1JM6

Pyruvate dehydrogenase kinase, isozyme 2, containing ADP

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
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1jm6a1	All alpha proteins	Bromodomain-like	alpha-ketoacid dehydrogenase kinase, N-terminal domain	alpha-ketoacid dehydrogenase kinase, N-terminal domain	Pyruvate dehydrogenase kinase	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A	d1jm6a2	Alpha and beta proteins (a+b)	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	alpha-ketoacid dehydrogenase kinase, C-terminal domain	Pyruvate dehydrogenase kinase	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B	d1jm6b1	All alpha proteins	Bromodomain-like	alpha-ketoacid dehydrogenase kinase, N-terminal domain	alpha-ketoacid dehydrogenase kinase, N-terminal domain	Pyruvate dehydrogenase kinase	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
B	d1jm6b2	Alpha and beta proteins (a+b)	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	alpha-ketoacid dehydrogenase kinase, C-terminal domain	Pyruvate dehydrogenase kinase	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	alpha-ketoacid dehydrogenase kinase, N-terminal domain	8024773	4002802	SCOP2 (2022-06-29)
A	SCOP2 Family	alpha-ketoacid dehydrogenase kinase, C-terminal domain	8024776	4003507	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	alpha-ketoacid dehydrogenase kinase, N-terminal domain	8037152	3001773	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	GHKL (Gyrase, Hsp90, Histidine Kinase, MutL) domain-like	8037155	3000091	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	alpha-ketoacid dehydrogenase kinase, N-terminal domain	8037152	3001773	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	GHKL (Gyrase, Hsp90, Histidine Kinase, MutL) domain-like	8037155	3000091	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	BCDHK_Adom3	e1jm6A1	A: alpha bundles	X: Bromodomain-like	H: alpha-ketoacid dehydrogenase kinase-N (From Topology)	T: alpha-ketoacid dehydrogenase kinase-N	F: BCDHK_Adom3	ECOD (1.6)
A	HATPase_c	e1jm6A2	A: a+b two layers	X: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like	H: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase (From Topology)	T: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	F: HATPase_c	ECOD (1.6)
B	BCDHK_Adom3	e1jm6B1	A: alpha bundles	X: Bromodomain-like	H: alpha-ketoacid dehydrogenase kinase-N (From Topology)	T: alpha-ketoacid dehydrogenase kinase-N	F: BCDHK_Adom3	ECOD (1.6)
B	HATPase_c	e1jm6B2	A: a+b two layers	X: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like	H: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase (From Topology)	T: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	F: HATPase_c	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.565.10	Alpha Beta	2-Layer Sandwich	Heat Shock Protein 90	Histidine kinase-like ATPase, C-terminal domain	CATH (4.3.0)
A	1.20.140.20	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)
B	3.30.565.10	Alpha Beta	2-Layer Sandwich	Heat Shock Protein 90	Histidine kinase-like ATPase, C-terminal domain	CATH (4.3.0)
B	1.20.140.20	Mainly Alpha	Up-down Bundle	Butyryl-CoA Dehydrogenase, subunit A	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02518	Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase (HATPase_c)	Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase	This family represents the structurally related ATPase domains of histidine kinase, DNA gyrase B and HSP90.	Domain
A, B	PF10436	Mitochondrial branched-chain alpha-ketoacid dehydrogenase kinase (BCDHK_Adom3)	Mitochondrial branched-chain alpha-ketoacid dehydrogenase kinase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Pyruvate dehydrogenase kinase, isozyme 2	protein serine/threonine kinase activity pyruvate dehydrogenase (acetyl-transferring) kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding protein serine/threonine kinase activity pyruvate dehydrogenase (acetyl-transferring) kinase activity catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding identical protein binding protein binding protein homodimerization activity protein dimerization activity protein-containing complex binding	cellular response to stimulus cellular response to nutrient levels response to nutrient levels cellular response to chemical stimulus response to stimulus response to chemical response to nutrient cellular response to nutrient cellular process monosaccharide metabolic process regulation of cellular process gluconeogenesis regulation of primary metabolic process regulation of small molecule metabolic process cellular response to stimulus cellular response to nutrient levels response to nutrient levels cellular response to chemical stimulus response to stimulus response to chemical response to nutrient cellular response to nutrient cellular process monosaccharide metabolic process regulation of cellular process gluconeogenesis regulation of primary metabolic process regulation of small molecule metabolic process small molecule metabolic process regulation of carbohydrate metabolic process regulation of glucose metabolic process regulation of biosynthetic process carbohydrate metabolic process regulation of biological process small molecule biosynthetic process carbohydrate biosynthetic process biological regulation hexose metabolic process primary metabolic process monosaccharide biosynthetic process hexose biosynthetic process biosynthetic process regulation of gluconeogenesis metabolic process regulation of carbohydrate biosynthetic process regulation of metabolic process glucose metabolic process signaling signal transduction by p53 class mediator cell death intracellular signal transduction cell communication apoptotic signaling pathway intrinsic apoptotic signaling pathway by p53 class mediator signal transduction apoptotic process intrinsic apoptotic signaling pathway programmed cell death chemical homeostasis homeostatic process regulation of pH monoatomic ion homeostasis monoatomic cation homeostasis cellular response to oxidative stress response to oxygen-containing compound cellular response to chemical stress cellular response to oxygen-containing compound response to reactive oxygen species cellular response to reactive oxygen species response to oxidative stress cellular response to stress response to stress cellular response to nitrogen compound response to peptide hormone insulin receptor signaling pathway cell surface receptor protein tyrosine kinase signaling pathway cellular response to endogenous stimulus response to hormone enzyme-linked receptor protein signaling pathway cellular response to hormone stimulus cell surface receptor signaling pathway response to endogenous stimulus cellular response to peptide hormone stimulus response to nitrogen compound response to insulin cellular response to insulin stimulus regulation of signaling regulation of signal transduction regulation of intracellular signal transduction regulation of response to stimulus calcium-mediated signaling intracellular signaling cassette regulation of calcium-mediated signaling regulation of cell communication protein phosphorylation phosphorylation peptidyl-serine modification peptidyl-serine phosphorylation macromolecule modification peptidyl-amino acid modification phosphate-containing compound metabolic process protein metabolic process macromolecule metabolic process protein modification process phosphorus metabolic process regulation of acyl-CoA biosynthetic process regulation of amide metabolic process oxoacid metabolic process regulation of lipid metabolic process acetyl-CoA metabolic process organic acid metabolic process nucleobase-containing compound metabolic process regulation of sulfur metabolic process regulation of phosphate metabolic process sulfur compound metabolic process thioester metabolic process regulation of nucleobase-containing compound metabolic process nucleoside phosphate metabolic process pyruvate metabolic process amide biosynthetic process regulation of ketone metabolic process sulfur compound biosynthetic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process regulation of fatty acid metabolic process regulation of phosphorus metabolic process monocarboxylic acid metabolic process acetyl-CoA biosynthetic process from pyruvate thioester biosynthetic process ketone metabolic process acyl-CoA metabolic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process acyl-CoA biosynthetic process regulation of acetyl-CoA biosynthetic process from pyruvate amide metabolic process fatty acid metabolic process carboxylic acid metabolic process nucleobase-containing compound biosynthetic process purine-containing compound metabolic process acetyl-CoA biosynthetic process organophosphate metabolic process lipid metabolic process glucose homeostasis carbohydrate homeostasis	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex catalytic complex oxidoreductase complex pyruvate dehydrogenase complex alpha-ketoacid dehydrogenase complex membrane-enclosed lumen membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex catalytic complex oxidoreductase complex pyruvate dehydrogenase complex alpha-ketoacid dehydrogenase complex membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR039028	PDK/BCKDK protein kinase	Family
A, B	IPR036784	Alpha-ketoacid/pyruvate dehydrogenase kinase, N-terminal domain superfamily	Homologous Superfamily
A, B	IPR036890	Histidine kinase/HSP90-like ATPase superfamily	Homologous Superfamily
A, B	IPR003594	Histidine kinase/HSP90-like ATPase domain	Domain
A, B	IPR018955	Branched-chain alpha-ketoacid dehydrogenase kinase/Pyruvate dehydrogenase kinase, N-terminal	Domain
A, B	IPR005467	Histidine kinase domain	Domain

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	[pyruvate dehydrogenase (acetyl-transferring)] kinase M-CSA #603	Mitochondrial Pyruvate Dehydrogenase kinase (PDK) regulates the activity of Pyruvate dehydrogenase complex (PDC) by phosphorylating a serine residue at the E1 subunit and thus inactivating it. Mitochondrial PDK is in a family of serine protein kinases that lacks sequence similarity with all other eukaryotic protein kinase but show similarity with key motifs of prokaryotic histidine protein kinases and a family of eukaryotic ATPases. In mammals, 4 isozymes of PDK have been found, PDK1, PDK2, PDK3, PDK4. PDK2 is found in many tissues but is low in amount in lung and spleen. It only phosphorylates site 2 and 3 serine residue of the E1 subunit.	Defined by 4 residues: HIS:A-247 [auth A-1239]GLU:A-251 [auth A-1243]LYS:A-254 [auth A-1246]ASN:A-255 [auth A-1247] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 2.7.1.99 (PDB Primary Data) Search M-CSA Motif + EC 2.7.1.99 EC: 2.7.11.2 (UniProt) Search M-CSA Motif + EC 2.7.11.2

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.