1X31

Crystal Structure of Heterotetrameric Sarcosine Oxidase from Corynebacterium sp. U-96

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	8091768	4000117	SCOP2 (2022-06-29)
A	SCOP2 Family	2Fe-2S ferredoxin domains from multidomain proteins	8091770	4000241	SCOP2 (2022-06-29)
A	SCOP2 Family	Sarcosine oxidase A3 domain-like	8091772	4007758	SCOP2 (2022-06-29)
A	SCOP2 Family	GcvT aminomethyltransferase-like	8091774	4000062	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Thioredoxin reductase-like	8091769	3000050	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	2Fe-2S ferredoxin-like	8091771	3000113	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Bfd-like	8091773	3002540	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Folate-binding domain-like	8091775	3000025	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Aminomethyltransferase beta-barrel domain-like	8091776	3000024	SCOP2 (2022-06-29)
B	SCOP2 Family	D-aminoacid oxidase-like	8091766	4000124	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Flavoreductase-like	8091767	3000055	SCOP2 (2022-06-29)
C	SCOP2 Family	Sarcosine oxidase, gamma subunit-like	8045654	4004595	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Folate-binding domain-like	8090858	3000025	SCOP2 (2022-06-29)
D	SCOP2 Family	Sarcosine oxidase delta subunit-like	8045651	4004593	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	Sarcosine oxidase delta subunit-like	8090855	3002464	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	GCV_T_C	e1x31A3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: GCV_T_C	ECOD (1.6)
A	soxA	e1x31A4	A: alpha arrays	X: HTH	H: bacterioferritin-associated ferredoxin (From Topology)	T: bacterioferritin-associated ferredoxin	F: soxA	ECOD (1.6)
A	Fer2_4	e1x31A5	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Fer2_4	ECOD (1.6)
A	GCV_T_N	e1x31A7	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	e1x31A6	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	e1x31A8	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	e1x31B3	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	e1x31B2	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	e1x31C1	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	e1x31D1	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	PF12831	FAD dependent oxidoreductase (FAD_oxidored)	FAD dependent oxidoreductase	-	Family
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	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 modified amino acid metabolic process metabolic process cellular process tetrahydrofolate metabolic process pteridine-containing compound metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm
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 modified amino acid metabolic process metabolic process cellular process tetrahydrofolate metabolic process pteridine-containing compound metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm
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 non-proteinogenic amino acid catabolic process carboxylic acid metabolic process modified amino acid metabolic process sarcosine metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process modified amino acid catabolic process alpha-amino acid metabolic process cellular catabolic process non-proteinogenic amino acid metabolic process alpha-amino acid catabolic process catabolic process oxoacid metabolic process non-proteinogenic amino acid catabolic process carboxylic acid metabolic process modified amino acid metabolic process sarcosine metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process modified amino acid catabolic process alpha-amino acid metabolic process cellular catabolic process non-proteinogenic amino acid metabolic process alpha-amino acid catabolic process sarcosine catabolic process carboxylic acid catabolic process metabolic process cellular process small molecule metabolic process small molecule catabolic process amino acid catabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm
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 modified amino acid metabolic process metabolic process cellular process tetrahydrofolate metabolic process pteridine-containing compound metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

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.