2CVZ | pdb_00002cvz

Structure of hydroxyisobutyrate dehydrogenase from thermus thermophilus HB8

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)
D	d2cvzd1	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	Hydroxyisobutyrate and 6-phosphogluconate dehydrogenase domain	Hydroxyisobutyrate dehydrogenase	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
D	d2cvzd2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	6-phosphogluconate dehydrogenase-like, N-terminal domain	Hydroxyisobutyrate dehydrogenase	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
C	d2cvzc1	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	Hydroxyisobutyrate and 6-phosphogluconate dehydrogenase domain	Hydroxyisobutyrate dehydrogenase	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
C	d2cvzc2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	6-phosphogluconate dehydrogenase-like, N-terminal domain	Hydroxyisobutyrate dehydrogenase	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
B	d2cvzb1	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	Hydroxyisobutyrate and 6-phosphogluconate dehydrogenase domain	Hydroxyisobutyrate dehydrogenase	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
B	d2cvzb2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	6-phosphogluconate dehydrogenase-like, N-terminal domain	Hydroxyisobutyrate dehydrogenase	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
A	d2cvza1	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	Hydroxyisobutyrate and 6-phosphogluconate dehydrogenase domain	Hydroxyisobutyrate dehydrogenase	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)
A	d2cvza2	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	6-phosphogluconate dehydrogenase-like, N-terminal domain	Hydroxyisobutyrate dehydrogenase	(Thermus thermophilus HB8 ) [TaxId: 300852 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	6-phosphogluconate dehydrogenase-like	8001103	3000048	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	6-phosphogluconate dehydrogenase-like	8001103	3000048	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	6-phosphogluconate dehydrogenase-like	8001103	3000048	SCOP2B (2022-06-29)
A	SCOP2 Family	Hydroxyisobutyrate dehydrogenase/6-phosphogluconate dehydrogenase-like	8001102	4000072	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	6-phosphogluconate dehydrogenase-like	8001103	3000048	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)
D		e2cvzD2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: FAD_binding_3	F:	ECOD (20:10:01)
D		e2cvzD3	A: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: MshEN	F:	ECOD (20:10:01)
C		e2cvzC2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: FAD_binding_3	F:	ECOD (20:10:01)
C		e2cvzC1	A: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: MshEN	F:	ECOD (20:10:01)
B		e2cvzB2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: FAD_binding_3	F:	ECOD (20:10:01)
B		e2cvzB1	A: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: MshEN	F:	ECOD (20:10:01)
A		e2cvzA1	A: 6-phosphogluconate dehydrogenase C-terminal domain-like	X: 6-phosphogluconate dehydrogenase C-terminal domain-like	H: 6-phosphogluconate dehydrogenase C-terminal domain-like	T: NAD_binding_11	F:	ECOD (20:10:01)
A		e2cvzA2	A: Rossmann-like	X: Rossmann-related	H: NAD(P)-binding Rossmann-fold domains	T: NAD_binding_2	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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
A, B, C, D	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	3-hydroxyisobutyrate dehydrogenase	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	IPR015815	3-hydroxyisobutyrate dehydrogenase-related	Family
A, B, C, D	IPR006115	6-phosphogluconate dehydrogenase, NADP-binding	Domain
A, B, C, D	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR013328	6-phosphogluconate dehydrogenase, domain 2	Homologous Superfamily
A, B, C, D	IPR029154	3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain	Domain
A, B, C, D	IPR002204	3-hydroxyisobutyrate dehydrogenase-related, conserved site	Conserved Site
A, B, C, D	IPR008927	6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily	Homologous Superfamily

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.