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Protein

Pyruvate dehydrogenase E1 component subunit beta, mitochondrial

Gene

PDHB

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

The pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO2, and thereby links the glycolytic pathway to the tricarboxylic cycle.2 Publications

Catalytic activityi

Pyruvate + [dihydrolipoyllysine-residue acetyltransferase] lipoyllysine = [dihydrolipoyllysine-residue acetyltransferase] S-acetyldihydrolipoyllysine + CO2.1 Publication

Cofactori

thiamine diphosphate2 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei89Thiamine pyrophosphate1 Publication1
Sitei319Important for interaction with DLAT1 Publication1

GO - Molecular functioni

  • pyruvate dehydrogenase (acetyl-transferring) activity Source: ProtInc
  • pyruvate dehydrogenase activity Source: UniProtKB

GO - Biological processi

Keywordsi

Molecular functionOxidoreductase
Biological processCarbohydrate metabolism, Glucose metabolism, Tricarboxylic acid cycle
LigandPyruvate, Thiamine pyrophosphate

Enzyme and pathway databases

BioCyciMetaCyc:HS09727-MONOMER
ReactomeiR-HSA-204174 Regulation of pyruvate dehydrogenase (PDH) complex
R-HSA-389661 Glyoxylate metabolism and glycine degradation
R-HSA-5362517 Signaling by Retinoic Acid
R-HSA-70268 Pyruvate metabolism
SABIO-RKiP11177

Names & Taxonomyi

Protein namesi
Recommended name:
Pyruvate dehydrogenase E1 component subunit beta, mitochondrial (EC:1.2.4.1)
Short name:
PDHE1-B
Gene namesi
Name:PDHB
Synonyms:PHE1B
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 3

Organism-specific databases

EuPathDBiHostDB:ENSG00000168291.12
HGNCiHGNC:8808 PDHB
MIMi179060 gene
neXtProtiNX_P11177

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Mitochondrion

Pathology & Biotechi

Involvement in diseasei

Pyruvate dehydrogenase E1-beta deficiency (PDHBD)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionAn 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.
See also OMIM:614111
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_030954132Y → C in PDHBD. 1 PublicationCorresponds to variant dbSNP:rs28935769EnsemblClinVar.1
Natural variantiVAR_021058344P → S in PDHBD. 1 PublicationCorresponds to variant dbSNP:rs28933391EnsemblClinVar.1

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi259E → A or Q: Does not affect interaction with DLAT. 1 Publication1
Mutagenesisi262E → A or Q: Does not affect interaction with DLAT. 1 Publication1
Mutagenesisi264E → A or Q: Does not affect interaction with DLAT. 1 Publication1
Mutagenesisi319D → A: Inhibits interaction with DLAT. Does not affect pyruvate decarboxylase activity. Loss of multienzyme pyruvate dehydrogenase complex activity. 1 Publication1
Mutagenesisi319D → N: Reduces interaction with DLAT. Reduces multienzyme pyruvate dehydrogenase complex activity. Does not affect pyruvate decarboxylase activity. 1 Publication1
Mutagenesisi359I → A: Reduces pyruvate decarboxylase and multienzyme pyruvate dehydrogenase complex activity. Does not affect interaction with DLAT. 1 Publication1
Mutagenesisi359Missing : Reduces pyruvate decarboxylase and multienzyme pyruvate dehydrogenase complex activity. Does not affect interaction with DLAT. 1 Publication1

Keywords - Diseasei

Disease mutation

Organism-specific databases

DisGeNETi5162
MalaCardsiPDHB
MIMi614111 phenotype
OpenTargetsiENSG00000168291
Orphaneti255138 Pyruvate dehydrogenase E1-beta deficiency
PharmGKBiPA33152

Chemistry databases

DrugBankiDB00157 NADH
DB00119 Pyruvic acid

Polymorphism and mutation databases

BioMutaiPDHB
DMDMi134044259

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transit peptidei1 – 30Mitochondrion2 PublicationsAdd BLAST30
ChainiPRO_000002045731 – 359Pyruvate dehydrogenase E1 component subunit beta, mitochondrialAdd BLAST329

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei67PhosphotyrosineBy similarity1
Modified residuei354N6-acetyllysineBy similarity1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiP11177
MaxQBiP11177
PaxDbiP11177
PeptideAtlasiP11177
PRIDEiP11177
ProteomicsDBi52715
52716 [P11177-2]
52717 [P11177-3]
TopDownProteomicsiP11177-1 [P11177-1]

2D gel databases

REPRODUCTION-2DPAGEiIPI00549885
SWISS-2DPAGEiP11177
UCD-2DPAGEiP11177

PTM databases

iPTMnetiP11177
PhosphoSitePlusiP11177
SwissPalmiP11177

Expressioni

Gene expression databases

BgeeiENSG00000168291 Expressed in 237 organ(s), highest expression level in myocardium
CleanExiHS_PDHB
ExpressionAtlasiP11177 baseline and differential
GenevisibleiP11177 HS

Organism-specific databases

HPAiCAB033794
HPA036744
HPA036745

Interactioni

Subunit structurei

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).5 Publications

Binary interactionsi

Protein-protein interaction databases

BioGridi111188, 73 interactors
ComplexPortaliCPX-376 Pyruvate dehydrogenase E1 heterotetramer
DIPiDIP-37651N
IntActiP11177, 33 interactors
MINTiP11177
STRINGi9606.ENSP00000307241

Structurei

Secondary structure

1359
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliP11177
SMRiP11177
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP11177

Family & Domainsi

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiKOG0524 Eukaryota
COG0022 LUCA
GeneTreeiENSGT00530000063423
HOGENOMiHOG000281450
HOVERGENiHBG000917
InParanoidiP11177
KOiK00162
OMAiSRMRHHC
OrthoDBiEOG091G0D37
PhylomeDBiP11177
TreeFamiTF105674

Family and domain databases

Gene3Di3.40.50.920, 1 hit
InterProiView protein in InterPro
IPR029061 THDP-binding
IPR009014 Transketo_C/PFOR_II
IPR005475 Transketolase-like_Pyr-bd
IPR033248 Transketolase_C
PfamiView protein in Pfam
PF02779 Transket_pyr, 1 hit
PF02780 Transketolase_C, 1 hit
SMARTiView protein in SMART
SM00861 Transket_pyr, 1 hit
SUPFAMiSSF52518 SSF52518, 1 hit
SSF52922 SSF52922, 1 hit

Sequences (3+)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 3 described isoforms and 2 potential isoforms that are computationally mapped.Show allAlign All

Isoform 1 (identifier: P11177-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide
        10         20         30         40         50
MAAVSGLVRR PLREVSGLLK RRFHWTAPAA LQVTVRDAIN QGMDEELERD
60 70 80 90 100
EKVFLLGEEV AQYDGAYKVS RGLWKKYGDK RIIDTPISEM GFAGIAVGAA
110 120 130 140 150
MAGLRPICEF MTFNFSMQAI DQVINSAAKT YYMSGGLQPV PIVFRGPNGA
160 170 180 190 200
SAGVAAQHSQ CFAAWYGHCP GLKVVSPWNS EDAKGLIKSA IRDNNPVVVL
210 220 230 240 250
ENELMYGVPF EFPPEAQSKD FLIPIGKAKI ERQGTHITVV SHSRPVGHCL
260 270 280 290 300
EAAAVLSKEG VECEVINMRT IRPMDMETIE ASVMKTNHLV TVEGGWPQFG
310 320 330 340 350
VGAEICARIM EGPAFNFLDA PAVRVTGADV PMPYAKILED NSIPQVKDII

FAIKKTLNI
Length:359
Mass (Da):39,233
Last modified:March 6, 2007 - v3
Checksum:iAB459B1259FBDBD3
GO
Isoform 2 (identifier: P11177-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     16-33: Missing.

Note: No experimental confirmation available.
Show »
Length:341
Mass (Da):37,200
Checksum:iB4F137127819BB38
GO
Isoform 3 (identifier: P11177-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     135-152: Missing.

Note: No experimental confirmation available.
Show »
Length:341
Mass (Da):37,514
Checksum:i89F0A32D89507E9D
GO

Computationally mapped potential isoform sequencesi

There are 2 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
C9J634C9J634_HUMAN
Pyruvate dehydrogenase E1 component...
PDHB
350Annotation score:
F8WF02F8WF02_HUMAN
Pyruvate dehydrogenase E1 component...
PDHB
251Annotation score:

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti9 – 13RRPLR → AETPS (PubMed:3422424).Curated5
Sequence conflicti43M → G AA sequence (PubMed:7895732).Curated1
Sequence conflicti160Q → G (PubMed:3422424).Curated1
Sequence conflicti213 – 221PPEAQSKDF → LRKLSQKIL (PubMed:3422424).Curated9
Sequence conflicti213P → L in AAA88097 (PubMed:2377599).Curated1
Sequence conflicti213P → L in BAA14123 (PubMed:2377599).Curated1
Sequence conflicti310 – 312MEG → NGS (PubMed:3422424).Curated3

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_00496731L → V2 Publications1
Natural variantiVAR_030954132Y → C in PDHBD. 1 PublicationCorresponds to variant dbSNP:rs28935769EnsemblClinVar.1
Natural variantiVAR_021058344P → S in PDHBD. 1 PublicationCorresponds to variant dbSNP:rs28933391EnsemblClinVar.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_01267516 – 33Missing in isoform 2. 1 PublicationAdd BLAST18
Alternative sequenceiVSP_043364135 – 152Missing in isoform 3. 1 PublicationAdd BLAST18

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M34479 mRNA Translation: AAA36428.1
M19123 mRNA Translation: AAA60052.1 Sequence problems.
M54788 mRNA Translation: AAA60053.1
M34055 mRNA Translation: AAA60233.1
M34056 mRNA Translation: AAA60054.1
D90086 Genomic DNA Translation: BAA14123.1
J03576 mRNA Translation: AAA88097.1
AL117618 mRNA Translation: CAB56017.1
CR541911 mRNA Translation: CAG46709.1
AK293153 mRNA Translation: BAG56698.1
AK313022 mRNA Translation: BAG35857.1
AC135507 Genomic DNA No translation available.
CH471055 Genomic DNA Translation: EAW65371.1
BC000439 mRNA Translation: AAH00439.1
BC001924 mRNA Translation: AAH01924.1
X57778 mRNA Translation: CAA40924.1
CCDSiCCDS2890.1 [P11177-1]
CCDS54602.1 [P11177-3]
CCDS82795.1 [P11177-2]
PIRiJU0145 DEHUPB
RefSeqiNP_000916.2, NM_000925.3 [P11177-1]
NP_001166939.1, NM_001173468.1 [P11177-3]
NP_001302465.1, NM_001315536.1 [P11177-2]
UniGeneiHs.161357

Genome annotation databases

EnsembliENST00000302746; ENSP00000307241; ENSG00000168291 [P11177-1]
ENST00000383714; ENSP00000373220; ENSG00000168291 [P11177-2]
ENST00000485460; ENSP00000417267; ENSG00000168291 [P11177-3]
GeneIDi5162
KEGGihsa:5162
UCSCiuc003dkf.4 human [P11177-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M34479 mRNA Translation: AAA36428.1
M19123 mRNA Translation: AAA60052.1 Sequence problems.
M54788 mRNA Translation: AAA60053.1
M34055 mRNA Translation: AAA60233.1
M34056 mRNA Translation: AAA60054.1
D90086 Genomic DNA Translation: BAA14123.1
J03576 mRNA Translation: AAA88097.1
AL117618 mRNA Translation: CAB56017.1
CR541911 mRNA Translation: CAG46709.1
AK293153 mRNA Translation: BAG56698.1
AK313022 mRNA Translation: BAG35857.1
AC135507 Genomic DNA No translation available.
CH471055 Genomic DNA Translation: EAW65371.1
BC000439 mRNA Translation: AAH00439.1
BC001924 mRNA Translation: AAH01924.1
X57778 mRNA Translation: CAA40924.1
CCDSiCCDS2890.1 [P11177-1]
CCDS54602.1 [P11177-3]
CCDS82795.1 [P11177-2]
PIRiJU0145 DEHUPB
RefSeqiNP_000916.2, NM_000925.3 [P11177-1]
NP_001166939.1, NM_001173468.1 [P11177-3]
NP_001302465.1, NM_001315536.1 [P11177-2]
UniGeneiHs.161357

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1NI4X-ray1.95B/D31-359[»]
2OZLX-ray1.90B/D32-359[»]
3EXEX-ray1.98B/D/F/H31-359[»]
3EXFX-ray3.00B/D/F/H31-359[»]
3EXGX-ray3.012/4/6/B/D/F/H/J/L/N/P/R/T/V/X/Z31-359[»]
3EXHX-ray2.44B/D/F/H31-359[»]
3EXIX-ray2.20B31-359[»]
6CERX-ray2.69B/D/F/H31-359[»]
6CFOX-ray2.70B/D31-359[»]
ProteinModelPortaliP11177
SMRiP11177
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi111188, 73 interactors
ComplexPortaliCPX-376 Pyruvate dehydrogenase E1 heterotetramer
DIPiDIP-37651N
IntActiP11177, 33 interactors
MINTiP11177
STRINGi9606.ENSP00000307241

Chemistry databases

DrugBankiDB00157 NADH
DB00119 Pyruvic acid

PTM databases

iPTMnetiP11177
PhosphoSitePlusiP11177
SwissPalmiP11177

Polymorphism and mutation databases

BioMutaiPDHB
DMDMi134044259

2D gel databases

REPRODUCTION-2DPAGEiIPI00549885
SWISS-2DPAGEiP11177
UCD-2DPAGEiP11177

Proteomic databases

EPDiP11177
MaxQBiP11177
PaxDbiP11177
PeptideAtlasiP11177
PRIDEiP11177
ProteomicsDBi52715
52716 [P11177-2]
52717 [P11177-3]
TopDownProteomicsiP11177-1 [P11177-1]

Protocols and materials databases

DNASUi5162
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000302746; ENSP00000307241; ENSG00000168291 [P11177-1]
ENST00000383714; ENSP00000373220; ENSG00000168291 [P11177-2]
ENST00000485460; ENSP00000417267; ENSG00000168291 [P11177-3]
GeneIDi5162
KEGGihsa:5162
UCSCiuc003dkf.4 human [P11177-1]

Organism-specific databases

CTDi5162
DisGeNETi5162
EuPathDBiHostDB:ENSG00000168291.12
GeneCardsiPDHB
HGNCiHGNC:8808 PDHB
HPAiCAB033794
HPA036744
HPA036745
MalaCardsiPDHB
MIMi179060 gene
614111 phenotype
neXtProtiNX_P11177
OpenTargetsiENSG00000168291
Orphaneti255138 Pyruvate dehydrogenase E1-beta deficiency
PharmGKBiPA33152
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0524 Eukaryota
COG0022 LUCA
GeneTreeiENSGT00530000063423
HOGENOMiHOG000281450
HOVERGENiHBG000917
InParanoidiP11177
KOiK00162
OMAiSRMRHHC
OrthoDBiEOG091G0D37
PhylomeDBiP11177
TreeFamiTF105674

Enzyme and pathway databases

BioCyciMetaCyc:HS09727-MONOMER
ReactomeiR-HSA-204174 Regulation of pyruvate dehydrogenase (PDH) complex
R-HSA-389661 Glyoxylate metabolism and glycine degradation
R-HSA-5362517 Signaling by Retinoic Acid
R-HSA-70268 Pyruvate metabolism
SABIO-RKiP11177

Miscellaneous databases

ChiTaRSiPDHB human
EvolutionaryTraceiP11177
GeneWikiiPyruvate_dehydrogenase_(lipoamide)_beta
GenomeRNAii5162
PROiPR:P11177
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000168291 Expressed in 237 organ(s), highest expression level in myocardium
CleanExiHS_PDHB
ExpressionAtlasiP11177 baseline and differential
GenevisibleiP11177 HS

Family and domain databases

Gene3Di3.40.50.920, 1 hit
InterProiView protein in InterPro
IPR029061 THDP-binding
IPR009014 Transketo_C/PFOR_II
IPR005475 Transketolase-like_Pyr-bd
IPR033248 Transketolase_C
PfamiView protein in Pfam
PF02779 Transket_pyr, 1 hit
PF02780 Transketolase_C, 1 hit
SMARTiView protein in SMART
SM00861 Transket_pyr, 1 hit
SUPFAMiSSF52518 SSF52518, 1 hit
SSF52922 SSF52922, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiODPB_HUMAN
AccessioniPrimary (citable) accession number: P11177
Secondary accession number(s): B2R7L0
, B4DDD7, Q6FH45, Q9BQ27, Q9UFK3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 1, 1989
Last sequence update: March 6, 2007
Last modified: November 7, 2018
This is version 215 of the entry and version 3 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 3
    Human chromosome 3: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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