3PDU | pdb_00003pdu

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

External Resource: Annotation


Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
Hd3pduh2 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)
Hd3pduh1 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)
Hd3pduh3 Artifacts Tags Tags Tags C-terminal Tags (Geobacter sulfurreducens ) [TaxId: 35554 ], SCOPe (2.08)
Gd3pdug2 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)
Gd3pdug1 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)
Fd3pduf2 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)
Fd3pduf1 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)
Fd3pduf3 Artifacts Tags Tags Tags C-terminal Tags (Geobacter sulfurreducens ) [TaxId: 35554 ], SCOPe (2.08)
Ed3pdue2 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)
Ed3pdue1 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)
Ed3pdue3 Artifacts Tags Tags Tags C-terminal Tags (Geobacter sulfurreducens ) [TaxId: 35554 ], SCOPe (2.08)
Dd3pdud2 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)
Dd3pdud1 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)
Dd3pdud3 Artifacts Tags Tags Tags C-terminal Tags (Geobacter sulfurreducens ) [TaxId: 35554 ], SCOPe (2.08)
Cd3pduc2 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)
Cd3pduc1 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)
Cd3pduc3 Artifacts Tags Tags Tags C-terminal Tags (Geobacter sulfurreducens ) [TaxId: 35554 ], SCOPe (2.08)
Bd3pdub2 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)
Bd3pdub1 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)
Bd3pdub3 Artifacts Tags Tags Tags C-terminal Tags (Geobacter sulfurreducens ) [TaxId: 35554 ], SCOPe (2.08)
Ad3pdua2 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)
Ad3pdua1 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)
Ad3pdua3 Artifacts Tags Tags Tags C-terminal Tags (Geobacter sulfurreducens ) [TaxId: 35554 ], SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
HNAD_binding_11e3pduH3 A: alpha arraysX: 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-likeF: NAD_binding_11ECOD (1.6)
HNAD_binding_2e3pduH2 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: NAD(P)-binding Rossmann-fold domainsF: NAD_binding_2ECOD (1.6)
GNAD_binding_11e3pduG3 A: alpha arraysX: 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-likeF: NAD_binding_11ECOD (1.6)
GNAD_binding_2e3pduG2 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: NAD(P)-binding Rossmann-fold domainsF: NAD_binding_2ECOD (1.6)
FNAD_binding_11e3pduF1 A: alpha arraysX: 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-likeF: NAD_binding_11ECOD (1.6)
FNAD_binding_2e3pduF2 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: NAD(P)-binding Rossmann-fold domainsF: NAD_binding_2ECOD (1.6)
ENAD_binding_11e3pduE1 A: alpha arraysX: 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-likeF: NAD_binding_11ECOD (1.6)
ENAD_binding_2e3pduE2 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: NAD(P)-binding Rossmann-fold domainsF: NAD_binding_2ECOD (1.6)
DNAD_binding_11e3pduD1 A: alpha arraysX: 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-likeF: NAD_binding_11ECOD (1.6)
DNAD_binding_2e3pduD2 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: NAD(P)-binding Rossmann-fold domainsF: NAD_binding_2ECOD (1.6)
CNAD_binding_11e3pduC1 A: alpha arraysX: 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-likeF: NAD_binding_11ECOD (1.6)
CNAD_binding_2e3pduC2 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: NAD(P)-binding Rossmann-fold domainsF: NAD_binding_2ECOD (1.6)
BNAD_binding_11e3pduB3 A: alpha arraysX: 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-likeF: NAD_binding_11ECOD (1.6)
BNAD_binding_2e3pduB2 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: NAD(P)-binding Rossmann-fold domainsF: NAD_binding_2ECOD (1.6)
ANAD_binding_11e3pduA3 A: alpha arraysX: 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-likeF: NAD_binding_11ECOD (1.6)
ANAD_binding_2e3pduA2 A: a/b three-layered sandwichesX: Rossmann-likeH: Rossmann-relatedT: NAD(P)-binding Rossmann-fold domainsF: NAD_binding_2ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
H3.40.50.720 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold NAD(P)-binding Rossmann-like DomainCATH (4.3.0)
H1.10.1040.10 Mainly Alpha Orthogonal Bundle N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase domain 2CATH (4.3.0)
G3.40.50.720 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold NAD(P)-binding Rossmann-like DomainCATH (4.3.0)
G1.10.1040.10 Mainly Alpha Orthogonal Bundle N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase domain 2CATH (4.3.0)
F3.40.50.720 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold NAD(P)-binding Rossmann-like DomainCATH (4.3.0)
F1.10.1040.10 Mainly Alpha Orthogonal Bundle N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase domain 2CATH (4.3.0)
E3.40.50.720 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold NAD(P)-binding Rossmann-like DomainCATH (4.3.0)
E1.10.1040.10 Mainly Alpha Orthogonal Bundle N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase domain 2CATH (4.3.0)
D3.40.50.720 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold NAD(P)-binding Rossmann-like DomainCATH (4.3.0)
D1.10.1040.10 Mainly Alpha Orthogonal Bundle N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase domain 2CATH (4.3.0)
C3.40.50.720 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold NAD(P)-binding Rossmann-like DomainCATH (4.3.0)
C1.10.1040.10 Mainly Alpha Orthogonal Bundle N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase domain 2CATH (4.3.0)
B3.40.50.720 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold NAD(P)-binding Rossmann-like DomainCATH (4.3.0)
B1.10.1040.10 Mainly Alpha Orthogonal Bundle N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase domain 2CATH (4.3.0)
A3.40.50.720 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold NAD(P)-binding Rossmann-like DomainCATH (4.3.0)
A1.10.1040.10 Mainly Alpha Orthogonal Bundle N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase domain 2CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, B, C, D, E
PF14833NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase (NAD_binding_11)NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase3-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
PF03446NAD binding domain of 6-phosphogluconate dehydrogenase (NAD_binding_2)NAD binding domain of 6-phosphogluconate dehydrogenaseThe NAD binding domain of 6-phosphogluconate dehydrogenase adopts a Rossmann fold. Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, B, C, D, E
3-hydroxyisobutyrate dehydrogenase family protein -

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A, B, C, D, E
IPR0158153-hydroxyisobutyrate dehydrogenase-relatedFamily
A, B, C, D, E
IPR0061156-phosphogluconate dehydrogenase, NADP-bindingDomain
A, B, C, D, E
IPR051265HIBADH-related NP60 subfamilyFamily
A, B, C, D, E
IPR036291NAD(P)-binding domain superfamilyHomologous Superfamily
A, B, C, D, E
IPR0133286-phosphogluconate dehydrogenase, domain 2Homologous Superfamily
A, B, C, D, E
IPR0291543-hydroxyisobutyrate dehydrogenase-like, NAD-binding domainDomain
A, B, C, D, E
IPR0022043-hydroxyisobutyrate dehydrogenase-related, conserved siteConserved Site
A, B, C, D, E
IPR0089276-phosphogluconate dehydrogenase-like, C-terminal domain superfamilyHomologous Superfamily