Annotations: 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
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	Amine oxidase-like	8001437	4000128	SCOP2 (2022-06-29)
A	SCOP2 Family	GcvT aminomethyltransferase-like	8001438	4000062	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Flavoreductase-like	8017496	3000055	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Folate-binding domain-like	8001552	3000025	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Aminomethyltransferase beta-barrel domain-like	8056079	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)
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 (v294.2)
A		e1pj5A4	A: beta barrels	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F:	ECOD (v294.2)
A	GCV_T	e1pj5A5	A: beta barrels	X: SMI1/KNR4-like	H: SMI1/KNR4-like	T: SMI1/KNR4-like	F: GCV_T	ECOD (v294.2)

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)

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 nucleotide binding heterocyclic compound binding small molecule binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR028896	Aminomethyltransferase-like	Family
A	IPR013977	Aminomethyltransferase, C-terminal domain	Domain
A	IPR027266	Aminomethyltransferase superfamily	Homologous Superfamily
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	GCVT, N-terminal domain	Domain

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)

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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.