This gene is a mitochondrial protein that functions as a phosphatase and is involved in the enzymatic resetting of the pyruvate dehydrogenase complex. Alternative splicing results in multiple transcript variants encoding the same protein. [provided by RefSeq, Aug 2016] See more...

Aliases for PDP2 Gene

Aliases for PDP2 Gene

  • Pyruvate Dehyrogenase Phosphatase Catalytic Subunit 2 2 3 5
  • [Pyruvate Dehydrogenase [Acetyl-Transferring]]-Phosphatase 2, Mitochondrial 3 4
  • Protein Phosphatase 2C, Magnesium-Dependent, Catalytic Subunit 2 2 3
  • Protein Phosphatase, Mg2+/Mn2+ Dependent 2B 2 3
  • EC 3.1.3.43 4 50
  • KIAA1348 2 4
  • PDPC 2 3 4
  • PPM2C2 2 3
  • PPM2B 2 3
  • [Pyruvate Dehydrogenase (Acetyl-Transferring)]-Phosphatase 2
  • Pyruvate Dehydrogenase Phosphatase Catalytic Subunit 2 4
  • Pyruvate Dehydrogenase Phosphatase Isoenzyme 2 3
  • EC 3.1.3 50
  • PDP 2 4
  • PDP2 5

External Ids for PDP2 Gene

Previous GeneCards Identifiers for PDP2 Gene

  • GC16P066690
  • GC16P065471
  • GC16P066914
  • GC16P052788

Summaries for PDP2 Gene

Entrez Gene Summary for PDP2 Gene

  • This gene is a mitochondrial protein that functions as a phosphatase and is involved in the enzymatic resetting of the pyruvate dehydrogenase complex. Alternative splicing results in multiple transcript variants encoding the same protein. [provided by RefSeq, Aug 2016]

GeneCards Summary for PDP2 Gene

PDP2 (Pyruvate Dehyrogenase Phosphatase Catalytic Subunit 2) is a Protein Coding gene. Among its related pathways are Metabolism and Pyruvate metabolism and Citric Acid (TCA) cycle. Gene Ontology (GO) annotations related to this gene include protein serine/threonine phosphatase activity and magnesium-dependent protein serine/threonine phosphatase activity. An important paralog of this gene is PDP1.

UniProtKB/Swiss-Prot Summary for PDP2 Gene

  • Catalyzes the dephosphorylation and concomitant reactivation of the alpha subunit of the E1 component of the pyruvate dehydrogenase complex.

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PDP2 Gene

Genomics for PDP2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PDP2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH16J066879 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 250.7 +2.1 2112 2.6 SP1 NCOR1 IKZF1 MYC SSRP1 ZNF580 ZNF592 KLF9 CEBPA ZNF10 PDP2 lnc-PDP2-3 CES2 B3GNT9 CTCF ENSG00000260465 CDH16 RRAD NAE1 ZDHHC1
GH16J066880 Promoter/Enhancer 1.1 Ensembl ENCODE 250.7 -0.3 -288 0.2 ZNF592 NR2C1 THRB SRF ETV1 POLR2A IKZF1 NR2F1 ATF4 NR2F6 PDP2 CA7 THAP11 CES2 CIAO2B NAE1
GH16J066877 Promoter 0.7 Ensembl 250.7 -0.7 -688 0.2 ZNF223 ATF2 IKZF1 ZSCAN21 EGR2 ZNF692 PATZ1 IKZF2 EED DPF2 PDP2 CA7 CES2 CIAO2B NAE1
GH16J066878 Promoter 0.7 EPDnew 250.7 0.0 -20 0.1 ZNF592 NR2F1 NR2F6 HNF4A RXRB PRDM4 EED RXRA LEF1 PDP2 lnc-PDP2-3 CA7 CES2 CIAO2B NAE1
GH16J066881 Enhancer 0.2 Ensembl 250.7 -1.5 -1488 0.2 PDP2 CA7 CES2 CIAO2B NAE1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PDP2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PDP2

Top Transcription factor binding sites by QIAGEN in the PDP2 gene promoter:
  • AML1a
  • C/EBPbeta
  • ITF-2
  • STAT3
  • Tal-1beta
  • USF-1
  • USF1
  • ZIC2

Genomic Locations for PDP2 Gene

Latest Assembly
chr16:66,878,589-66,895,754
(GRCh38/hg38)
Size:
17,166 bases
Orientation:
Plus strand

Previous Assembly
chr16:66,914,418-66,925,004
(GRCh37/hg19 by Entrez Gene)
Size:
10,587 bases
Orientation:
Plus strand

chr16:66,912,492-66,929,657
(GRCh37/hg19 by Ensembl)
Size:
17,166 bases
Orientation:
Plus strand

Genomic View for PDP2 Gene

Genes around PDP2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PDP2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PDP2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PDP2 Gene

Proteins for PDP2 Gene

  • Protein details for PDP2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9P2J9-PDP2_HUMAN
    Recommended name:
    [Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 2, mitochondrial
    Protein Accession:
    Q9P2J9
    Secondary Accessions:
    • A8K924

    Protein attributes for PDP2 Gene

    Size:
    529 amino acids
    Molecular mass:
    59978 Da
    Cofactor:
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    • Heterodimer of a catalytic subunit and a FAD protein of unknown function.
    SequenceCaution:
    • Sequence=BAA92586.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for PDP2 Gene

Selected DME Specific Peptides for PDP2 Gene

Q9P2J9:
  • LASDGLW
  • ARMYRDDIT
  • PEVTYHRLRPQDKFLVLA
  • QAVSERLFYY
  • VAFSGATAC

Post-translational modifications for PDP2 Gene

  • Ubiquitination at Lys438 and Lys459
  • Modification sites at PhosphoSitePlus

Domains & Families for PDP2 Gene

Gene Families for PDP2 Gene

HGNC:
Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for PDP2 Gene

Suggested Antigen Peptide Sequences for PDP2 Gene

GenScript: Design optimal peptide antigens:
  • Pyruvate dehydrogenase phosphatase catalytic subunit 2 (PDP2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9P2J9

UniProtKB/Swiss-Prot:

PDP2_HUMAN :
  • Belongs to the PP2C family.
Family:
  • Belongs to the PP2C family.
genes like me logo Genes that share domains with PDP2: view

Function for PDP2 Gene

Molecular function for PDP2 Gene

UniProtKB/Swiss-Prot Function:
Catalyzes the dephosphorylation and concomitant reactivation of the alpha subunit of the E1 component of the pyruvate dehydrogenase complex.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=H2O + O-phospho-L-seryl-[pyruvate dehydrogenase E1 alpha subunit] = L-seryl-[pyruvate dehydrogenase E1 alpha subunit] + phosphate; Xref=Rhea:RHEA:12669, Rhea:RHEA-COMP:13689, Rhea:RHEA-COMP:13690, ChEBI:CHEBI:15377, ChEBI:CHEBI:29999, ChEBI:CHEBI:43474, ChEBI:CHEBI:83421; EC=3.1.3.43;.

Enzyme Numbers (IUBMB) for PDP2 Gene

Phenotypes From GWAS Catalog for PDP2 Gene

Gene Ontology (GO) - Molecular Function for PDP2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003824 catalytic activity IEA --
GO:0004721 phosphoprotein phosphatase activity IEA --
GO:0004722 protein serine/threonine phosphatase activity IEA --
GO:0004724 magnesium-dependent protein serine/threonine phosphatase activity IBA 21873635
GO:0004741 [pyruvate dehydrogenase (lipoamide)] phosphatase activity IBA 21873635
genes like me logo Genes that share ontologies with PDP2: view
genes like me logo Genes that share phenotypes with PDP2: view

Animal Models for research

  • Taconic Biosciences Mouse Models for PDP2

miRNA for PDP2 Gene

miRTarBase miRNAs that target PDP2

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PDP2

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PDP2 Gene

Localization for PDP2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PDP2 Gene

Mitochondrion matrix.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PDP2 gene
Compartment Confidence
mitochondrion 5
nucleus 2
cytosol 2
plasma membrane 1
extracellular 1
cytoskeleton 1
peroxisome 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PDP2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IBA 21873635
GO:0005759 mitochondrial matrix TAS --
genes like me logo Genes that share ontologies with PDP2: view

Pathways & Interactions for PDP2 Gene

genes like me logo Genes that share pathways with PDP2: view

SIGNOR curated interactions for PDP2 Gene

Activates:
Inactivates:

Gene Ontology (GO) - Biological Process for PDP2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006470 protein dephosphorylation IEA,IBA 21873635
GO:0010510 regulation of acetyl-CoA biosynthetic process from pyruvate TAS --
GO:1904184 positive regulation of pyruvate dehydrogenase activity IBA 21873635
genes like me logo Genes that share ontologies with PDP2: view

Drugs & Compounds for PDP2 Gene

(4) Drugs for PDP2 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
FAD Approved Pharma 0
Magnesium Approved, Experimental, Investigational Pharma 0
Water Approved Pharma 0
Phosphate Experimental Pharma 0
genes like me logo Genes that share compounds with PDP2: view

Transcripts for PDP2 Gene

mRNA/cDNA for PDP2 Gene

8 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :
9 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PDP2

Alternative Splicing Database (ASD) splice patterns (SP) for PDP2 Gene

ExUns: 1a · 1b · 1c · 1d · 1e · 1f · 1g · 1h · 1i ^ 2 ^ 3a · 3b · 3c · 3d · 3e · 3f · 3g
SP1:
SP2: - - - -
SP3: - - -
SP4: - - - - -
SP5: -
SP6: - -

Relevant External Links for PDP2 Gene

GeneLoc Exon Structure for
PDP2

Expression for PDP2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PDP2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PDP2 Gene

This gene is overexpressed in Lung (43.7) and Breast (24.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PDP2 Gene



Protein tissue co-expression partners for PDP2 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PDP2

SOURCE GeneReport for Unigene cluster for PDP2 Gene:

Hs.632214

Evidence on tissue expression from TISSUES for PDP2 Gene

  • Nervous system(4.8)
  • Skin(2.1)
  • Kidney(2)
genes like me logo Genes that share expression patterns with PDP2: view

Primer products for research

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PDP2 Gene

Orthologs for PDP2 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for PDP2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia PDP2 29 30
  • 99.43 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia PDP2 29 30
  • 88.34 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia PDP2 29 30
  • 87.12 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Pdp2 29
  • 83.49 (n)
Mouse
(Mus musculus)
Mammalia Pdp2 29 16 30
  • 83.27 (n)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia PDP2 30
  • 76 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia PDP2 30
  • 67 (a)
OneToOne
Chicken
(Gallus gallus)
Aves PDP2 29 30
  • 65.4 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia PDP2 30
  • 61 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia pdp2 29
  • 63.46 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.17333 29
Zebrafish
(Danio rerio)
Actinopterygii pdp2 29 30
  • 62.07 (n)
OneToOne
Fruit Fly
(Drosophila melanogaster)
Insecta Pdp 30
  • 38 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea pdp-1 30
  • 35 (a)
OneToMany
A. gosspyii yeast
(Eremothecium gossypii)
Saccharomycetes AGOS_ACL083C 29
  • 46.63 (n)
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PTC5 29 30
  • 46.34 (n)
OneToMany
K. Lactis Yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0C13706g 29
  • 45.27 (n)
Bread mold
(Neurospora crassa)
Ascomycetes NCU01767 29
  • 46.12 (n)
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPAC10F6.17c 29
  • 45.7 (n)
Species where no ortholog for PDP2 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for PDP2 Gene

ENSEMBL:
Gene Tree for PDP2 (if available)
TreeFam:
Gene Tree for PDP2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PDP2: view image
Alliance of Genome Resources:
Additional Orthologs for PDP2

Paralogs for PDP2 Gene

(2) SIMAP similar genes for PDP2 Gene using alignment to 7 proteins:

  • PDP2_HUMAN
  • H3BQX2_HUMAN
  • H3BRB7_HUMAN
  • H3BSA5_HUMAN
  • H3BTU5_HUMAN
  • H3BUJ9_HUMAN
  • H3BV50_HUMAN
genes like me logo Genes that share paralogs with PDP2: view

Variants for PDP2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PDP2 Gene

SNP ID Clinical significance and condition Chr 16 pos Variation AA Info Type
rs193921129 Uncertain Significance: Malignant tumor of prostate 66,885,174(+) A/G
NM_020786.4(PDP2):c.890A>G (p.Asn297Ser)
MISSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for PDP2 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for PDP2 Gene

Variant ID Type Subtype PubMed ID
nsv572904 CNV loss 21841781

Variation tolerance for PDP2 Gene

Residual Variation Intolerance Score: 12.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.08; 22.05% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PDP2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PDP2
Leiden Open Variation Database (LOVD)
PDP2

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PDP2 Gene

Disorders for PDP2 Gene

Additional Disease Information for PDP2

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform

No disorders were found for PDP2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PDP2 Gene

Publications for PDP2 Gene

  1. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 40
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  3. Prediction of the coding sequences of unidentified human genes. XVI. The complete sequences of 150 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10718198) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2000) 3 4
  4. Isoenzymes of pyruvate dehydrogenase phosphatase. DNA-derived amino acid sequences, expression, and regulation. (PMID: 9651365) Huang B … Popov KM (The Journal of biological chemistry 1998) 2 3
  5. CYLD Regulates Centriolar Satellites Proteostasis by Counteracting the E3 Ligase MIB1. (PMID: 31067453) Douanne T … Bidère N (Cell reports 2019) 3

Products for PDP2 Gene

Sources for PDP2 Gene