1C0P

D-AMINO ACIC OXIDASE IN COMPLEX WITH D-ALANINE AND A PARTIALLY OCCUPIED BIATOMIC SPECIES

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1c0pa1	Alpha and beta proteins (a/b)	Nucleotide-binding domain	Nucleotide-binding domain	D-aminoacid oxidase, N-terminal domain	D-aminoacid oxidase, N-terminal domain	(Rhodotorula toruloides ) [TaxId: 5286 ],	SCOPe (2.08)
A	d1c0pa2	Alpha and beta proteins (a+b)	FAD-linked reductases, C-terminal domain	FAD-linked reductases, C-terminal domain	D-aminoacid oxidase-like	D-aminoacid oxidase	(Rhodotorula toruloides ) [TaxId: 5286 ],	SCOPe (2.08)
A	d1c0pa3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Rhodotorula toruloides ) [TaxId: 5286 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	D-aminoacid oxidase-like	8001377	4000124	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Flavoreductase-like	8001378	3000055	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	DAO_2nd	e1c0pA1	A: a+b two layers	X: FAD-linked reductases, C-terminal domain-like	H: FAD-linked reductases-C (From Topology)	T: FAD-linked reductases-C	F: DAO_2nd	ECOD (1.6)
A	DAO_1st	e1c0pA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F: DAO_1st	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
A	3.30.9.10	Alpha Beta	2-Layer Sandwich	D-Amino Acid Oxidase	Chain A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01266	FAD dependent oxidoreductase (DAO)	FAD dependent oxidoreductase	This family includes various FAD dependent oxidoreductases: Glycerol-3-phosphate dehydrogenase EC:1.1.99.5, Sarcosine oxidase beta subunit EC:1.5.3.1, D-alanine oxidase EC:1.4.99.1, D-aspartate oxidase EC:1.4.3.1.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	D-AMINO ACID OXIDASE	oxidoreductase activity, acting on the CH-NH2 group of donors oxidoreductase activity oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor D-amino-acid oxidase activity primary methylamine oxidase activity catalytic activity FAD binding flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding nucleotide binding oxidoreductase activity, acting on the CH-NH2 group of donors oxidoreductase activity oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor D-amino-acid oxidase activity primary methylamine oxidase activity catalytic activity FAD binding flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding nucleotide binding heterocyclic compound binding small molecule binding D-glutamate oxidase activity	catabolic process oxoacid metabolic process non-proteinogenic amino acid catabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process cellular catabolic process non-proteinogenic amino acid metabolic process alpha-amino acid catabolic process carboxylic acid catabolic process D-amino acid metabolic process catabolic process oxoacid metabolic process non-proteinogenic amino acid catabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process cellular catabolic process non-proteinogenic amino acid metabolic process alpha-amino acid catabolic process carboxylic acid catabolic process D-amino acid metabolic process metabolic process cellular process small molecule metabolic process small molecule catabolic process D-amino acid catabolic process amino acid catabolic process response to nutrient levels cellular homeostasis chemical homeostasis response to stimulus homeostatic process intracellular nitrogen homeostasis nitrogen utilization intracellular chemical homeostasis	peroxisomal matrix membrane-bounded organelle intracellular anatomical structure peroxisome membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle microbody lumen microbody cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR006181	D-amino acid oxidase, conserved site	Conserved Site
A	IPR006076	FAD dependent oxidoreductase	Domain
A	IPR023209	D-amino-acid oxidase	Family

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	D-amino-acid oxidase M-CSA #110	D amino acid oxidase (DAAO) acts to oxidise D amino acids to their imino counterparts, using FAD as a cofactor. The imino acid then undergoes hydrolysis outside of the enzyme's active site. This reaction has been found to play an important role in the degradation of certain neurotransmitters such as D-serine in mammals, but the enzyme is also found in other eukaryotes and its function has not been fully characterised. It shows mechanistic correlation with other enzymes able to oxidise amino groups. Yeast and mammalian DAAOs share features such as the basic catalytic mechanism. However, they differ in important aspects such as catalytic efficiency, substrate specificity, aggregation state, stability, kinetic mechanism, and mode and effectiveness of FAD binding. Thus, DAAO from the yeast Rhodotorula gracilis (RgDAAO) has a kcat value ≈20,000 minute−1 compared to 600 minute−1 for pig kidney DAAO (pkDAAO) with D-alanine as substrate.	Defined by 3 residues: ASN:A-56 [auth A-1054]SER:A-337 [auth A-1335]GLN:A-341 [auth A-1339] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.4.3.3 (PDB Primary Data) Search M-CSA Motif + EC 1.4.3.3

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.