1Y9E

Crystal structure of Bacillus subtilis protein yhfP with NAD bound

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	d1y9ea1	All beta proteins	GroES-like	GroES-like	Alcohol dehydrogenase-like, N-terminal domain	Hypothetical protein YhfP	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
A	d1y9ea2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Alcohol dehydrogenase-like, C-terminal domain	Hypothetical protein YhfP	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d1y9eb1	All beta proteins	GroES-like	GroES-like	Alcohol dehydrogenase-like, N-terminal domain	Hypothetical protein YhfP	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
B	d1y9eb2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Alcohol dehydrogenase-like, C-terminal domain	Hypothetical protein YhfP	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
C	d1y9ec1	All beta proteins	GroES-like	GroES-like	Alcohol dehydrogenase-like, N-terminal domain	Hypothetical protein YhfP	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
C	d1y9ec2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Alcohol dehydrogenase-like, C-terminal domain	Hypothetical protein YhfP	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
D	d1y9ed1	All beta proteins	GroES-like	GroES-like	Alcohol dehydrogenase-like, N-terminal domain	Hypothetical protein YhfP	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
D	d1y9ed2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Alcohol dehydrogenase-like, C-terminal domain	Hypothetical protein YhfP	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
E	d1y9ee1	All beta proteins	GroES-like	GroES-like	Alcohol dehydrogenase-like, N-terminal domain	Hypothetical protein YhfP	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
E	d1y9ee2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Alcohol dehydrogenase-like, C-terminal domain	Hypothetical protein YhfP	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
F	d1y9ef1	All beta proteins	GroES-like	GroES-like	Alcohol dehydrogenase-like, N-terminal domain	Hypothetical protein YhfP	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
F	d1y9ef2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Alcohol dehydrogenase-like, C-terminal domain	Hypothetical protein YhfP	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	GroES-like	8057548	3000002	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Zinc-containing alcohol dehydrogenase-like	8057549	3000040	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	GroES-like	8057548	3000002	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Zinc-containing alcohol dehydrogenase-like	8057549	3000040	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Zinc-containing alcohol dehydrogenase-like	8057549	3000040	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	GroES-like	8057548	3000002	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	GroES-like	8057548	3000002	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Zinc-containing alcohol dehydrogenase-like	8057549	3000040	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Zinc-containing alcohol dehydrogenase-like	8057549	3000040	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	GroES-like	8057548	3000002	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	GroES-like	8057548	3000002	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Zinc-containing alcohol dehydrogenase-like	8057549	3000040	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	ADH_N	e1y9eA1	A: beta barrels	X: GroES-like	H: GroES-related	T: Alcohol dehydrogenase-like, N-terminal domain	F: ADH_N	ECOD (1.6)
A	ADH_zinc_N	e1y9eA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: ADH_zinc_N	ECOD (1.6)
B	ADH_N	e1y9eB1	A: beta barrels	X: GroES-like	H: GroES-related	T: Alcohol dehydrogenase-like, N-terminal domain	F: ADH_N	ECOD (1.6)
B	ADH_zinc_N	e1y9eB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: ADH_zinc_N	ECOD (1.6)
C	ADH_N	e1y9eC1	A: beta barrels	X: GroES-like	H: GroES-related	T: Alcohol dehydrogenase-like, N-terminal domain	F: ADH_N	ECOD (1.6)
C	ADH_zinc_N	e1y9eC2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: ADH_zinc_N	ECOD (1.6)
D	ADH_N	e1y9eD1	A: beta barrels	X: GroES-like	H: GroES-related	T: Alcohol dehydrogenase-like, N-terminal domain	F: ADH_N	ECOD (1.6)
D	ADH_zinc_N	e1y9eD2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: ADH_zinc_N	ECOD (1.6)
E	ADH_N	e1y9eE1	A: beta barrels	X: GroES-like	H: GroES-related	T: Alcohol dehydrogenase-like, N-terminal domain	F: ADH_N	ECOD (1.6)
E	ADH_zinc_N	e1y9eE2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: ADH_zinc_N	ECOD (1.6)
F	ADH_N	e1y9eF1	A: beta barrels	X: GroES-like	H: GroES-related	T: Alcohol dehydrogenase-like, N-terminal domain	F: ADH_N	ECOD (1.6)
F	ADH_zinc_N	e1y9eF2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: ADH_zinc_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.180.10	Alpha Beta	Alpha-Beta Complex	Quinone Oxidoreductase	Chain A, domain 1	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)
B	3.90.180.10	Alpha Beta	Alpha-Beta Complex	Quinone Oxidoreductase	Chain A, domain 1	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)
C	3.90.180.10	Alpha Beta	Alpha-Beta Complex	Quinone Oxidoreductase	Chain A, domain 1	CATH (4.3.0)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
D	3.90.180.10	Alpha Beta	Alpha-Beta Complex	Quinone Oxidoreductase	Chain A, domain 1	CATH (4.3.0)
D	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
E	3.90.180.10	Alpha Beta	Alpha-Beta Complex	Quinone Oxidoreductase	Chain A, domain 1	CATH (4.3.0)
E	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
F	3.90.180.10	Alpha Beta	Alpha-Beta Complex	Quinone Oxidoreductase	Chain A, domain 1	CATH (4.3.0)
F	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF00107	Zinc-binding dehydrogenase (ADH_zinc_N)	Zinc-binding dehydrogenase	-	Domain
A, B, C, D, E A, B, C, D, E, F	PF08240	Alcohol dehydrogenase GroES-like domain (ADH_N)	Alcohol dehydrogenase GroES-like domain	This is the catalytic domain of alcohol dehydrogenases. Many of them contain an inserted zinc binding domain. This domain has a GroES-like structure [1-2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	hypothetical protein yhfP	oxidoreductase activity oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor acryloyl-CoA reductase (NADPH) activity oxidoreductase activity, acting on the CH-CH group of donors catalytic activity	-	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR013154	Alcohol dehydrogenase-like, N-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR051397	Zinc-containing alcohol dehydrogenase-like protein	Family
A, B, C, D, E A, B, C, D, E, F	IPR011032	GroES-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR013149	Alcohol dehydrogenase-like, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR014188	Acrylyl-CoA reductase AcuI	Family
A, B, C, D, E A, B, C, D, E, F	IPR020843	Polyketide synthase, enoylreductase 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.