Human Gene PDP1 (ENST00000297598.5) Description and Page Index
  Description: Homo sapiens pyruvate dehyrogenase phosphatase catalytic subunit 1 (PDP1), transcript variant 5, mRNA. (from RefSeq NM_018444)
RefSeq Summary (NM_018444): Pyruvate dehydrogenase (E1) is one of the three components (E1, E2, and E3) of the large pyruvate dehydrogenase complex. Pyruvate dehydrogenase kinases catalyze phosphorylation of serine residues of E1 to inactivate the E1 component and inhibit the complex. Pyruvate dehydrogenase phosphatases catalyze the dephosphorylation and activation of the E1 component to reverse the effects of pyruvate dehydrogenase kinases. Pyruvate dehydrogenase phosphatase is a heterodimer consisting of catalytic and regulatory subunits. Two catalytic subunits have been reported; one is predominantly expressed in skeletal muscle and another one is is much more abundant in the liver. The catalytic subunit, encoded by this gene, is the former, and belongs to the protein phosphatase 2C (PP2C) superfamily. Along with the pyruvate dehydrogenase complex and pyruvate dehydrogenase kinases, this enzyme is located in the mitochondrial matrix. Mutation in this gene causes pyruvate dehydrogenase phosphatase deficiency. Multiple alternatively spliced transcript variants encoding different isoforms have been identified.[provided by RefSeq, Jun 2009].
Gencode Transcript: ENST00000297598.5
Gencode Gene: ENSG00000164951.16
Transcript (Including UTRs)
   Position: hg38 chr8:93,916,923-93,926,068 Size: 9,146 Total Exon Count: 2 Strand: +
Coding Region
   Position: hg38 chr8:93,922,060-93,923,673 Size: 1,614 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated: 2019-09-04

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr8:93,916,923-93,926,068)mRNA (may differ from genome)Protein (537 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsHGNC
HPRDLynxMGIneXtProtOMIMPubMed
ReactomeStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: PDP1_HUMAN
DESCRIPTION: RecName: Full=[Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 1, mitochondrial; Short=PDP 1; EC=3.1.3.43; AltName: Full=Protein phosphatase 2C; AltName: Full=Pyruvate dehydrogenase phosphatase catalytic subunit 1; Short=PDPC 1; Flags: Precursor;
FUNCTION: Catalyzes the dephosphorylation and concomitant reactivation of the alpha subunit of the E1 component of the pyruvate dehydrogenase complex (By similarity).
CATALYTIC ACTIVITY: [Pyruvate dehydrogenase (acetyl-transferring)] phosphate + H(2)O = [pyruvate dehydrogenase (acetyl-transferring)] + phosphate.
COFACTOR: Binds 2 magnesium ions per subunit (By similarity).
SUBUNIT: Heterodimer of a catalytic (PDP1) and a regulatory (PDPR) subunit (By similarity).
SUBCELLULAR LOCATION: Mitochondrion matrix (By similarity).
DISEASE: Defects in PDP1 are the cause of pyruvate dehydrogenase phosphatase deficiency (PDP deficiency) [MIM:608782]. PDP deficiency results in lactic acidosis leading to neurological dysfunction.
SIMILARITY: Belongs to the PP2C family.
SEQUENCE CAUTION: Sequence=AAF67480.1; Type=Erroneous initiation;

-  MalaCards Disease Associations
  MalaCards Gene Search: PDP1
Diseases sorted by gene-association score: pyruvate dehydrogenase phosphatase deficiency* (1390), atypical autism (16), lactic acidosis (11), sarcosinemia (10), tularemia (4), peroxisome disorders (4), leigh syndrome (1), diabetes mellitus, noninsulin-dependent (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 27.05 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 304.67 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -89.40201-0.445 Picture PostScript Text
3' UTR -573.902395-0.240 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001932 - PP2C-like
IPR000222 - PP2C_Mn2_Asp60_BS
IPR015655 - Protein_Pase_2C

Pfam Domains:
PF00481 - Protein phosphatase 2C

ModBase Predicted Comparative 3D Structure on Q9P0J1
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003824 catalytic activity
GO:0004721 phosphoprotein phosphatase activity
GO:0004722 protein serine/threonine phosphatase activity
GO:0004741 [pyruvate dehydrogenase (lipoamide)] phosphatase activity
GO:0005515 protein binding
GO:0016787 hydrolase activity
GO:0043169 cation binding
GO:0046872 metal ion binding

Biological Process:
GO:0006470 protein dephosphorylation
GO:0010510 regulation of acetyl-CoA biosynthetic process from pyruvate
GO:0035970 peptidyl-threonine dephosphorylation

Cellular Component:
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix


-  Descriptions from all associated GenBank mRNAs
  BC047619 - Homo sapiens protein phosphatase 2C, magnesium-dependent, catalytic subunit, mRNA (cDNA clone MGC:50991 IMAGE:4824168), complete cds.
AK057079 - Homo sapiens cDNA FLJ32517 fis, clone SMINT1000117, highly similar to Pyruvate dehydrogenase (lipoamide)-phosphatase 1 (EC 3.1.3.43).
BC064978 - Homo sapiens protein phosphatase 2C, magnesium-dependent, catalytic subunit, mRNA (cDNA clone IMAGE:6158636), partial cds.
AF155661 - Homo sapiens pyruvate dehydrogenase (PDH) mRNA, complete cds.
AB590483 - Synthetic construct DNA, clone: pFN21AE2019, Homo sapiens PDP1 gene for pyruvate dehyrogenase phosphatase catalytic subunit 1, without stop codon, in Flexi system.
AK302651 - Homo sapiens cDNA FLJ56179 complete cds, highly similar to Pyruvate dehydrogenase (lipoamide)-phosphatase 1 (EC 3.1.3.43).
AK126862 - Homo sapiens cDNA FLJ44914 fis, clone BRAMY3009782, highly similar to Pyruvate dehydrogenase (lipoamide)-phosphatase 1 (EC 3.1.3.43).
BC098343 - Homo sapiens protein phosphatase 2C, magnesium-dependent, catalytic subunit, mRNA (cDNA clone MGC:119646 IMAGE:40010016), complete cds.
KJ894053 - Synthetic construct Homo sapiens clone ccsbBroadEn_03447 PDP1 gene, encodes complete protein.
AK022057 - Homo sapiens cDNA FLJ11995 fis, clone HEMBB1001443, highly similar to Rattus norvegicus pyruvate dehydrogenase phosphatase isoenzyme 1 mRNA.
JD292690 - Sequence 273714 from Patent EP1572962.
JD180787 - Sequence 161811 from Patent EP1572962.
JD549070 - Sequence 530094 from Patent EP1572962.
JD549069 - Sequence 530093 from Patent EP1572962.
JD295105 - Sequence 276129 from Patent EP1572962.
JD303581 - Sequence 284605 from Patent EP1572962.
JD168830 - Sequence 149854 from Patent EP1572962.
JD323684 - Sequence 304708 from Patent EP1572962.
JD063661 - Sequence 44685 from Patent EP1572962.
JD490497 - Sequence 471521 from Patent EP1572962.
JD357384 - Sequence 338408 from Patent EP1572962.
JD544729 - Sequence 525753 from Patent EP1572962.
JD332654 - Sequence 313678 from Patent EP1572962.
JD265967 - Sequence 246991 from Patent EP1572962.
JD455040 - Sequence 436064 from Patent EP1572962.
JD275377 - Sequence 256401 from Patent EP1572962.
JD188479 - Sequence 169503 from Patent EP1572962.
JD539243 - Sequence 520267 from Patent EP1572962.
JD297940 - Sequence 278964 from Patent EP1572962.
JD244407 - Sequence 225431 from Patent EP1572962.
JD524081 - Sequence 505105 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9P0J1 (Reactome details) participates in the following event(s):

R-HSA-204169 PDP dephosphorylates p-lipo-PDH
R-HSA-204174 Regulation of pyruvate dehydrogenase (PDH) complex
R-HSA-70268 Pyruvate metabolism
R-HSA-71406 Pyruvate metabolism and Citric Acid (TCA) cycle
R-HSA-1428517 The citric acid (TCA) cycle and respiratory electron transport
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: B3KX71, NM_018444, PDP, PDP1_HUMAN, PPM2C, Q5U5K1, Q9P0J1, uc003yge.1, uc003yge.2, uc003yge.3, uc003yge.4, uc003yge.5
UCSC ID: uc003yge.5
RefSeq Accession: NM_018444
Protein: Q9P0J1 (aka PDP1_HUMAN)
CCDS: CCDS6259.1, CCDS55262.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.