1Y56

Crystal structure of L-proline dehydrogenase from P.horikoshii

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Thioredoxin reductase/Flavin-dependent monoxygenase-like	8091751	4000117	SCOP2 (2022-06-29)
A	SCOP2 Family	Sarcosine oxidase A3 domain-like	8091753	4007758	SCOP2 (2022-06-29)
A	SCOP2 Family	2Fe-2S ferredoxin domains from multidomain proteins	8091755	4000241	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Thioredoxin reductase-like	8091752	3000050	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Bfd-like	8091754	3002540	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	2Fe-2S ferredoxin-like	8091756	3000113	SCOP2 (2022-06-29)
B	SCOP2 Family	D-aminoacid oxidase-like	8064391	4000124	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Flavoreductase-like	8064392	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	Fer2_BFD	e1y56A3	A: alpha arrays	X: HTH	H: bacterioferritin-associated ferredoxin (From Topology)	T: bacterioferritin-associated ferredoxin	F: Fer2_BFD	ECOD (1.6)
A	Fer2_4	e1y56A2	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Fer2_4	ECOD (1.6)
A	FAD_binding_3_1st	e1y56A1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F: FAD_binding_3_1st	ECOD (1.6)
B	DAO_2nd_1	e1y56B2	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_1	ECOD (1.6)
B	DAO_1st	e1y56B1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: DAO_1st	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.20.440	Alpha Beta	Roll	Ubiquitin-like (UB roll)	2Fe-2S iron-sulphur cluster binding domain, sarcosine oxidase, alpha subunit, N-terminal domain	CATH (4.3.0)
A	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
A	1.10.10.1100	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	BFD-like [2Fe-2S]-binding domain	CATH (4.3.0)
B	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
B	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	PF17806	Sarcosine oxidase A3 domain (SO_alpha_A3)	Sarcosine oxidase A3 domain	This short domain is found in Heterotetrameric Sarcosine Oxidase's alpha A3 domain [1]. This domain binds to FMN in sarcosine oxidase. This domain is related to Pfam:PF04324 but lacks its iron binding cysteine residues.	Domain
A	PF07992	Pyridine nucleotide-disulphide oxidoreductase (Pyr_redox_2)	Pyridine nucleotide-disulphide oxidoreductase	This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. This domain is actually a small NADH binding domain within a larger FAD binding domain.	Domain
A	PF13510	2Fe-2S iron-sulfur cluster binding domain (Fer2_4)	2Fe-2S iron-sulfur cluster binding domain	The 2Fe-2S ferredoxin family have a general core structure consisting of beta(2)-alpha-beta(2) which a beta-grasp type fold. The domain is around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated. Th ...	The 2Fe-2S ferredoxin family have a general core structure consisting of beta(2)-alpha-beta(2) which a beta-grasp type fold. The domain is around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated. This cluster appears within sarcosine oxidase proteins.	Domain
B	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	hypothetical protein PH1363	oxidoreductase activity catalytic activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding oxidoreductase activity catalytic activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding	-	-
B	sarcosine oxidase	binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding	-	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR051691	Metabolic Enzymes: Cyanogenesis, Opine Oxidation, G-3-P Dehydrogenation	Family
A	IPR041117	SoxA, A3 domain	Domain
A	IPR023753	FAD/NAD(P)-binding domain	Domain
A	IPR041854	BFD-like [2Fe-2S]-binding domain superfamily	Homologous Superfamily
A	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
A	IPR042204	2Fe-2S iron-sulfur cluster binding domain, N-terminal	Homologous Superfamily
B	IPR006076	FAD dependent oxidoreductase	Domain
B	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily

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.