2YIC

Crystal structure of the SucA domain of Mycobacterium smegmatis alpha- ketoglutarate decarboxylase (triclinic form)

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	2-oxoglutarate dehydrogenase C-terminal domain-like	8046276	4004996	SCOP2 (2022-06-29)
A	SCOP2 Family	Branched-chain alpha-keto acid dehydrogenase PP module	8093317	4003592	SCOP2 (2022-06-29)
A	SCOP2 Family	TK-like Pyr module	8093318	4003561	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	TK C-terminal domain-like	8093316	3000424	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8093319	3001790	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8093320	3001790	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	TK C-terminal domain-like	8093316	3000424	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8093319	3001790	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8093320	3001790	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8093319	3001790	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8093320	3001790	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	TK C-terminal domain-like	8093316	3000424	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8093320	3001790	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8093319	3001790	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	TK C-terminal domain-like	8093316	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	e2yicA4	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	e2yicA6	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	e2yicA5	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	e2yicB3	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	e2yicB1	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	e2yicB2	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)
C	OxoGdeHyase_C	e2yicC4	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)
C	E1_dh	e2yicC6	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)
C	Transket_pyr	e2yicC5	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)
D	OxoGdeHyase_C	e2yicD4	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)
D	E1_dh	e2yicD1	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)
D	Transket_pyr	e2yicD5	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.287.1150	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	TPP helical domain	CATH (4.3.0)
A	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (4.3.0)
A	3.40.50.12470	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	3.40.50.11610	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal domain	CATH (4.3.0)
B	1.10.287.1150	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	TPP helical domain	CATH (4.3.0)
B	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (4.3.0)
B	3.40.50.12470	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
B	3.40.50.11610	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal domain	CATH (4.3.0)
C	1.10.287.1150	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	TPP helical domain	CATH (4.3.0)
C	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (4.3.0)
C	3.40.50.12470	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
C	3.40.50.11610	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal domain	CATH (4.3.0)
D	1.10.287.1150	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	TPP helical domain	CATH (4.3.0)
D	3.40.50.970	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains	CATH (4.3.0)
D	3.40.50.12470	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
D	3.40.50.11610	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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, C, D	PF16870	2-oxoglutarate dehydrogenase C-terminal (OxoGdeHyase_C)	2-oxoglutarate dehydrogenase C-terminal	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	2-OXOGLUTARATE DECARBOXYLASE	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding 2-oxoglutarate decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity 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 cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding 2-oxoglutarate decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity 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 S-succinyltransferase activity catalytic activity, acting on a protein acyltransferase activity acyltransferase activity, transferring groups other than amino-acyl groups transferase activity S-acyltransferase activity dihydrolipoyllysine-residue succinyltransferase activity succinyltransferase activity vitamin binding thiamine pyrophosphate binding organic cyclic compound binding anion binding quaternary ammonium group binding heterocyclic compound binding sulfur compound binding 2-hydroxy-3-oxoadipate synthase activity transketolase or transaldolase activity	aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds cellular metabolic process metabolic process cellular process primary metabolic process generation of precursor metabolites and energy	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR001078	2-oxoacid dehydrogenase acyltransferase, catalytic domain	Domain
A, B, C, D	IPR031717	Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal	Domain
A, B, C, D	IPR042179	Multifunctional 2-oxoglutarate metabolism enzyme, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D	IPR029061	Thiamin diphosphate-binding fold	Homologous Superfamily
A, B, C, D	IPR023213	Chloramphenicol acetyltransferase-like domain superfamily	Homologous Superfamily
A, B, C, D	IPR032106	2-oxoglutarate dehydrogenase E1 component, N-terminal domain	Domain
A, B, C, D	IPR005475	Transketolase-like, pyrimidine-binding domain	Domain
A, B, C, D	IPR011603	2-oxoglutarate dehydrogenase E1 component	Family
A, B, C, D	IPR001017	Dehydrogenase, E1 component	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.