PP_0544 is a 12-transmembrane-helix cytoplasmic-membrane permease of the APC (amino acid-polyamine-organocation) superfamily, encoded in Pseudomonas putida KT2440 between the ethanolamine ammonia-lyase genes eutB/eutC and an aldehyde dehydrogenase, next to a sigma-54-dependent regulator. It belongs to the ethanolamine permease family (NCBIfam TIGR00908, InterPro IPR004757; Eat), whose members are encoded beside ethanolamine-catabolism genes, and it is therefore predicted to take up ethanolamine for catabolism to acetaldehyde and ammonia. It is unrelated to the enterobacterial EutH ethanolamine channel, and its transport activity, substrate range and coupling ion have not been measured directly.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005886 plasma membrane | IEA GO_REF:0000044 | ACCEPT | Summary: PP_0544 is a predicted 12-pass plasma-membrane protein. Reason: Phobius predicts twelve helical transmembrane segments (34-56 through 440-457) and the protein belongs to the APC transporter superfamily (InterPro IPR050367, IPR002293; Pfam AA_permease_2), whose bacterial members are cytoplasmic-membrane permeases. In a Gram-negative bacterium a 12-pass APC permease with no outer-membrane beta-barrel signature belongs in the inner (plasma) membrane. The UniProt SUBCELLULAR LOCATION line rests only on an ARBA rule and is not cited; the support is sequence features plus family membership. Supporting Evidence: file:PSEPK/PP_0544/PP_0544-uniprot.txt FT TRANSMEM 34..56 file:PSEPK/PP_0544/PP_0544-uniprot.txt FT TRANSMEM 440..457 file:PSEPK/PP_0544/PP_0544-uniprot.txt DR InterPro; IPR050367; APC_superfamily. |
| GO:0016020 membrane | IEA GO_REF:0000002 | MODIFY | Summary: Generic membrane localization from the IPR002293 transporter-family mapping; correct but less specific than the plasma membrane location the protein already carries. Reason: Correct but general. Twelve predicted TM helices and APC-family membership place PP_0544 in the cytoplasmic (plasma) membrane, which the gene already carries (GO:0005886, SubCell row); replace with that specific term. Proposed replacements: plasma membrane Supporting Evidence: file:PSEPK/PP_0544/PP_0544-uniprot.txt FT TRANSMEM 34..56 file:PSEPK/PP_0544/PP_0544-uniprot.txt FT TRANSMEM 440..457 file:PSEPK/PP_0544/PP_0544-uniprot.txt InterPro; IPR002293; AA/rel_permease1. |
| GO:0022857 transmembrane transporter activity | IEA GO_REF:0000002 | MODIFY | Summary: PP_0544 is a 12-TM APC-superfamily transporter; its specific family model (NCBIfam TIGR00908 / InterPro IPR004757, ethanolamine permease) and conserved eat-eutBC locus predict ethanolamine as the substrate. Reason: The multipass APC-family protein has the specific IPR004757/TIGR00908 ethanolamine-permease classification and lies beside eutBC in KT2440. These are coherent family/locus clues, but not independent transport experiments: the model itself was defined using related gene neighborhoods. Refine the generic MF to predicted ethanolamine transmembrane transport. The reviewed sources do not directly measure PP_0544 transport. In PAO1, the separate Eat/PA4023 deletion retained growth at pH 7.0 and 20 mM ethanolamine, whereas deletion of the transcriptional regulator EatR/PA4021 abolished growth. Regulatory essentiality does not demonstrate transporter specificity, and the Eat result does not exclude transport at limiting substrate or another pH. No substrate charge, coupling ion, rate or universal requirement is inferred. Proposed replacements: ethanolamine transmembrane transporter activity Supporting Evidence: file:PSEPK/PP_0544/PP_0544-uniprot.txt InterPro; IPR004757; EtNH_permease file:PSEPK/PP_0544/PP_0544-bioinformatics/RESULTS.md The three genes used as the seed for this model (from Burkholderia pseudomallei, Pseudomonas aeruginosa and Clostridium acetobutylicum are all adjacent to genes for the catabolism of ethanolamine. Most if not all of the hits to this model have a similar arrangement of genes. file:PSEPK/PP_0544/PP_0544-bioinformatics/RESULTS.md | Q88QF1 | PP_0543 | Ethanolamine ammonia-lyase large subunit (EAL large subunit) (EC 4.3.1.7) | PMID:27325678 This pathway is encoded by the PA4022-eat-eutBC operon and consists of a transport protein (Eat), an ethanolamine-ammonia lyase (EutBC), and an acetaldehyde dehydrogenase (PA4022). file:PSEAE/PA4022/PA4022-source-analysis/primary-assay-scope.yaml The growth of the Ξ eat mutant on ethanolamine was identical to that of wild-type (WT) P. aeruginosa PAO1. |
| GO:0055085 transmembrane transport | IEA GO_REF:0000002 | MODIFY | Summary: A multi-pass APC-family permease participates in transmembrane transport; the predicted substrate is ethanolamine. Reason: The multipass APC-family protein has the specific IPR004757/TIGR00908 ethanolamine-permease classification and lies beside eutBC in KT2440. These are coherent family/locus clues, but not independent transport experiments: the model itself was defined using related gene neighborhoods. Refine the generic transport process to predicted ethanolamine transport; this is substrate-specific reinterpretation rather than an is_a-descendant replacement. The reviewed sources do not directly measure PP_0544 transport. In PAO1, the separate Eat/PA4023 deletion retained growth at pH 7.0 and 20 mM ethanolamine, whereas deletion of the transcriptional regulator EatR/PA4021 abolished growth. Regulatory essentiality does not demonstrate transporter specificity, and the Eat result does not exclude transport at limiting substrate or another pH. No substrate charge, coupling ion, rate or universal requirement is inferred. Proposed replacements: ethanolamine transport Supporting Evidence: file:PSEPK/PP_0544/PP_0544-bioinformatics/RESULTS.md The three genes used as the seed for this model (from Burkholderia pseudomallei, Pseudomonas aeruginosa and Clostridium acetobutylicum are all adjacent to genes for the catabolism of ethanolamine. Most if not all of the hits to this model have a similar arrangement of genes. file:PSEPK/PP_0544/PP_0544-bioinformatics/RESULTS.md | Q88QF1 | PP_0543 | Ethanolamine ammonia-lyase large subunit (EAL large subunit) (EC 4.3.1.7) | PMID:27325678 This pathway is encoded by the PA4022-eat-eutBC operon and consists of a transport protein (Eat), an ethanolamine-ammonia lyase (EutBC), and an acetaldehyde dehydrogenase (PA4022). file:PSEAE/PA4022/PA4022-source-analysis/primary-assay-scope.yaml The growth of the Ξ eat mutant on ethanolamine was identical to that of wild-type (WT) P. aeruginosa PAO1. |
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Download this section (compressed HTML)Q: Does PP_0544 transport protonated ethanolamine, and what coupling ion and substrate range does it use?
Q: Does PP_0544 become important when uncharged ethanolamine is limiting, despite normal growth of a PAO1 eat mutant at pH 7.0 and 20 mM ethanolamine?
Experiment: Measure radiolabeled ethanolamine uptake in wild type, PP_0544 deletion, and complemented strains across pH and ion gradients.
Type: membrane transport assay
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