1VRQ

Crystal Structure of Heterotetrameric Sarcosine Oxidase from Corynebacterium sp. U-96 in complex with Folinic Acid

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	SCOP2B Superfamily	Folate-binding domain-like	8091775	3000025	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Aminomethyltransferase beta-barrel domain-like	8091776	3000024	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Thioredoxin reductase-like	8091769	3000050	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	2Fe-2S ferredoxin-like	8091771	3000113	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Bfd-like	8091773	3002540	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Flavoreductase-like	8091767	3000055	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Folate-binding domain-like	8090858	3000025	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Sarcosine oxidase delta subunit-like	8090855	3002464	SCOP2B (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	GCV_T_C	e1vrqA3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: GCV_T_C	ECOD (1.6)
A	soxA	e1vrqA4	A: alpha arrays	X: HTH	H: bacterioferritin-associated ferredoxin (From Topology)	T: bacterioferritin-associated ferredoxin	F: soxA	ECOD (1.6)
A	Fer2_4	e1vrqA5	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Fer2_4	ECOD (1.6)
A	GCV_T_N	e1vrqA8	A: a+b two layers	X: Alpha-beta plaits	H: Aminomethyltransferase folate-binding domain (From Topology)	T: Aminomethyltransferase folate-binding domain	F: GCV_T_N	ECOD (1.6)
A	GCV_T_N1	e1vrqA7	A: a+b two layers	X: Alpha-beta plaits	H: Aminomethyltransferase folate-binding domain (From Topology)	T: Aminomethyltransferase folate-binding domain	F: GCV_T_N1	ECOD (1.6)
A	FAD_binding_3_1st	e1vrqA6	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	e1vrqB3	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	FAD_binding_3_1st	e1vrqB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: FAD_binding_3_1st	ECOD (1.6)
C	SoxG	e1vrqC1	A: a+b two layers	X: Alpha-beta plaits	H: Aminomethyltransferase folate-binding domain (From Topology)	T: Aminomethyltransferase folate-binding domain	F: SoxG	ECOD (1.6)
D	SoxD	e1vrqD1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: SoxD	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.1360.120	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	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)
C	3.30.1360.120	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
C	3.30.70.1520	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Heterotetrameric sarcosine oxidase	CATH (4.3.0)
D	3.30.2270.10	Alpha Beta	2-Layer Sandwich	Folate-binding fold	Folate-binding superfamily	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	PF12831	FAD dependent oxidoreductase (FAD_oxidored)	FAD dependent oxidoreductase	-	Family
A	PF01571	Aminomethyltransferase folate-binding domain (GCV_T)	Aminomethyltransferase folate-binding domain	This is a family of glycine cleavage T-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl tran ...	This is a family of glycine cleavage T-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl transferase.	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
A	PF08669	Glycine cleavage T-protein C-terminal barrel domain (GCV_T_C)	Glycine cleavage T-protein C-terminal barrel domain	This is a family of glycine cleavage T-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl tran ...	This is a family of glycine cleavage T-proteins, part of the glycine cleavage multienzyme complex (GCV) found in bacteria and the mitochondria of eukaryotes. GCV catalyses the catabolism of glycine in eukaryotes. The T-protein is an aminomethyl transferase.	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
C	PF04268	Sarcosine oxidase, gamma subunit family (SoxG)	Sarcosine oxidase, gamma subunit family	-	Family
D	PF04267	Sarcosine oxidase, delta subunit family (SoxD)	Sarcosine oxidase, delta subunit family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Sarcosine oxidase alpha subunit	binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on the CH-NH group of donors, oxygen as acceptor sarcosine oxidase activity oxidoreductase activity, acting on the CH-NH group of donors catalytic activity	folic acid-containing compound metabolic process cellular metabolic process metabolic process cellular process tetrahydrofolate metabolic process pteridine-containing compound metabolic process cellular modified amino acid metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity
B	Sarcosine oxidase beta subunit	binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on the CH-NH group of donors, oxygen as acceptor sarcosine oxidase activity oxidoreductase activity, acting on the CH-NH group of donors catalytic activity	folic acid-containing compound metabolic process cellular metabolic process metabolic process cellular process tetrahydrofolate metabolic process pteridine-containing compound metabolic process cellular modified amino acid metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity
C	Sarcosine oxidase gamma subunit	oxidoreductase activity oxidoreductase activity, acting on the CH-NH group of donors, oxygen as acceptor sarcosine oxidase activity oxidoreductase activity, acting on the CH-NH group of donors catalytic activity	catabolic process oxoacid metabolic process amino acid metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process cellular catabolic process non-proteinogenic amino acid metabolic process sarcosine catabolic process carboxylic acid catabolic process small molecule metabolic process amino acid catabolic process non-proteinogenic amino acid catabolic process cellular metabolic process catabolic process oxoacid metabolic process amino acid metabolic process organic acid catabolic process organic acid metabolic process alpha-amino acid metabolic process cellular catabolic process non-proteinogenic amino acid metabolic process sarcosine catabolic process carboxylic acid catabolic process small molecule metabolic process amino acid catabolic process non-proteinogenic amino acid catabolic process cellular metabolic process carboxylic acid metabolic process sarcosine metabolic process primary metabolic process cellular modified amino acid metabolic process alpha-amino acid catabolic process metabolic process cellular process small molecule catabolic process cellular modified amino acid catabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity
D	Sarcosine oxidase delta subunit	cation binding ion binding binding metal ion binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on the CH-NH group of donors, oxygen as acceptor sarcosine oxidase activity oxidoreductase activity, acting on the CH-NH group of donors catalytic activity	folic acid-containing compound metabolic process cellular metabolic process metabolic process cellular process tetrahydrofolate metabolic process pteridine-containing compound metabolic process cellular modified amino acid metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR028896	Aminomethyltransferase-like	Family
A	IPR013977	Aminomethyltransferase, C-terminal domain	Domain
A	IPR041117	SoxA, A3 domain	Domain
A	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
A	IPR006222	Aminomethyltransferase, folate-binding domain	Domain
A	IPR006277	Sarcosine oxidase, alpha subunit	Family
A	IPR029043	Glycine cleavage T-protein/YgfZ, C-terminal	Homologous Superfamily
A	IPR042204	2Fe-2S iron-sulfur cluster binding domain, N-terminal	Homologous Superfamily
A	IPR027266	GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1	Homologous Superfamily
B	IPR001763	Rhodanese-like domain	Domain
B	IPR006076	FAD dependent oxidoreductase	Domain
B	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
B	IPR006278	Sarcosine oxidase subunit beta	Family
C	IPR006280	Sarcosine oxidase, gamma subunit, heterotetrameric	Family
C	IPR007375	Sarcosine oxidase, gamma subunit	Family
C	IPR027266	GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1	Homologous Superfamily
D	IPR006279	Sarcosine oxidase, delta subunit, heterotetrameric	Family
D	IPR038561	Sarcosine oxidase subunit delta 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.