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	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 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 Superfamily	Bfd-like	8091773	3002540	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Aminomethyltransferase beta-barrel domain-like	8091776	3000024	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Folate-binding domain-like	8091775	3000025	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)
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	PF08669	e1x31A3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: PF08669	ECOD (1.6)
A	PF17806	e1x31A4	A: alpha arrays	X: HTH	H: bacterioferritin-associated ferredoxin (From Topology)	T: bacterioferritin-associated ferredoxin	F: PF17806	ECOD (1.6)
A	PF13510	e1x31A5	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF13510	ECOD (1.6)
A	PF01571	e1x31A7	A: a+b two layers	X: Alpha-beta plaits	H: Aminomethyltransferase folate-binding domain (From Topology)	T: Aminomethyltransferase folate-binding domain	F: PF01571	ECOD (1.6)
A	PF07992	e1x31A8	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F: PF07992	ECOD (1.6)
B	F_UNCLASSIFIED	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: F_UNCLASSIFIED	ECOD (1.6)
B	PF01266	e1x31B2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: PF01266	ECOD (1.6)
C	PF04268	e1x31C1	A: a+b two layers	X: Alpha-beta plaits	H: Aminomethyltransferase folate-binding domain (From Topology)	T: Aminomethyltransferase folate-binding domain	F: PF04268	ECOD (1.6)
D	PF04267	e1x31D1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: PF04267	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	organic cyclic compound metabolic process organic substance metabolic process organonitrogen compound metabolic process 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	organic cyclic compound metabolic process organic substance metabolic process organonitrogen compound metabolic process 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 organic substance metabolic process sarcosine catabolic process carboxylic acid catabolic process small molecule metabolic process amino acid catabolic process organonitrogen compound catabolic 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 organic substance metabolic process sarcosine catabolic process carboxylic acid catabolic process small molecule metabolic process amino acid catabolic process organonitrogen compound catabolic process organonitrogen compound metabolic 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 organic substance 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	organic cyclic compound metabolic process organic substance metabolic process organonitrogen compound metabolic process 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	IPR013977	Glycine cleavage T-protein, C-terminal barrel domain	Domain
A	IPR028896	Aminomethyltransferase-like	Family
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 National Science Foundation (DBI-1832184), 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 R01GM133198.