1PS9

The Crystal Structure and Reaction Mechanism of E. coli 2,4-Dienoyl CoA Reductase

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	d1ps9a1	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	FMN-linked oxidoreductases	FMN-linked oxidoreductases	2,4-dienoyl-CoA reductase, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1ps9a2	Alpha and beta proteins (a/b)	FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	C-terminal domain of adrenodoxin reductase-like	2,4-dienoyl-CoA reductase, C-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d1ps9a3	Alpha and beta proteins (a/b)	Nucleotide-binding domain	Nucleotide-binding domain	N-terminal domain of adrenodoxin reductase-like	2,4-dienoyl-CoA reductase, middle domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	FMN-linked oxidoreductases	8001461	4000080	SCOP2 (2022-06-29)
A	SCOP2 Family	Adrenodoxin reductase-like	8001459	4000129	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	FMN-linked oxidoreductases	8017586	3000014	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Thioredoxin reductase-like	8017588	3000050	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	Oxidored_FMN	e1ps9A1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Oxidored_FMN	ECOD (1.6)
A	Pyr_redox_2_1	e1ps9A2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Pyr_redox_2_1	ECOD (1.6)
A	Pyr_redox_2	e1ps9A3	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Nucleotide-binding domain	F: Pyr_redox_2	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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	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	2,4-dienoyl-CoA reductase	oxidoreductase activity oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on the CH-CH group of donors catalytic activity 2,4-dienoyl-CoA reductase (NADPH) activity binding nucleotide binding FMN binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding heterocyclic compound binding carbohydrate derivative binding oxidoreductase activity oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on the CH-CH group of donors catalytic activity 2,4-dienoyl-CoA reductase (NADPH) 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 iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding FAD binding flavin adenine dinucleotide binding cation binding metal ion binding	catabolic process oxoacid metabolic process organic acid catabolic process organic acid metabolic process cellular lipid catabolic process cellular catabolic process organic substance metabolic process monocarboxylic acid catabolic process fatty acid oxidation carboxylic acid catabolic process fatty acid beta-oxidation small molecule metabolic process lipid oxidation fatty acid metabolic process catabolic process oxoacid metabolic process organic acid catabolic process organic acid metabolic process cellular lipid catabolic process cellular catabolic process organic substance metabolic process monocarboxylic acid catabolic process fatty acid oxidation carboxylic acid catabolic process fatty acid beta-oxidation small molecule metabolic process lipid oxidation fatty acid metabolic process lipid catabolic process cellular metabolic process carboxylic acid metabolic process primary metabolic process lipid modification fatty acid catabolic process fatty acid beta-oxidation, unsaturated, even number, reductase/isomerase pathway cellular lipid metabolic process metabolic process cellular process monocarboxylic acid metabolic process small molecule catabolic process organic substance catabolic process fatty acid beta-oxidation, unsaturated, even number lipid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001155	NADH:flavin oxidoreductase/NADH oxidase, N-terminal	Domain
A	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A	IPR023753	FAD/NAD(P)-binding domain	Domain
A	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	2,4-dienoyl-CoA reductase (NADPH) M-CSA #108	2,4-dienoyl-CoA reductase (DCR) in E. coli is an iron-sulfur flavoenzyme which contains FMN, FAD, and a 4Fe-4S cluster. It is also a monomer, unlike that of its eukaryotic counterparts which form homotetramers and lack the flavin and iron-sulfur cofactors. DCR utilises NADPH to remove the C4-C5 double bond of unsaturated fatty acids. DCR is unusual in that it lacks stereospecificity, catalysing the reduction of both natural fatty acids with cis double bonds, as well as substrates containing trans double bonds, this might be explained by the large size of the substrate binding pocket [PMID:12840019].	Defined by 5 residues: GLU:A-164TYR:A-166ARG:A-214HIS:A-252GLN:A-339 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.3.1.34 (PDB Primary Data) Search M-CSA Motif + EC 1.3.1.34

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.