1PJ5

Crystal structure of dimethylglycine oxidase of Arthrobacter globiformis in complex with acetate

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1pj5a1	All beta proteins	Elongation factor/aminomethyltransferase common domain	Aminomethyltransferase beta-barrel domain	Aminomethyltransferase beta-barrel domain	N,N-dimethylglycine oxidase, C-terminal domain	(Arthrobacter globiformis ) [TaxId: 1665 ],	SCOPe (2.08)
A	d1pj5a2	Alpha and beta proteins (a/b)	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	FAD-linked reductases, N-terminal domain	N,N-dimethylglycine oxidase	(Arthrobacter globiformis ) [TaxId: 1665 ],	SCOPe (2.08)
A	d1pj5a3	Alpha and beta proteins (a+b)	FAD-linked reductases, C-terminal domain	FAD-linked reductases, C-terminal domain	L-aminoacid/polyamine oxidase	N,N-dimethylglycine oxidase	(Arthrobacter globiformis ) [TaxId: 1665 ],	SCOPe (2.08)
A	d1pj5a4	Alpha and beta proteins (a+b)	Folate-binding domain	Folate-binding domain	Aminomethyltransferase folate-binding domain	N,N-dimethylglycine oxidase domain 3	(Arthrobacter globiformis ) [TaxId: 1665 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	GcvT aminomethyltransferase-like	8001438	4000062	SCOP2 (2022-06-29)
A	SCOP2 Family	Amine oxidase-like	8001437	4000128	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Aminomethyltransferase beta-barrel domain-like	8056079	3000024	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Folate-binding domain-like	8001552	3000025	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Flavoreductase-like	8017496	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	GCV_T_C	e1pj5A1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: GCV_T_C	ECOD (1.6)
A	KOG2844	e1pj5A3	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: KOG2844	ECOD (1.6)
A	GCV_T_N	e1pj5A6	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	e1pj5A5	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	DAO_1st	e1pj5A4	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	3.50.50.60	Alpha Beta	3-Layer(bba) Sandwich	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	CATH (4.3.0)
A	3.30.9.10	Alpha Beta	2-Layer Sandwich	D-Amino Acid Oxidase	Chain A, domain 2	CATH (4.3.0)
A	3.30.1360.120	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.3.0)
A	3.30.70.1400	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Aminomethyltransferase beta-barrel domains	CATH (4.3.0)
A	2.40.30.110	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF16350	FAD dependent oxidoreductase central domain (FAO_M)	FAD dependent oxidoreductase central domain	-	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	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
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	N,N-dimethylglycine oxidase	dimethylglycine oxidase activity oxidoreductase activity oxidoreductase activity, acting on the CH-NH group of donors, oxygen as acceptor oxidoreductase activity, acting on the CH-NH group of donors catalytic activity binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding small molecule binding	-	-

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	IPR032503	FAD dependent oxidoreductase, central domain	Domain
A	IPR029043	Glycine cleavage T-protein/YgfZ, C-terminal	Homologous Superfamily
A	IPR006076	FAD dependent oxidoreductase	Domain
A	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
A	IPR006222	Aminomethyltransferase, folate-binding domain	Domain
A	IPR027266	GTP-binding protein TrmE/Aminomethyltransferase GcvT, domain 1	Homologous Superfamily

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	dimethylglycine oxidase (tetrahydrofolate utilising) M-CSA #879	Catalyses the oxidative demethylation of N,N-dimethylglycine to yield sarcosine, 5,10-methylenetetrahydrofolate and hydrogen peroxide. The oxidation of dimethylglycine is coupled to the synthesis of 5,10-methylenetetrahydrofolate through an unusual substrate channelling mechanism. This channelling occurs by non-biased diffusion of the iminium intermediate through a large solvent cavity connecting active site 1 (N-terminus) and active site 2 (C-terminus). The synthesis of 5,10-methylenetetrahydrofolate (at active site 2) prevents the accumulation of formaldehyde (not shown), formed by hydrolysis of the iminium intermediate product (at active site 1).	Defined by 3 residues: HIS:A-225TYR:A-259ASP:A-552 \| Explore in 3D: M-CSA Motif Definition Extent of motif is too large to support Structure Motif searching. EC: 1.5.3.10 (PDB Primary Data)

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.