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PDPR pyruvate dehydrogenase phosphatase regulatory subunit [ Homo sapiens (human) ]

Gene ID: 55066, updated on 2-Nov-2024

Summary

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Official Symbol
PDPRprovided by HGNC
Official Full Name
pyruvate dehydrogenase phosphatase regulatory subunitprovided by HGNC
Primary source
HGNC:HGNC:30264
See related
Ensembl:ENSG00000090857 MIM:617835; AllianceGenome:HGNC:30264
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
PDP3
Summary
Pyruvate dehydrogenase complex (PDC) catalyzes the oxidative decarboxylation of pyruvate and links glycolysis to the tricarboxylic acid cycle and fatty acid synthesis. The dephosphorylation and reactivation of PDC is catalyzed by pyruvate dehydrogenase phosphatase (PDP). The dimeric PDP has a catalytic subunit and a regulatory subunit. This gene encodes the FAD-containing regulatory subunit of PDP. The encoded protein acts to decrease the sensitivity of the PDP catalytic subunit to magnesium ions. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2017]
Expression
Ubiquitous expression in testis (RPKM 9.0), brain (RPKM 8.9) and 25 other tissues See more
Orthologs
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Genomic context

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See PDPR in Genome Data Viewer
Location:
16q22.1
Exon count:
23
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (70113626..70163427)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (75922058..75974584)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (70147529..70196440)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:70099725-70100338 Neighboring gene uncharacterized LOC124903706 Neighboring gene ribosomal protein S10 pseudogene 24 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:70121188-70121409 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11049 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:70148769-70149711 Neighboring gene uncharacterized LOC400541 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:70200631-70201130 Neighboring gene C-type lectin domain family 18 member C Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:70221261-70222190 Neighboring gene uncharacterized LOC105371328

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. PDPR Gene Variants Predisposing to Papillary Thyroid Cancer. Brock P, et al. Thyroid, 2024 May. PMID 38062777,
  2. Purification and properties of pyruvate dehydrogenase phosphatase from bovine heart and kidney. Teague WM, et al. Biochemistry, 1982 Oct 26. PMID 6293549
  3. Cloning, expression, and properties of the regulatory subunit of bovine pyruvate dehydrogenase phosphatase. Lawson JE, et al. J Biol Chem, 1997 Dec 12. PMID 9395502
  4. Novel association strategy with copy number variation for identifying new risk Loci of human diseases. Chen X, et al. PLoS One, 2010 Aug 20. PMID 20808825, Free PMC Article
  5. Recent advances in mechanisms regulating glucose oxidation at the level of the pyruvate dehydrogenase complex by PDKs. Sugden MC, et al. Am J Physiol Endocrinol Metab, 2003 May. PMID 12676647

See all (38) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. PDPR Gene Variants Predisposing to Papillary Thyroid Cancer.
    Title: PDPR Gene Variants Predisposing to Papillary Thyroid Cancer.
  2. Observational study of gene-disease association. (HuGE Navigator)
    Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
  3. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
    Title: Novel association strategy with copy number variation for identifying new risk Loci of human diseases.
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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ10079, DKFZp686A088, DKFZp686D16130

Gene Ontology Provided by GOA

Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in mitochondrial matrix IBA
Inferred from Biological aspect of Ancestor
more info
  
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
  
located_in mitochondrion NAS
Non-traceable Author Statement
more info
 PubMed 
part_of pyruvate dehydrogenase (lipoamide) phosphatase complex NAS
Non-traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial
NP_001309046.1
NP_001309047.1
NP_001309048.1
NP_060460.4
XP_005256072.1
XP_005256073.1
XP_006721287.1
XP_006721288.1
XP_011521492.1
XP_016878877.1
XP_047290258.1
XP_047290259.1
XP_047290260.1
XP_047290261.1
XP_047290262.1
XP_047290263.1
XP_047290264.1
XP_047290265.1
XP_047290266.1
XP_047302562.1
XP_047302564.1
XP_047302565.1
XP_047302566.1
XP_047302567.1
XP_047302568.1
XP_047302569.1
XP_047302570.1
XP_047302571.1
XP_047302572.1
XP_047302573.1

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_052842.1 RefSeqGene

    Range
    5707..53912
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001322117.1 → NP_001309046.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform 1 precursor

    Status: REVIEWED

    Source sequence(s)
    AC009022, AC009060
    Consensus CDS
    CCDS45520.1
    UniProtKB/Swiss-Prot
    A7E298, A8K8Y7, B3KSE1, Q6AI20, Q6AWC9, Q8NCN5
    UniProtKB/TrEMBL
    B4DZL5
    Related
    ENSP00000457916.1, ENST00000568530.5
    Conserved Domains (4) summary
    COG0665
    Location:39 → 426
    DadA; Glycine/D-amino acid oxidase (deaminating) [Amino acid transport and metabolism]
    pfam01571
    Location:463 → 736
    GCV_T; Aminomethyltransferase folate-binding domain
    pfam08669
    Location:786 → 852
    GCV_T_C; Glycine cleavage T-protein C-terminal barrel domain
    pfam16350
    Location:405 → 459
    FAO_M; FAD dependent oxidoreductase central domain

  2. NM_001322118.1 → NP_001309047.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC009022, AC009060, AK302987
    Consensus CDS
    CCDS82007.1
    UniProtKB/TrEMBL
    A8MT40, B4DZL5
    Related
    ENSP00000381190.3, ENST00000398122.7
    Conserved Domains (5) summary
    COG0404
    Location:353 → 730
    GcvT; Glycine cleavage system T protein (aminomethyltransferase) [Amino acid transport and metabolism]
    COG0665
    Location:1 → 326
    DadA; Glycine/D-amino acid oxidase (deaminating) [Amino acid transport and metabolism]
    pfam01571
    Location:363 → 636
    GCV_T; Aminomethyltransferase folate-binding domain
    pfam08669
    Location:648 → 752
    GCV_T_C; Glycine cleavage T-protein C-terminal barrel domain
    pfam16350
    Location:305 → 360
    FAO_M; FAD dependent oxidoreductase central domain

  3. NM_001322119.1 → NP_001309048.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC009022, AC009060
    Conserved Domains (4) summary
    COG0404
    Location:51 → 428
    GcvT; Glycine cleavage system T protein (aminomethyltransferase) [Amino acid transport and metabolism]
    pfam01571
    Location:61 → 334
    GCV_T; Aminomethyltransferase folate-binding domain
    pfam08669
    Location:346 → 450
    GCV_T_C; Glycine cleavage T-protein C-terminal barrel domain
    pfam16350
    Location:3 → 58
    FAO_M; FAD dependent oxidoreductase central domain

  4. NM_017990.5 → NP_060460.4  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform 1 precursor

    See identical proteins and their annotated locations for NP_060460.4

    Status: REVIEWED

    Source sequence(s)
    AC009022, AC009060
    Consensus CDS
    CCDS45520.1
    UniProtKB/Swiss-Prot
    A7E298, A8K8Y7, B3KSE1, Q6AI20, Q6AWC9, Q8NCN5
    UniProtKB/TrEMBL
    B4DZL5
    Related
    ENSP00000288050.5, ENST00000288050.9
    Conserved Domains (4) summary
    COG0665
    Location:39 → 426
    DadA; Glycine/D-amino acid oxidase (deaminating) [Amino acid transport and metabolism]
    pfam01571
    Location:463 → 736
    GCV_T; Aminomethyltransferase folate-binding domain
    pfam08669
    Location:786 → 852
    GCV_T_C; Glycine cleavage T-protein C-terminal barrel domain
    pfam16350
    Location:405 → 459
    FAO_M; FAD dependent oxidoreductase central domain

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
    70113626..70163427
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017023388.3 → XP_016878877.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X5

    Related
    ENST00000561920.5

  2. XM_047434302.1 → XP_047290258.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X1

    UniProtKB/Swiss-Prot
    A7E298, A8K8Y7, B3KSE1, Q6AI20, Q6AWC9, Q8NCN5
    Conserved Domains (4) summary
    COG0665
    Location:39 → 426
    DadA; Glycine/D-amino acid oxidase (deaminating) [Amino acid transport and metabolism]
    pfam01571
    Location:463 → 736
    GCV_T; Aminomethyltransferase folate-binding domain
    pfam08669
    Location:786 → 852
    GCV_T_C; Glycine cleavage T-protein C-terminal barrel domain
    pfam16350
    Location:405 → 459
    FAO_M; FAD dependent oxidoreductase central domain

  3. XM_047434303.1 → XP_047290259.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X2

  4. XM_047434304.1 → XP_047290260.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X3

  5. XM_047434306.1 → XP_047290262.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X4

  6. XM_005256015.3 → XP_005256072.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X1

    See identical proteins and their annotated locations for XP_005256072.1

    UniProtKB/Swiss-Prot
    A7E298, A8K8Y7, B3KSE1, Q6AI20, Q6AWC9, Q8NCN5
    UniProtKB/TrEMBL
    B4DZL5
    Conserved Domains (4) summary
    COG0665
    Location:39 → 426
    DadA; Glycine/D-amino acid oxidase (deaminating) [Amino acid transport and metabolism]
    pfam01571
    Location:463 → 736
    GCV_T; Aminomethyltransferase folate-binding domain
    pfam08669
    Location:786 → 852
    GCV_T_C; Glycine cleavage T-protein C-terminal barrel domain
    pfam16350
    Location:405 → 459
    FAO_M; FAD dependent oxidoreductase central domain

  7. XM_006721224.3 → XP_006721287.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X2

    UniProtKB/TrEMBL
    B4DZL5
    Conserved Domains (6) summary
    COG0404
    Location:453 → 769
    GcvT; Glycine cleavage system T protein (aminomethyltransferase) [Amino acid transport and metabolism]
    COG0665
    Location:39 → 426
    DadA; Glycine/D-amino acid oxidase (deaminating) [Amino acid transport and metabolism]
    pfam01571
    Location:463 → 684
    GCV_T; Aminomethyltransferase folate-binding domain
    pfam08669
    Location:687 → 791
    GCV_T_C; Glycine cleavage T-protein C-terminal barrel domain
    pfam16350
    Location:405 → 460
    FAO_M; FAD dependent oxidoreductase central domain
    cl21454
    Location:5 → 74
    NADB_Rossmann; Rossmann-fold NAD(P)(+)-binding proteins

  8. XM_006721225.4 → XP_006721288.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X3

    UniProtKB/TrEMBL
    B4DZL5
    Conserved Domains (6) summary
    COG0404
    Location:373 → 750
    GcvT; Glycine cleavage system T protein (aminomethyltransferase) [Amino acid transport and metabolism]
    COG0665
    Location:39 → 346
    DadA; Glycine/D-amino acid oxidase (deaminating) [Amino acid transport and metabolism]
    pfam01571
    Location:383 → 656
    GCV_T; Aminomethyltransferase folate-binding domain
    pfam08669
    Location:668 → 772
    GCV_T_C; Glycine cleavage T-protein C-terminal barrel domain
    pfam16350
    Location:325 → 380
    FAO_M; FAD dependent oxidoreductase central domain
    cl21454
    Location:5 → 74
    NADB_Rossmann; Rossmann-fold NAD(P)(+)-binding proteins

  9. XM_047434305.1 → XP_047290261.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X4

  10. XM_011523190.4 → XP_011521492.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X6

    Conserved Domains (5) summary
    COG0404
    Location:453 → 655
    GcvT; Glycine cleavage system T protein (aminomethyltransferase) [Amino acid transport and metabolism]
    COG0665
    Location:39 → 426
    DadA; Glycine/D-amino acid oxidase (deaminating) [Amino acid transport and metabolism]
    pfam01571
    Location:463 → 655
    GCV_T; Aminomethyltransferase folate-binding domain
    pfam16350
    Location:405 → 460
    FAO_M; FAD dependent oxidoreductase central domain
    cl21454
    Location:5 → 74
    NADB_Rossmann; Rossmann-fold NAD(P)(+)-binding proteins

  11. XM_047434310.1 → XP_047290266.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X9

    UniProtKB/TrEMBL
    H3BQG3
    Related
    ENSP00000455764.1, ENST00000565186.5

  12. XM_047434307.1 → XP_047290263.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X4

  13. XM_005256016.4 → XP_005256073.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X1

    See identical proteins and their annotated locations for XP_005256073.1

    UniProtKB/Swiss-Prot
    A7E298, A8K8Y7, B3KSE1, Q6AI20, Q6AWC9, Q8NCN5
    UniProtKB/TrEMBL
    B4DZL5
    Conserved Domains (4) summary
    COG0665
    Location:39 → 426
    DadA; Glycine/D-amino acid oxidase (deaminating) [Amino acid transport and metabolism]
    pfam01571
    Location:463 → 736
    GCV_T; Aminomethyltransferase folate-binding domain
    pfam08669
    Location:786 → 852
    GCV_T_C; Glycine cleavage T-protein C-terminal barrel domain
    pfam16350
    Location:405 → 459
    FAO_M; FAD dependent oxidoreductase central domain

  14. XM_047434308.1 → XP_047290264.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X7

  15. XM_047434309.1 → XP_047290265.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X8

RNA

  1. XR_007064891.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    75922058..75974584
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047446613.1 → XP_047302569.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X5

  2. XM_047446609.1 → XP_047302565.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X1

  3. XM_047446611.1 → XP_047302567.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X2

  4. XM_047446606.1 → XP_047302562.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X1

  5. XM_047446610.1 → XP_047302566.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X2

  6. XM_047446612.1 → XP_047302568.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X3

  7. XM_047446614.1 → XP_047302570.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X6

  8. XM_047446617.1 → XP_047302573.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X9

  9. XM_047446608.1 → XP_047302564.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X1

  10. XM_047446615.1 → XP_047302571.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X7

  11. XM_047446616.1 → XP_047302572.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X8

RNA

  1. XR_007086598.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8NCN5.2 GenPept UniProtKB/Swiss-Prot:Q8NCN5

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