1U8V

Crystal Structure of 4-Hydroxybutyryl-CoA Dehydratase from Clostridium aminobutyricum: Radical catalysis involving a [4Fe-4S] cluster and flavin

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 Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1u8va1	All alpha proteins	Bromodomain-like	Acyl-CoA dehydrogenase C-terminal domain-like	Medium chain acyl-CoA dehydrogenase-like, C-terminal domain	4-hydroxybutyryl-CoA dehydratase AbfD, C-terminal domain	(Clostridium aminobutyricum ) [TaxId: 33953 ],	SCOPe (2.08)
A	d1u8va2	Multi-domain proteins (alpha and beta)	Acyl-CoA dehydrogenase NM domain-like	Acyl-CoA dehydrogenase NM domain-like	Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains	4-hydroxybutyryl-CoA dehydratase AbfD, NM domains	(Clostridium aminobutyricum ) [TaxId: 33953 ],	SCOPe (2.08)
B	d1u8vb1	All alpha proteins	Bromodomain-like	Acyl-CoA dehydrogenase C-terminal domain-like	Medium chain acyl-CoA dehydrogenase-like, C-terminal domain	4-hydroxybutyryl-CoA dehydratase AbfD, C-terminal domain	(Clostridium aminobutyricum ) [TaxId: 33953 ],	SCOPe (2.08)
B	d1u8vb2	Multi-domain proteins (alpha and beta)	Acyl-CoA dehydrogenase NM domain-like	Acyl-CoA dehydrogenase NM domain-like	Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains	4-hydroxybutyryl-CoA dehydratase AbfD, NM domains	(Clostridium aminobutyricum ) [TaxId: 33953 ],	SCOPe (2.08)
C	d1u8vc1	All alpha proteins	Bromodomain-like	Acyl-CoA dehydrogenase C-terminal domain-like	Medium chain acyl-CoA dehydrogenase-like, C-terminal domain	4-hydroxybutyryl-CoA dehydratase AbfD, C-terminal domain	(Clostridium aminobutyricum ) [TaxId: 33953 ],	SCOPe (2.08)
C	d1u8vc2	Multi-domain proteins (alpha and beta)	Acyl-CoA dehydrogenase NM domain-like	Acyl-CoA dehydrogenase NM domain-like	Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains	4-hydroxybutyryl-CoA dehydratase AbfD, NM domains	(Clostridium aminobutyricum ) [TaxId: 33953 ],	SCOPe (2.08)
D	d1u8vd1	All alpha proteins	Bromodomain-like	Acyl-CoA dehydrogenase C-terminal domain-like	Medium chain acyl-CoA dehydrogenase-like, C-terminal domain	4-hydroxybutyryl-CoA dehydratase AbfD, C-terminal domain	(Clostridium aminobutyricum ) [TaxId: 33953 ],	SCOPe (2.08)
D	d1u8vd2	Multi-domain proteins (alpha and beta)	Acyl-CoA dehydrogenase NM domain-like	Acyl-CoA dehydrogenase NM domain-like	Medium chain acyl-CoA dehydrogenase, NM (N-terminal and middle) domains	4-hydroxybutyryl-CoA dehydratase AbfD, NM domains	(Clostridium aminobutyricum ) [TaxId: 33953 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Medium chain acyl-CoA dehydrogenase C-terminal domain-like	8030463	4000821	SCOP2 (2022-06-29)
A	SCOP2 Family	Medium chain acyl-CoA dehydrogenase FAD-binding domain-like	8030464	4002751	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Acyl-CoA dehydrogenase C-terminal domain-like	8042842	3001580	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Acyl-CoA dehydrogenase N-terminal lobe-like	8042843	3001701	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Acyl-CoA dehydrogenase N-terminal lobe-like	8042843	3001701	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Acyl-CoA dehydrogenase C-terminal domain-like	8042842	3001580	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Acyl-CoA dehydrogenase N-terminal lobe-like	8042843	3001701	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Acyl-CoA dehydrogenase C-terminal domain-like	8042842	3001580	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Acyl-CoA dehydrogenase C-terminal domain-like	8042842	3001580	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Acyl-CoA dehydrogenase N-terminal lobe-like	8042843	3001701	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	HpaB_N_C	e1u8vA1	A: beta complex topology	X: Acyl-CoA dehydrogenase middle domain-like (From Topology)	H: Acyl-CoA dehydrogenase middle domain-like (From Topology)	T: Acyl-CoA dehydrogenase middle domain-like	F: HpaB_N_C	ECOD (1.6)
A	HpaB_N_N	e1u8vA2	A: alpha arrays	X: Acyl-CoA dehydrogenase N-terminal domain-like (From Topology)	H: Acyl-CoA dehydrogenase N-terminal domain-like (From Topology)	T: Acyl-CoA dehydrogenase N-terminal domain-like	F: HpaB_N_N	ECOD (1.6)
A	HpaB	e1u8vA3	A: alpha bundles	X: Bromodomain-like	H: Acyl-CoA dehydrogenase C-terminal domain-like (From Topology)	T: Acyl-CoA dehydrogenase C-terminal domain-like	F: HpaB	ECOD (1.6)
B	HpaB_N_C	e1u8vB1	A: beta complex topology	X: Acyl-CoA dehydrogenase middle domain-like (From Topology)	H: Acyl-CoA dehydrogenase middle domain-like (From Topology)	T: Acyl-CoA dehydrogenase middle domain-like	F: HpaB_N_C	ECOD (1.6)
B	HpaB_N_N	e1u8vB2	A: alpha arrays	X: Acyl-CoA dehydrogenase N-terminal domain-like (From Topology)	H: Acyl-CoA dehydrogenase N-terminal domain-like (From Topology)	T: Acyl-CoA dehydrogenase N-terminal domain-like	F: HpaB_N_N	ECOD (1.6)
B	HpaB	e1u8vB3	A: alpha bundles	X: Bromodomain-like	H: Acyl-CoA dehydrogenase C-terminal domain-like (From Topology)	T: Acyl-CoA dehydrogenase C-terminal domain-like	F: HpaB	ECOD (1.6)
C	HpaB_N_C	e1u8vC1	A: beta complex topology	X: Acyl-CoA dehydrogenase middle domain-like (From Topology)	H: Acyl-CoA dehydrogenase middle domain-like (From Topology)	T: Acyl-CoA dehydrogenase middle domain-like	F: HpaB_N_C	ECOD (1.6)
C	HpaB_N_N	e1u8vC2	A: alpha arrays	X: Acyl-CoA dehydrogenase N-terminal domain-like (From Topology)	H: Acyl-CoA dehydrogenase N-terminal domain-like (From Topology)	T: Acyl-CoA dehydrogenase N-terminal domain-like	F: HpaB_N_N	ECOD (1.6)
C	HpaB	e1u8vC3	A: alpha bundles	X: Bromodomain-like	H: Acyl-CoA dehydrogenase C-terminal domain-like (From Topology)	T: Acyl-CoA dehydrogenase C-terminal domain-like	F: HpaB	ECOD (1.6)
D	HpaB_N_C	e1u8vD1	A: beta complex topology	X: Acyl-CoA dehydrogenase middle domain-like (From Topology)	H: Acyl-CoA dehydrogenase middle domain-like (From Topology)	T: Acyl-CoA dehydrogenase middle domain-like	F: HpaB_N_C	ECOD (1.6)
D	HpaB_N_N	e1u8vD2	A: alpha arrays	X: Acyl-CoA dehydrogenase N-terminal domain-like (From Topology)	H: Acyl-CoA dehydrogenase N-terminal domain-like (From Topology)	T: Acyl-CoA dehydrogenase N-terminal domain-like	F: HpaB_N_N	ECOD (1.6)
D	HpaB	e1u8vD3	A: alpha bundles	X: Bromodomain-like	H: Acyl-CoA dehydrogenase C-terminal domain-like (From Topology)	T: Acyl-CoA dehydrogenase C-terminal domain-like	F: HpaB	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.3140.10	Mainly Alpha	Orthogonal Bundle	4-hydroxybutyryl-coa dehydratase, domain 1	4-hydroxybutyryl-coa dehydratase, domain 1	CATH (4.3.0)
A	2.40.110.10	Mainly Beta	Beta Barrel	Butyryl-CoA Dehydrogenase, subunit A	domain 2	CATH (4.3.0)
A	1.20.140.10	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
B	1.10.3140.10	Mainly Alpha	Orthogonal Bundle	4-hydroxybutyryl-coa dehydratase, domain 1	4-hydroxybutyryl-coa dehydratase, domain 1	CATH (4.3.0)
B	2.40.110.10	Mainly Beta	Beta Barrel	Butyryl-CoA Dehydrogenase, subunit A	domain 2	CATH (4.3.0)
B	1.20.140.10	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
C	1.10.3140.10	Mainly Alpha	Orthogonal Bundle	4-hydroxybutyryl-coa dehydratase, domain 1	4-hydroxybutyryl-coa dehydratase, domain 1	CATH (4.3.0)
C	2.40.110.10	Mainly Beta	Beta Barrel	Butyryl-CoA Dehydrogenase, subunit A	domain 2	CATH (4.3.0)
C	1.20.140.10	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
D	1.10.3140.10	Mainly Alpha	Orthogonal Bundle	4-hydroxybutyryl-coa dehydratase, domain 1	4-hydroxybutyryl-coa dehydratase, domain 1	CATH (4.3.0)
D	2.40.110.10	Mainly Beta	Beta Barrel	Butyryl-CoA Dehydrogenase, subunit A	domain 2	CATH (4.3.0)
D	1.20.140.10	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF11794	4-hydroxyphenylacetate 3-hydroxylase N terminal (HpaB_N)	4-hydroxyphenylacetate 3-hydroxylase N terminal	-	Family
A, B, C, D	PF03241	4-hydroxyphenylacetate 3-hydroxylase C terminal (HpaB)	4-hydroxyphenylacetate 3-hydroxylase C terminal	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Gamma-aminobutyrate metabolism dehydratase/isomerase	hydro-lyase activity 4-hydroxybutanoyl-CoA dehydratase activity lyase activity catalytic activity carbon-oxygen lyase activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion binding oxidoreductase activity hydro-lyase activity 4-hydroxybutanoyl-CoA dehydratase activity lyase activity catalytic activity carbon-oxygen lyase activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion binding oxidoreductase activity oxidoreductase activity, acting on the CH-CH group of donors isomerase activity intramolecular oxidoreductase activity, transposing C=C bonds intramolecular oxidoreductase activity vinylacetyl-CoA delta-isomerase activity	metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR009100	Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily	Homologous Superfamily
A, B, C, D	IPR024719	HpaB/PvcC/4-BUDH C-terminal	Domain
A, B, C, D	IPR046373	Acyl-CoA oxidase/dehydrogenase, middle domain superfamily	Homologous Superfamily
A, B, C, D	IPR004925	HpaB/PvcC/4-BUDH	Family
A, B, C, D	IPR036250	Acyl-CoA dehydrogenase-like, C-terminal	Homologous Superfamily
A, B, C, D	IPR024674	HpaB/PvcC/4-BUDH N-terminal	Domain

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

Chains	Enzyme Name	Description	Catalytic Residues
A	4-hydroxybutanoyl-CoA dehydratase M-CSA #750	4-hydroxybutyryl-CoA dehydratase (4-BUDH) catalyses the dehydration of 4-hydroxybutanoyl-CoA to crotonyl-CoA, as well as the isomerisation of vinylacetyl-CoA to crotonyl-CoA. The reaction is mechanistically the most demanding step in the fermentation of gamma-aminobutyrate to ammonia, acetate and butyrate by Clostridium aminobutyricum.	Defined by 8 residues: CYS:A-99CYS:A-103THR:A-190GLU:A-257HIS:A-292TYR:A-296CYS:A-299GLU:A-455 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 4.2 (PDB Primary Data) Search M-CSA Motif + EC 4.2 EC: 5.3.3.3 (PDB Primary Data) Search M-CSA Motif + EC 5.3.3.3

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.