PgsA (PP_4097; UniProt Q88FJ8) is the Pseudomonas putida KT2440 CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase. It is a four-helix integral membrane protein of the CDP-alcohol phosphatidyltransferase class-I family that transfers the phosphatidyl group of CDP-diacylglycerol to sn-glycerol 3-phosphate, forming phosphatidylglycerol phosphate. This is the first, committed step of phosphatidylglycerol synthesis, which in turn supplies cardiolipin synthesis. Phosphatidylglycerol and cardiolipin are major KT2440 membrane lipids.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005737 cytoplasm | IEA GO_REF:0000117 | REMOVE | Summary: ARBA-assigned cytoplasm conflicts with the four-helix membrane topology of PgsA. Reason: Phobius predicts four transmembrane helices, and the family (CDP-alcohol phosphatidyltransferase class-I) contains integral membrane enzymes whose donor substrate CDP-diacylglycerol is a bilayer lipid. No soluble form is known. This machine-learned row has no supporting feature in the entry, while the plasma membrane row gives the correct compartment. Supporting Evidence: file:PSEPK/pgsA/pgsA-uniprot.txt TRANSMEM 6..23 file:PSEPK/pgsA/pgsA-uniprot.txt TRANSMEM 157..176 file:PSEPK/pgsA/pgsA-uniprot.txt IPR043130; CDP-OH_PTrfase_TM_dom. |
| GO:0005886 plasma membrane | IEA GO_REF:0000118 | ACCEPT | Summary: Plasma membrane is the correct compartment for this multi-pass phosphatidyltransferase. Reason: Phobius predicts four transmembrane helices and the protein has the CDP-alcohol phosphatidyltransferase transmembrane domain. The E. coli orthologue is an experimentally located inner-membrane protein. In a Gram-negative bacterium, plasma membrane is the GO term for the inner membrane. Supporting Evidence: file:PSEPK/pgsA/pgsA-uniprot.txt TRANSMEM 6..23 file:PSEPK/pgsA/pgsA-uniprot.txt IPR043130; CDP-OH_PTrfase_TM_dom. |
| GO:0008444 CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity | IEA GO_REF:0000120 | ACCEPT | Summary: The specific CDP-diacylglycerol--glycerol-3-phosphate phosphatidyltransferase activity. Reason: Family-level support. Q88FJ8 matches the substrate-specific NCBIfam TIGR00560 pgsA model and the InterPro phosphatidylglycerophosphate synthase family (IPR004570), within the CDP-alcohol phosphatidyltransferase class-I family (Pfam PF01066, PROSITE PS00379). These classifiers define EC 2.7.8.5, which is experimentally established for E. coli PgsA. No enzyme assay on the KT2440 protein is available. Supporting Evidence: file:PSEPK/pgsA/pgsA-uniprot.txt TIGR00560; pgsA; 1. file:PSEPK/pgsA/pgsA-uniprot.txt IPR004570; Phosphatidylglycerol_P_synth. |
| GO:0008610 lipid biosynthetic process | IEA GO_REF:0000117 | MODIFY | Summary: Lipid biosynthetic process is correct but a broad ancestor of phosphatidylglycerol biosynthesis. Reason: The specific supported process is phosphatidylglycerol biosynthetic process. Proposed replacements: phosphatidylglycerol biosynthetic process Supporting Evidence: file:PSEPK/pgsA/pgsA-uniprot.txt IPR004570; Phosphatidylglycerol_P_synth. |
| GO:0008654 phospholipid biosynthetic process | IEA GO_REF:0000120 | MODIFY | Summary: Phospholipid biosynthetic process is correct but a broad ancestor of phosphatidylglycerol biosynthesis. Reason: The specific supported process is phosphatidylglycerol biosynthetic process. Proposed replacements: phosphatidylglycerol biosynthetic process Supporting Evidence: file:PSEPK/pgsA/pgsA-uniprot.txt IPR004570; Phosphatidylglycerol_P_synth. |
| GO:0016020 membrane | IEA GO_REF:0000120 | MODIFY | Summary: Membrane is correct but less specific than plasma membrane. Reason: The specific location, plasma (inner) membrane, is already carried by this gene. Proposed replacements: plasma membrane Supporting Evidence: file:PSEPK/pgsA/pgsA-uniprot.txt IPR043130; CDP-OH_PTrfase_TM_dom. |
| GO:0016780 phosphotransferase activity, for other substituted phosphate groups | IEA GO_REF:0000120 | MODIFY | Summary: The generic phosphotransferase parent is correct but less specific than the PGP synthase activity. Reason: GO:0008444 is the specific descendant supported by the pgsA family assignment. Proposed replacements: CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase activity Supporting Evidence: file:PSEPK/pgsA/pgsA-uniprot.txt TIGR00560; pgsA; 1. |
| GO:0019637 organophosphate metabolic process | IEA GO_REF:0000117 | MODIFY | Summary: Organophosphate metabolic process is correct but a broad ancestor of phosphatidylglycerol biosynthesis. Reason: Phosphatidylglycerol biosynthetic process is a descendant of this term and is the specific supported process. Proposed replacements: phosphatidylglycerol biosynthetic process Supporting Evidence: file:PSEPK/pgsA/pgsA-uniprot.txt IPR004570; Phosphatidylglycerol_P_synth. |
| GO:0036094 small molecule binding | IEA GO_REF:0000117 | MARK AS OVER ANNOTATED | Summary: Small molecule binding restates substrate binding during catalysis rather than a function. Reason: PgsA binds sn-glycerol 3-phosphate only as a substrate during phosphatidyl transfer. No binding role separate from catalysis is known, so this machine-learned binding annotation claims more than the catalytic evidence supports. The molecular function is captured by GO:0008444. Supporting Evidence: file:PSEPK/pgsA/pgsA-uniprot.txt PS00379; CDP_ALCOHOL_P_TRANSF; 1. |
| GO:0046474 glycerophospholipid biosynthetic process | IEA GO_REF:0000118 | MODIFY | Summary: Glycerophospholipid biosynthetic process is correct but less specific than phosphatidylglycerol biosynthesis. Reason: TreeGrafter transfers the generic term placed at the PTHR14269 phosphatidyltransferase root (see the PTHR14269 family review). For PgsA the specific descendant is phosphatidylglycerol biosynthetic process. This matches the treatment of the same row on E. coli PgsA. Proposed replacements: phosphatidylglycerol biosynthetic process Supporting Evidence: file:PSEPK/pgsA/pgsA-uniprot.txt IPR004570; Phosphatidylglycerol_P_synth. |
| GO:0050793 regulation of developmental process | IEA GO_REF:0000117 | REMOVE | Summary: Regulation of developmental process is not supported for this bacterial phosphatidyltransferase. Reason: This ARBA prediction has no basis in the domain content or the biology of a bacterial membrane-lipid biosynthetic enzyme. Bacteria have no developmental program to which a PGP synthase is known to contribute regulation. Supporting Evidence: file:PSEPK/pgsA/pgsA-uniprot.txt TIGR00560; pgsA; 1. |
| GO:0006655 phosphatidylglycerol biosynthetic process | ISS PMID:3003065 Structure and expression of the gene locus encoding the phos... | NEW | Summary: Phosphatidylglycerol biosynthesis, by similarity to E. coli PgsA. Reason: Q88FJ8 matches the substrate-specific pgsA family models (NCBIfam TIGR00560, InterPro IPR004570) that include E. coli PgsA, whose gene product is the experimentally defined PGP synthase. The KT2440 lipid study places pgsA at the head of the PG branch. No GOA row gives the specific pathway process, which the broader rows below are refined to. Supporting Evidence: PMID:3003065 This paper presents definitive results which establishes a direct gene-protein product relationship between the pgsA gene and the phosphatidylglycerophosphate synthase of Escherichia coli. file:PSEPK/pgsA/pgsA-uniprot.txt TIGR00560; pgsA; 1. PMID:21895997 pgsA– CDP‐diacylglycerol‐glycerol‐3‐phosphate‐3‐phosphatidyltransferase |
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Experiment: Quantify phosphatidylglycerol phosphate, phosphatidylglycerol and cardiolipin after conditional pgsA depletion by targeted lipidomics.
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