DsdA (PA3357) is a cytoplasmic pyridoxal 5'-phosphate-dependent D-serine dehydratase (D-serine ammonia-lyase) of the serine/threonine dehydratase family. It deaminates D-serine to pyruvate and ammonia and also accepts D-threonine, but not L-amino acids (Km for D-serine about 330 ΞΌM). In PAO1 the chromosomal gene is cryptic. It is not induced by D-serine, and growth on D-serine depends on the broad-specificity D-amino acid dehydrogenase DadA. Supplied on a plasmid, dsdA restores growth on D-serine as sole carbon and nitrogen source to a dadA dsdA mutant.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0006520 amino acid metabolic process | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro2GO from the serine/threonine dehydratase PLP-binding signature. Reason: True, and entailed by the accepted GO:0036088 D-serine catabolic process, which is_a amino acid metabolic process. Supporting Evidence: PMID:26957519 supporting the proposed biochemical function of DsdA in the conversion of D-serine into pyruvate and ammonia |
| GO:0008721 D-serine ammonia-lyase activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN000034699, seeded by E. coli DsdA (IDA) and by this gene (expected self-seed, from its own IDA row). Reason: Core activity, directly assayed on this protein. The IBD stands on the E. coli seed too. Supporting Evidence: PMID:26957519 Among D- and L-amino acids tested, only D-serine and D-threonine could serve as the substrates of DsdA, and the Km of DsdA with D-serine was calculated to be 330 ΞΌM. |
| GO:0008721 D-serine ammonia-lyase activity | IDA PMID:26957519 The Cryptic dsdA Gene Encodes a Functional D-Serine Dehydrat... | ACCEPT | Summary: PseudoCAP seed row for PTN000034699. Substrate screen and Km determination for DsdA. Reason: Seed verdict SOUND. The abstract states the kinetic measurement made on DsdA itself. Supporting Evidence: PMID:26957519 Among D- and L-amino acids tested, only D-serine and D-threonine could serve as the substrates of DsdA, and the Km of DsdA with D-serine was calculated to be 330 ΞΌM. |
| GO:0008721 D-serine ammonia-lyase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Combined IEA from the DsdA family signature and EC 4.3.1.18. Reason: Consistent with the direct assay. Supporting Evidence: PMID:26957519 Among D- and L-amino acids tested, only D-serine and D-threonine could serve as the substrates of DsdA, and the Km of DsdA with D-serine was calculated to be 330 ΞΌM. |
| GO:0016829 lyase activity | IEA GO_REF:0000117 | TOO GENERAL | Summary: ARBA machine-learning lyase activity. Reason: True, and entailed by the accepted GO:0008721 D-serine ammonia-lyase activity, which is_a lyase activity. Supporting Evidence: PMID:26957519 Among D- and L-amino acids tested, only D-serine and D-threonine could serve as the substrates of DsdA, and the Km of DsdA with D-serine was calculated to be 330 ΞΌM. |
| GO:0016836 hydro-lyase activity | IEA GO_REF:0000104 | MODIFY | Summary: UniRule IEA hydro-lyase activity. Reason: The "dehydratase" name reflects the PLP mechanism, which eliminates water before the aminoacrylate is hydrolysed. The overall reaction (D-serine to pyruvate and ammonia) is classed as an ammonia-lyase (EC 4.3.1.18), and GO:0008721 sits under carbon-nitrogen lyase activity, not under hydro-lyase activity. Lateral correction to the specific supported term, which the gene already carries. Proposed replacements: D-serine ammonia-lyase activity Supporting Evidence: file:PSEAE/dsdA/dsdA-uniprot.txt Reaction=D-serine = pyruvate + NH4(+) |
| GO:0030170 pyridoxal phosphate binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO PLP binding; HAMAP places the PLP lysine at K119. Reason: Correct cofactor binding for a fold-type II PLP enzyme. It supports the core activity but is not itself the function. Supporting Evidence: file:PSEAE/dsdA/dsdA-uniprot.txt N6-(pyridoxal phosphate)lysine |
| GO:0036088 D-serine catabolic process | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN000034699, seeded by E. coli DsdA. Reason: DsdA performs the one-step degradation of D-serine to pyruvate and ammonia, and plasmid dsdA restores D-serine catabolism to a dadA dsdA mutant. The chromosomal gene is cryptic under laboratory conditions; the process is the one the enzyme carries out, not necessarily the main route of D-serine use in PAO1. Supporting Evidence: PMID:26957519 However, when complemented by dsdA on a plasmid, the double mutant was able to grow on D-serine as the sole source of carbon and nitrogen, supporting the proposed biochemical function of DsdA in the conversion of D-serine into pyruvate and ammonia. |
| GO:0036088 D-serine catabolic process | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO from the DsdA family signature. Reason: Same claim as the IBA row. Supporting Evidence: PMID:26957519 supporting the proposed biochemical function of DsdA in the conversion of D-serine into pyruvate and ammonia |
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