the C20 product remain unresolved. Supporting Evidence: file:FLAJ1/Fjoh_1584/Fjoh_1584-uniprot.txt Prenyltransferase that catalyzes the transfer of the geranylgeranyl moiety of geranylgeranyl diphosphate (GGPP) to the C3 hydroxyl of sn-glycerol-1-phosphate (G1P). PMID:24684232 family enzymes catalyse the formation of an ether bond between glycerol-1-phosphate and polyprenyl diphosphates |
| GO:0047294 phosphoglycerol geranylgeranyltransferase activity | EXP PMID:24684232 A comprehensive analysis of the geranylgeranylglyceryl phosp... | ACCEPT | Summary: The specific ether-forming prenyltransferase reaction is supported. Reason: PMID:24684232 characterizes bacterial group II GGGPS, including fjGGGPS, and the curated target FUNCTION statement specifies the C20 GGPP/G1P reaction. Figure 5 distinguishes engineered I90A acceptance of HepPP from wild type; that mutant capacity does not establish native C35 synthesis. Supporting Evidence: file:FLAJ1/Fjoh_1584/Fjoh_1584-uniprot.txt Prenyltransferase that catalyzes the transfer of the geranylgeranyl moiety of geranylgeranyl diphosphate (GGPP) to the C3 hydroxyl of sn-glycerol-1-phosphate (G1P). file:analysis/module_audits/bacterial_heptaprenylglyceryl_ether_lipid/comparative-members/PMID24684232-fulltext-scope.md The I90A mutant clearly accepted HepPP as substrate, in contrast to the wild-type enzyme |
| GO:0047294 phosphoglycerol geranylgeranyltransferase activity | IEA GO_REF:0000120 | ACCEPT | Summary: The specific ether-forming prenyltransferase reaction is supported. Reason: The electronic substrate-specific claim agrees with the target experimental row and curated FUNCTION statement linked to PMID:24684232. Acceptance rests on this independent characterization, not on ARBA alone. The engineered I90A HepPP result does not extend wild-type specificity to C35. Supporting Evidence: file:FLAJ1/Fjoh_1584/Fjoh_1584-uniprot.txt Prenyltransferase that catalyzes the transfer of the geranylgeranyl moiety of geranylgeranyl diphosphate (GGPP) to the C3 hydroxyl of sn-glycerol-1-phosphate (G1P). file:analysis/module_audits/bacterial_heptaprenylglyceryl_ether_lipid/comparative-members/PMID24684232-fulltext-scope.md The I90A mutant clearly accepted HepPP as substrate, in contrast to the wild-type enzyme |
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Download this section (compressed HTML)Q: What is the native role of the C20 GGGP product, and which enzymes use it in UW101?
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: The physiological function and downstream fate of the native C20 ether product in F. johnsoniae are unresolved.
OPEN BIOLOGY BP_DARK
What is known: The C20 ether-forming reaction is established in biochemical assays. Its native cellular role, product abundance, and downstream transformations in F. johnsoniae UW101 remain unresolved.
What would resolve it: Identify native lipid products and perturb downstream candidate genes, coupling lipidomics to rescue and envelope phenotypes.
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