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Q38799

- ODPB1_ARATH

UniProt

Q38799 - ODPB1_ARATH

Protein

Pyruvate dehydrogenase E1 component subunit beta-1, mitochondrial

Gene

PDH2

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 129 (01 Oct 2014)
      Sequence version 2 (06 Jun 2002)
      Previous versions | rss
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    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

    Thiamine pyrophosphate.

    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

    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.

    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: Chromosome 5

    Organism-specific databases

    TAIRiAT5G50850.

    Subcellular locationi

    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

    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

    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.
    OMAiDPKVFVM.
    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

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    MLGILRQRAI DGASTLRRTR FALVSARSYA AGAKEMTVRD ALNSAIDEEM    50
    SADPKVFVMG EEVGQYQGAY KITKGLLEKY GPERVYDTPI TEAGFTGIGV 100
    GAAYAGLKPV VEFMTFNFSM QAIDHIINSA AKSNYMSAGQ INVPIVFRGP 150
    NGAAAGVGAQ HSQCYAAWYA SVPGLKVLAP YSAEDARGLL KAAIRDPDPV 200
    VFLENELLYG ESFPISEEAL DSSFCLPIGK AKIEREGKDV TIVTFSKMVG 250
    FALKAAEKLA EEGISAEVIN LRSIRPLDRA TINASVRKTS RLVTVEEGFP 300
    QHGVCAEICA SVVEESFSYL DAPVERIAGA DVPMPYAANL ERLALPQIED 350
    IVRASKRACY RSK 363
    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:
    EMBL
    GenBank
    DDBJ
    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:
    EMBL
    GenBank
    DDBJ
    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 .
    RefSeqi NP_199898.1. NM_124463.3.
    UniGenei At.24270.

    3D structure databases

    ProteinModelPortali Q38799.
    SMRi Q38799. Positions 35-357.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 20403. 2 interactions.
    IntActi Q38799. 2 interactions.

    2D gel databases

    SWISS-2DPAGE Q38799.

    Proteomic databases

    PaxDbi Q38799.
    PRIDEi Q38799.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT5G50850.1 ; AT5G50850.1 ; AT5G50850 .
    GeneIDi 835157.
    KEGGi ath:AT5G50850.

    Organism-specific databases

    GeneFarmi 2003.
    TAIRi AT5G50850.

    Phylogenomic databases

    eggNOGi COG0022.
    HOGENOMi HOG000281450.
    InParanoidi Q38799.
    KOi K00162.
    OMAi DPKVFVM.
    PhylomeDBi Q38799.

    Enzyme and pathway databases

    BioCyci ARA:AT5G50850-MONOMER.
    RETL1328306-WGS:GSTH-5057-MONOMER.

    Miscellaneous databases

    PROi Q38799.

    Gene expression databases

    Genevestigatori Q38799.

    Family and domain databases

    Gene3Di 3.40.50.920. 1 hit.
    3.40.50.970. 1 hit.
    InterProi IPR027110. PDHB.
    IPR029061. THDP-binding.
    IPR009014. Transketo_C/Pyr-ferredox_oxred.
    IPR005475. Transketolase-like_Pyr-bd.
    IPR005476. Transketolase_C.
    [Graphical view ]
    PANTHERi PTHR11624:SF56. PTHR11624:SF56. 1 hit.
    Pfami PF02779. Transket_pyr. 1 hit.
    PF02780. Transketolase_C. 1 hit.
    [Graphical view ]
    SMARTi SM00861. Transket_pyr. 1 hit.
    [Graphical view ]
    SUPFAMi SSF52518. SSF52518. 1 hit.
    SSF52922. SSF52922. 1 hit.
    ProtoNeti Search...

    Publicationsi

    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: October 1, 2014
    This is version 129 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