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

Gene ID: 57546, updated on 2-Nov-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

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