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Protein

Pyruvate dehydrogenase protein X component, mitochondrial

Gene

PDHX

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

Functioni

Required for anchoring dihydrolipoamide dehydrogenase (E3) to the dihydrolipoamide transacetylase (E2) core of the pyruvate dehydrogenase complexes of eukaryotes. This specific binding is essential for a functional PDH complex.

GO - Molecular functioni

GO - Biological processi

  • mitochondrial acetyl-CoA biosynthetic process from pyruvate Source: MGI

Enzyme and pathway databases

BioCyciMetaCyc:ENSG00000110435-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
SIGNORiO00330

Names & Taxonomyi

Protein namesi
Recommended name:
Pyruvate dehydrogenase protein X component, mitochondrial
Alternative name(s):
Dihydrolipoamide dehydrogenase-binding protein of pyruvate dehydrogenase complex
E3-binding protein
Short name:
E3BP
Lipoyl-containing pyruvate dehydrogenase complex component X
proX
Gene namesi
Name:PDHX
Synonyms:PDX1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 11

Organism-specific databases

EuPathDBiHostDB:ENSG00000110435.11
HGNCiHGNC:21350 PDHX
MIMi608769 gene
neXtProtiNX_O00330

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 E3-binding protein deficiency (PDHXD)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA metabolic disorder characterized by decreased activity of the pyruvate dehydrogenase complex without observable reduction in the activities of enzymes E1, E2, or E3. Clinical features include hypotonia and psychomotor retardation.
See also OMIM:245349

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi183R → A: Strongly decreased DLD binding. 1 Publication1
Mutagenesisi185S → A: Strongly decreased DLD binding. 1 Publication1
Mutagenesisi186P → A: Strongly decreased DLD binding. 1 Publication1
Mutagenesisi187A → M: Strongly decreased DLD binding. 1 Publication1
Mutagenesisi189R → A: Strongly decreased DLD binding. 1 Publication1
Mutagenesisi190N → A: Decreased DLD binding. 2 Publications1
Mutagenesisi190N → K: Moderately decreased interaction with DLD. 1 Publication1
Mutagenesisi193E → A: Strongly decreased DLD binding. 1 Publication1
Mutagenesisi208R → A: Strongly decreased DLD binding. 1 Publication1
Mutagenesisi208R → D: Decreased interaction with DLD. 1 Publication1
Mutagenesisi210I → A: Strongly decreased DLD binding. 1 Publication1
Mutagenesisi210I → R: Decreased interaction with DLD. 1 Publication1
Mutagenesisi210I → S: Decreased interaction with DLD. 1 Publication1
Mutagenesisi213K → A: Strongly decreased DLD binding. 1 Publication1
Mutagenesisi214E → A: Strongly decreased DLD binding. 1 Publication1

Organism-specific databases

DisGeNETi8050
MalaCardsiPDHX
MIMi245349 phenotype
OpenTargetsiENSG00000110435
Orphaneti255182 Pyruvate dehydrogenase E3-binding protein deficiency
PharmGKBiPA134976445

Polymorphism and mutation databases

BioMutaiPDHX

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Transit peptidei1 – 53MitochondrionBy similarityAdd BLAST53
ChainiPRO_000002048454 – 501Pyruvate dehydrogenase protein X component, mitochondrialAdd BLAST448

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei97N6-lipoyllysinePROSITE-ProRule annotation1 Publication1
Modified residuei194N6-acetyllysineCombined sources1
Modified residuei196PhosphoserineCombined sources1
Modified residuei394N6-succinyllysineBy similarity1

Post-translational modificationi

Delipoylated at Lys-97 by SIRT4, delipoylation decreases the PHD complex activity.1 Publication

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiO00330
MaxQBiO00330
PaxDbiO00330
PeptideAtlasiO00330
PRIDEiO00330
ProteomicsDBi47851

PTM databases

iPTMnetiO00330
PhosphoSitePlusiO00330
SwissPalmiO00330

Expressioni

Gene expression databases

BgeeiENSG00000110435 Expressed in 233 organ(s), highest expression level in skeletal muscle tissue
CleanExiHS_PDHX
HS_PDX1
ExpressionAtlasiO00330 baseline and differential
GenevisibleiO00330 HS

Organism-specific databases

HPAiHPA038484
HPA038485

Interactioni

Subunit structurei

Part of the inner core of the multimeric pyruvate dehydrogenase complex that is composed of about 48 DLAT and 12 PDHX molecules (PubMed:14638692, PubMed:20361979). This core binds multiple copies of pyruvate dehydrogenase (subunits PDH1A and PDHB, E1), dihydrolipoamide acetyltransferase (DLAT, E2) and lipoamide dehydrogenase (DLD, E3) (PubMed:14638692). Interacts with SIRT4 (PubMed:25525879). Interacts with DLD (PubMed:20385101, PubMed:16263718, PubMed:16442803, PubMed:20160912, PubMed:20361979).7 Publications

Binary interactionsi

Protein-protein interaction databases

BioGridi113737, 32 interactors
DIPiDIP-29026N
IntActiO00330, 16 interactors
MINTiO00330
STRINGi9606.ENSP00000227868

Structurei

Secondary structure

1501
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliO00330
SMRiO00330
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO00330

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini56 – 132Lipoyl-bindingPROSITE-ProRule annotationAdd BLAST77
Domaini183 – 220Peripheral subunit-binding (PSBD)PROSITE-ProRule annotationAdd BLAST38

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi149 – 170Pro-richAdd BLAST22

Sequence similaritiesi

Belongs to the 2-oxoacid dehydrogenase family.Curated

Keywords - Domaini

Lipoyl, Transit peptide

Phylogenomic databases

eggNOGiKOG0557 Eukaryota
COG0508 LUCA
GeneTreeiENSGT00890000139393
HOGENOMiHOG000281566
HOVERGENiHBG005063
InParanoidiO00330
KOiK13997
OMAiHSTQWLR
OrthoDBiEOG091G0CAV
PhylomeDBiO00330
TreeFamiTF332256

Family and domain databases

Gene3Di3.30.559.10, 1 hit
4.10.320.10, 1 hit
InterProiView protein in InterPro
IPR003016 2-oxoA_DH_lipoyl-BS
IPR001078 2-oxoacid_DH_actylTfrase
IPR000089 Biotin_lipoyl
IPR023213 CAT-like_dom_sf
IPR036625 E3-bd_dom_sf
IPR004167 PSBD
IPR011053 Single_hybrid_motif
PfamiView protein in Pfam
PF00198 2-oxoacid_dh, 1 hit
PF00364 Biotin_lipoyl, 1 hit
PF02817 E3_binding, 1 hit
SUPFAMiSSF47005 SSF47005, 1 hit
SSF51230 SSF51230, 1 hit
PROSITEiView protein in PROSITE
PS50968 BIOTINYL_LIPOYL, 1 hit
PS00189 LIPOYL, 1 hit
PS51826 PSBD, 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 3 potential isoforms that are computationally mapped.Show allAlign All

Isoform 1 (identifier: O00330-1) [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
MAASWRLGCD PRLLRYLVGF PGRRSVGLVK GALGWSVSRG ANWRWFHSTQ
60 70 80 90 100
WLRGDPIKIL MPSLSPTMEE GNIVKWLKKE GEAVSAGDAL CEIETDKAVV
110 120 130 140 150
TLDASDDGIL AKIVVEEGSK NIRLGSLIGL IVEEGEDWKH VEIPKDVGPP
160 170 180 190 200
PPVSKPSEPR PSPEPQISIP VKKEHIPGTL RFRLSPAARN ILEKHSLDAS
210 220 230 240 250
QGTATGPRGI FTKEDALKLV QLKQTGKITE SRPTPAPTAT PTAPSPLQAT
260 270 280 290 300
AGPSYPRPVI PPVSTPGQPN AVGTFTEIPA SNIRRVIAKR LTESKSTVPH
310 320 330 340 350
AYATADCDLG AVLKVRQDLV KDDIKVSVND FIIKAAAVTL KQMPDVNVSW
360 370 380 390 400
DGEGPKQLPF IDISVAVATD KGLLTPIIKD AAAKGIQEIA DSVKALSKKA
410 420 430 440 450
RDGKLLPEEY QGGSFSISNL GMFGIDEFTA VINPPQACIL AVGRFRPVLK
460 470 480 490 500
LTEDEEGNAK LQQRQLITVT MSSDSRVVDD ELATRFLKSF KANLENPIRL

A
Length:501
Mass (Da):54,122
Last modified:January 24, 2001 - v3
Checksum:i9CF0C1DAE9E12EF9
GO
Isoform 2 (identifier: O00330-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     115-341: Missing.

Note: No experimental confirmation available.
Show »
Length:274
Mass (Da):29,906
Checksum:i7657F43CA5F9B61D
GO
Isoform 3 (identifier: O00330-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     2-53: AASWRLGCDP...RWFHSTQWLR → QSGGAEGSPG...ISSGAPDFPG

Note: No experimental confirmation available. Gene prediction based on EST data.
Show »
Length:486
Mass (Da):51,460
Checksum:iC0682D60CAC5BDF5
GO

Computationally mapped potential isoform sequencesi

There are 3 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
E9PLU0E9PLU0_HUMAN
Pyruvate dehydrogenase protein X co...
PDHX
151Annotation score:
E9PRI6E9PRI6_HUMAN
Pyruvate dehydrogenase protein X co...
PDHX
182Annotation score:
H0YD97H0YD97_HUMAN
Pyruvate dehydrogenase protein X co...
PDHX
189Annotation score:

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti41A → R in AAC39661 (PubMed:9467010).Curated1
Sequence conflicti251A → S in AAB66315 (PubMed:9242632).Curated1
Sequence conflicti251A → S in CAA73606 (PubMed:9399911).Curated1
Sequence conflicti344P → S in BAG62924 (PubMed:14702039).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_04661923R → C1 PublicationCorresponds to variant dbSNP:rs1049306EnsemblClinVar.1
Natural variantiVAR_046620101T → A. Corresponds to variant dbSNP:rs11539202EnsemblClinVar.1
Natural variantiVAR_046621370D → V1 PublicationCorresponds to variant dbSNP:rs17850649Ensembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0538172 – 53AASWR…TQWLR → QSGGAEGSPGAGRTGRGPGS GKAPPAEISSGAPDFPG in isoform 3. CuratedAdd BLAST52
Alternative sequenceiVSP_045271115 – 341Missing in isoform 2. CuratedAdd BLAST227

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF001437 mRNA Translation: AAB66315.1
Y13145 mRNA Translation: CAA73606.1
U82328 mRNA Translation: AAC39661.1
AJ298105 Genomic DNA Translation: CAC18649.1
AK301384 mRNA Translation: BAG62924.1
AC107928 Genomic DNA No translation available.
AL138810 Genomic DNA No translation available.
AL356215 Genomic DNA No translation available.
CH471064 Genomic DNA Translation: EAW68158.1
CH471064 Genomic DNA Translation: EAW68160.1
BC010389 mRNA Translation: AAH10389.1
U79296 mRNA Translation: AAB50223.1
CCDSiCCDS44569.1 [O00330-3]
CCDS53616.1 [O00330-2]
CCDS7896.1 [O00330-1]
RefSeqiNP_001128496.1, NM_001135024.1 [O00330-3]
NP_001159630.1, NM_001166158.1 [O00330-2]
NP_003468.2, NM_003477.2 [O00330-1]
UniGeneiHs.502315

Genome annotation databases

EnsembliENST00000227868; ENSP00000227868; ENSG00000110435 [O00330-1]
ENST00000430469; ENSP00000415695; ENSG00000110435 [O00330-2]
ENST00000448838; ENSP00000389404; ENSG00000110435 [O00330-3]
GeneIDi8050
KEGGihsa:8050
UCSCiuc001mvt.4 human [O00330-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF001437 mRNA Translation: AAB66315.1
Y13145 mRNA Translation: CAA73606.1
U82328 mRNA Translation: AAC39661.1
AJ298105 Genomic DNA Translation: CAC18649.1
AK301384 mRNA Translation: BAG62924.1
AC107928 Genomic DNA No translation available.
AL138810 Genomic DNA No translation available.
AL356215 Genomic DNA No translation available.
CH471064 Genomic DNA Translation: EAW68158.1
CH471064 Genomic DNA Translation: EAW68160.1
BC010389 mRNA Translation: AAH10389.1
U79296 mRNA Translation: AAB50223.1
CCDSiCCDS44569.1 [O00330-3]
CCDS53616.1 [O00330-2]
CCDS7896.1 [O00330-1]
RefSeqiNP_001128496.1, NM_001135024.1 [O00330-3]
NP_001159630.1, NM_001166158.1 [O00330-2]
NP_003468.2, NM_003477.2 [O00330-1]
UniGeneiHs.502315

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1ZY8X-ray2.59K/L/M/N/O54-274[»]
2DNCNMR-A57-141[»]
2F5ZX-ray2.18K/L/M/N/O173-228[»]
2F60X-ray1.55K173-228[»]
ProteinModelPortaliO00330
SMRiO00330
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi113737, 32 interactors
DIPiDIP-29026N
IntActiO00330, 16 interactors
MINTiO00330
STRINGi9606.ENSP00000227868

PTM databases

iPTMnetiO00330
PhosphoSitePlusiO00330
SwissPalmiO00330

Polymorphism and mutation databases

BioMutaiPDHX

Proteomic databases

EPDiO00330
MaxQBiO00330
PaxDbiO00330
PeptideAtlasiO00330
PRIDEiO00330
ProteomicsDBi47851

Protocols and materials databases

DNASUi8050
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000227868; ENSP00000227868; ENSG00000110435 [O00330-1]
ENST00000430469; ENSP00000415695; ENSG00000110435 [O00330-2]
ENST00000448838; ENSP00000389404; ENSG00000110435 [O00330-3]
GeneIDi8050
KEGGihsa:8050
UCSCiuc001mvt.4 human [O00330-1]

Organism-specific databases

CTDi8050
DisGeNETi8050
EuPathDBiHostDB:ENSG00000110435.11
GeneCardsiPDHX
HGNCiHGNC:21350 PDHX
HPAiHPA038484
HPA038485
MalaCardsiPDHX
MIMi245349 phenotype
608769 gene
neXtProtiNX_O00330
OpenTargetsiENSG00000110435
Orphaneti255182 Pyruvate dehydrogenase E3-binding protein deficiency
PharmGKBiPA134976445
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0557 Eukaryota
COG0508 LUCA
GeneTreeiENSGT00890000139393
HOGENOMiHOG000281566
HOVERGENiHBG005063
InParanoidiO00330
KOiK13997
OMAiHSTQWLR
OrthoDBiEOG091G0CAV
PhylomeDBiO00330
TreeFamiTF332256

Enzyme and pathway databases

BioCyciMetaCyc:ENSG00000110435-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
SIGNORiO00330

Miscellaneous databases

ChiTaRSiPDHX human
EvolutionaryTraceiO00330
GeneWikiiE3_binding_protein
GenomeRNAii8050
PROiPR:O00330
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000110435 Expressed in 233 organ(s), highest expression level in skeletal muscle tissue
CleanExiHS_PDHX
HS_PDX1
ExpressionAtlasiO00330 baseline and differential
GenevisibleiO00330 HS

Family and domain databases

Gene3Di3.30.559.10, 1 hit
4.10.320.10, 1 hit
InterProiView protein in InterPro
IPR003016 2-oxoA_DH_lipoyl-BS
IPR001078 2-oxoacid_DH_actylTfrase
IPR000089 Biotin_lipoyl
IPR023213 CAT-like_dom_sf
IPR036625 E3-bd_dom_sf
IPR004167 PSBD
IPR011053 Single_hybrid_motif
PfamiView protein in Pfam
PF00198 2-oxoacid_dh, 1 hit
PF00364 Biotin_lipoyl, 1 hit
PF02817 E3_binding, 1 hit
SUPFAMiSSF47005 SSF47005, 1 hit
SSF51230 SSF51230, 1 hit
PROSITEiView protein in PROSITE
PS50968 BIOTINYL_LIPOYL, 1 hit
PS00189 LIPOYL, 1 hit
PS51826 PSBD, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiODPX_HUMAN
AccessioniPrimary (citable) accession number: O00330
Secondary accession number(s): B4DW62
, D3DR11, E9PB14, E9PBP7, O60221, Q96FV8, Q99783
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 15, 1999
Last sequence update: January 24, 2001
Last modified: November 7, 2018
This is version 188 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, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  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
  6. Human chromosome 11
    Human chromosome 11: entries, gene names and cross-references to MIM
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