liuA (PA2015) encodes isovaleryl-CoA dehydrogenase, the first gene of the liuRABCDE (leucine and isovalerate utilization) cluster of Pseudomonas aeruginosa. LiuA is a FAD-dependent member of the acyl-CoA dehydrogenase family that oxidises isovaleryl-CoA (3-methylbutanoyl-CoA) to 3-methylcrotonyl-CoA, the first of three steps converting isovaleryl-CoA to 3-hydroxy-3-methylglutaryl-CoA in leucine catabolism. The purified recombinant enzyme uses isovaleryl-CoA with a Km of 2.3 microM and also butyryl-CoA, but not isobutyryl-CoA, octanoyl-CoA or the terpene-derived acyl-CoAs citronellyl-CoA and 5-methylhex-4-enoyl-CoA. liuA insertion mutants cannot grow on leucine or isovalerate and, like mutants in the other liu genes, also fail to grow on acyclic terpenes such as citronellol, whose Atu pathway joins the Liu pathway at 3-methylcrotonyl-CoA.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003995 acyl-CoA dehydrogenase activity | IBA GO_REF:0000033 | TOO GENERAL | Summary: Acyl-CoA dehydrogenase activity by IBA from PTN000744030 (14 seeds, including human IVD P26440, SBCAD P45954, SCAD P16219, VLCAD P49748 and ACAD9 Q9H845). Reason: The IBD is sound: the node term is the shared activity of a broad ACAD clade, and every seed is a characterised acyl-CoA dehydrogenase. For LiuA the substrate is known, and GO:0008470 3-methylbutanoyl-CoA dehydrogenase activity, accepted in this review, is_a GO:0003995. Q9I296 in WITH/FROM reflects its own IDA and is expected. Supporting Evidence: PMID:18625020 LiuA purified from recombinant E. coli revealed acyl-CoA dehydrogenase activity with isovaleryl-CoA (KM 2.3 microM) and butyryl-CoA as substrates. |
| GO:0003995 acyl-CoA dehydrogenase activity | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro mapping to acyl-CoA dehydrogenase activity. Reason: Entailed by the accepted GO:0008470 rows. |
| GO:0006552 L-leucine catabolic process | IBA GO_REF:0000033 | ACCEPT | Summary: L-leucine catabolism by IBA from the IVD subclade node PTN005188837. Reason: Isovaleryl-CoA dehydrogenation is a step of leucine catabolism; liuA mutants cannot use leucine or isovalerate, and the purified enzyme acts on isovaleryl-CoA. Supporting Evidence: PMID:18625020 Mutants with insertion in any of the liu genes were unable to utilize acyclic terpenes or leucine/isovalerate and confirmed the importance of the liu genes for catabolism of methyl-branched compounds. file:PSEAE/liuA/liuA-uniprot.txt IPR034183; IVD. |
| GO:0008300 isoprenoid catabolic process | IMP PMID:16517656 The atu and liu clusters are involved in the catabolic pathw... | MARK AS OVER ANNOTATED | Summary: PseudoCAP IMP: the atu and liu clusters are both needed for growth on acyclic monoterpenes of the citronellol family. Not an IBD seed. Reason: Abstract only. The liu cluster is needed for terpene growth, and a complemented liuA mutant fails to grow on terpenes (PMID:18625020). But the Atu pathway enters the Liu pathway at 3-methylcrotonyl-CoA, the product of LiuA, and purified LiuA does not oxidise the terpene-derived acyl-CoAs tested. On the present pathway, LiuA performs no step of terpene catabolism, and the growth defect is unexplained necessity, not demonstrated participation. Contrast liuC and liuE, which act downstream of the entry point and were kept (MODIFY to GO:0016100 and TOO_GENERAL respectively) in their reviews. Supporting Evidence: PMID:18625020 Other acyl-CoA compounds such as isobutyryl-CoA, 3-hydroxybutyryl-CoA, octanoyl-CoA, citronellyl-CoA or 5-methyl-hex-4-enoyl-CoA were not utilized. PMID:16272386 enters that of leucine/isovalerate (Liu, leucine and isovalerate utilization) at the level of methylcrotonyl-CoA |
| GO:0008470 3-methylbutanoyl-CoA dehydrogenase activity | IDA PMID:18625020 Biochemical characterization of isovaleryl-CoA dehydrogenase... | ACCEPT | Summary: PseudoCAP IDA, a seed (via its GO:0003995 parent) of the PTN000744030 IBD. Purified recombinant LiuA dehydrogenates isovaleryl-CoA (Km 2.3 microM) and butyryl-CoA. Reason: Abstract only, but the abstract reports the purified-enzyme assay with kinetics, which is the decisive fact. Seed verdict SOUND. Supporting Evidence: PMID:18625020 LiuA purified from recombinant E. coli revealed acyl-CoA dehydrogenase activity with isovaleryl-CoA (KM 2.3 microM) and butyryl-CoA as substrates. |
| GO:0008470 3-methylbutanoyl-CoA dehydrogenase activity | IEA GO_REF:0000120 | ACCEPT | Summary: EC 1.3.8.4 / ARBA mapping to isovaleryl-CoA dehydrogenase activity. Reason: Same claim as the IDA row. The ARBA-derived protein name on this unreviewed entry calls the bacterial protein "mitochondrial", which is wrong for P. aeruginosa; recorded as a UniProt defect. Supporting Evidence: PMID:18625020 LiuA purified from recombinant E. coli revealed acyl-CoA dehydrogenase activity with isovaleryl-CoA (KM 2.3 microM) and butyryl-CoA as substrates. |
| GO:0008470 3-methylbutanoyl-CoA dehydrogenase activity | IMP PMID:16517656 The atu and liu clusters are involved in the catabolic pathw... | ACCEPT | Summary: PseudoCAP IMP for isovaleryl-CoA dehydrogenase activity from the atu/liu mutagenesis paper; a second seed of the PTN000744030 IBD. Reason: Abstract only. The term is right for LiuA (purified-enzyme evidence in PMID:18625020), so the row's claim stands. The abstract describes growth and metabolite phenotypes of atuF and liuD mutants and does not mention a liuA mutant or an isovaleryl-CoA dehydrogenase assay, so the seed's own basis is UNVERIFIABLE from what can be read. No defect is recorded: the full text may contain the experiment. Supporting Evidence: PMID:16517656 Mutagenesis of the atu and liu clusters showed that both are involved in AMTC and leucine catabolism by encoding the enzymes related to the geranyl-CoA and the 3-methylcrotonyl-CoA pathways, respectively. |
| GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors | IEA GO_REF:0000002 | TOO GENERAL | Summary: Generic CH-CH oxidoreductase activity from ACAD domain InterPro entries. Reason: Entailed by the accepted GO:0008470 rows. |
| GO:0050660 flavin adenine dinucleotide binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: FAD binding from ACAD N-terminal domain InterPro entries. Reason: Acyl-CoA dehydrogenases are FAD flavoproteins, so the term is correct, but it is a cofactor-binding term subsumed in the catalytic function. Supporting Evidence: file:PSEAE/liuA/liuA-uniprot.txt Belongs to the acyl-CoA dehydrogenase family. |
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Download this section (compressed HTML)Q: Why does a complemented liuA mutant fail to grow on acyclic terpenes, when the Atu pathway is thought to join the Liu pathway at 3-methylcrotonyl-CoA, downstream of LiuA, and LiuA does not oxidise the terpene-derived acyl-CoAs tested?
Experiment: Profile acyl-CoA intermediates in a liuA mutant grown on citronellol (with an alternative carbon source) and test purified LiuA against other terpene-derived acyl-CoAs, to find whether LiuA catalyses an unrecognised step of the Atu pathway.
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