DadA2 (PA5084) is the second of two DadA-family FAD-dependent D-amino acid dehydrogenases encoded by Pseudomonas aeruginosa PAO1, a paralog of the experimentally characterised DadA1 (PA5304). It carries the complete DadA family signature (HAMAP MF_01202, DAO/FAD-dependent oxidoreductase domain) and is predicted to oxidatively deaminate D-amino acids to 2-oxo acids and ammonia, passing electrons to a membrane acceptor as E. coli DadA does. No experimental study of the PA5084 product has been found. Loss of dadA1 alone abolishes growth on D-alanine and several other D-amino acids as nitrogen source, so DadA2 does not replace DadA1 under those conditions, and its physiological substrates and expression conditions are unknown.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA cytoplasm from the deep DAO-family node PTN000354057 (eukaryotic and bacterial seeds). Reason: DadA-family enzymes lack a signal peptide and act at the cytoplasmic face of the inner membrane, so a cytoplasmic location is plausible; it is not where the function is specifically known to act and there are no data on PA5084 itself. Supporting Evidence: file:PSEAE/dadA2/dadA2-uniprot.txt Belongs to the DadA oxidoreductase family. |
| GO:0005886 plasma membrane | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA plasma membrane from the E. coli DadA seed (P0A6J5, IDA membrane association). Reason: E. coli DadA is membrane-associated and donates electrons to the respiratory chain; DadA2 is in the same HAMAP family, so the membrane association is a reasonable inheritance, but it is untested for PA5084. Supporting Evidence: file:PSEAE/dadA2/dadA2-uniprot.txt Belongs to the DadA oxidoreductase family. |
| GO:0008718 D-amino-acid dehydrogenase activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN008552203 (DadA clade; 3 seeds, 10 leaf IBAs in 8 taxa). Seeds are E. coli DadA (P0A6J5, IDA), P. aeruginosa DadA1 (Q9HTQ0, PseudoCAP IDA, PMID:21378189, sound) and DadA2 itself (PseudoCAP IDA, PMID:17021207, wrong reference). Reason: The node term suits a DadA clade, and the IBD stands on the E. coli DadA and DadA1 seeds without the DadA2 seed. DadA2 carries the full DadA family signature, so inheriting the activity is reasonable. This IBA and the IEA rows are the real support for the term on DadA2; the DadA2 seed itself contributes nothing. Supporting Evidence: file:PSEAE/dadA2/dadA2-uniprot.txt HAMAP; MF_01202; DadA; 1. PMID:21378189 purified recombinant DadA alone was sufficient to demonstrate the proposed enzymatic activity with very broad substrate specificity |
| GO:0008718 D-amino-acid dehydrogenase activity | IDA PMID:17021207 The AauR-AauS two-component system regulates uptake and meta... | ACCEPT | Summary: PseudoCAP IDA for D-amino-acid dehydrogenase activity, citing a paper on the AauR-AauS two-component system of Pseudomonas putida KT2440. This row is a seed of the PTN008552203 IBD. Reason: Full text read. PMID:17021207 studies acidic amino acid uptake and its regulation in P. putida KT2440; it never mentions DadA, PA5084 or any D-amino acid dehydrogenase assay, so it gives no experimental support for this row. The term itself is accepted on the DadA family homology captured by the IBA and IEA rows, not on this citation. Seed verdict WRONG (reference), recorded as a PseudoCAP source defect. Supporting Evidence: PMID:17021207 Here, we show that the two-component system encoded by PP1067-PP1066 ( aauS-aauR ) is required for efficient growth of P. putida KT2440 on acidic amino acids (Glu and Asp) and their amides (Gln and Asn). file:PSEAE/dadA2/dadA2-uniprot.txt HAMAP; MF_01202; DadA; 1. |
| GO:0008718 D-amino-acid dehydrogenase activity | IEA GO_REF:0000120 | ACCEPT | Summary: UniRule/InterPro DadA family mapping (IPR023080, RHEA:18125). Reason: The DadA family signature is complete; consistent with the IBA. Supporting Evidence: file:PSEAE/dadA2/dadA2-uniprot.txt HAMAP; MF_01202; DadA; 1. |
| GO:0019478 D-amino acid catabolic process | IEA GO_REF:0000120 | ACCEPT | Summary: UniRule/InterPro mapping to D-amino acid catabolic process. Reason: As precise as the evidence allows for an uncharacterised DadA paralog: a D-amino acid dehydrogenase degrades D-amino acids, but which ones DadA2 acts on in vivo is unknown. Supporting Evidence: file:PSEAE/dadA2/dadA2-uniprot.txt Belongs to the DadA oxidoreductase family. |
| GO:0055130 D-alanine catabolic process | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: IBA D-alanine catabolic process from the E. coli DadA seed (P0A6J5, IMP). Reason: In P. aeruginosa the D-alanine catabolic role belongs to DadA1 (dadRAX locus): a dadA1 mutant can no longer use D-alanine as nitrogen source, so DadA2 does not contribute measurably to D-alanine catabolism under the tested conditions. The node-level inheritance is reasonable for the clade (E. coli DadA, DadA1), but for this paralog the specific process is not supported. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN008552203 · PTN008552203 SUPPORTS SOURCE BUT NOT TARGET DadA clade node; the GO:0055130 IBD rests on E. coli DadA alone and suits the clade's main members, but the P. aeruginosa paralog DadA2 is not the D-alanine catabolic enzyme. UniProtKB:P0A6J5 · E. coli DadA SUPPORTS SOURCE BUT NOT TARGET IMP evidence for D-alanine catabolism in E. coli; valid for E. coli and for DadA1. Supporting Evidence: PMID:21378189 the results from this study clearly demonstrate DadA to be the enzyme solely responsible for the proposed D-amino acid dehydrogenase activity of broad substrate specificity |
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Download this section (compressed HTML)Q: Under what conditions is dadA2 (PA5084) expressed, and which D-amino acids, if any, does it oxidise that DadA1 does not?
Experiment: Purify recombinant DadA2 and measure dehydrogenase activity with a panel of D-amino acids (DCPIP or ferricyanide acceptor); test growth of dadA1, dadA2 and double mutants on each D-amino acid as sole nitrogen or carbon source.
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: The substrates, expression conditions and physiological role of the DadA2 paralog are unknown; DadA1 alone accounts for D-alanine and several other D-amino acid utilisation.
BIOLOGY
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