3PDU | pdb_00003pdu

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	Ribosomal_L25p	e3pduA2	A: alpha bundles	X: ETN0001 domain-like	H: ETN0001 domain-like	T: NAC/WRKY/GCM/WOPR domain	F: Ribosomal_L25p	ECOD (develop294)
A	Amidase_2	e3pduA3	A: alpha bundles	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: Amidase_2	ECOD (develop294)
B	V-set	e3pduB2	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: V-set	ECOD (develop294)
B	Amidase_2	e3pduB3	A: alpha bundles	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: Amidase_2	ECOD (develop294)
C	V-set	e3pduC2	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: V-set	ECOD (develop294)
C	Amidase_2	e3pduC1	A: alpha bundles	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: Amidase_2	ECOD (develop294)
D	V-set	e3pduD2	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: V-set	ECOD (develop294)
D	Amidase_2	e3pduD1	A: alpha bundles	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: Amidase_2	ECOD (develop294)
E	V-set	e3pduE2	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: V-set	ECOD (develop294)
E	Amidase_2	e3pduE1	A: alpha bundles	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: Amidase_2	ECOD (develop294)
F	V-set	e3pduF2	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: V-set	ECOD (develop294)
F	Amidase_2	e3pduF1	A: alpha bundles	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: Amidase_2	ECOD (develop294)
G	V-set	e3pduG2	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: V-set	ECOD (develop294)
G	Amidase_2	e3pduG3	A: alpha bundles	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: Amidase_2	ECOD (develop294)
H	V-set	e3pduH2	A: alpha bundles	X: beta-Grasp	H: HTH	T: winged helix domain	F: V-set	ECOD (develop294)
H	Amidase_2	e3pduH3	A: alpha bundles	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: Amidase_2	ECOD (develop294)

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 catalytic activity binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule binding NAD binding	catabolic process small molecule metabolic process metabolic process cellular process organic acid catabolic process organic acid metabolic process small molecule 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	IPR051265	HIBADH-related NP60 subfamily	Family
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