PA4088 is an uncharacterized pyridoxal 5'-phosphate (PLP)-dependent enzyme of Pseudomonas aeruginosa of the class-III aminotransferase fold, in the glutamate-1-semialdehyde aminomutase (GSAM)-like family. Its crystal structure shows PLP bound as a Schiff base to Lys286, and a K286A mutant structure contains pyridoxamine 5'-phosphate. PA4088 is a distant paralog of the canonical P. aeruginosa GSAM HemL (PA3977), sharing only about 27% identity with HemL enzymes, and its close paralog in the same genome is PA5523. Its substrate and reaction are not known; no catalytic activity of the purified protein has been reported in the abstract of the structural study.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0030170 pyridoxal phosphate binding | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN000241365 (GSAM family root, seeded by E. coli HemL and Arabidopsis GSA). Reason: Confirmed directly by the structure, which shows PLP bound to Lys286. Supporting Evidence: PMID:29684343 Continuous electron density indicates the presence of a PLP cofactor with a Schiff base linkage between the PLP cofactor and the Ξ΅-amino group of Lys286 PMID:29684343 A crystal structure of a K286A mutant in complex with PMP is also reported |
| GO:0030170 pyridoxal phosphate binding | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO from the Aminotran_3 domain. Reason: Same claim; shown by the structure. Supporting Evidence: PMID:29684343 Continuous electron density indicates the presence of a PLP cofactor with a Schiff base linkage between the PLP cofactor and the Ξ΅-amino group of Lys286 file:PSEAE/PA4088/PA4088-uniprot.txt PF00202; Aminotran_3 |
| GO:0042286 glutamate-1-semialdehyde 2,1-aminomutase activity | EXP PMID:29684343 Crystal structure of a glutamate-1-semialdehyde-aminomutase ... | MARK AS OVER ANNOTATED | Summary: PseudoCAP EXP GSAM activity citing the crystal structure paper, and a seed of both PTN000241365 (isomerase activity) and PTN000241400 (GSAM activity). The abstract assigns PA4088 to the GSAM family from its structure and calls the gene uncharacterized; no activity assay is described there. Reason: Seed verdict OVER-SPECIFIC. A structure that places a protein in the GSAM-like family and shows bound PLP supports PLP binding, not GSAM activity. P. aeruginosa has a dedicated, reviewed HemL (PA3977, P48247), and PA4088 is only about 27% identical to HemL enzymes, against 66% between the E. coli and P. aeruginosa HemLs. The full text was not read, so the row is not removed. Supporting Evidence: PMID:29684343 we crystallized the expression product of the uncharacterized pa4088 gene from the opportunistic pathogen Pseudomonas aeruginosa PAO1 PMID:29684343 The resulting high-resolution structure confirms it to be a member of the GSAM family file:PSEAE/PA4088/PA4088-bioinformatics/RESULTS.md | E. coli HemL vs PA4088 | 26.9 | file:PSEAE/PA4088/PA4088-bioinformatics/RESULTS.md | E. coli HemL P23893 vs PAO1 HemL P48247 | 65.7 | |
| GO:0042286 glutamate-1-semialdehyde 2,1-aminomutase activity | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: IBA from PTN000241400 (15 leaves, 12 taxa, taxon constraint Proteobacteria), seeded by E. coli HemL P23893 and PA4088 itself. The topology, checked with panther_tree.py on 2026-11-05, is a Proteobacteria SPECIATION node whose 15 leaves are all PTHR43713:SF3 and 13 of which are named hemL; PA4088 sits in a Pseudomonas-specific DUPLICATION (PTN002463962) with PA5523 and PAO1 HemL (P48247). Reason: The function is well established for the canonical HemLs at this node, and the node is placed correctly for them. PA4088 reaches the term only as a diverged copy of a Pseudomonas-specific duplication whose sister kept HemL function (P48247): it is about 27% identical to HemL enzymes, versus 66% between HemL orthologs, in an organism that has its own HemL. The transfer to PA4088 is unsupported by anything except PA4088's own questionable seed. Propagation Review Root cause: PROPAGATION BAD Failure modes: WRONG ORTHOLOG OR PARALOG SOURCE EVIDENCE WEAK Sources checked: PANTHER:PTN000241400 Β· PTN000241400 SUPPORTS SOURCE BUT NOT TARGET Proteobacteria SPECIATION node of 15 SF3 leaves, 13 of them named hemL. No child clade separates the Pseudomonas paralogs from PAO1 HemL: PA4088, PA5523 and P48247 are the three children of one DUPLICATION (PTN002463962), so the GSAM IBD cannot be moved off PA4088 and the divergence has to be recorded on the paralog branches themselves. UniProtKB:P23893 Β· E. coli HemL SUPPORTS SOURCE BUT NOT TARGET Sound seed for canonical HemL orthologs; 27% identity to PA4088. UniProtKB:Q9HWU0 Β· PA4088 (self; PseudoCAP EXP seed) SOURCE WEAK OR INFERRED Structure-only paper; activity not described in the abstract. Supporting Evidence: file:PSEAE/PA4088/PA4088-bioinformatics/RESULTS.md | E. coli HemL vs PA4088 | 26.9 | file:PSEAE/PA4088/PA4088-bioinformatics/RESULTS.md | E. coli HemL P23893 vs PAO1 HemL P48247 | 65.7 | PMID:29684343 The resulting high-resolution structure confirms it to be a member of the GSAM family |
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Download this section (compressed HTML)Q: Does the full text of PMID:29684343 report any GSAM (or other aminotransferase) activity assay for purified PA4088?
Experiment: Assay purified PA4088 and PA5523 for glutamate-1-semialdehyde 2,1-aminomutase activity, and screen them against amino donor/acceptor panels typical of class-III aminotransferases; test whether either complements a hemL (PA3977) deletion.
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