1UMD | pdb_00001umd

branched-chain 2-oxo acid dehydrogenase (E1) from Thermus thermophilus HB8 with 4-methyl-2-oxopentanoate as an intermediate

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	d1umdd1	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	Branched-chain alpha-keto acid dehydrogenase Pyr module	Branched-chain alpha-keto acid dehydrogenase, Pyr module	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
D	d1umdd2	Alpha and beta proteins (a/b)	TK C-terminal domain-like	TK C-terminal domain-like	Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain	Branched-chain alpha-keto acid dehydrogenase	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
B	d1umdb1	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	Branched-chain alpha-keto acid dehydrogenase Pyr module	Branched-chain alpha-keto acid dehydrogenase, Pyr module	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
B	d1umdb2	Alpha and beta proteins (a/b)	TK C-terminal domain-like	TK C-terminal domain-like	Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain	Branched-chain alpha-keto acid dehydrogenase	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
C	d1umdc_	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	Branched-chain alpha-keto acid dehydrogenase PP module	Branched-chain alpha-keto acid dehydrogenase, PP module	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)
A	d1umda_	Alpha and beta proteins (a/b)	Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	Branched-chain alpha-keto acid dehydrogenase PP module	Branched-chain alpha-keto acid dehydrogenase, PP module	(Thermus thermophilus ) [TaxId: 274 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	TK C-terminal domain-like	8041901	3000424	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8041900	3001790	SCOP2B (2022-06-29)
B	SCOP2 Family	Branched-chain alpha-keto acid dehydrogenase Pyr module	8029521	4003570	SCOP2 (2022-06-29)
B	SCOP2 Family	BCKDE1B C-terminal domain-like	8029522	4000496	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8041900	3001790	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	TK C-terminal domain-like	8041901	3000424	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8041906	3001790	SCOP2B (2022-06-29)
A	SCOP2 Family	Branched-chain alpha-keto acid dehydrogenase PP module	8029527	4003592	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8041906	3001790	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	Pribosyltran	e1umdD1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Pribosyltran	ECOD (v294.1)
D	E1_dh	e1umdD2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: E1_dh	ECOD (v294.1)
B	Pribosyltran	e1umdB1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Pribosyltran	ECOD (v294.1)
B	E1_dh	e1umdB2	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: E1_dh	ECOD (v294.1)
C	Esterase	e1umdC1	A: a/b three-layered sandwiches	X: HTH	H: HTH	T: winged helix domain	F: Esterase	ECOD (v294.1)
A	E1_dh	e1umdA1	A: a/b three-layered sandwiches	X: Thiamin diphosphate-binding fold (THDP-binding)	H: Thiamin diphosphate-binding fold (THDP-binding)	T: Thiamin diphosphate-binding fold (THDP-binding)	F: E1_dh	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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	3.40.50.920	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		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	3.40.50.920	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		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)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, 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
B, D	PF02780	Transketolase, C-terminal domain (Transketolase_C)	Transketolase, C-terminal domain	The C-terminal domain of transketolase has been proposed as a regulatory molecule binding site [2].	Domain
A, C	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
B, D	2-oxo acid dehydrogenase beta subunit	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 branched-chain 2-oxo acid dehydrogenase activity catalytic activity	-	-
A, C	2-oxo acid dehydrogenase alpha subunit	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 branched-chain 2-oxo acid dehydrogenase activity catalytic activity cation binding ion binding binding metal ion binding small molecule binding	catabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process branched-chain amino acid catabolic process carboxylic acid catabolic process metabolic process cellular process small molecule metabolic process branched-chain amino acid metabolic process small molecule catabolic process catabolic process oxoacid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid catabolic process organic acid metabolic process branched-chain amino acid catabolic process carboxylic acid catabolic process metabolic process cellular process small molecule metabolic process branched-chain amino acid metabolic process small molecule catabolic process amino acid catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR005475	Transketolase-like, pyrimidine-binding domain	Domain
B, D	IPR029061	Thiamin diphosphate-binding fold	Homologous Superfamily
B, D	IPR009014	Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II	Homologous Superfamily
B, D	IPR033248	Transketolase, C-terminal domain	Domain
A, C	IPR029061	Thiamin diphosphate-binding fold	Homologous Superfamily
A, C	IPR050771	Alpha-ketoacid dehydrogenase complex E1 component	Family
A, C	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.