2TMD

CORRELATION OF X-RAY DEDUCED AND EXPERIMENTAL AMINO ACID SEQUENCES OF TRIMETHYLAMINE DEHYDROGENASE

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	d2tmda1	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	d2tmda2	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	d2tmda3	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	d2tmdb1	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	d2tmdb2	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	d2tmdb3	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	SCOP2B Superfamily	Thioredoxin reductase-like	8017579	3000050	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	FMN-linked oxidoreductases	8017577	3000014	SCOP2B (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	PF00724	e2tmdA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF00724	ECOD (1.6)
A	PF22620	e2tmdA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: PF22620	ECOD (1.6)
A	PF07992	e2tmdA3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F: PF07992	ECOD (1.6)
B	PF00724	e2tmdB1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF00724	ECOD (1.6)
B	PF22620	e2tmdB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: PF22620	ECOD (1.6)
B	PF07992	e2tmdB3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F: PF07992	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	PF07992	Pyridine nucleotide-disulphide oxidoreductase (Pyr_redox_2)	Pyridine nucleotide-disulphide oxidoreductase	This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases. This domain is actually a small NADH binding domain within a larger FAD binding domain.	Domain
A, B	PF00724	NADH:flavin oxidoreductase / NADH oxidase family (Oxidored_FMN)	NADH:flavin oxidoreductase / NADH oxidase family	-	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	IPR001155	NADH:flavin oxidoreductase/NADH oxidase, N-terminal	Domain
A, B	IPR037348	Trimethylamine dehydrogenase/Dimethylamine dehydrogenase, FMN-binding domain	Domain
A, B	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A, B	IPR023753	FAD/NAD(P)-binding domain	Domain
A, B	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily

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

Chains	Enzyme Name	Description	Catalytic Residues
A	trimethylamine dehydrogenase M-CSA #114	Trimethylamine dehydrogenase (TMADH) is an iron-sulfur flavoprotein that catalyses the oxidative demethylation of trimethylamine to form dimethylamine and formaldehyde. It contains a unique flavin, in the form of a 6-S-cysteinyl FMN, which is bent by approximately 25 degrees along the N5-N10 axis of the flavin isoalloxazine ring.	Defined by 4 residues: CYS:A-30TYR:A-169HIS:A-172ASP:A-267 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.5.99.7 (PDB Primary Data) Search M-CSA Motif + EC 1.5.99.7

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.