Skip to main content

 4GBJ | pdb_00004gbj

Crystal structure of NAD-binding 6-phosphogluconate dehydrogenase from Dyadobacter fermentans

External Resource: Annotation


Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
DFtsJe4gbjD2 A: alpha arraysX: beta-GraspH: Ubiquitin-relatedT: Ubiquitin-likeF: FtsJECOD (v295.2)
DAldedhe4gbjD1 A: alpha arraysX: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4F: AldedhECOD (v295.2)
CFtsJe4gbjC2 A: alpha arraysX: beta-GraspH: Ubiquitin-relatedT: Ubiquitin-likeF: FtsJECOD (v295.2)
CAldedhe4gbjC1 A: alpha arraysX: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4F: AldedhECOD (v295.2)
BFtsJe4gbjB2 A: alpha arraysX: beta-GraspH: Ubiquitin-relatedT: Ubiquitin-likeF: FtsJECOD (v295.2)
BAldedhe4gbjB3 A: alpha arraysX: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4F: AldedhECOD (v295.2)
Ae4gbjA1 A: alpha arraysX: Flavodoxin-likeH: Precorrin-8X methylmutase CbiC/CobHT: Precorrin-8X methylmutase CbiC/CobHF:ECOD (v295.2)
AAldedhe4gbjA2 A: alpha arraysX: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4F: AldedhECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
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
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
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
6-phosphogluconate dehydrogenase NAD-binding - -

InterPro: Protein Family Classification InterPro Database Homepage

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