PDHB pyruvate dehydrogenase E1 subunit beta [Homo sapiens (human)] - Gene

Summary

Official Symbol: PDHBprovided by HGNC
Official Full Name: pyruvate dehydrogenase E1 subunit betaprovided by HGNC
Primary source: HGNC:HGNC:8808
See related: Ensembl:ENSG00000168291 MIM:179060; AllianceGenome:HGNC:8808
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: PDHBD; PHE1B; E1beta; PDHE1B; PDHE1-B
Summary: 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]
Expression: Ubiquitous expression in heart (RPKM 60.3), kidney (RPKM 43.5) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3p14.3

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (58427630..58433832, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (58468008..58474213, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (58413357..58419559, complement)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Integrated single-cell and bulk characterization of cuproptosis key regulator PDHB and association with tumor microenvironment infiltration in clear cell renal cell carcinoma.
Title: Integrated single-cell and bulk characterization of cuproptosis key regulator PDHB and association with tumor microenvironment infiltration in clear cell renal cell carcinoma.
Pyruvate dehydrogenase B regulates myogenic differentiation via the FoxP1-Arih2 axis.
Title: Pyruvate dehydrogenase B regulates myogenic differentiation via the FoxP1-Arih2 axis.
Building on evidence that PDH activity depends on the stability of a multi-protein PDH complex, the authors found that the PDH-E1beta subunit of the PDH complex is downregulated to inhibit PDH activity under conditions of prolonged hypoxia which establishs the specific mechanism through which PDH acts as an oncogenic factor by tuning glycolytic metabolism in cancer cells.
Title: Pyruvate Dehydrogenase PDH-E1β Controls Tumor Progression by Altering the Metabolic Status of Cancer Cells.
PDHB was downregulated in nasopharyngeal carcinoma cells. Forced expression of PDHB in NPC cells inhibited cell growth and migration, while knocking down the expression of PDHB promoted the growth, migration, and tumorigenesis of NPC cells. PDHB inhibited ERK signaling and cell growth driven by RasV12.
Title: Pyruvate dehydrogenase B promoted the growth and migration of the nasopharyngeal carcinoma cells.
Data indicate that (pro)renin receptor ATP6PA2 interacts with the E1 beta subunit of pyruvate dehydrogenase and controlling its protein stability
Title: ATP6AP2/(pro)renin receptor contributes to glucose metabolism via stabilizing the pyruvate dehydrogenase E1 β subunit.
PHD3 depletion did not affect the expression of the PDH-E1alpha, E1beta, and E2 subunits, or the phosphorylation status of E1alpha, but destabilized the PDH complex (PDC), resulting in less functional PDC.
Title: Prolyl-hydroxylase PHD3 interacts with pyruvate dehydrogenase (PDH)-E1β and regulates the cellular PDH activity.
Sequencing of PDHB reveals a homozygous point mutation (c.302T>C), causing a predicted amino acid change in patient 1. Patient 2 is compound heterozygote for mutations c.301A>G (p.M101V) and c.313G>A (p.R105Q).
Title: PDH E1β deficiency with novel mutations in two patients with Leigh syndrome.
Observational study of gene-disease association. (HuGE Navigator)
Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
Data indicate that PDH deficiency in our patient involves a post-translational modification in which EGFR-PTK-mediated tyrosine phosphorylation of the E1beta protein leads to enhanced ubiquitination followed by proteasome-mediated degradation.
Title: Pyruvate dehydrogenase complex deficiency caused by ubiquitination and proteasome-mediated degradation of the E1 subunit.
clinical findings are similar to those of PDHA1 deficiency, except that ataxia was more frequent in PDHA1 cases and consanguinity was found only in PDHB families.
Title: Mutations of the E1beta subunit gene (PDHB) in four families with pyruvate dehydrogenase deficiency.

Submit: New GeneRIF Correction See all GeneRIFs (11)

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

Associated conditions

Description	Tests
Pyruvate dehydrogenase E1-beta deficiency MedGen: C3279841 OMIM: 614111 GeneReviews: Primary Pyruvate Dehydrogenase Complex Deficiency Overview	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	Tandem affinity purification and mass spectrometry analysis identify pyruvate dehydrogenase subunit beta (PDHB), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Gag-Pol	gag-pol	Tandem affinity purification and mass spectrometry analysis identify pyruvate dehydrogenase subunit beta (PDHB), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Nef	nef	Tandem affinity purification and mass spectrometry analysis identify pyruvate dehydrogenase subunit beta (PDHB), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Pr55(Gag)	gag	Tandem affinity purification and mass spectrometry analysis identify pyruvate dehydrogenase subunit beta (PDHB), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

GDB:181220 (e-PCR)
- UniSTS:155188

STS-J03576 (e-PCR)
- UniSTS:1849

D1S3203 (e-PCR)
- UniSTS:22631

D7S3207 (e-PCR)
- UniSTS:229489

D1S1423 (e-PCR)
- UniSTS:149619

D1S1425 (e-PCR)
- UniSTS:149621

L30092 (e-PCR)
- UniSTS:57478

D13S1553 (e-PCR)
- UniSTS:473482

G44720 (e-PCR)
- UniSTS:95195

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables metal ion binding	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
contributes_to pyruvate dehydrogenase (acetyl-transferring) activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in acetyl-CoA biosynthetic process from pyruvate	IBA Inferred from Biological aspect of Ancestor more info
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
involved_in glucose metabolic process	IEA Inferred from Electronic Annotation more info
involved_in tricarboxylic acid cycle	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in mitochondrial matrix	TAS Traceable Author Statement more info
located_in mitochondrion	HTP more info	PubMed
is_active_in mitochondrion	IDA Inferred from Direct Assay more info	PubMed
located_in mitochondrion	IDA Inferred from Direct Assay more info
located_in mitochondrion	NAS Non-traceable Author Statement more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleus	HDA 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 E1 component subunit beta, mitochondrial

Names: epididymis secretory sperm binding protein; pyruvate dehydrogenase (lipoamide) beta; pyruvate dehydrogenase E1 beta subunit; pyruvate dehydrogenase, E1 beta polypeptide

NP_000916.2

EC 1.2.4.1

NP_001166939.1

EC 1.2.4.1

NP_001302465.1

EC 1.2.4.1

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

NG_016860.2 RefSeqGene

Range

5000..11202

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_000925.4 → NP_000916.2 pyruvate dehydrogenase E1 component subunit beta, mitochondrial isoform 1 precursor

See identical proteins and their annotated locations for NP_000916.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the predominant transcript and encodes the longest isoform (1).

Source sequence(s)

AC135507

Consensus CDS

CCDS2890.1

UniProtKB/Swiss-Prot

B2R7L0, B4DDD7, P11177, Q6FH45, Q9BQ27, Q9UFK3

UniProtKB/TrEMBL

A0A384MDR8, C9J634

Related

ENSP00000307241.6, ENST00000302746.11

Conserved Domains (1) summary

PRK11892
Location:32 → 355

PRK11892; pyruvate dehydrogenase subunit beta; Provisional
NM_001173468.2 → NP_001166939.1 pyruvate dehydrogenase E1 component subunit beta, mitochondrial isoform 2 precursor

See identical proteins and their annotated locations for NP_001166939.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks a segment in the coding region compared to variant 1. The resulting protein (isoform 2) is shorter but has the same N- and C-termini compared to isoform 1.

Source sequence(s)

AK293153, BM971427, DA965753

Consensus CDS

CCDS54602.1

UniProtKB/Swiss-Prot

P11177

Related

ENSP00000417267.1, ENST00000485460.5

Conserved Domains (1) summary

cl27364
Location:32 → 337

Transketolase_C; Transketolase, C-terminal domain
NM_001315536.2 → NP_001302465.1 pyruvate dehydrogenase E1 component subunit beta, mitochondrial isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AC135507

Consensus CDS

CCDS82795.1

UniProtKB/TrEMBL

C9J634

Related

ENSP00000373220.4, ENST00000383714.8

Conserved Domains (1) summary

PRK11892
Location:11 → 337

PRK11892; pyruvate dehydrogenase subunit beta; Provisional

RNA

NR_033384.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (3) is alternatively spliced at the 5' end compared to variant 1. It is represented as non-coding because the use of the 5'-most translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC135507

Related

ENST00000461692.5