id: A0A7E6FSU6 gene_symbol: DDO product_type: PROTEIN status: IN_PROGRESS taxon: id: NCBITaxon:6645 label: Octopus vulgaris description: >- 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. reference_proteome_assessments: - reference_proteomes: - UP001162480 status: NO_SUPPORTED_COUNTERPART reviewed_on: '2026-10-19' reason: Retain A0A7E6FSU6 as the primary Swiss-Prot accession. The four returned oxidase-family hits have only about 25-27% global identity and incomplete query coverage. They do not establish a D-aspartate oxidase counterpart; a D-amino-acid oxidase-like label is not evidence of matching substrate specificity. No supported counterpart was identified by this search. evidence: - type: PROTEOME_SEARCH description: MMseqs2 searched 29,931 sequences across UP001162480 at E <= 1e-5 and sensitivity 7.5, returning 4 hits. Every returned sequence was globally aligned using BLOSUM62 with gap-open -10 and extension -0.5. Scores and sequences for all 4 returned candidates are retained, with 4 detailed alignment files. The heuristic search does not establish genomic absence or unique locus identity. supported_by: - reference_id: file:OCTVU/DDO/DDO-record-evidence.yaml supporting_text: 'target_sequence_count: 29931' - reference_id: file:OCTVU/DDO/DDO-record-evidence.yaml supporting_text: 'candidate_count: 4' - type: PROTEOME_MEMBERSHIP description: The primary accession is outside every searched exact-taxon reference proteome. supported_by: - reference_id: file:OCTVU/DDO/DDO-record-evidence.yaml supporting_text: 'primary_in_any_reference_proteome: false' - type: RECORD_HISTORY description: 'Sampled UniSave observation: 27-NOV-2024, entry version 16.: UP000515154. This dated observation does not establish uninterrupted membership/absence, the exact change date, or UniProt''s motivation.' supported_by: - reference_id: file:OCTVU/DDO/DDO-record-evidence.yaml supporting_text: |- entry_date: 27-NOV-2024, entry version 16. proteomes: - UP000515154 existing_annotations: # --- IEA annotations --- - term: id: GO:0003884 label: D-amino-acid oxidase activity evidence_type: IEA original_reference_id: GO_REF:0000120 qualifier: enables review: 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. action: MODIFY 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_replacement_terms: - id: GO:0008445 label: D-aspartate oxidase activity supported_by: - reference_id: PMID:8103425 supporting_text: >- 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 - reference_id: PMID:7915543 supporting_text: >- The properties of D-aspartate oxidase from Octopus vulgaris (EC 1.4.3.1) have been investigated - term: id: GO:0005737 label: cytoplasm evidence_type: IEA original_reference_id: GO_REF:0000118 qualifier: located_in review: summary: >- TreeGrafter-derived cytoplasm annotation. It is a true but broad parent of the peroxisomal matrix location already annotated by ISS, so it is retained as non-core rather than rejected. action: KEEP_AS_NON_CORE reason: >- GO:0005737 cytoplasm is an ancestor of GO:0005782 peroxisomal matrix in the ontology (peroxisomal matrix is part_of peroxisome, part_of cytoplasm), so the TreeGrafter call is entailed by the more specific location rather than in conflict with it: DDO is a soluble monomeric FAD flavoenzyme with a C-terminal SKL microbody targeting signal, and there is no membrane or extracellular assignment that the broad term would contradict. Per the project rule that a broad-but-true compartment is not an over-annotation, this is kept as non-core; the informative location remains GO:0005782. - term: id: GO:0005782 label: peroxisomal matrix evidence_type: IEA original_reference_id: GO_REF:0000044 qualifier: located_in review: 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). action: ACCEPT 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. - term: id: GO:0008445 label: D-aspartate oxidase activity evidence_type: IEA original_reference_id: GO_REF:0000003 qualifier: enables review: 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. action: ACCEPT 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. - term: id: GO:0019478 label: D-amino acid catabolic process evidence_type: IEA original_reference_id: GO_REF:0000118 qualifier: involved_in review: 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]. action: ACCEPT 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]. - term: id: GO:0046416 label: D-amino acid metabolic process evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: involved_in review: 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. action: KEEP_AS_NON_CORE 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. - term: id: GO:0071949 label: FAD binding evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: enables review: 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]. action: ACCEPT 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. # --- ISS annotations --- - term: id: GO:0005782 label: peroxisomal matrix evidence_type: ISS original_reference_id: GO_REF:0000024 qualifier: located_in review: 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. action: ACCEPT 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. # Second ISS annotation for peroxisomal matrix (from bovine DDO P31228) - term: id: GO:0005782 label: peroxisomal matrix evidence_type: ISS original_reference_id: GO_REF:0000024 qualifier: located_in review: 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. action: ACCEPT reason: >- Redundant with the other ISS annotation but from a different ortholog (bovine P31228 vs human Q99489). Both support peroxisomal matrix localization consistently. supported_by: - reference_id: PMID:7915543 supporting_text: >- 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 # --- Experimental annotations --- - term: id: GO:0047821 label: D-glutamate oxidase activity evidence_type: EXP original_reference_id: PMID:7915543 qualifier: enables review: 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. action: ACCEPT 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]. supported_by: - reference_id: PMID:7915543 supporting_text: >- 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 - reference_id: PMID:8103425 supporting_text: >- 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 - term: id: GO:0008445 label: D-aspartate oxidase activity evidence_type: IDA original_reference_id: PMID:7915543 qualifier: enables review: 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. action: ACCEPT reason: >- This is the core molecular function of the enzyme, directly demonstrated by enzyme purification and kinetic characterization [PMID:7915543, PMID:8103425]. supported_by: - reference_id: PMID:7915543 supporting_text: >- 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 - reference_id: PMID:8103425 supporting_text: >- 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 - reference_id: PMID:15491279 supporting_text: >- 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 - term: id: GO:0019478 label: D-amino acid catabolic process evidence_type: IDA original_reference_id: PMID:7915543 qualifier: involved_in review: 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. action: ACCEPT 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]. supported_by: - reference_id: PMID:7903300 supporting_text: >- 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 - reference_id: PMID:7903300 supporting_text: >- 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 - term: id: GO:0071949 label: FAD binding evidence_type: IDA original_reference_id: PMID:7915543 qualifier: enables review: 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. action: ACCEPT reason: >- FAD binding is directly demonstrated by spectrophotometric characterization and cofactor stoichiometry [PMID:7915543]. FAD is essential for catalytic activity. supported_by: - reference_id: PMID:7915543 supporting_text: >- 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 references: - id: file:OCTVU/DDO/DDO-record-evidence.yaml title: Compact archived record and sequence evidence for A0A7E6FSU6 - id: GO_REF:0000002 title: Gene Ontology annotation through association of InterPro records with GO terms findings: [] - id: GO_REF:0000003 title: Gene Ontology annotation based on Enzyme Commission mapping findings: [] - id: GO_REF:0000024 title: Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity findings: [] - id: GO_REF:0000044 title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt findings: [] - id: GO_REF:0000118 title: TreeGrafter-generated GO annotations findings: [] - id: GO_REF:0000120 title: Combined Automated Annotation using Multiple IEA Methods findings: [] - id: PMID:7915543 title: Properties of the flavoenzyme D-aspartate oxidase from Octopus vulgaris. findings: - statement: >- DDO is a 37 kDa FAD-dependent monomer with KM 4.3 mM for D-Asp and 9.7 mM for D-Glu. Two active-site residues with pKa 7.1 and 9.1 are critical for catalysis. - statement: >- The enzyme exists in active (FAD-bound) and inactive (6-OH-FAD-bound) forms; the inactive form is a purification artifact. - statement: >- Structural similarities to bovine D-aspartate oxidase and porcine D-amino acid oxidase in amino-acid composition and N-terminal sequence. - id: PMID:7903300 title: Biological role of D-amino acid oxidase and D-aspartate oxidase. Effects of D-amino acids. findings: - statement: >- D-amino acids administered to animals are oxidized in vivo by D-amino acid oxidase and D-aspartate oxidase in tissues, producing NH3, H2O2, and the corresponding keto acid. - statement: >- Inverse relationship between oxidase levels and D-amino acid concentrations: younger animals have lower oxidase and higher D-amino acids. - statement: >- Biological role is detoxification of D-amino acids that accumulate during aging. - statement: >- DDO expression in liver and kidney increases progressively during postnatal development. - id: PMID:8103425 title: Further study on the specificity of D-amino acid oxidase and D-aspartate oxidase and time course for complete oxidation of D-amino acids. findings: - statement: >- D-AspO from Octopus and beef kidney specifically oxidizes D-Asp, D-Glu, D-Asn, D-Gln, D-Asp-dimethyl-ester, and N-methyl-D-Asp. - statement: >- D-Pro, D-Leu, D-Ala, D-Met oxidized at very low rates (0.2-0.6% of D-Asp rate). - statement: >- All L-amino acids are not oxidized, confirming strict D-stereoselectivity. - statement: >- D-AspO is clearly distinct from D-amino acid oxidase (D-AAO) in substrate specificity. - id: PMID:8446003 title: Occurrence of free D-aspartic acid in the circumsoesophageal ganglia of Aplysia fasciata. findings: - statement: >- Free D-Asp found at high concentrations in CNS of cephalopods (O. vulgaris, L. vulgaris, S. officinalis) and Aplysia, constituting 8.3% of total aspartate in ganglia. - statement: >- D-Asp may have a specific neurological function in molluscan CNS. - statement: >- Octopus D-AspO was used as analytical tool to measure D-Asp levels. - id: PMID:18703100 title: Control of GnRH expression in the olfactory lobe of Octopus vulgaris. findings: - statement: >- NMDA receptors are present in Octopus olfactory lobes and NMDA enhances GnRH mRNA expression in a dose-response manner. - statement: >- L-glutamate/NMDA/NO pathway controls reproductive maturation in O. vulgaris. - statement: >- D-aspartate acts as NMDA receptor agonist, implicating DDO in neuromodulation through regulation of D-Asp levels. - id: PMID:15491279 title: Cephalopod vision involves dicarboxylic amino acids - D-aspartate, L-aspartate and L-glutamate. findings: - statement: >- High concentrations of free D-aspartate in cephalopod retina: O. vulgaris 2.30 +/- 0.25 umol/g, S. officinalis 2.60 +/- 0.30 umol/g, L. vulgaris 1.60 +/- 0.20 umol/g tissue. - statement: >- Purified octopus D-AspO degrades D-Asp in retinal extracts, abolishing the D-Asp HPLC peak, confirming enzyme activity against the retinal D-Asp pool. - statement: >- Radiotracer experiments indicate D-Asp is synthesized in optic lobes and transported to the retina, establishing dynamic D-Asp handling in cephalopod visual circuitry. - statement: >- DDO also oxidizes NMDA (N-methyl-D-aspartate), in addition to D-Asp and D-Glu. - id: PMID:34250021 title: Human D-aspartate oxidase - a key player in D-aspartate metabolism. findings: - statement: >- DDO/DASPO is a peroxisomal enzyme in mammals; D-Asp and DDO are localized in neurons within peroxisomes, emphasizing compartmentalization and H2O2 handling. - statement: >- DDO inhibition could raise endogenous D-Asp to modulate NMDA-receptor-related physiology as a potential therapeutic strategy for neuropsychiatric disorders. - statement: >- Human DASPO operates by a ternary-complex mechanism where oxygen reacts with the reduced flavin-imino acid complex before product release, with hydride transfer from substrate alpha-carbon to flavin N5. core_functions: - description: >- DDO is a D-aspartate oxidase (EC 1.4.3.1) that catalyzes the FAD-dependent oxidative deamination of D-aspartate to oxaloacetate + H2O2 + NH4+, with KM 4.3 mM and kcat 6.8 s-1. It also oxidizes D-glutamate (KM 9.7 mM, kcat 11 s-1) and other acidic D-amino acid derivatives (D-Asn, D-Gln, NMDA). This is the primary catalytic function of the enzyme. molecular_function: id: GO:0008445 label: D-aspartate oxidase activity directly_involved_in: - id: GO:0019478 label: D-amino acid catabolic process locations: - id: GO:0005782 label: peroxisomal matrix supported_by: - reference_id: PMID:7915543 supporting_text: >- 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 - reference_id: PMID:7903300 supporting_text: >- 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 - reference_id: PMID:15491279 supporting_text: >- S. officinalis contains the highest quantity of D -Asp (2.60±0.30 μmol/g of tissue) followed by O. vulgaris and L. vulgaris , with concentrations of 2.30±0.25 and 1.60±0.20 μmol/g of tissue respectively - description: >- In the cephalopod visual system, free D-aspartate is present at high concentrations in retina (2.30 +/- 0.25 umol/g in O. vulgaris) and optic lobes. Radiotracer experiments show D-Asp is synthesized in optic lobes and transported to retina. DDO is implicated in regulating the D-Asp pool that may serve as a neuromodulator or signaling molecule in visual circuitry, though direct DDO localization in retina has not been demonstrated. DDO was purified from hepatopancreas, where it shows substantial activity consistent with metabolic clearance of dietary D-amino acids. molecular_function: id: GO:0008445 label: D-aspartate oxidase activity directly_involved_in: - id: GO:0019478 label: D-amino acid catabolic process supported_by: - reference_id: PMID:15491279 supporting_text: >- D -Asp is synthesized in the optic lobes and is then transported actively into the retina - reference_id: PMID:15491279 supporting_text: >- 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 suggested_questions: - question: >- 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]. - question: >- 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. suggested_experiments: - description: >- 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. - description: >- 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.