2GAG | pdb_00002gag

Heteroteterameric sarcosine: structure of a diflavin metaloenzyme at 1.85 a resolution

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
C	SCOP2 Family	Sarcosine oxidase, gamma subunit-like	8045655	4004595	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Folate-binding domain-like	8090859	3000025	SCOP2 (2022-06-29)
D	SCOP2 Family	Sarcosine oxidase delta subunit-like	8045652	4004593	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	Sarcosine oxidase delta subunit-like	8090856	3002464	SCOP2 (2022-06-29)
B	SCOP2 Family	D-aminoacid oxidase-like	8064389	4000124	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Flavoreductase-like	8064390	3000055	SCOP2 (2022-06-29)
A	SCOP2 Family	Thioredoxin reductase/Flavin-dependent monoxygenase-like	8091757	4000117	SCOP2 (2022-06-29)
A	SCOP2 Family	2Fe-2S ferredoxin domains from multidomain proteins	8091759	4000241	SCOP2 (2022-06-29)
A	SCOP2 Family	Sarcosine oxidase A3 domain-like	8091761	4007758	SCOP2 (2022-06-29)
A	SCOP2 Family	GcvT aminomethyltransferase-like	8091763	4000062	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Thioredoxin reductase-like	8091758	3000050	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	2Fe-2S ferredoxin-like	8091760	3000113	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Bfd-like	8091762	3002540	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Folate-binding domain-like	8091764	3000025	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Aminomethyltransferase beta-barrel domain-like	8091765	3000024	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)
C	SoxG	e2gagC1	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	e2gagD1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: SoxD	ECOD (1.6)
B	DAO_2nd_1	e2gagB3	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	e2gagB2	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)
A	GCV_T_C	e2gagA3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: GCV_T_C	ECOD (1.6)
A	soxA	e2gagA4	A: alpha arrays	X: HTH	H: bacterioferritin-associated ferredoxin (From Topology)	T: bacterioferritin-associated ferredoxin	F: soxA	ECOD (1.6)
A	UNK_F_TYPE	e2gagA8	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: UNK_F_TYPE	ECOD (1.6)
A	GCV_T_N	e2gagA7	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	e2gagA6	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	e2gagA5	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F: FAD_binding_3_1st	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.30.1360.120	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.2.0)
C	3.30.70.1520	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Heterotetrameric sarcosine oxidase	CATH (4.2.0)
D	3.30.2270.10	Alpha Beta	2-Layer Sandwich	Folate-binding fold	Folate-binding superfamily	CATH (4.2.0)
B	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.2.0)
B	3.30.9.10	Alpha Beta	2-Layer Sandwich	D-Amino Acid Oxidase	Chain A, domain 2	CATH (4.2.0)
A	3.30.1360.120	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (utative)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	heterotetrameric 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 non-proteinogenic amino acid metabolic process alpha-amino acid catabolic process sarcosine 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 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	-
D	heterotetrameric 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	-
B	heterotetrameric sarcosine oxidase beta-subunit	binding nucleoside phosphate 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
A	heterotetrameric sarcosine oxidase alpha-subunit	transferase activity, transferring nitrogenous groups transaminase activity transferase activity catalytic activity binding nucleoside phosphate 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	folic acid-containing compound metabolic process modified amino acid metabolic process metabolic process cellular process tetrahydrofolate metabolic process pteridine-containing compound metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR027266	Aminomethyltransferase superfamily	Homologous Superfamily
C	IPR006280	Sarcosine oxidase, gamma subunit, heterotetrameric	Family
C	IPR007375	Sarcosine oxidase, gamma subunit	Family
D	IPR006279	Sarcosine oxidase, delta subunit, heterotetrameric	Family
D	IPR038561	Sarcosine oxidase subunit delta superfamily	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
A	IPR013977	Aminomethyltransferase, C-terminal domain	Domain
A	IPR028896	Aminomethyltransferase-like	Family
A	IPR027266	Aminomethyltransferase superfamily	Homologous Superfamily
A	IPR041117	SoxA, A3 domain	Domain
A	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
A	IPR006222	GCVT, N-terminal domain	Domain
A	IPR006277	Sarcosine oxidase, alpha subunit	Family
A	IPR029043	Glycine cleavage T-protein/YgfZ, C-terminal	Homologous Superfamily
A	IPR023753	FAD/NAD(P)-binding domain	Domain
A	IPR042204	2Fe-2S iron-sulfur cluster binding domain, N-terminal	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.