2BFD | pdb_00002bfd

Reactivity modulation of human branched-chain alpha-ketoacid dehydrogenase by an internal molecular switch

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d2bfdb1	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	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2bfdb2	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	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2bfda1	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	HUMAN (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8037947	3001790	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	TK C-terminal domain-like	8037948	3000424	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Thiamin diphosphate-binding fold (THDP-binding)	8032827	3001790	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)
B		e2bfdB1	A: Flavodoxin-like	X: Class I glutamine amidotransferase-like	H: TK C-terminal domain-like	T: Transketolase_C	F:	ECOD (20:10:01)
B		e2bfdB2	A: Thiamin diphosphate-binding fold (THDP-binding)	X: Thiamin diphosphate-binding fold (THDP-binding)	H: Thiamin diphosphate-binding fold (THDP-binding)	T: Transket_pyr	F:	ECOD (20:10:01)
A		e2bfdA1	A: Thiamin diphosphate-binding fold (THDP-binding)	X: Thiamin diphosphate-binding fold (THDP-binding)	H: Thiamin diphosphate-binding fold (THDP-binding)	T: E1_dh	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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	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	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	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	2-OXOISOVALERATE 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	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 nucleobase-containing compound metabolic process acyl-CoA metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process sulfur compound metabolic process fatty-acyl-CoA metabolic process phosphorus metabolic process branched-chain alpha-keto acid decarboxylation to branched-chain acyl-CoA nucleoside phosphate metabolic process purine-containing compound metabolic process fatty acid derivative metabolic process organophosphate metabolic process lipid metabolic process response to nutrient levels response to stimulus response to chemical response to nutrient	protein-containing complex catalytic complex branched-chain alpha-ketoacid dehydrogenase complex oxidoreductase complex transferase complex alpha-ketoacid dehydrogenase complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex catalytic complex branched-chain alpha-ketoacid dehydrogenase complex oxidoreductase complex transferase complex alpha-ketoacid dehydrogenase complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membraneless organelle nucleolus intracellular organelle lumen organelle lumen membraneless organelle nuclear lumen nucleoplasm mitochondrial matrix
A	2-OXOISOVALERATE 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 carboxy-lyase activity lyase activity carbon-carbon lyase activity	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 nucleobase-containing compound metabolic process acyl-CoA metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process sulfur compound metabolic process fatty-acyl-CoA metabolic process phosphorus metabolic process branched-chain alpha-keto acid decarboxylation to branched-chain acyl-CoA nucleoside phosphate metabolic process purine-containing compound metabolic process fatty acid derivative metabolic process organophosphate metabolic process lipid metabolic process	protein-containing complex catalytic complex branched-chain alpha-ketoacid dehydrogenase complex oxidoreductase complex transferase complex alpha-ketoacid dehydrogenase complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex catalytic complex branched-chain alpha-ketoacid dehydrogenase complex oxidoreductase complex transferase complex alpha-ketoacid dehydrogenase complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR029061	Thiamin diphosphate-binding fold	Homologous Superfamily
B	IPR009014	Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II	Homologous Superfamily
B	IPR005475	Transketolase-like, pyrimidine-binding domain	Domain
B	IPR033248	Transketolase, C-terminal domain	Domain
A	IPR029061	Thiamin diphosphate-binding fold	Homologous Superfamily
A	IPR050771	Alpha-ketoacid dehydrogenase complex E1 component	Family
A	IPR001017	Dehydrogenase, E1 component	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: P21953	maple syrup urine disease Maple syrup urine disease, type 1B medulloblastoma psoriasis atopic eczema idiopathic scoliosis intellectual disability interstitial cystitis lung carcinoma osteosarcoma tuberculosis atypical teratoid rhabdoid tumor glioblastoma inborn errors of metabolism intermediate maple syrup urine disease maple syrup urine disease Maple syrup urine disease, type 1B medulloblastoma psoriasis atopic eczema idiopathic scoliosis intellectual disability interstitial cystitis lung carcinoma osteosarcoma tuberculosis atypical teratoid rhabdoid tumor glioblastoma inborn errors of metabolism intermediate maple syrup urine disease large cell medulloblastoma malignant ependymoma pancreatic ductal adenocarcinoma classic maple syrup urine disease inherited organic acidemia intermittent maple syrup urine disease lung cancer malignant mesothelioma
A	Pharos: P12694	maple syrup urine disease classic maple syrup urine disease heart disease inherited organic acidemia intermittent maple syrup urine disease Maple syrup urine disease, type 1B myocardial infarction colorectal cancer intellectual disability osteoarthritis inborn errors of metabolism intermediate maple syrup urine disease prostate carcinoma

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.