3PDU

Crystal structure of gamma-hydroxybutyrate dehydrogenase from Geobacter sulfurreducens in complex with NADP+

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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	d3pdua2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	(Geobacter sulfurreducens ) [TaxId: 35554 ],	SCOPe (2.08)
A	d3pdua1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Geobacter sulfurreducens ) [TaxId: 35554 ],	SCOPe (2.08)
A	d3pdua3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Geobacter sulfurreducens ) [TaxId: 35554 ],	SCOPe (2.08)
B	d3pdub2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	(Geobacter sulfurreducens ) [TaxId: 35554 ],	SCOPe (2.08)
B	d3pdub1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Geobacter sulfurreducens ) [TaxId: 35554 ],	SCOPe (2.08)
B	d3pdub3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Geobacter sulfurreducens ) [TaxId: 35554 ],	SCOPe (2.08)
C	d3pduc2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	(Geobacter sulfurreducens ) [TaxId: 35554 ],	SCOPe (2.08)
C	d3pduc1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Geobacter sulfurreducens ) [TaxId: 35554 ],	SCOPe (2.08)
C	d3pduc3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Geobacter sulfurreducens ) [TaxId: 35554 ],	SCOPe (2.08)
D	d3pdud2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	(Geobacter sulfurreducens ) [TaxId: 35554 ],	SCOPe (2.08)
D	d3pdud1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Geobacter sulfurreducens ) [TaxId: 35554 ],	SCOPe (2.08)
D	d3pdud3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Geobacter sulfurreducens ) [TaxId: 35554 ],	SCOPe (2.08)
E	d3pdue2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	(Geobacter sulfurreducens ) [TaxId: 35554 ],	SCOPe (2.08)
E	d3pdue1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Geobacter sulfurreducens ) [TaxId: 35554 ],	SCOPe (2.08)
E	d3pdue3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Geobacter sulfurreducens ) [TaxId: 35554 ],	SCOPe (2.08)
F	d3pduf2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	(Geobacter sulfurreducens ) [TaxId: 35554 ],	SCOPe (2.08)
F	d3pduf1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Geobacter sulfurreducens ) [TaxId: 35554 ],	SCOPe (2.08)
F	d3pduf3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Geobacter sulfurreducens ) [TaxId: 35554 ],	SCOPe (2.08)
G	d3pdug2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	(Geobacter sulfurreducens ) [TaxId: 35554 ],	SCOPe (2.08)
G	d3pdug1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Geobacter sulfurreducens ) [TaxId: 35554 ],	SCOPe (2.08)
H	d3pduh2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	(Geobacter sulfurreducens ) [TaxId: 35554 ],	SCOPe (2.08)
H	d3pduh1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Geobacter sulfurreducens ) [TaxId: 35554 ],	SCOPe (2.08)
H	d3pduh3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Geobacter sulfurreducens ) [TaxId: 35554 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	NAD_binding_11	e3pduA3	A: alpha arrays	X: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	H: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: NAD_binding_11	ECOD (1.6)
A	NAD_binding_2	e3pduA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: NAD_binding_2	ECOD (1.6)
B	NAD_binding_11	e3pduB3	A: alpha arrays	X: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	H: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: NAD_binding_11	ECOD (1.6)
B	NAD_binding_2	e3pduB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: NAD_binding_2	ECOD (1.6)
C	NAD_binding_11	e3pduC1	A: alpha arrays	X: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	H: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: NAD_binding_11	ECOD (1.6)
C	NAD_binding_2	e3pduC2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: NAD_binding_2	ECOD (1.6)
D	NAD_binding_11	e3pduD1	A: alpha arrays	X: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	H: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: NAD_binding_11	ECOD (1.6)
D	NAD_binding_2	e3pduD2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: NAD_binding_2	ECOD (1.6)
E	NAD_binding_11	e3pduE1	A: alpha arrays	X: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	H: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: NAD_binding_11	ECOD (1.6)
E	NAD_binding_2	e3pduE2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: NAD_binding_2	ECOD (1.6)
F	NAD_binding_11	e3pduF1	A: alpha arrays	X: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	H: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: NAD_binding_11	ECOD (1.6)
F	NAD_binding_2	e3pduF2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: NAD_binding_2	ECOD (1.6)
G	NAD_binding_11	e3pduG3	A: alpha arrays	X: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	H: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: NAD_binding_11	ECOD (1.6)
G	NAD_binding_2	e3pduG2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: NAD_binding_2	ECOD (1.6)
H	NAD_binding_11	e3pduH3	A: alpha arrays	X: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	H: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: NAD_binding_11	ECOD (1.6)
H	NAD_binding_2	e3pduH2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: NAD_binding_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
A	1.10.1040.10	Mainly Alpha	Orthogonal Bundle	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase	domain 2	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	1.10.1040.10	Mainly Alpha	Orthogonal Bundle	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase	domain 2	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)
C	1.10.1040.10	Mainly Alpha	Orthogonal Bundle	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase	domain 2	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)
D	1.10.1040.10	Mainly Alpha	Orthogonal Bundle	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase	domain 2	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)
E	1.10.1040.10	Mainly Alpha	Orthogonal Bundle	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase	domain 2	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)
F	1.10.1040.10	Mainly Alpha	Orthogonal Bundle	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase	domain 2	CATH (4.3.0)
G	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
G	1.10.1040.10	Mainly Alpha	Orthogonal Bundle	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase	domain 2	CATH (4.3.0)
H	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
H	1.10.1040.10	Mainly Alpha	Orthogonal Bundle	N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase	domain 2	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, G, H	PF14833	NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase (NAD_binding_11)	NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase	3-Hydroxyisobutyrate is a central metabolite in the valine catabolic pathway, and is reversibly oxidised to methylmalonate semi-aldehyde by a specific dehydrogenase belonging to the 3-hydroxyacid dehydrogenase family. The reaction is NADP-dependent a ...	3-Hydroxyisobutyrate is a central metabolite in the valine catabolic pathway, and is reversibly oxidised to methylmalonate semi-aldehyde by a specific dehydrogenase belonging to the 3-hydroxyacid dehydrogenase family. The reaction is NADP-dependent and this region of the enzyme binds NAD. The NAD-binding domain of 6-phosphogluconate dehydrogenase adopts an alpha helical structure [1].	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	PF03446	NAD binding domain of 6-phosphogluconate dehydrogenase (NAD_binding_2)	NAD binding domain of 6-phosphogluconate dehydrogenase	The NAD binding domain of 6-phosphogluconate dehydrogenase adopts a Rossmann fold.	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, G, H	3-hydroxyisobutyrate dehydrogenase family protein	oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors catalytic activity binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule binding NAD binding	catabolic process cellular metabolic process organic acid catabolic process organic acid metabolic process cellular catabolic process organic substance metabolic process small molecule metabolic process metabolic process cellular process small molecule catabolic process organic substance catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR015815	3-hydroxyisobutyrate dehydrogenase-related	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR006115	6-phosphogluconate dehydrogenase, NADP-binding	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR013328	6-phosphogluconate dehydrogenase, domain 2	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR029154	3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR002204	3-hydroxyisobutyrate dehydrogenase-related, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR008927	6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily	Homologous Superfamily