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    PDP2 pyruvate dehydrogenase phosphatase catalytic subunit 2 [ Homo sapiens (human) ]

    Gene ID: 57546, updated on 28-Oct-2024

    Summary

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    Official Symbol
    PDP2provided by HGNC
    Official Full Name
    pyruvate dehydrogenase phosphatase catalytic subunit 2provided by HGNC
    Primary source
    HGNC:HGNC:30263
    See related
    Ensembl:ENSG00000172840 MIM:615499; AllianceGenome:HGNC:30263
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PPM2B; PDPC 2; PPM2C2
    Summary
    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]
    Expression
    Ubiquitous expression in thyroid (RPKM 4.8), kidney (RPKM 4.0) and 25 other tissues See more
    Orthologs
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    Genomic context

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    See PDP2 in Genome Data Viewer
    Location:
    16q22.1
    Exon count:
    3
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (66880515..66891101)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (72674823..72685405)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (66914418..66925004)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene NEDD8 activating enzyme E1 subunit 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7568 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:66864603-66865103 Neighboring gene uncharacterized LOC124903699 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:66878245-66878746 Neighboring gene carbonic anhydrase 7 Neighboring gene MPRA-validated peak2618 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr16:66898937-66899130 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10942 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10943 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66914460-66915232 Neighboring gene uncharacterized LOC124903700 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66933011-66933906 Neighboring gene uncharacterized LOC107984821 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:66933907-66934800 Neighboring gene VISTA enhancer hs1760

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Autocrine phosphatase PDP2 inhibits ferroptosis by dephosphorylating ACSL4 in the Luminal A Breast Cancer. Zhu JJ, et al. PLoS One, 2024. PMID 38466744, Free PMC Article
    2. Crystallization and preliminary crystallographic studies of the catalytic subunits of human pyruvate dehydrogenase phosphatase isoforms 1 and 2. Kato J, et al. Acta Crystallogr Sect F Struct Biol Cryst Commun, 2010 Mar 1. PMID 20208177, Free PMC Article
    3. Activation and mitochondrial translocation of protein kinase Cdelta are necessary for insulin stimulation of pyruvate dehydrogenase complex activity in muscle and liver cells. Caruso M, et al. J Biol Chem, 2001 Nov 30. PMID 11577086
    4. Isoenzymes of pyruvate dehydrogenase phosphatase. DNA-derived amino acid sequences, expression, and regulation. Huang B, et al. J Biol Chem, 1998 Jul 10. PMID 9651365
    5. Pyruvate dehydrogenase phosphatase catalytic subunit 2 limits Th17 differentiation. Kono M, et al. Proc Natl Acad Sci U S A, 2018 Sep 11. PMID 30150402, Free PMC Article

    See all (23) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Autocrine phosphatase PDP2 inhibits ferroptosis by dephosphorylating ACSL4 in the Luminal A Breast Cancer.
      Title: Autocrine phosphatase PDP2 inhibits ferroptosis by dephosphorylating ACSL4 in the Luminal A Breast Cancer.
    2. ICER was found to bind to the Pdp2 promoter and suppress its expression. Furthermore, forced expression of PDP2 in CD4(+) cells reduced the in vitro Th17 differentiation, whereas shRNA-based suppression of PDP2 expression increased in vitro Th17 differentiation
      Title: Pyruvate dehydrogenase phosphatase catalytic subunit 2 limits Th17 differentiation.
    3. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    4. catalytic subunit of PDP2 crystals belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 53.6, b = 69.1, c = 109.7 A.
      Title: Crystallization and preliminary crystallographic studies of the catalytic subunits of human pyruvate dehydrogenase phosphatase isoforms 1 and 2.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1348

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables [pyruvate dehydrogenase (acetyl-transferring)]-phosphatase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables [pyruvate dehydrogenase (acetyl-transferring)]-phosphatase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in T-helper cell differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein dephosphorylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in signal transduction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in mitochondrial matrix TAS
    Traceable Author Statement
    more info
    		  
    located_in mitochondrion HTP PubMed 
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    [Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 2, mitochondrial
    Names
    protein phosphatase 2C, magnesium-dependent, catalytic subunit 2
    protein phosphatase, Mg2+/Mn2+ dependent 2B
    pyruvate dehydrogenase phosphatase isoenzyme 2
    pyruvate dehyrogenase phosphatase catalytic subunit 2
    NP_001316857.1
    NP_001316858.1
    NP_001316859.1
    NP_001316860.1
    NP_001316861.1
    NP_001316862.1
    NP_001316863.1
    NP_065837.1

    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.

    Genomic

    1. NG_051332.2 RefSeqGene

      Range
      5155..15741
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_1088

    mRNA and Protein(s)

    1. NM_001329928.2 → NP_001316857.1  [Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 2, mitochondrial precursor

      Status: REVIEWED

      Source sequence(s)
      AC044802
      Consensus CDS
      CCDS10822.1
      UniProtKB/Swiss-Prot
      A8K924, Q9P2J9
      Conserved Domains (1) summary
      cd00143
      Location:109 → 517
      PP2Cc; Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence ...

    2. NM_001329929.2 → NP_001316858.1  [Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 2, mitochondrial precursor

      Status: REVIEWED

      Source sequence(s)
      AC044802
      Consensus CDS
      CCDS10822.1
      UniProtKB/Swiss-Prot
      A8K924, Q9P2J9
      Conserved Domains (1) summary
      cd00143
      Location:109 → 517
      PP2Cc; Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence ...

    3. NM_001329930.2 → NP_001316859.1  [Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 2, mitochondrial precursor

      Status: REVIEWED

      Source sequence(s)
      AC044802
      Consensus CDS
      CCDS10822.1
      UniProtKB/Swiss-Prot
      A8K924, Q9P2J9
      Conserved Domains (1) summary
      cd00143
      Location:109 → 517
      PP2Cc; Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence ...

    4. NM_001329931.2 → NP_001316860.1  [Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 2, mitochondrial precursor

      Status: REVIEWED

      Source sequence(s)
      AC044802
      Consensus CDS
      CCDS10822.1
      UniProtKB/Swiss-Prot
      A8K924, Q9P2J9
      Conserved Domains (1) summary
      cd00143
      Location:109 → 517
      PP2Cc; Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence ...

    5. NM_001329932.2 → NP_001316861.1  [Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 2, mitochondrial precursor

      Status: REVIEWED

      Source sequence(s)
      AC044802, DA107466, HY057277
      Consensus CDS
      CCDS10822.1
      UniProtKB/Swiss-Prot
      A8K924, Q9P2J9
      Conserved Domains (1) summary
      cd00143
      Location:109 → 517
      PP2Cc; Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence ...

    6. NM_001329933.2 → NP_001316862.1  [Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 2, mitochondrial precursor

      Status: REVIEWED

      Source sequence(s)
      AC044802
      Consensus CDS
      CCDS10822.1
      UniProtKB/Swiss-Prot
      A8K924, Q9P2J9
      Conserved Domains (1) summary
      cd00143
      Location:109 → 517
      PP2Cc; Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence ...

    7. NM_001329934.2 → NP_001316863.1  [Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 2, mitochondrial precursor

      Status: REVIEWED

      Source sequence(s)
      AC044802
      Consensus CDS
      CCDS10822.1
      UniProtKB/Swiss-Prot
      A8K924, Q9P2J9
      Conserved Domains (1) summary
      cd00143
      Location:109 → 517
      PP2Cc; Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence ...

    8. NM_020786.4 → NP_065837.1  [Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 2, mitochondrial precursor

      See identical proteins and their annotated locations for NP_065837.1

      Status: REVIEWED

      Source sequence(s)
      AC044802, AK292539, BM668681
      Consensus CDS
      CCDS10822.1
      UniProtKB/Swiss-Prot
      A8K924, Q9P2J9
      Related
      ENSP00000309548.2, ENST00000311765.4
      Conserved Domains (1) summary
      cd00143
      Location:109 → 517
      PP2Cc; Serine/threonine phosphatases, family 2C, catalytic domain; The protein architecture and deduced catalytic mechanism of PP2C phosphatases are similar to the PP1, PP2A, PP2B family of protein Ser/Thr phosphatases, with which PP2C shares no sequence ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      66880515..66891101
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      72674823..72685405
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9P2J9.2 GenPept UniProtKB/Swiss-Prot:Q9P2J9

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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