1DJN

STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF RECOMBINANT WILD TYPE TRIMETHYLAMINE DEHYDROGENASE FROM METHYLOPHILUS METHYLOTROPHUS (SP. W3A1)

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1djna1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	FMN-linked oxidoreductases	FMN-linked oxidoreductases	Trimethylamine dehydrogenase, N-terminal domain	(Methylophilus methylotrophus W3A1 ) [TaxId: 2327 ],	SCOPe (2.08)
A	d1djna2	Alpha and beta proteins (a/b)	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	C-terminal domain of adrenodoxin reductase-like	Trimethylamine dehydrogenase, C-terminal domain	(Methylophilus methylotrophus W3A1 ) [TaxId: 2327 ],	SCOPe (2.08)
A	d1djna3	Alpha and beta proteins (a/b)	Nucleotide-binding domain	Nucleotide-binding domain	N-terminal domain of adrenodoxin reductase-like	Trimethylamine dehydrogenase, middle domain	(Methylophilus methylotrophus W3A1 ) [TaxId: 2327 ],	SCOPe (2.08)
B	d1djnb1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	FMN-linked oxidoreductases	FMN-linked oxidoreductases	Trimethylamine dehydrogenase, N-terminal domain	(Methylophilus methylotrophus W3A1 ) [TaxId: 2327 ],	SCOPe (2.08)
B	d1djnb2	Alpha and beta proteins (a/b)	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	C-terminal domain of adrenodoxin reductase-like	Trimethylamine dehydrogenase, C-terminal domain	(Methylophilus methylotrophus W3A1 ) [TaxId: 2327 ],	SCOPe (2.08)
B	d1djnb3	Alpha and beta proteins (a/b)	Nucleotide-binding domain	Nucleotide-binding domain	N-terminal domain of adrenodoxin reductase-like	Trimethylamine dehydrogenase, middle domain	(Methylophilus methylotrophus W3A1 ) [TaxId: 2327 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Adrenodoxin reductase-like	8001448	4000129	SCOP2 (2022-06-29)
A	SCOP2 Family	FMN-linked oxidoreductases	8001449	4000080	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Thioredoxin reductase-like	8017579	3000050	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	FMN-linked oxidoreductases	8017577	3000014	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Thioredoxin reductase-like	8017579	3000050	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	FMN-linked oxidoreductases	8017577	3000014	SCOP2B (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	Oxidored_FMN	e1djnA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Oxidored_FMN	ECOD (1.6)
A	mycofact_OYE_2	e1djnA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: mycofact_OYE_2	ECOD (1.6)
A	FAD_binding_3_1st	e1djnA3	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	Oxidored_FMN	e1djnB1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Oxidored_FMN	ECOD (1.6)
B	mycofact_OYE_2	e1djnB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: mycofact_OYE_2	ECOD (1.6)
B	FAD_binding_3_1st	e1djnB3	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)
A	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
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)
B	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00724	NADH:flavin oxidoreductase / NADH oxidase family (Oxidored_FMN)	NADH:flavin oxidoreductase / NADH oxidase family	-	Domain
A, B	PF22620	OYE-like second alpha/beta domain (OYE-like_second_a-b)	OYE-like second alpha/beta domain	This domain is found in a group of diverse dehydrogenases from the old yellow enzyme (OYE)-like family, such as histamine dehydrogenase from Nocardioides simplex, trimethylamine dehydrogenase from Methylophilus methylotrophus (sp. W(3)A(1)) and 2-nap ...	This domain is found in a group of diverse dehydrogenases from the old yellow enzyme (OYE)-like family, such as histamine dehydrogenase from Nocardioides simplex, trimethylamine dehydrogenase from Methylophilus methylotrophus (sp. W(3)A(1)) and 2-naphthoyl-CoA reductase (NCR) [1-4], which has been described as a small, second alpha/beta domain [3,4].	Domain
A, B	PF13450	NAD(P)-binding Rossmann-like domain (NAD_binding_8)	NAD(P)-binding Rossmann-like domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	TRIMETHYLAMINE DEHYDROGENASE	binding nucleotide binding FMN binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on the CH-NH group of donors trimethylamine dehydrogenase activity binding nucleotide binding FMN binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on the CH-NH group of donors trimethylamine dehydrogenase activity catalytic activity oxidoreductase activity, acting on the CH-NH group of donors, flavin as acceptor iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding cation binding metal ion binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR037348	TMADH/DMDH, FMN-binding domain	Domain
A, B	IPR001155	NADH:flavin oxidoreductase/NADH oxidase, N-terminal	Domain
A, B	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A, B	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
A, B	IPR051793	NADH:flavin oxidoreductase/NADH oxidase	Family
A, B	IPR054428	TMADH/DMDH/HD, second alpha/beta domain	Domain

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.