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Aliases for PDHB Gene

Aliases for PDHB Gene

  • Pyruvate Dehydrogenase (Lipoamide) Beta 2 3 5
  • EC 4 61
  • PDHE1-B 3 4
  • PHE1B 3 4
  • Pyruvate Dehydrogenase E1 Component Subunit Beta, Mitochondrial 3
  • Pyruvate Dehydrogenase, E1 Beta Polypeptide 3
  • PDHBD 3

External Ids for PDHB Gene

Previous GeneCards Identifiers for PDHB Gene

  • GC03M057277
  • GC03M057782
  • GC03M058268
  • GC03M058370

Summaries for PDHB Gene

Entrez Gene Summary for PDHB Gene

  • The pyruvate dehydrogenase (PDH) complex is a nuclear-encoded mitochondrial multienzyme complex that catalyzes the overall conversion of pyruvate to acetyl-CoA and carbon dioxide, and provides the primary link between glycolysis and the tricarboxylic acid (TCA) cycle. The PDH complex is composed of multiple copies of three enzymatic components: pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2) and lipoamide dehydrogenase (E3). The E1 enzyme is a heterotetramer of two alpha and two beta subunits. This gene encodes the E1 beta subunit. Mutations in this gene are associated with pyruvate dehydrogenase E1-beta deficiency. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Mar 2012]

GeneCards Summary for PDHB Gene

PDHB (Pyruvate Dehydrogenase (Lipoamide) Beta) is a Protein Coding gene. Diseases associated with PDHB include Pyruvate Dehydrogenase E1-Beta Deficiency and Pyruvate Dehydrogenase E1-Alpha Deficiency. Among its related pathways are Metabolism and Citrate cycle (TCA cycle). GO annotations related to this gene include pyruvate dehydrogenase (acetyl-transferring) activity and pyruvate dehydrogenase activity. An important paralog of this gene is BCKDHB.

UniProtKB/Swiss-Prot for PDHB Gene

  • The pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2), and thereby links the glycolytic pathway to the tricarboxylic cycle.

Gene Wiki entry for PDHB Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PDHB Gene

Genomics for PDHB Gene

Regulatory Elements for PDHB Gene

Enhancers for PDHB Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH03F058462 1.2 Ensembl ENCODE 19.7 -29.8 -29766 1.6 ELF3 CBX3 PKNOX1 ARID4B THRB RAD21 RARA RFX5 ZNF143 RCOR1 PDHB RPP14 PXK KCTD6 ACOX2 ENSG00000255154 ENSG00000243384 FAM107A ENSG00000272360
GH03F058469 1.1 FANTOM5 Ensembl ENCODE 19.2 -37.8 -37768 3.4 PKNOX1 ARID4B SIN3A FEZF1 ZNF2 YY1 SLC30A9 FOS SP3 SP5 RPP14 PXK PDHB LOC105377110 KCTD6 ACOX2 ENSG00000255154 FAM107A ENSG00000243384 ENSG00000272182
GH03F058458 0.8 Ensembl 18.9 -24.5 -24544 0.4 ZBTB33 RPP14 PDHB ACOX2 PXK ENSG00000243384 FAM107A ENSG00000255154 ENSG00000272360
GH03F058432 1 ENCODE 8.5 -0.7 -651 3.6 HDGF PKNOX1 MLX ARID4B SIN3A DMAP1 YY1 SLC30A9 ZNF143 FOS RPP14 PXK PDHB ABHD6 ENSG00000272360
GH03F058437 0.4 ENCODE 8.4 -3.6 -3600 0.7 CTCF ZNF654 SMC3 RAD21 PXK ACOX2 PDHB ENSG00000272360
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around PDHB on UCSC Golden Path with GeneCards custom track

Promoters for PDHB Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001365405 457 1601 HDGF PKNOX1 MLX ARID4B SIN3A DMAP1 YY1 SLC30A9 ZNF143 SP3

Genomic Location for PDHB Gene

58,427,630 bp from pter
58,433,857 bp from pter
6,228 bases
Minus strand

Genomic View for PDHB Gene

Genes around PDHB on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PDHB Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PDHB Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PDHB Gene

Proteins for PDHB Gene

  • Protein details for PDHB Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Pyruvate dehydrogenase E1 component subunit beta, mitochondrial
    Protein Accession:
    Secondary Accessions:
    • B2R7L0
    • B4DDD7
    • Q6FH45
    • Q9BQ27
    • Q9UFK3

    Protein attributes for PDHB Gene

    359 amino acids
    Molecular mass:
    39233 Da
    Name=thiamine diphosphate; Xref=ChEBI:CHEBI:58937;
    Quaternary structure:
    • Heterotetramer of two PDHA1 and two PDHB subunits. The heterotetramer interacts with DLAT, and is part of the multimeric pyruvate dehydrogenase complex that contains multiple copies of pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (DLAT, E2) and lipoamide dehydrogenase (DLD, E3). These subunits are bound to an inner core composed of about 48 DLAT and 12 PDHX molecules.

    Three dimensional structures from OCA and Proteopedia for PDHB Gene

    Alternative splice isoforms for PDHB Gene


neXtProt entry for PDHB Gene

Selected DME Specific Peptides for PDHB Gene


Post-translational modifications for PDHB Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PDHB Gene

Domains & Families for PDHB Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PDHB: view

No data available for Gene Families and UniProtKB/Swiss-Prot for PDHB Gene

Function for PDHB Gene

Molecular function for PDHB Gene

GENATLAS Biochemistry:
pyruvate dehydrogenase,E1 beta subunit
UniProtKB/Swiss-Prot CatalyticActivity:
Pyruvate + [dihydrolipoyllysine-residue acetyltransferase] lipoyllysine = [dihydrolipoyllysine-residue acetyltransferase] S-acetyldihydrolipoyllysine + CO(2).
UniProtKB/Swiss-Prot Function:
The pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2), and thereby links the glycolytic pathway to the tricarboxylic cycle.

Enzyme Numbers (IUBMB) for PDHB Gene

Gene Ontology (GO) - Molecular Function for PDHB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004738 pyruvate dehydrogenase activity IDA 19081061
GO:0004739 pyruvate dehydrogenase (acetyl-transferring) activity IEA --
GO:0005515 protein binding IPI 18206651
GO:0016491 oxidoreductase activity IEA --
GO:0034604 contributes_to pyruvate dehydrogenase (NAD+) activity IDA 18164639
genes like me logo Genes that share ontologies with PDHB: view
genes like me logo Genes that share phenotypes with PDHB: view

Human Phenotype Ontology for PDHB Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for PDHB Gene

Localization for PDHB Gene

Subcellular locations from UniProtKB/Swiss-Prot for PDHB Gene

Mitochondrion matrix.

Subcellular locations from

Jensen Localization Image for PDHB Gene COMPARTMENTS Subcellular localization image for PDHB gene
Compartment Confidence
extracellular 5
mitochondrion 5
nucleus 5
cytosol 1

Gene Ontology (GO) - Cellular Components for PDHB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 21630459
GO:0005654 nucleoplasm IDA --
GO:0005739 mitochondrion IDA --
GO:0005759 mitochondrial matrix IEA,TAS --
GO:0045254 pyruvate dehydrogenase complex IDA 19081061
genes like me logo Genes that share ontologies with PDHB: view

Pathways & Interactions for PDHB Gene

genes like me logo Genes that share pathways with PDHB: view

Gene Ontology (GO) - Biological Process for PDHB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005975 carbohydrate metabolic process IEA --
GO:0006006 glucose metabolic process IEA --
GO:0006086 acetyl-CoA biosynthetic process from pyruvate IEA,IDA 19081061
GO:0006090 pyruvate metabolic process TAS --
GO:0006099 tricarboxylic acid cycle IEA,IDA 19081061
genes like me logo Genes that share ontologies with PDHB: view

No data available for SIGNOR curated interactions for PDHB Gene

Drugs & Compounds for PDHB Gene

(11) Drugs for PDHB Gene - From: DrugBank, DGIdb, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Pyruvic acid Approved Nutra Target 0
Carbon dioxide Approved, Vet_approved Pharma 0
2-Ketobutyric acid Experimental Pharma 0
alpha-ketoisovalerate Experimental Pharma 0
thiamin diphosphate Experimental Pharma 0

(3) Additional Compounds for PDHB Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
2-(a-Hydroxyethyl)thiamine diphosphate
  • 2-(alpha-Hydroxyethyl)thiamine diphosphate
  • 2-Hydroxyethyl-ThPP
  • 3-[(4-Amino-2-methyl-5-pyrimidinyl)methyl]-2-(1-hydroxyethyl)-4-methyl-5-(4,6,6-trihydroxy-3,5-dioxa-4,6-diphosphahex-1-yl)- P,P'-dioxide
  • 3-[(4-Amino-2-methyl-5-pyrimidinyl)methyl]-2-(1-hydroxyethyl)-5-(2-hydroxyethyl)-4-methyl- 5-(trihydrogen pyrophosphate) (8CI)
  • Thiazolium
  • Ac-CoA
  • Ac-Coenzyme A
  • Ac-S-CoA
  • Ac-S-Coenzyme A
  • Acetyl coenzyme-A
  • Dihydrolipoyllysine-residue acetyltransferase]S-acetyldihydrolipoyllysine
genes like me logo Genes that share compounds with PDHB: view

Transcripts for PDHB Gene

Unigene Clusters for PDHB Gene

Pyruvate dehydrogenase (lipoamide) beta:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for PDHB Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b · 2c ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6a · 6b · 6c ^ 7a · 7b ^ 8a · 8b · 8c ^ 9a · 9b ^ 10a · 10b · 10c
SP1: - - - - - -
SP2: - - - - - -
SP3: - - - - -
SP4: - - - - - -
SP5: - - - - - - -
SP6: - - - - - - - - - - - -
SP7: - -
SP8: - -
SP9: - - - - - -

Relevant External Links for PDHB Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PDHB Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PDHB Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PDHB Gene

This gene is overexpressed in Heart (10.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PDHB Gene

Protein tissue co-expression partners for PDHB Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PDHB Gene:


SOURCE GeneReport for Unigene cluster for PDHB Gene:

genes like me logo Genes that share expression patterns with PDHB: view

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for PDHB Gene

Orthologs for PDHB Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PDHB Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PDHB 34 35
  • 99.44 (n)
(Canis familiaris)
Mammalia -- 35
  • 96 (a)
-- 35
  • 95 (a)
  • 92.66 (n)
(Bos Taurus)
Mammalia PDHB 34 35
  • 91.74 (n)
(Ornithorhynchus anatinus)
Mammalia PDHB 35
  • 91 (a)
(Monodelphis domestica)
Mammalia PDHB 35
  • 90 (a)
(Mus musculus)
Mammalia Pdhb 34 16 35
  • 88.39 (n)
(Rattus norvegicus)
Mammalia Pdhb 34
  • 88.21 (n)
(Gallus gallus)
Aves PDHB 34 35
  • 77.35 (n)
(Anolis carolinensis)
Reptilia PDHB 35
  • 83 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia pdhb 34
  • 76.88 (n)
Str.4760 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.372 34
(Danio rerio)
Actinopterygii pdhb 34 35
  • 73.26 (n)
wufc76a05 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010421 34
  • 62.71 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG11876 36 34 35
  • 62.58 (n)
(Caenorhabditis elegans)
Secernentea C04C3.3 36
  • 66 (a)
pdhb-1 34 35
  • 60.73 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F09603g 34
  • 61.09 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PDB1 34 35 37
  • 60.63 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AAR167C 34
  • 59.33 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons MAB1 34
  • 60.15 (n)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.1955 34
(Oryza sativa)
Liliopsida Os08g0536000 34
  • 58.89 (n)
(Hordeum vulgare)
Liliopsida Hv.6624 34
(Zea mays)
Liliopsida Zm.433 34
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10514 35
  • 71 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU03004 34
  • 60.1 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes pdb1 34
  • 59.9 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4730 34
Species where no ortholog for PDHB was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PDHB Gene

Gene Tree for PDHB (if available)
Gene Tree for PDHB (if available)

Paralogs for PDHB Gene

Paralogs for PDHB Gene

(1) SIMAP similar genes for PDHB Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with PDHB: view

Variants for PDHB Gene

Sequence variations from dbSNP and Humsavar for PDHB Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
rs28933391 Pyruvate dehydrogenase E1-beta deficiency (PDHBD) [MIM:614111], Pathogenic 58,428,084(-) CTATA(C/T)CTCAG nc-transcript-variant, reference, missense
rs28935769 Pyruvate dehydrogenase E1-beta deficiency (PDHBD) [MIM:614111], Pathogenic 58,430,851(-) CTACT(A/G)CATGT nc-transcript-variant, reference, missense
rs863225125 Pathogenic 58,431,586(-) GCAGC(-/TATGGTATGTA)ATACT intron-variant, splice-donor-variant
rs863224158 Likely pathogenic 58,430,827(-) GCCTG(A/T)GCCTA intron-variant, nc-transcript-variant, reference, missense
rs1126551 Likely benign 58,430,808(-) AGAGG(A/G)CCCAA intron-variant, nc-transcript-variant, reference, synonymous-codon

Variation tolerance for PDHB Gene

Residual Variation Intolerance Score: 20.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.59; 12.71% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PDHB Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for PDHB Gene

Disorders for PDHB Gene

MalaCards: The human disease database

(3) MalaCards diseases for PDHB Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
pyruvate dehydrogenase e1-beta deficiency
  • pyruvate dehydrogenase e1 b deficiency
pyruvate dehydrogenase e1-alpha deficiency
  • pyruvate decarboxylase deficiency
leigh syndrome
  • leigh syndrome due to mitochondrial complex i deficiency
- elite association - COSMIC cancer census association via MalaCards
Search PDHB in MalaCards View complete list of genes associated with diseases


  • Pyruvate dehydrogenase E1-beta deficiency (PDHBD) [MIM:614111]: An enzymatic defect causing primary lactic acidosis in children. It is associated with a broad clinical spectrum ranging from fatal lactic acidosis in the newborn to chronic neurologic dysfunction with structural abnormalities in the central nervous system without systemic acidosis. {ECO:0000269 PubMed:15138885}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Genatlas disease for PDHB Gene

ataxia,intermittent,congenital lactate acidosis,progressive neurologic dysfunction (PDH complex deficiency)

Relevant External Links for PDHB

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with PDHB: view

Publications for PDHB Gene

  1. Characterization of two cDNA clones for pyruvate dehydrogenase E1 beta subunit and its regulation in tricarboxylic acid cycle-deficient fibroblast. (PMID: 2376596) Huh T.L. … Song B.J. (J. Biol. Chem. 1990) 3 4 22 64
  2. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson S.L. … O'Brien S.J. (PLoS ONE 2010) 3 46 64
  3. Mutations of the E1beta subunit gene (PDHB) in four families with pyruvate dehydrogenase deficiency. (PMID: 18164639) Okajima K. … Kerr D.S. (Mol. Genet. Metab. 2008) 3 22 64
  4. Structural basis for inactivation of the human pyruvate dehydrogenase complex by phosphorylation: role of disordered phosphorylation loops. (PMID: 19081061) Kato M. … Chuang D.T. (Structure 2008) 3 4 64
  5. Activity of pyruvate dehydrogenase A (PDHA) in hamster spermatozoa correlates positively with hyperactivation and is associated with sperm capacitation. (PMID: 16855207) Kumar V. … Shivaji S. (Biol. Reprod. 2006) 22 25 64

Products for PDHB Gene

Sources for PDHB Gene

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