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Protein

Pyruvate dehydrogenase E1 component subunit beta-1, mitochondrial

Gene

PDH2

Organism
Arabidopsis thaliana (Mouse-ear cress)
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. It contains multiple copies of three enzymatic components: pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2) and lipoamide dehydrogenase (E3).

Catalytic activityi

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

Cofactori

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei92 – 921Thiamine pyrophosphateBy similarity

GO - Molecular functioni

  1. pyruvate dehydrogenase (acetyl-transferring) activity Source: UniProtKB-EC

GO - Biological processi

  1. acetyl-CoA biosynthetic process from pyruvate Source: InterPro
  2. defense response to bacterium Source: TAIR
  3. glycolytic process Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Glycolysis

Keywords - Ligandi

Pyruvate, Thiamine pyrophosphate

Enzyme and pathway databases

BioCyciARA:AT5G50850-MONOMER.
RETL1328306-WGS:GSTH-5057-MONOMER.
ReactomeiREACT_285305. Signaling by Retinoic Acid.
REACT_290601. Pyruvate metabolism.
REACT_307000. Regulation of pyruvate dehydrogenase (PDH) complex.

Names & Taxonomyi

Protein namesi
Recommended name:
Pyruvate dehydrogenase E1 component subunit beta-1, mitochondrial (EC:1.2.4.1)
Short name:
PDHE1-B
Alternative name(s):
Protein MACCI-BOU
Gene namesi
Name:PDH2
Synonyms:MAB1
Ordered Locus Names:At5g50850
ORF Names:K16E14.1
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
ProteomesiUP000006548 Componenti: Chromosome 5

Organism-specific databases

TAIRiAT5G50850.

Subcellular locationi

  1. Mitochondrion matrix 1 Publication

GO - Cellular componenti

  1. apoplast Source: TAIR
  2. mitochondrial matrix Source: UniProtKB-SubCell
  3. mitochondrion Source: TAIR
  4. nucleolus Source: TAIR
  5. vacuolar membrane Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 2929MitochondrionBy similarityAdd
BLAST
Chaini30 – 363334Pyruvate dehydrogenase E1 component subunit beta-1, mitochondrialPRO_0000020462Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Cross-linki34 – 34Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki247 – 247Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki254 – 254Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication

Keywords - PTMi

Isopeptide bond, Ubl conjugation

Proteomic databases

PaxDbiQ38799.
PRIDEiQ38799.

2D gel databases

SWISS-2DPAGEQ38799.

Expressioni

Tissue specificityi

Expressed in roots, immature rosettes, and mature rosettes.1 Publication

Gene expression databases

ExpressionAtlasiQ38799. baseline and differential.
GenevestigatoriQ38799.

Interactioni

Subunit structurei

Tetramer of 2 alpha and 2 beta subunits.By similarity

Protein-protein interaction databases

BioGridi20403. 2 interactions.
IntActiQ38799. 2 interactions.

Structurei

3D structure databases

ProteinModelPortaliQ38799.
SMRiQ38799. Positions 35-357.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Keywords - Domaini

Transit peptide

Phylogenomic databases

eggNOGiCOG0022.
HOGENOMiHOG000281450.
InParanoidiQ38799.
KOiK00162.
OMAiAMKLAMR.
PhylomeDBiQ38799.

Family and domain databases

Gene3Di3.40.50.920. 1 hit.
3.40.50.970. 1 hit.
InterProiIPR027110. PDHB.
IPR029061. THDP-binding.
IPR009014. Transketo_C/Pyr-ferredox_oxred.
IPR005475. Transketolase-like_Pyr-bd.
IPR005476. Transketolase_C.
[Graphical view]
PANTHERiPTHR11624: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.

Sequencei

Sequence statusi: Complete.

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

Q38799-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MLGILRQRAI DGASTLRRTR FALVSARSYA AGAKEMTVRD ALNSAIDEEM
60 70 80 90 100
SADPKVFVMG EEVGQYQGAY KITKGLLEKY GPERVYDTPI TEAGFTGIGV
110 120 130 140 150
GAAYAGLKPV VEFMTFNFSM QAIDHIINSA AKSNYMSAGQ INVPIVFRGP
160 170 180 190 200
NGAAAGVGAQ HSQCYAAWYA SVPGLKVLAP YSAEDARGLL KAAIRDPDPV
210 220 230 240 250
VFLENELLYG ESFPISEEAL DSSFCLPIGK AKIEREGKDV TIVTFSKMVG
260 270 280 290 300
FALKAAEKLA EEGISAEVIN LRSIRPLDRA TINASVRKTS RLVTVEEGFP
310 320 330 340 350
QHGVCAEICA SVVEESFSYL DAPVERIAGA DVPMPYAANL ERLALPQIED
360
IVRASKRACY RSK
Length:363
Mass (Da):39,176
Last modified:June 6, 2002 - v2
Checksum:iD044E3A336D4EC52
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti334 – 3341M → I in AAA52225 (PubMed:8061040).Curated
Sequence conflicti337 – 3371A → T in AAA52225 (PubMed:8061040).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U09137 mRNA. Translation: AAA52225.1.
AB026637 Genomic DNA. Translation: BAA98121.1.
CP002688 Genomic DNA. Translation: AED96001.1.
AY070728 mRNA. Translation: AAL50070.1.
BT000839 mRNA. Translation: AAN38676.1.
RefSeqiNP_199898.1. NM_124463.3.
UniGeneiAt.24270.

Genome annotation databases

EnsemblPlantsiAT5G50850.1; AT5G50850.1; AT5G50850.
GeneIDi835157.
KEGGiath:AT5G50850.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U09137 mRNA. Translation: AAA52225.1.
AB026637 Genomic DNA. Translation: BAA98121.1.
CP002688 Genomic DNA. Translation: AED96001.1.
AY070728 mRNA. Translation: AAL50070.1.
BT000839 mRNA. Translation: AAN38676.1.
RefSeqiNP_199898.1. NM_124463.3.
UniGeneiAt.24270.

3D structure databases

ProteinModelPortaliQ38799.
SMRiQ38799. Positions 35-357.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi20403. 2 interactions.
IntActiQ38799. 2 interactions.

2D gel databases

SWISS-2DPAGEQ38799.

Proteomic databases

PaxDbiQ38799.
PRIDEiQ38799.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT5G50850.1; AT5G50850.1; AT5G50850.
GeneIDi835157.
KEGGiath:AT5G50850.

Organism-specific databases

GeneFarmi2003.
TAIRiAT5G50850.

Phylogenomic databases

eggNOGiCOG0022.
HOGENOMiHOG000281450.
InParanoidiQ38799.
KOiK00162.
OMAiAMKLAMR.
PhylomeDBiQ38799.

Enzyme and pathway databases

BioCyciARA:AT5G50850-MONOMER.
RETL1328306-WGS:GSTH-5057-MONOMER.
ReactomeiREACT_285305. Signaling by Retinoic Acid.
REACT_290601. Pyruvate metabolism.
REACT_307000. Regulation of pyruvate dehydrogenase (PDH) complex.

Miscellaneous databases

PROiQ38799.

Gene expression databases

ExpressionAtlasiQ38799. baseline and differential.
GenevestigatoriQ38799.

Family and domain databases

Gene3Di3.40.50.920. 1 hit.
3.40.50.970. 1 hit.
InterProiIPR027110. PDHB.
IPR029061. THDP-binding.
IPR009014. Transketo_C/Pyr-ferredox_oxred.
IPR005475. Transketolase-like_Pyr-bd.
IPR005476. Transketolase_C.
[Graphical view]
PANTHERiPTHR11624: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...

Publicationsi

« Hide 'large scale' publications
  1. "The nucleotide and deduced amino acid sequences of a cDNA encoding the E1 beta-subunit of the Arabidopsis thaliana mitochondrial pyruvate dehydrogenase complex."
    Luethy M.H., Miernyk J.A., Randall D.D.
    Biochim. Biophys. Acta 1187:95-98(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], TISSUE SPECIFICITY.
    Strain: cv. Columbia.
  2. "Structural analysis of Arabidopsis thaliana chromosome 5. XI."
    Kaneko T., Katoh T., Asamizu E., Sato S., Nakamura Y., Kotani H., Tabata S.
    Submitted (APR-1999) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  3. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  4. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
    , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
    Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: cv. Columbia.
  5. "Experimental analysis of the Arabidopsis mitochondrial proteome highlights signaling and regulatory components, provides assessment of targeting prediction programs, and indicates plant-specific mitochondrial proteins."
    Heazlewood J.L., Tonti-Filippini J.S., Gout A.M., Day D.A., Whelan J., Millar A.H.
    Plant Cell 16:241-256(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
    Strain: cv. Landsberg erecta.
  6. "Multidimensional protein identification technology (MudPIT) analysis of ubiquitinated proteins in plants."
    Maor R., Jones A., Nuehse T.S., Studholme D.J., Peck S.C., Shirasu K.
    Mol. Cell. Proteomics 6:601-610(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-34; LYS-247 AND LYS-254.
    Strain: cv. Landsberg erecta.

Entry informationi

Entry nameiODPB1_ARATH
AccessioniPrimary (citable) accession number: Q38799
Secondary accession number(s): Q9LSM8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1999
Last sequence update: June 6, 2002
Last modified: April 1, 2015
This is version 133 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names

External Data

Dasty 3

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 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.