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Aliases for PDHB Gene

Aliases for PDHB Gene

  • Pyruvate Dehydrogenase E1 Beta Subunit 2 3 5
  • Pyruvate Dehydrogenase (Lipoamide) Beta 2 3
  • PDHE1-B 3 4
  • PHE1B 3 4
  • Pyruvate Dehydrogenase E1 Component Subunit Beta, Mitochondrial 3
  • Pyruvate Dehydrogenase, E1 Beta Polypeptide 3
  • EC 4
  • PDHE1B 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 E1 Beta Subunit) 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 Central carbon metabolism in cancer and Metabolism. Gene Ontology (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

Additional gene information for PDHB Gene

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

Genomics for PDHB Gene

GeneHancer (GH) Regulatory Elements for PDHB Gene

Promoters and enhancers for PDHB Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03J058432 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 658.5 -0.7 -650 3.6 HDGF PKNOX1 FOXA2 SMAD1 MLX ARNT ARID4B SIN3A DMAP1 YY1 PDHB RPP14 PXK ABHD6 ENSG00000272360
GH03J058469 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 19.2 -37.8 -37768 3.4 PKNOX1 CLOCK FOXA2 ARID4B NEUROD1 SIN3A FEZF1 ZNF2 YY1 SLC30A9 RPP14 PXK PDHB LOC105377110 KCTD6 ACOX2 HTD2 FAM107A ENSG00000243384 ENSG00000272182
GH03J058462 Enhancer 1.1 Ensembl ENCODE 19.8 -29.8 -29782 1.6 PKNOX1 FOXA2 SMAD1 ARID4B YY1 ZNF207 ZNF143 ATF7 RUNX3 DEK PDHB RPP14 PXK DENND6A KCTD6 ACOX2 HTD2 ENSG00000243384 FAM107A FLNB-AS1
GH03J058305 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 5.6 +126.5 126548 3.3 FOXA2 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 IRF4 YY1 SLC30A9 RPP14 HTD2 DENND6A ABHD6 PDHB ENSG00000273493 PXK PIR62243
GH03J058382 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 7 +47.5 47458 6.9 NCOA3 TAF1 JUN MAX RAD21 YY1 ZNF664 CTBP1 GATA3 ZNF316 PXK RPP14 FAM107A HTD2 ACOX2 ENSG00000243384 PDHB FLNB-AS1 ENSG00000275607 ENSG00000272182
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PDHB on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PDHB gene promoter:
  • SREBP-1c
  • SREBP-1b
  • SREBP-1a
  • ARP-1
  • Roaz
  • IRF-7A
  • STAT3
  • SRF
  • SRF (504 AA)
  • FOXJ2 (long isoform)

Genomic Locations for PDHB Gene

Genomic Locations for PDHB Gene
6,228 bases
Minus strand
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 (PubMed:12651851, PubMed:17474719, PubMed:19081061). 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) (PubMed:14638692). These subunits are bound to an inner core composed of about 48 DLAT and 12 PDHX molecules (PubMed:14638692). Interacts with DLAT (PubMed:20160912).

    Three dimensional structures from OCA and Proteopedia for PDHB Gene

    Alternative splice isoforms for PDHB Gene


neXtProt entry for PDHB Gene

Post-translational modifications for PDHB Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PDHB Gene

No data available for DME Specific Peptides for PDHB Gene

Domains & Families for PDHB Gene

Gene Families for PDHB Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins

Graphical View of Domain Structure for InterPro Entry

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

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

Function for PDHB Gene

Molecular function for PDHB Gene

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.
UniProtKB/Swiss-Prot CatalyticActivity:
Pyruvate + [dihydrolipoyllysine-residue acetyltransferase] lipoyllysine = [dihydrolipoyllysine-residue acetyltransferase] S-acetyldihydrolipoyllysine + CO(2).
GENATLAS Biochemistry:
pyruvate dehydrogenase,E1 beta subunit

Enzyme Numbers (IUBMB) for PDHB Gene

Phenotypes From GWAS Catalog 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 TAS,IEA --
GO:0005515 protein binding IPI 12651851
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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PDHB

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

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PDHB gene
Compartment Confidence
extracellular 5
mitochondrion 5
nucleus 5
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Mitochondria (3)
  • Nucleoplasm (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PDHB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus HDA 21630459
GO:0005654 nucleoplasm IDA --
GO:0005739 mitochondrion IDA --
GO:0005759 mitochondrial matrix 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 IDA 19081061
GO:0006090 pyruvate metabolic process TAS --
GO:0006099 tricarboxylic acid cycle IDA,TAS 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

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

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

(4) 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
  • 2-(a-Hydroxyethyl)thiamine diphosphoric acid
  • 2-(alpha-Hydroxyethyl)thiamine diphosphoric acid
  • 2-(α-hydroxyethyl)thiamine diphosphate
  • AcCoA
  • Acetyl coenzyme A
  • S-Acetyl-CoA
  • S-Acetyl-coenzyme A
  • Ac-CoA
  • 8-S-Acetyldihydrolipoamide
  • Dihydrolipoyllysine-residue acetyltransferase]S-acetyldihydrolipoyllysine
Thiamine pyrophosphate
  • Thiamin diphosphate
  • Thiamin pyrophosphate
  • Thiamine diphosphate
  • THPP
  • TPP
genes like me logo Genes that share compounds with PDHB: view

Transcripts for PDHB Gene

mRNA/cDNA for PDHB Gene

Unigene Clusters for PDHB Gene

Pyruvate dehydrogenase (lipoamide) beta:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PDHB

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 CGAP 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, 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:


Evidence on tissue expression from TISSUES for PDHB Gene

  • Nervous system(4.9)
  • Lung(4.5)
  • Heart(4.4)
  • Liver(4.4)
  • Muscle(2.5)
  • Kidney(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PDHB Gene

Germ Layers:
  • ectoderm
  • mesoderm
  • nervous
  • skeletal muscle
Head and neck:
  • brain
  • head
genes like me logo Genes that share expression patterns with PDHB: view

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 33
  • 99.44 (n)
(Canis familiaris)
Mammalia -- 34
  • 96 (a)
-- 34
  • 95 (a)
  • 92.66 (n)
(Bos Taurus)
Mammalia PDHB 34 33
  • 91.74 (n)
(Ornithorhynchus anatinus)
Mammalia PDHB 34
  • 91 (a)
(Monodelphis domestica)
Mammalia PDHB 34
  • 90 (a)
(Mus musculus)
Mammalia Pdhb 16 34 33
  • 88.39 (n)
(Rattus norvegicus)
Mammalia Pdhb 33
  • 88.21 (n)
(Gallus gallus)
Aves PDHB 34 33
  • 77.35 (n)
(Anolis carolinensis)
Reptilia PDHB 34
  • 83 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia pdhb 33
  • 76.88 (n)
Str.4760 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.372 33
(Danio rerio)
Actinopterygii pdhb 34 33
  • 73.26 (n)
wufc76a05 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010421 33
  • 62.71 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG11876 34 35 33
  • 62.58 (n)
(Caenorhabditis elegans)
Secernentea C04C3.3 35
  • 66 (a)
pdhb-1 34 33
  • 60.73 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0F09603g 33
  • 61.09 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PDB1 36 34 33
  • 60.63 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AAR167C 33
  • 59.33 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons MAB1 33
  • 60.15 (n)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.1955 33
(Oryza sativa)
Liliopsida Os08g0536000 33
  • 58.89 (n)
(Hordeum vulgare)
Liliopsida Hv.6624 33
(Zea mays)
Liliopsida Zm.433 33
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10514 34
  • 71 (a)
Cin.4730 33
bread mold
(Neurospora crassa)
Ascomycetes NCU03004 33
  • 60.1 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes pdb1 33
  • 59.9 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4730 33
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)
Evolutionary constrained regions (ECRs) for PDHB: view image

Paralogs for PDHB Gene

Paralogs for PDHB Gene

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

  • C9J634_HUMAN
  • F8WF02_HUMAN
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 Variation AA Info Type
rs1126551 likely-benign, benign, not specified, Pyruvate dehydrogenase complex deficiency 58,430,808(-) C/T coding_sequence_variant, intron_variant, non_coding_transcript_variant, synonymous_variant
rs1126722 benign, Pyruvate dehydrogenase complex deficiency 58,427,791(-) T/G 3_prime_UTR_variant, non_coding_transcript_variant
rs1126735 benign, Pyruvate dehydrogenase complex deficiency 58,427,681(-) A/G/T 3_prime_UTR_variant, non_coding_transcript_variant
rs1126737 benign, Pyruvate dehydrogenase complex deficiency 58,427,678(-) T/C 3_prime_UTR_variant, non_coding_transcript_variant
rs11542399 benign, uncertain-significance, not specified, Pyruvate dehydrogenase complex deficiency 58,431,949(-) A/G coding_sequence_variant, non_coding_transcript_variant, synonymous_variant

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)

Additional Variant Information for PDHB Gene

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

SNP Genotyping and Copy Number Assay Products

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: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

- 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)

Additional Disease Information for PDHB

Genetic Association Database
Human Genome Epidemiology 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 TL … Song BJ (The Journal of biological chemistry 1990) 3 4 22 58
  2. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 44 58
  3. Pyruvate dehydrogenase complex deficiency caused by ubiquitination and proteasome-mediated degradation of the E1 subunit. (PMID: 17923481) Han Z … Stacpoole PW (The Journal of biological chemistry 2008) 2 3 58
  4. Mutations of the E1beta subunit gene (PDHB) in four families with pyruvate dehydrogenase deficiency. (PMID: 18164639) Okajima K … Kerr DS (Molecular genetics and metabolism 2008) 3 22 58
  5. Structural basis for inactivation of the human pyruvate dehydrogenase complex by phosphorylation: role of disordered phosphorylation loops. (PMID: 19081061) Kato M … Chuang DT (Structure (London, England : 1993) 2008) 3 4 58

Products for PDHB Gene

Sources for PDHB Gene

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