6VEF

Cryo-EM Structure of Escherichia coli 2-oxoglutarate dehydrogenase E1 component sucA

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8093314	3001790	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	TK C-terminal domain-like	8093311	3000424	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8093315	3001790	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8093314	3001790	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8093315	3001790	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	TK C-terminal domain-like	8093311	3000424	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	OxoGdeHyase_C	e6vefA1	A: a/b three-layered sandwiches	X: TK C-terminal domain-like (From Topology)	H: TK C-terminal domain-like (From Topology)	T: TK C-terminal domain-like	F: OxoGdeHyase_C	ECOD (1.6)
A	E1_dh	e6vefA3	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: E1_dh	ECOD (1.6)
A	Transket_pyr	e6vefA2	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: Transket_pyr	ECOD (1.6)
B	OxoGdeHyase_C	e6vefB3	A: a/b three-layered sandwiches	X: TK C-terminal domain-like (From Topology)	H: TK C-terminal domain-like (From Topology)	T: TK C-terminal domain-like	F: OxoGdeHyase_C	ECOD (1.6)
B	E1_dh	e6vefB2	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: E1_dh	ECOD (1.6)
B	Transket_pyr	e6vefB1	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	H: Thiamin diphosphate-binding fold (THDP-binding) (From Topology)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: Transket_pyr	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02779	Transketolase, pyrimidine binding domain (Transket_pyr)	Transketolase, pyrimidine binding domain	This family includes transketolase enzymes, pyruvate dehydrogenases, and branched chain alpha-keto acid decarboxylases.	Domain
A, B	PF16870	2-oxoglutarate dehydrogenase C-terminal (OxoGdeHyase_C)	2-oxoglutarate dehydrogenase C-terminal	-	Family
A, B	PF00676	Dehydrogenase E1 component (E1_dh)	Dehydrogenase E1 component	This family uses thiamine pyrophosphate as a cofactor. This family includes pyruvate dehydrogenase, 2-oxoglutarate dehydrogenase and 2-oxoisovalerate dehydrogenase.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	2-oxoglutarate dehydrogenase E1 component	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor oxidoreductase activity oxidoreductase activity, acting on the aldehyde or oxo group of donors oxoglutarate dehydrogenase (succinyl-transferring) activity catalytic activity nucleoside phosphate binding nucleotide binding heterocyclic compound binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor oxidoreductase activity oxidoreductase activity, acting on the aldehyde or oxo group of donors oxoglutarate dehydrogenase (succinyl-transferring) activity catalytic activity nucleoside phosphate binding nucleotide binding heterocyclic compound binding vitamin binding thiamine pyrophosphate binding anion binding quaternary ammonium group binding sulfur compound binding identical protein binding protein binding	aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process metabolic process cellular process generation of precursor metabolites and energy	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex oxoglutarate dehydrogenase complex catalytic complex oxidoreductase complex tricarboxylic acid cycle heteromeric enzyme complex alpha-ketoacid dehydrogenase complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR042179	Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal domain superfamily	Homologous Superfamily
A, B	IPR029061	Thiamin diphosphate-binding fold	Homologous Superfamily
A, B	IPR032106	2-oxoglutarate dehydrogenase E1 component, N-terminal domain	Domain
A, B	IPR005475	Transketolase-like, pyrimidine-binding domain	Domain
A, B	IPR011603	2-oxoglutarate dehydrogenase E1 component	Family
A, B	IPR031717	2-oxoglutarate dehydrogenase E1 component/KDG, C-terminal	Domain
A, B	IPR001017	Dehydrogenase, E1 component	Domain

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.