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

Summary

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Official Symbol: PDHBprovided by HGNC
Official Full Name: pyruvate dehydrogenase (lipoamide) betaprovided by HGNC
Primary source: HGNC:8808
See related: Ensembl:ENSG00000168291; HPRD:01530; MIM:179060; Vega:OTTHUMG00000159157
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; 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]

Genomic context

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Location :: 3p21.1-p14.2

Sequence :: Chromosome: 3; NC_000003.11 (58413357..58419579, complement)

See PDHB in Epigenomics, MapViewer

Chromosome 3 - NC_000003.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence

Go to nucleotideGraphics FASTA GenBank

Go to reference sequence details

Bibliography

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GeneRIFs: Gene References Into Functions What's a GeneRIF?

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.
Species specificity in the interaction between hE1beta and hE2 in pyruvate dehydrogenase complex.
Title: Binding of pyruvate dehydrogenase to the core of the human pyruvate dehydrogenase complex.

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

Pyruvate dehydrogenase e1-beta deficiency

MIM: 614111

Genetic Testing Registry

Interactions

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Products	Interactant	Other Gene	Source	Pubs	Description
P11177	P08559	PDHA1	HPRD	PubMed
P11177	P29803	PDHA2	HPRD	PubMed
P11177	P11177	PDHB	HPRD	PubMed
P11177	O00330	PDHX	HPRD	PubMed
BioGRID:111188	BioGRID:106807	ANXA7	BioGRID	PubMed	Two-hybrid
BioGRID:111188	BioGRID:120937	CAND1	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111188	BioGRID:107460	CDKN1A	BioGRID	PubMed	Two-hybrid
BioGRID:111188	BioGRID:114030	CUL3	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111188	BioGRID:108081	DLAT	BioGRID	PubMed	Reconstituted Complex
BioGRID:111188	BioGRID:114023	DYRK2	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111188	BioGRID:108223	ECT2	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111188	BioGRID:108298	EIF5	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111188	BioGRID:117654	FBXO6	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111188	BioGRID:108499	FCER1A	BioGRID	PubMed	Two-hybrid
BioGRID:111188	BioGRID:108621	FN1	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111188	BioGRID:109045	GNB2	BioGRID	PubMed	Two-hybrid
BioGRID:111188	BioGRID:109143	GRB7	BioGRID	PubMed	Two-hybrid
BioGRID:111188	BioGRID:109894	ITGB1	BioGRID	PubMed	Two-hybrid
BioGRID:111188	BioGRID:115014	MDC1	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111188	BioGRID:111017	OGDH	BioGRID	PubMed	Co-fractionation
BioGRID:111188	BioGRID:111791	PCYT2	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111188	BioGRID:111186	PDHA1	BioGRID	PubMed	Co-fractionation; Co-purification
BioGRID:111188	BioGRID:111187	PDHA2	BioGRID	PubMed	Co-purification
BioGRID:111188	BioGRID:113737	PDHX	BioGRID	PubMed	Co-fractionation; Co-purification
BioGRID:111188	BioGRID:111223	PFDN1	BioGRID	PubMed	Two-hybrid
BioGRID:111188	BioGRID:111843	RAP1B	BioGRID	PubMed	Two-hybrid
BioGRID:111188	BioGRID:107529	RCC1	BioGRID	PubMed	Two-hybrid
BioGRID:111188	BioGRID:110115	RPSA	BioGRID	PubMed	Co-fractionation
BioGRID:111188	BioGRID:115608	RRAGB	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111188	BioGRID:112516	SNRPD1	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111188	BioGRID:117071	SRRM2	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111188	BioGRID:124195	TRIM63	BioGRID	PubMed	Two-hybrid
BioGRID:111188	BioGRID:114374	TSC22D1	BioGRID	PubMed	Two-hybrid
BioGRID:111188	BioGRID:113164	UBC	BioGRID	PubMed	Affinity Capture-MS
BioGRID:111188	BioGRID:113363	YWHAE	BioGRID	PubMed	Affinity Capture-MS

Pathways from BioSystems

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Butanoate metabolism, organism-specific biosystem (from KEGG)
Butanoate metabolism, organism-specific biosystem
Butanoate metabolism
Butanoate metabolism, conserved biosystem (from KEGG)
Butanoate metabolism, conserved biosystem
Butanoate metabolism
Citrate cycle (TCA cycle), organism-specific biosystem (from KEGG)
Citrate cycle (TCA cycle), organism-specific biosystemThe citrate cycle (TCA cycle, Krebs cycle) is an important aerobic pathway for the final steps of the oxidation of carbohydrates and fatty acids. The cycle starts with acetyl-CoA, the activated form ...
Citrate cycle (TCA cycle), conserved biosystem (from KEGG)
Citrate cycle (TCA cycle), conserved biosystemThe citrate cycle (TCA cycle, Krebs cycle) is an important aerobic pathway for the final steps of the oxidation of carbohydrates and fatty acids. The cycle starts with acetyl-CoA, the activated form ...
Glycolysis / Gluconeogenesis, organism-specific biosystem (from KEGG)
Glycolysis / Gluconeogenesis, organism-specific biosystemGlycolysis is the process of converting glucose into pyruvate and generating small amounts of ATP (energy) and NADH (reducing power). It is a central pathway that produces important precursor metabol...
Glycolysis / Gluconeogenesis, conserved biosystem (from KEGG)
Glycolysis / Gluconeogenesis, conserved biosystemGlycolysis is the process of converting glucose into pyruvate and generating small amounts of ATP (energy) and NADH (reducing power). It is a central pathway that produces important precursor metabol...
Glycolysis and Gluconeogenesis, organism-specific biosystem (from WikiPathways)
Glycolysis and Gluconeogenesis, organism-specific biosystem
Glycolysis and Gluconeogenesis
HIF-1 signaling pathway, organism-specific biosystem (from KEGG)
HIF-1 signaling pathway, organism-specific biosystemHypoxia-inducible factor 1 (HIF-1) is a transcription factor that functions as a master regulator of oxygen homeostasis. It consists of two subunits: an inducibly-expressed HIF-1alpha subunit and a c...
Metabolism, organism-specific biosystem (from REACTOME)
Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
Pyruvate metabolism, organism-specific biosystem (from REACTOME)
Pyruvate metabolism, organism-specific biosystemPyruvate sits at an intersection of key pathways of energy metabolism. It is the end product of glycolysis and the starting point for gluconeogenesis, and can be generated by transamination of alanin...
Pyruvate metabolism, organism-specific biosystem (from KEGG)
Pyruvate metabolism, organism-specific biosystem
Pyruvate metabolism
Pyruvate metabolism, conserved biosystem (from KEGG)
Pyruvate metabolism, conserved biosystem
Pyruvate metabolism
Pyruvate metabolism and Citric Acid (TCA) cycle, organism-specific biosystem (from REACTOME)
Pyruvate metabolism and Citric Acid (TCA) cycle, organism-specific biosystemPyruvate metabolism and the citric acid (TCA) cycle together link the processes of energy metabolism in a human cell with one another and with key biosynthetic reactions. Pyruvate, derived from the r...
Pyruvate oxidation, pyruvate => acetyl-CoA, organism-specific biosystem (from KEGG)
Pyruvate oxidation, pyruvate => acetyl-CoA, organism-specific biosystemPathway module; Carbohydrate and lipid metabolism; Central carbohydrate metabolism
Pyruvate oxidation, pyruvate => acetyl-CoA, conserved biosystem (from KEGG)
Pyruvate oxidation, pyruvate => acetyl-CoA, conserved biosystemPathway module; Carbohydrate and lipid metabolism; Central carbohydrate metabolism
Regulation of pyruvate dehydrogenase (PDH) complex, organism-specific biosystem (from REACTOME)
Regulation of pyruvate dehydrogenase (PDH) complex, organism-specific biosystemThe mitochondrial pyruvate dehydrogenase (PDH) complex catalyzes the oxidative decarboxylation of pyruvate, linking glycolysis to the tricarboxylic acid cycle and fatty acid synthesis. PDH inactivati...
The citric acid (TCA) cycle and respiratory electron transport, organism-specific biosystem (from REACTOME)
The citric acid (TCA) cycle and respiratory electron transport, organism-specific biosystemThe metabolism of pyruvate provides one source of acetyl-CoA which enters the citric acid (TCA, tricarboxylic acid) cycle to generate energy and the reducing equivalent NADH. These reducing equivalen...
pyruvate decarboxylation to acetyl CoA, organism-specific biosystem (from BIOCYC)
pyruvate decarboxylation to acetyl CoA, organism-specific biosystem2-oxo acid dehydrogenase complexes convert 2-oxo acids to the corresponding acyl-CoA derivatives and produce NADH and : CARBON-DIOXIDE in an irreversible reaction. Five members of this family are kno...
pyruvate decarboxylation to acetyl CoA, conserved biosystem (from BIOCYC)
pyruvate decarboxylation to acetyl CoA, conserved biosystemGeneral Background 2-oxo acid dehydrogenase complexes convert 2-oxo acids to the corresponding acyl-CoA derivatives and produce NADH and |FRAME: CARBON-DIOXIDE| in an irreversible reaction. Five mem...

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

Genotypes

See PDHB SNP Geneview Report
See PDHB SNP Genotype Report
See PDHB SNP Variation Viewer Report

Homology

Homologs of the PDHB gene: The PDHB gene is conserved in Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, fruit fly, mosquito, C.elegans, S.cerevisiae, K.lactis, E.gossypii, S.pombe, M.oryzae, N.crassa, A.thaliana, and rice.
Map Viewer (Mouse, Rat)
OrthoDB: The Hierarchical Catalog of Eukaryotic Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
pyruvate dehydrogenase (acetyl-transferring) activity	IEA Inferred from Electronic Annotation more info
pyruvate dehydrogenase activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
acetyl-CoA biosynthetic process from pyruvate	IDA Inferred from Direct Assay more info	PubMed
glucose metabolic process	IEA Inferred from Electronic Annotation more info
pyruvate metabolic process	TAS Traceable Author Statement more info
regulation of acetyl-CoA biosynthetic process from pyruvate	TAS Traceable Author Statement more info
small molecule metabolic process	TAS Traceable Author Statement more info
tricarboxylic acid cycle	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
mitochondrial matrix	TAS Traceable Author Statement more info
pyruvate dehydrogenase complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: pyruvate dehydrogenase E1 component subunit beta, mitochondrial

Names: pyruvate dehydrogenase E1 component subunit beta, mitochondrial; pyruvate dehydrogenase, E1 beta polypeptide

NP_000916.2

EC 1.2.4.1

NP_001166939.1

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_016860.1 RefSeqGene

Range

5001..11223

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_000925.3 → NP_000916.2 pyruvate dehydrogenase E1 component subunit beta, mitochondrial isoform 1 precursor

Status: REVIEWED

Description

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

Source sequence(s)

AK225569, AK293153, BM971427, DA965753

Consensus CDS

CCDS2890.1

UniProtKB/Swiss-Prot

P11177

Related

ENSP00000307241, OTTHUMP00000214202, ENST00000302746, OTTHUMT00000353558

Conserved Domains (3) summary

cd07036
Location:37 – 203
Blast Score: 807

TPP_PYR_E1-PDHc-beta_like; Pyrimidine (PYR) binding domain of the beta subunits of the E1 components of human pyruvate dehydrogenase complex (E1- PDHc) and related proteins.

PLN02683
Location:6 – 356
Blast Score: 1404

PLN02683; pyruvate dehydrogenase E1 component subunit beta

pfam02780
Location:226 – 348
Blast Score: 372

Transketolase_C; Transketolase, C-terminal domain
NM_001173468.1 → NP_001166939.1 pyruvate dehydrogenase E1 component subunit beta, mitochondrial isoform 2 precursor

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, OTTHUMP00000214203, ENST00000485460, OTTHUMT00000353562

Conserved Domains (3) summary

cd07036
Location:37 – 185
Blast Score: 710

TPP_PYR_E1-PDHc-beta_like; Pyrimidine (PYR) binding domain of the beta subunits of the E1 components of human pyruvate dehydrogenase complex (E1- PDHc) and related proteins.

PLN02683
Location:6 – 338
Blast Score: 1301

PLN02683; pyruvate dehydrogenase E1 component subunit beta

pfam02780
Location:208 – 330
Blast Score: 372

Transketolase_C; Transketolase, C-terminal domain

RNA

NR_033384.1 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)

AK225569, AK293153, BM971427, DB039833

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 104

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh37.p10 Primary Assembly

Genomic

NC_000003.11 Reference GRCh37.p10 Primary Assembly

Range

58413357..58419579, complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

AC_000135.1 Alternate HuRef

Range

58509470..58515692, complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.0

Genomic

NC_018914.1 Alternate CHM1_1.0

Range

58365707..58371932, complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Nucleotide		Protein
Heading	Accession and Version	Protein
genomic	ABBA01024384.1 (7670..13892)	None
genomic	AC135507.2 (128888..135084)	None
genomic	AMYH01013229.1 (109114..115339)	None
genomic	CH471055.1	EAW65371.1
		EAW65372.1
		EAW65373.1
genomic	D90086.1	BAA14123.1
mRNA	AB209241.1	BAD92478.1
mRNA	AK225569.1	None
mRNA	AK225621.1	None
mRNA	AK293153.1	BAG56698.1
mRNA	AK311514.1	None
mRNA	AK313022.1	BAG35857.1
mRNA	AL117618.1	CAB56017.1
mRNA	AL706543.1	None
mRNA	BC000439.2	AAH00439.1
mRNA	BC001924.1	AAH01924.1
mRNA	BC004115.2	None
mRNA	BM971427.1	None
mRNA	CR541911.1	CAG46709.1
mRNA	DA965753.1	None
mRNA	DB039833.1	None
mRNA	J03576.1	AAA88097.1
mRNA	M19123.1	AAA60052.1
mRNA	M34055.1	AAA60233.1
mRNA	M34056.1	AAA60054.1
mRNA	M34479.1	AAA36428.1
mRNA	M54788.1	AAA60053.1
mRNA	X57778.1	CAA40924.1
other-genetic	AM392999.1	CAL37877.1
other-genetic	AM393278.1	CAL38156.1
other-genetic	DQ891366.2	ABM82292.1
other-genetic	DQ894546.2	ABM85472.1