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PDHX pyruvate dehydrogenase complex component X [ Homo sapiens (human) ]

Gene ID: 8050, updated on 3-Nov-2024

Summary

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Official Symbol
PDHXprovided by HGNC
Official Full Name
pyruvate dehydrogenase complex component Xprovided by HGNC
Primary source
HGNC:HGNC:21350
See related
Ensembl:ENSG00000110435 MIM:608769; AllianceGenome:HGNC:21350
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
E3BP; OPDX; PDX1; proX; DLDBP; PDHXD
Summary
The pyruvate dehydrogenase (PDH) complex is located in the mitochondrial matrix and catalyzes the conversion of pyruvate to acetyl coenzyme A. The PDH complex thereby links glycolysis to Krebs cycle. The PDH complex contains three catalytic subunits, E1, E2, and E3, two regulatory subunits, E1 kinase and E1 phosphatase, and a non-catalytic subunit, E3 binding protein (E3BP). This gene encodes the E3 binding protein subunit; also known as component X of the pyruvate dehydrogenase complex. This protein tethers E3 dimers to the E2 core of the PDH complex. Defects in this gene are a cause of pyruvate dehydrogenase deficiency which results in neurological dysfunction and lactic acidosis in infancy and early childhood. This protein is also a minor antigen for antimitochondrial antibodies. These autoantibodies are present in nearly 95% of patients with the autoimmune liver disease primary biliary cirrhosis (PBC). In PBC, activated T lymphocytes attack and destroy epithelial cells in the bile duct where this protein is abnormally distributed and overexpressed. PBC eventually leads to cirrhosis and liver failure. Alternative splicing results in multiple transcript variants encoding distinct isoforms.[provided by RefSeq, Oct 2009]
Expression
Ubiquitous expression in heart (RPKM 24.7), testis (RPKM 13.6) and 25 other tissues See more
Orthologs
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Genomic context

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See PDHX in Genome Data Viewer
Location:
11p13
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (34915920..34996128)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (35054373..35134137)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (34937985..35017675)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102723568 Neighboring gene uncharacterized LOC105376625 Neighboring gene uncharacterized LOC105376624 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3253 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3254 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4608 Neighboring gene APAF1 interacting protein Neighboring gene microRNA 1343 Neighboring gene uncharacterized LOC105376626 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4609 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:35051560-35052759 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4611 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4612 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4613 Neighboring gene uncharacterized LOC105376627 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4614 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4615 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4616

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. Defects in the E2 lipoyl transacetylase and the X-lipoyl containing component of the pyruvate dehydrogenase complex in patients with lactic acidemia. Robinson BH, et al. J Clin Invest, 1990 Jun. PMID 2112155, Free PMC Article
  2. Identification of PDHX as a metabolic target for esophageal squamous cell carcinoma. Inoue J, et al. Cancer Sci, 2021 Jul. PMID 33964039, Free PMC Article
  3. Leigh's disease due to a new mutation in the PDHX gene. Schiff M, et al. Ann Neurol, 2006 Apr. PMID 16566017
  4. Quantitative proteomics: the copy number of pyruvate dehydrogenase is more than 10(2)-fold lower than that of complex III in human mitochondria. Murray J, et al. FEBS Lett, 2002 Oct 9. PMID 12372595
  5. PDC-E3BP is not a dominant T-cell autoantigen in primary biliary cirrhosis. McHugh A, et al. Liver Int, 2006 May. PMID 16629643

See all (96) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Cuproptosis-related gene PDHX and heat stress-related HSPD1 as potential key drivers associated with cell stemness, aberrant metabolism and immunosuppression in esophageal carcinoma.
    Title: Cuproptosis-related gene PDHX and heat stress-related HSPD1 as potential key drivers associated with cell stemness, aberrant metabolism and immunosuppression in esophageal carcinoma.
  2. Identification of PDHX as a metabolic target for esophageal squamous cell carcinoma.
    Title: Identification of PDHX as a metabolic target for esophageal squamous cell carcinoma.
  3. PDHX is a functional target of miR-27b and that this interaction has consequential effects on cell metabolism which facilitate cell growth and progression in breast cancer.
    Title: Suppression of PDHX by microRNA-27b deregulates cell metabolism and promotes growth in breast cancer.
  4. We propose testing for the R446* mutation in PDHX as a rapid first screening in Roma infants with metabolic acidosis.
    Title: Founder p.Arg 446* mutation in the PDHX gene explains over half of cases with congenital lactic acidosis in Roma children.
  5. MiR-26a regulates glucose metabolism of colorectal cancer cells by direct targeting PDHX.
    Title: MicroRNA-26a regulates glucose metabolism by direct targeting PDHX in colorectal cancer cells.
  6. New mutation in PDHX gene found in two unrelated patients with Pyruvate dehydrogenase deficiency.
    Title: Pyruvate dehydrogenase deficiency caused by a new mutation of PDHX gene in two Moroccan patients.
  7. genetic association with systemic lupus erythematosus to a haplotype between PDHX and CD44 was established.
    Title: Identification of a systemic lupus erythematosus susceptibility locus at 11p13 between PDHX and CD44 in a multiethnic study.
  8. Observational study of gene-disease association. (HuGE Navigator)
    Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
  9. determination that PDH and complex III exist at a steady-state ratio of 1:100, 1:128 and 1:202 in HeLa cell extracts, fibroblast mitochondria and heart tissue mitochondria, respectively
    Title: Quantitative proteomics: the copy number of pyruvate dehydrogenase is more than 10(2)-fold lower than that of complex III in human mitochondria.
  10. model of the pyruvate dehydrogenase complex formed by E2 and E2 plus the E3-binding protein and binding of the E1 and E3 components
    Title: Organization of the cores of the mammalian pyruvate dehydrogenase complex formed by E2 and E2 plus the E3-binding protein and their capacities to bind the E1 and E3 components.
Submit: New GeneRIF Correction See all GeneRIFs (14)

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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables acyltransferase activity IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
contributes_to pyruvate dehydrogenase (NAD+) activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
acts_upstream_of_or_within acetyl-CoA biosynthetic process from pyruvate IC
Inferred by Curator
more info
 PubMed 
involved_in acetyl-CoA biosynthetic process from pyruvate IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in acetyl-CoA biosynthetic process from pyruvate ISS
Inferred from Sequence or Structural Similarity
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
  
located_in mitochondrion NAS
Non-traceable Author Statement
more info
 PubMed 
part_of pyruvate dehydrogenase complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of pyruvate dehydrogenase complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of pyruvate dehydrogenase complex IPI
Inferred from Physical Interaction
more info
 PubMed 
part_of pyruvate dehydrogenase complex ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
pyruvate dehydrogenase protein X component, mitochondrial
Names
dihydrolipoamide dehydrogenase-binding protein of pyruvate dehydrogenase complex
lipoyl-containing pyruvate dehydrogenase complex component X
pyruvate dehydrogenase complex, E3-binding protein subunit
pyruvate dehydrogenase complex, lipoyl-containing component X
NP_001128496.2
NP_001159630.1
NP_003468.2
XP_011518692.1

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_013368.1 RefSeqGene

    Range
    5489..84999
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001135024.2 → NP_001128496.2  pyruvate dehydrogenase protein X component, mitochondrial isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks a segment in the 5' region, resulting in upstream in-frame AUG start codon, as compared to variant 1. The resulting isoform (2) has a shorter and distinct N-terminus, as compared to isoform 1.
    Source sequence(s)
    AC107928, AL138810
    Consensus CDS
    CCDS44569.2
    UniProtKB/TrEMBL
    A0A8C8MSB2, B2R673
    Related
    ENSP00000389404.3, ENST00000448838.8
    Conserved Domains (1) summary
    TIGR01349
    Location:1 → 440
    PDHac_trf_mito; pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form

  2. NM_001166158.2 → NP_001159630.1  pyruvate dehydrogenase protein X component, mitochondrial isoform 3 precursor

    See identical proteins and their annotated locations for NP_001159630.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks multiple in-frame exons in the central coding region, compared to variant 1, resulting in a protein (isoform 3) that lacks 227 aa, compared to isoform 1.
    Source sequence(s)
    AA282215, AC107928, AF001437, BC010389
    Consensus CDS
    CCDS53616.1
    UniProtKB/Swiss-Prot
    O00330
    Related
    ENSP00000415695.2, ENST00000430469.6
    Conserved Domains (2) summary
    PRK11892
    Location:56 → 114
    PRK11892; pyruvate dehydrogenase subunit beta; Provisional
    pfam00198
    Location:109 → 273
    2-oxoacid_dh; 2-oxoacid dehydrogenases acyltransferase (catalytic domain)

  3. NM_003477.3 → NP_003468.2  pyruvate dehydrogenase protein X component, mitochondrial isoform 1 precursor

    See identical proteins and their annotated locations for NP_003468.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AA282215, AC107928, AF001437, BC010389
    Consensus CDS
    CCDS7896.1
    UniProtKB/Swiss-Prot
    B4DW62, D3DR11, E9PB14, E9PBP7, O00330, O60221, Q96FV8, Q99783
    UniProtKB/TrEMBL
    B2R673
    Related
    ENSP00000227868.4, ENST00000227868.9
    Conserved Domains (1) summary
    TIGR01349
    Location:58 → 500
    PDHac_trf_mito; pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form

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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    34915920..34996128
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011520390.2 → XP_011518692.1  pyruvate dehydrogenase protein X component, mitochondrial isoform X1

    UniProtKB/TrEMBL
    A0A8C8MSB2, B2R673
    Conserved Domains (1) summary
    TIGR01349
    Location:1 → 440
    PDHac_trf_mito; pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase, long form

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    35054373..35134137
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O00330.3 GenPept UniProtKB/Swiss-Prot:O00330

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