D-aspartate oxidase (EC 1.4.3.1) is a FAD-dependent flavoenzyme that selectively catalyzes the oxidative deamination of acidic D-amino acids, primarily D-aspartate and D-glutamate. It is a 37 kDa monomer containing one FAD per molecule, purified from O. vulgaris hepatopancreas. DDO protects the organism from D-amino acid toxicity and regulates D-aspartate levels in the CNS, where D-Asp acts as an NMDA receptor agonist. Expression increases postnatally in liver and kidney. Localized to the peroxisomal matrix by similarity.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003884 D-amino-acid oxidase activity | IEA GO_REF:0000120 | MODIFY | Summary: GO:0003884 (D-amino-acid oxidase activity) describes oxidative deamination of neutral/basic D-amino acids (D-Ala, D-Met, D-Pro, etc.). DDO is specifically a D-aspartate oxidase (EC 1.4.3.1), which is functionally distinct from D-amino acid oxidase (EC 1.4.3.3). DDO acts on acidic D-amino acids (D-Asp, D-Glu) and has negligible activity on neutral D-amino acids [PMID:8103425]. The IEA mapping from InterPro/PANTHER assigns the broader parent family activity, but GO:0008445 (D-aspartate oxidase activity) is the correct specific term for this enzyme. Reason: DDO is a D-aspartate oxidase, not a D-amino acid oxidase. D-AspO specifically oxidizes D-Asp, D-Glu, and their derivatives, whereas D-AAO oxidizes neutral D-amino acids [PMID:8103425]. DDO oxidizes D-Pro, D-Leu, D-Ala, D-Met at only 0.2-0.6% of the D-Asp rate [PMID:8103425]. The correct term is GO:0008445 (D-aspartate oxidase activity), which is already annotated with IDA evidence. Proposed replacements: D-aspartate oxidase activity Supporting Evidence: PMID:8103425 D-Aspartate oxidase (D-Aspo) either purified from Octopus vulgaris or from beef kidney oxidizes only D-Asp, D-Glu and their following derivatives: D-Asn, D-Gln, D-Asp-dimethyl-ester and N-methyl-D-Asp PMID:7915543 The properties of D-aspartate oxidase from Octopus vulgaris (EC 1.4.3.1) have been investigated |
| GO:0005737 cytoplasm | IEA GO_REF:0000118 | MARK AS OVER ANNOTATED | Summary: TreeGrafter-derived annotation placing DDO in the cytoplasm. UniProt annotates DDO to the peroxisome matrix by similarity to human DDO (Q99489), which has a C-terminal peroxisomal targeting signal (SKL motif at residues 334-336). The cytoplasm annotation is not wrong per se (peroxisomes are in the cytoplasm), but it is too general. The more specific peroxisomal matrix annotation is preferred and already present. Reason: DDO has a C-terminal SKL microbody targeting signal (residues 334-336) and is annotated to peroxisomal matrix (GO:0005782) by ISS to human and bovine orthologs. Cytoplasm is too general and adds no information beyond the more specific peroxisomal matrix annotation. |
| GO:0005782 peroxisomal matrix | IEA GO_REF:0000044 | ACCEPT | Summary: IEA annotation from UniProt subcellular location mapping. DDO has a C-terminal SKL microbody targeting signal (residues 334-336 in the O. vulgaris sequence) consistent with peroxisomal matrix localization. This is further supported by ISS annotations to human DDO (Q99489) and bovine DDO (P31228). Reason: Peroxisomal matrix localization is well-supported by the conserved SKL peroxisomal targeting signal at the C-terminus and by sequence similarity to mammalian orthologs known to localize to the peroxisome matrix. |
| GO:0008445 D-aspartate oxidase activity | IEA GO_REF:0000003 | ACCEPT | Summary: IEA annotation from EC number mapping (EC 1.4.3.1). This is the correct molecular function for DDO, directly supported by experimental characterization in PMID:7915543. The EC-to-GO mapping is accurate here. Reason: D-aspartate oxidase activity (EC 1.4.3.1) is the experimentally verified catalytic function of this enzyme [PMID:7915543]. This IEA annotation is consistent with the IDA annotation from the same GO term. |
| GO:0019478 D-amino acid catabolic process | IEA GO_REF:0000118 | ACCEPT | Summary: TreeGrafter-derived annotation for involvement in D-amino acid catabolism. DDO catalyzes the oxidative deamination of D-Asp and D-Glu, producing the corresponding keto acids (oxaloacetate and 2-oxoglutarate), H2O2, and NH4+. This is a bona fide catabolic process for D-amino acids [PMID:7903300]. Reason: DDO directly participates in D-amino acid catabolism by oxidatively deaminating D-aspartate and D-glutamate. The biological role as a D-amino acid detoxifying enzyme is well-established [PMID:7903300, PMID:8103425]. |
| GO:0046416 D-amino acid metabolic process | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro-derived annotation for D-amino acid metabolic process. This is a parent term of GO:0019478 (D-amino acid catabolic process), which is already annotated with both IEA and IDA evidence. The metabolic process term is not incorrect but is less specific than the catabolic process term. Reason: This is a valid but more general parent of GO:0019478 (D-amino acid catabolic process). Since the more specific catabolic term is already annotated with IDA evidence, this broader term adds minimal information but is not wrong. Kept as non-core. |
| GO:0071949 FAD binding | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro-derived annotation for FAD binding. DDO contains one mol FAD per mol protein, with multiple FAD-binding residues identified by similarity (positions 34, 35, 41, 42, 304, 308, 309). FAD is the essential cofactor for catalytic activity [PMID:7915543]. Reason: FAD binding is experimentally established. DDO is a flavoenzyme containing stoichiometric FAD as cofactor [PMID:7915543]. This IEA is consistent with the IDA annotation for the same term. |
| GO:0005782 peroxisomal matrix | ISS GO_REF:0000024 | ACCEPT | Summary: ISS annotation transferred from human DDO (Q99489). DDO has a conserved C-terminal SKL peroxisomal targeting signal (microbody targeting signal at residues 334-336). The subcellular location annotation in UniProt also specifies peroxisome matrix by similarity. Reason: Peroxisomal matrix localization is well-supported by the conserved SKL targeting signal at the C-terminus and orthology to human DDO (Q99489), which is experimentally localized to peroxisomes. |
| GO:0005782 peroxisomal matrix | ISS GO_REF:0000024 | ACCEPT | Summary: Second ISS annotation for peroxisomal matrix, transferred from bovine DDO (P31228). This provides additional orthologous support for peroxisomal localization. PMID:7915543 notes structural similarities between Octopus DDO and bovine D-aspartate oxidase. Reason: Redundant with the other ISS annotation but from a different ortholog (bovine P31228 vs human Q99489). Both support peroxisomal matrix localization consistently. Supporting Evidence: PMID:7915543 Structural investigations show similarities in both the amino-acid composition and the N-terminal amino-acid sequence to bovine D-aspartate oxidase and porcine D-amino-acid oxidase |
| GO:0047821 D-glutamate oxidase activity | EXP PMID:7915543 Properties of the flavoenzyme D-aspartate oxidase from Octop... | ACCEPT | Summary: Experimental annotation for D-glutamate oxidase activity. PMID:7915543 reports kinetic characterization of DDO with D-glutamate as substrate: KM 9.7 mM, kcat 11 s-1. PMID:8103425 confirms DDO oxidizes D-Glu, D-Gln, and derivatives. D-glutamate is a legitimate substrate with catalytic efficiency comparable to D-aspartate. Reason: D-glutamate oxidase activity is directly demonstrated with kinetic parameters (KM 9.7 mM, kcat 11 s-1) [PMID:7915543]. D-Glu is among the primary substrates of DDO [PMID:8103425]. Supporting Evidence: PMID:7915543 kinetic analyses suggest that two active-site residues with pKa of 7.1 and 9.1 are critical for catalysis, and that the ionization of such residues has different effects on the catalytic activity depending whether mono- or dicarboxylic D-amino acids are used as substrate PMID:8103425 D-Aspartate oxidase (D-Aspo) either purified from Octopus vulgaris or from beef kidney oxidizes only D-Asp, D-Glu and their following derivatives: D-Asn, D-Gln, D-Asp-dimethyl-ester and N-methyl-D-Asp |
| GO:0008445 D-aspartate oxidase activity | IDA PMID:7915543 Properties of the flavoenzyme D-aspartate oxidase from Octop... | ACCEPT | Summary: IDA annotation for D-aspartate oxidase activity, the primary catalytic function of DDO. PMID:7915543 reports comprehensive biochemical characterization: the enzyme is a 37 kDa FAD-dependent monomer with KM 4.3 mM for D-Asp, kcat 6.8 s-1. It selectively oxidizes acidic D-amino acids and is classified as EC 1.4.3.1. Reason: This is the core molecular function of the enzyme, directly demonstrated by enzyme purification and kinetic characterization [PMID:7915543, PMID:8103425]. Supporting Evidence: PMID:7915543 The properties of D-aspartate oxidase from Octopus vulgaris (EC 1.4.3.1) have been investigated. The protein is a monomer of M(r) 37,000 containing one mol flavin/mol protein PMID:8103425 D-Aspartate oxidase (D-Aspo) either purified from Octopus vulgaris or from beef kidney oxidizes only D-Asp, D-Glu and their following derivatives: D-Asn, D-Gln, D-Asp-dimethyl-ester and N-methyl-D-Asp PMID:15491279 a D - A sp O ( D -aspartate oxidase; EC 1.4.3.1), the enzyme which specifically oxidizes D -Asp into oxaloacetate has been found in various animals, and has been purified from O. vulgaris |
| GO:0019478 D-amino acid catabolic process | IDA PMID:7915543 Properties of the flavoenzyme D-aspartate oxidase from Octop... | ACCEPT | Summary: IDA annotation for involvement in D-amino acid catabolic process. PMID:7915543 demonstrates that DDO catalyzes the oxidative deamination of D-Asp to oxaloacetate and D-Glu to 2-oxoglutarate, with release of NH4+ and H2O2. PMID:7903300 establishes the biological role as detoxification of D-amino acids that accumulate during aging. Reason: DDO directly catabolizes D-amino acids. The enzyme's catalytic products (keto acids, H2O2, NH4+) confirm this is a catabolic/degradative process [PMID:7915543]. The detoxification role is well-established in vivo [PMID:7903300]. Supporting Evidence: PMID:7903300 D-Amino acids administered to animals are absorbed by the intestine and transported through the blood-stream to solid tissues where they are oxidized in vivo by D-amino acid oxidase and D-aspartate oxidase to produce the same compounds they do in vitro; i.e. NH3, H2O2, and the keto acid corresponding to the amino acid ingested PMID:7903300 the in vivo biological role of these oxidases in animals is to act as detoxifying agents to metabolize D-amino acids which may have accumulated during aging |
| GO:0071949 FAD binding | IDA PMID:7915543 Properties of the flavoenzyme D-aspartate oxidase from Octop... | ACCEPT | Summary: IDA annotation for FAD binding. PMID:7915543 demonstrates that DDO contains stoichiometric FAD (one mol FAD per mol protein) and that the enzyme exists in active (FAD-bound) and inactive (6-OH-FAD-bound, purification artifact) forms. The spectrophotometric properties conform to the oxidase class of flavoproteins. Reason: FAD binding is directly demonstrated by spectrophotometric characterization and cofactor stoichiometry [PMID:7915543]. FAD is essential for catalytic activity. Supporting Evidence: PMID:7915543 The protein is a monomer of M(r) 37,000 containing one mol flavin/mol protein. The enzyme as isolated exists at least in two forms, one containing FAD and the other, which is catalytically inactive, probably containing 6-OH-FAD |
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Download this section (compressed HTML)Q: Does DDO play a direct role in modulating NMDA receptor-mediated signaling in octopus CNS by controlling D-aspartate levels? D-Asp is present at high concentrations in cephalopod CNS [PMID:8446003] and NMDA receptors are functional in octopus brain [PMID:18703100].
Q: Is DDO expressed in octopus CNS tissue, or only in peripheral organs (liver, kidney)? The developmental expression data from PMID:7903300 focuses on liver and kidney; CNS expression would support a direct neuromodulatory role.
Experiment: Immunohistochemistry or in situ hybridization for DDO expression in O. vulgaris brain tissue (specifically olfactory and optic lobes) to determine whether DDO is expressed in the CNS where D-Asp is present at high levels.
Hypothesis: DDO is expressed in octopus CNS and directly regulates D-Asp levels for NMDA receptor-mediated neuromodulation.
Experiment: CRISPR/Cas9 or morpholino knockdown of DDO in O. vulgaris to assess the effect on D-Asp levels in CNS and on NMDA receptor-dependent behaviors.
Hypothesis: DDO knockdown leads to elevated D-Asp in CNS, altering NMDA receptor signaling and downstream GnRH-mediated reproductive maturation.
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