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Protein

Pyruvate dehydrogenase E1 component subunit beta, mitochondrial

Gene

PDHB

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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

GO - Molecular functioni

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

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Carbohydrate metabolism, Glucose metabolism, Tricarboxylic acid cycle

Keywords - Ligandi

Pyruvate, Thiamine pyrophosphate

Enzyme and pathway databases

BioCyciMetaCyc:HS09727-MONOMER.
ZFISH: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-RKP11177.

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

HGNCiHGNC:8808. PDHB.

Subcellular locationi

GO - Cellular componenti

  • extracellular exosome Source: UniProtKB
  • mitochondrial matrix Source: Reactome
  • mitochondrion Source: HPA
  • nucleoplasm Source: HPA
  • nucleus Source: UniProtKB
  • pyruvate dehydrogenase complex Source: UniProtKB
Complete GO annotation...

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 rs28935769dbSNPEnsembl.1
Natural variantiVAR_021058344P → S in PDHBD. 1 PublicationCorresponds to variant rs28933391dbSNPEnsembl.1

Keywords - Diseasei

Disease mutation

Organism-specific databases

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

Chemistry databases

DrugBankiDB00119. 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.
TopDownProteomicsiP11177-1. [P11177-1]

2D gel databases

REPRODUCTION-2DPAGEIPI00549885.
SWISS-2DPAGEP11177.
UCD-2DPAGEP11177.

PTM databases

iPTMnetiP11177.
PhosphoSitePlusiP11177.
SwissPalmiP11177.

Expressioni

Gene expression databases

BgeeiENSG00000168291.
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. 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.4 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
DLATP105157EBI-1035872,EBI-2959723

Protein-protein interaction databases

BioGridi111188. 62 interactors.
DIPiDIP-37651N.
IntActiP11177. 24 interactors.
MINTiMINT-3007546.
STRINGi9606.ENSP00000307241.

Structurei

Secondary structure

1359
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi32 – 34Combined sources3
Helixi35 – 49Combined sources15
Beta strandi53 – 57Combined sources5
Turni58 – 61Combined sources4
Turni69 – 72Combined sources4
Helixi73 – 77Combined sources5
Turni79 – 81Combined sources3
Beta strandi82 – 84Combined sources3
Helixi89 – 101Combined sources13
Beta strandi105 – 109Combined sources5
Helixi113 – 119Combined sources7
Helixi120 – 124Combined sources5
Turni125 – 129Combined sources5
Helixi130 – 133Combined sources4
Turni134 – 136Combined sources3
Beta strandi143 – 147Combined sources5
Helixi156 – 158Combined sources3
Helixi163 – 167Combined sources5
Beta strandi173 – 175Combined sources3
Helixi180 – 192Combined sources13
Beta strandi193 – 195Combined sources3
Beta strandi197 – 201Combined sources5
Turni203 – 207Combined sources5
Beta strandi209 – 211Combined sources3
Helixi214 – 217Combined sources4
Beta strandi229 – 232Combined sources4
Beta strandi235 – 241Combined sources7
Helixi245 – 257Combined sources13
Turni258 – 260Combined sources3
Beta strandi263 – 267Combined sources5
Beta strandi270 – 272Combined sources3
Helixi276 – 286Combined sources11
Beta strandi289 – 292Combined sources4
Helixi301 – 311Combined sources11
Helixi315 – 317Combined sources3
Beta strandi323 – 325Combined sources3
Beta strandi329 – 331Combined sources3
Helixi336 – 340Combined sources5
Helixi346 – 357Combined sources12

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[»]
ProteinModelPortaliP11177.
SMRiP11177.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP11177.

Family & Domainsi

Keywords - Domaini

Transit peptide

Phylogenomic databases

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

Family and domain databases

Gene3Di3.40.50.920. 1 hit.
3.40.50.970. 1 hit.
InterProiIPR027110. PDHB.
IPR029061. THDP-binding.
IPR009014. Transketo_C/PFOR_II.
IPR005475. Transketolase-like_Pyr-bd.
IPR033248. Transketolase_C.
IPR033247. Transketolase_fam.
[Graphical view]
PANTHERiPTHR11624. PTHR11624. 1 hit.
PTHR11624:SF56. PTHR11624:SF56. 1 hit.
PfamiPF02779. Transket_pyr. 1 hit.
PF02780. Transketolase_C. 1 hit.
[Graphical view]
SMARTiSM00861. Transket_pyr. 1 hit.
[Graphical view]
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

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

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 → V.2 Publications1
Natural variantiVAR_030954132Y → C in PDHBD. 1 PublicationCorresponds to variant rs28935769dbSNPEnsembl.1
Natural variantiVAR_021058344P → S in PDHBD. 1 PublicationCorresponds to variant rs28933391dbSNPEnsembl.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

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[»]
ProteinModelPortaliP11177.
SMRiP11177.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi111188. 62 interactors.
DIPiDIP-37651N.
IntActiP11177. 24 interactors.
MINTiMINT-3007546.
STRINGi9606.ENSP00000307241.

Chemistry databases

DrugBankiDB00119. Pyruvic acid.

PTM databases

iPTMnetiP11177.
PhosphoSitePlusiP11177.
SwissPalmiP11177.

Polymorphism and mutation databases

BioMutaiPDHB.
DMDMi134044259.

2D gel databases

REPRODUCTION-2DPAGEIPI00549885.
SWISS-2DPAGEP11177.
UCD-2DPAGEP11177.

Proteomic databases

EPDiP11177.
MaxQBiP11177.
PaxDbiP11177.
PeptideAtlasiP11177.
PRIDEiP11177.
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.
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.
OMAiRKTHHLV.
OrthoDBiEOG091G0D37.
PhylomeDBiP11177.
TreeFamiTF105674.

Enzyme and pathway databases

BioCyciMetaCyc:HS09727-MONOMER.
ZFISH: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-RKP11177.

Miscellaneous databases

ChiTaRSiPDHB. human.
EvolutionaryTraceiP11177.
GeneWikiiPyruvate_dehydrogenase_(lipoamide)_beta.
GenomeRNAii5162.
PROiP11177.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000168291.
CleanExiHS_PDHB.
ExpressionAtlasiP11177. baseline and differential.
GenevisibleiP11177. HS.

Family and domain databases

Gene3Di3.40.50.920. 1 hit.
3.40.50.970. 1 hit.
InterProiIPR027110. PDHB.
IPR029061. THDP-binding.
IPR009014. Transketo_C/PFOR_II.
IPR005475. Transketolase-like_Pyr-bd.
IPR033248. Transketolase_C.
IPR033247. Transketolase_fam.
[Graphical view]
PANTHERiPTHR11624. PTHR11624. 1 hit.
PTHR11624:SF56. PTHR11624:SF56. 1 hit.
PfamiPF02779. Transket_pyr. 1 hit.
PF02780. Transketolase_C. 1 hit.
[Graphical view]
SMARTiSM00861. Transket_pyr. 1 hit.
[Graphical view]
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 historyi
Integrated into UniProtKB/Swiss-Prot: July 1, 1989
Last sequence update: March 6, 2007
Last modified: November 30, 2016
This is version 198 of the entry and version 3 of the sequence. [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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.