Pdk2 pyruvate dehydrogenase kinase 2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Pdk2provided by RGD
Official Full Name: pyruvate dehydrogenase kinase 2provided by RGD
Primary source: RGD:69428
See related: EnsemblRapid:ENSRNOG00000004172 AllianceGenome:RGD:69428
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Enables ATP binding activity; identical protein binding activity; and pyruvate dehydrogenase (acetyl-transferring) kinase activity. Involved in peptidyl-serine phosphorylation. Part of pyruvate dehydrogenase complex. Orthologous to human PDK2 (pyruvate dehydrogenase kinase 2). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Heart (RPKM 552.7), Kidney (RPKM 548.8) and 8 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 10q26

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	10	NC_086028.1 (80469388..80483988, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	10	NC_051345.1 (79972550..79987074, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	10	NC_005109.4 (82838270..82852758, complement)

Chromosome 10 - NC_086028.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

PDK2/4 induction and the subsequent lactate surge induce the metabolic shift in the diabetic dorsal root ganglion thereby contributing to the pathogenesis of painful diabetic neuropathy.
Title: Pyruvate Dehydrogenase Kinase-mediated Glycolytic Metabolic Shift in the Dorsal Root Ganglion Drives Painful Diabetic Neuropathy.
The Pdk2 and Pdk1 interaction site was identified with nuclear magnetic resonance and mass spectrometry.
Title: Elucidation of the interaction loci of the human pyruvate dehydrogenase complex E2·E3BP core with pyruvate dehydrogenase kinase 1 and kinase 2 by H/D exchange mass spectrometry and nuclear magnetic resonance.
Inactivation of pyruvate dehydrogenase kinase 2 by mitochondrial reactive oxygen species.
Title: Inactivation of pyruvate dehydrogenase kinase 2 by mitochondrial reactive oxygen species.
Mobility of adenosine triphosphate (ATP) lid is central to allosteric regulation of pyruvate dehydrogenase kinase-2 activity serving as a conformational switch required for communication between active site and allosteric sites in the kinase molecule.
Title: Allosteric coupling in pyruvate dehydrogenase kinase 2.
persistently elevated levels of circulating free fatty acid in normal and diabetic OLETF rats play an important role in stimulating PDK2 and PDK4 expression in liver
Title: Increased expression of hepatic pyruvate dehydrogenase kinases 2 and 4 in young and middle-aged Otsuka Long-Evans Tokushima Fatty rats: induction by elevated levels of free fatty acids.
Carboxy-terminal truncation variants of PDK2 display a greatly diminished capacity for phosphorylation of holo-pyruvate dehydrogenase complex(PDC), due to inability of transacetylase component of PDC to promote phosphorylation catalyzed by truncated PDK2.
Title: The carboxy-terminal tail of pyruvate dehydrogenase kinase 2 is required for the kinase activity.
Y80 and D117 are required for the communication between the dichloroacetate-binding site and active site of PDK2.
Title: Amino acid residues responsible for the recognition of dichloroacetate by pyruvate dehydrogenase kinase 2.
The results show that hepatic PDK4 up-regulation can be achieved by heterodimerization of either PPARalpha or TR with the RXR receptor and that effects of PPARalpha activation on hepatic PDK2 and PDK4 expression favour a switch towards expression of PDK4.
Title: Investigation of potential mechanisms regulating protein expression of hepatic pyruvate dehydrogenase kinase isoforms 2 and 4 by fatty acids and thyroid hormone.
mRNA levels not changed in skeletal muscle during fasting
Title: Pyruvate dehydrogenase activation and kinase expression in human skeletal muscle during fasting.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

MARC_7915-7916:996688163:1 (e-PCR)
- UniSTS:269854

RH141314 (e-PCR)
- UniSTS:223310

Pdk2 (e-PCR), detects polymorphism
- UniSTS:518558

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables ATP binding	IDA Inferred from Direct Assay more info	PubMed
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables ATP binding	ISO Inferred from Sequence Orthology more info
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IEA Inferred from Electronic Annotation more info
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info
enables protein kinase activity	IEA Inferred from Electronic Annotation more info
enables protein serine/threonine kinase activity	IDA Inferred from Direct Assay more info	PubMed
enables protein-containing complex binding	IDA Inferred from Direct Assay more info	PubMed
enables pyruvate dehydrogenase (acetyl-transferring) kinase activity	IBA Inferred from Biological aspect of Ancestor more info
enables pyruvate dehydrogenase (acetyl-transferring) kinase activity	IDA Inferred from Direct Assay more info	PubMed
enables pyruvate dehydrogenase (acetyl-transferring) kinase activity	IEA Inferred from Electronic Annotation more info
enables pyruvate dehydrogenase (acetyl-transferring) kinase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables pyruvate dehydrogenase (acetyl-transferring) kinase activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in cellular response to nutrient	IEA Inferred from Electronic Annotation more info
involved_in cellular response to nutrient	ISO Inferred from Sequence Orthology more info
involved_in cellular response to nutrient	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to reactive oxygen species	IEA Inferred from Electronic Annotation more info
involved_in cellular response to reactive oxygen species	ISO Inferred from Sequence Orthology more info
involved_in glucose homeostasis	IEA Inferred from Electronic Annotation more info
involved_in glucose homeostasis	ISO Inferred from Sequence Orthology more info
involved_in glucose homeostasis	ISS Inferred from Sequence or Structural Similarity more info
involved_in insulin receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in insulin receptor signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in insulin receptor signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in intrinsic apoptotic signaling pathway by p53 class mediator	IEA Inferred from Electronic Annotation more info
involved_in intrinsic apoptotic signaling pathway by p53 class mediator	ISO Inferred from Sequence Orthology more info
involved_in peptidyl-serine phosphorylation	IDA Inferred from Direct Assay more info	PubMed
involved_in protein phosphorylation	IDA Inferred from Direct Assay more info	PubMed
involved_in protein phosphorylation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of acetyl-CoA biosynthetic process from pyruvate	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of acetyl-CoA biosynthetic process from pyruvate	IEA Inferred from Electronic Annotation more info
involved_in regulation of acetyl-CoA biosynthetic process from pyruvate	ISO Inferred from Sequence Orthology more info
involved_in regulation of acetyl-CoA biosynthetic process from pyruvate	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of calcium-mediated signaling	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of calcium-mediated signaling	ISO Inferred from Sequence Orthology more info
involved_in regulation of gluconeogenesis	IEA Inferred from Electronic Annotation more info
involved_in regulation of gluconeogenesis	ISO Inferred from Sequence Orthology more info
involved_in regulation of gluconeogenesis	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of glucose metabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of glucose metabolic process	ISO Inferred from Sequence Orthology more info
involved_in regulation of glucose metabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of ketone metabolic process	ISO Inferred from Sequence Orthology more info
involved_in regulation of ketone metabolic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of pH	IEA Inferred from Electronic Annotation more info
involved_in regulation of pH	ISO Inferred from Sequence Orthology more info
involved_in regulation of pH	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in mitochondrial matrix	IEA Inferred from Electronic Annotation more info
is_active_in mitochondrion	IBA Inferred from Biological aspect of Ancestor more info
located_in mitochondrion	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
part_of pyruvate dehydrogenase complex	IDA Inferred from Direct Assay more info	PubMed
part_of pyruvate dehydrogenase complex	IEA Inferred from Electronic Annotation more info
part_of pyruvate dehydrogenase complex	ISO Inferred from Sequence Orthology more info
part_of pyruvate dehydrogenase complex	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: pyruvate dehydrogenase kinase, isozyme 2

Names: PDH kinase 2; PDK P45; [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial; [Pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial; pyruvate dehydrogenase 2; pyruvate dehydrogenase kinase, isoenzyme 2

NP_110499.1

EC 2.7.11.2

XP_038942857.1

EC 2.7.11.2

XP_063126011.1

EC 2.7.11.2

XP_063126012.1

EC 2.7.11.2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_030872.2 → NP_110499.1 pyruvate dehydrogenase kinase, isozyme 2

See identical proteins and their annotated locations for NP_110499.1

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000010

UniProtKB/Swiss-Prot

Q64536

UniProtKB/TrEMBL

A6HI79

Conserved Domains (2) summary

cd16929
Location:196 → 361

HATPase_PDK-like; Histidine kinase-like ATPase domain of pyruvate dehydrogenase kinase, branched-chain alpha-ketoacid dehydrogenase kinase and related domains

pfam10436
Location:30 → 192

BCDHK_Adom3; Mitochondrial branched-chain alpha-ketoacid dehydrogenase kinase

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

NC_086028.1 Reference GRCr8

Range

80469388..80483988 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063269941.1 → XP_063126011.1 pyruvate dehydrogenase kinase, isozyme 2 isoform X1

UniProtKB/TrEMBL

A0A8I6AJH2
XM_039086929.2 → XP_038942857.1 pyruvate dehydrogenase kinase, isozyme 2 isoform X2

UniProtKB/TrEMBL

A0A8I6AJH2

Related

ENSRNOP00000093282.2, ENSRNOT00000102681.2

Conserved Domains (2) summary

cd16929
Location:175 → 340

HATPase_PDK-like; Histidine kinase-like ATPase domain of pyruvate dehydrogenase kinase, branched-chain alpha-ketoacid dehydrogenase kinase and related domains

pfam10436
Location:16 → 171

BCDHK_Adom3; Mitochondrial branched-chain alpha-ketoacid dehydrogenase kinase
XM_063269942.1 → XP_063126012.1 pyruvate dehydrogenase kinase, isozyme 2 isoform X3

UniProtKB/TrEMBL

F1LMM8, Q9JID3