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Protein

Pyruvate, phosphate dikinase 1, chloroplastic

Gene

PPDK

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Formation of phosphoenolpyruvate. May be involved in regulating the flux of carbon into starch and fatty acids of seeds and in the remobilization of nitrogen reserves in senescing leaves.4 Publications

Catalytic activityi

ATP + pyruvate + phosphate = AMP + phosphoenolpyruvate + diphosphate.2 Publications

Cofactori

Mg2+By similarity

Enzyme regulationi

Activated by light-induced dephosphorylation. Inhibited by dark-induced phosphorylation. Both reactions are catalyzed by PDRP1.By similarity

Kineticsi

  1. KM=17 µM for pyruvate1 Publication
  2. KM=292 µM for phosphoenolpyruvate1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Active sitei545Tele-phosphohistidine intermediateBy similarity1
    Binding sitei651SubstrateBy similarity1
    Binding sitei707SubstrateBy similarity1
    Metal bindingi836MagnesiumBy similarity1
    Binding sitei836SubstrateBy similarity1
    Binding sitei857Substrate; via carbonyl oxygenBy similarity1
    Binding sitei858Substrate; via amide nitrogenBy similarity1
    Binding sitei859SubstrateBy similarity1
    Metal bindingi860MagnesiumBy similarity1
    Binding sitei860Substrate; via amide nitrogenBy similarity1
    Active sitei922Proton donorBy similarity1

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Kinase, Transferase

    Keywords - Biological processi

    Photosynthesis

    Keywords - Ligandi

    ATP-binding, Magnesium, Metal-binding, Nucleotide-binding, Pyruvate

    Enzyme and pathway databases

    BioCyciARA:AT4G15530-MONOMER.
    BRENDAi2.7.11.32. 399.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Pyruvate, phosphate dikinase 1, chloroplastic (EC:2.7.9.1)
    Alternative name(s):
    Pyruvate, orthophosphate dikinase 1
    Gene namesi
    Name:PPDK
    Ordered Locus Names:At4g15530
    ORF Names:dl3805c, FCAALL.325
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    Proteomesi
    • UP000006548 Componenti: Chromosome 4

    Organism-specific databases

    TAIRiAT4G15530.

    Subcellular locationi

    • Plastidchloroplast 1 Publication
    • Cytoplasm 1 Publication

    • Note: Isoform 1 is targeted to the chloroplast while isoform 2 is found in the cytoplasm.

    GO - Cellular componenti

    • chloroplast Source: TAIR
    • chloroplast stroma Source: TAIR
    • cytosol Source: TAIR
    • nucleus Source: TAIR
    Complete GO annotation...

    Keywords - Cellular componenti

    Chloroplast, Cytoplasm, Plastid

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi543T → D: Loss of phosphorylation. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Transit peptidei1 – 87ChloroplastSequence analysisAdd BLAST87
    ChainiPRO_000034351588 – 963Pyruvate, phosphate dikinase 1, chloroplasticAdd BLAST876

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei543Phosphothreonine; by PDRP1Combined sources1

    Post-translational modificationi

    Phosphorylation of Thr-543 in the dark inactivates the enzyme. Dephosphorylation upon light stimulation reactivates the enzyme.By similarity

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    PaxDbiO23404.
    PRIDEiO23404.

    PTM databases

    iPTMnetiO23404.

    Expressioni

    Tissue specificityi

    Isoform 1 is expressed in leaves, flowers and siliques. Isoform 2 is found in cotyledons, rosette and cauline leaves, petioles, flowers and siliques.1 Publication

    Developmental stagei

    Both isoforms 1 and 2 increase up to 7 days after sowing, but then decline.1 Publication

    Inductioni

    Isoform 2, but not isoform 1, is induced during darkness.2 Publications

    Gene expression databases

    ExpressionAtlasiO23404. baseline and differential.
    GenevisibleiO23404. AT.

    Interactioni

    Subunit structurei

    Homotetramer. Interacts with RP1 and RP2.By similarity1 Publication

    Protein-protein interaction databases

    BioGridi12523. 4 interactors.
    STRINGi3702.AT4G15530.5.

    Structurei

    3D structure databases

    ProteinModelPortaliO23404.
    SMRiO23404.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domaini

    The catalytic core domain alone is sufficient for the binding to PDRP1 but not for the binding to PDRP2.1 Publication
    The N-terminal domain contains the ATP/Pi binding site, the central domain the pyrophosphate/phosphate carrier histidine, and the C-terminal domain the pyruvate binding site.By similarity

    Sequence similaritiesi

    Belongs to the PEP-utilizing enzyme family.Curated

    Keywords - Domaini

    Transit peptide

    Phylogenomic databases

    eggNOGiENOG410IIM3. Eukaryota.
    COG0574. LUCA.
    HOGENOMiHOG000039664.
    InParanoidiO23404.
    KOiK01006.
    OMAiVRRETNP.
    OrthoDBiEOG0936014R.
    PhylomeDBiO23404.

    Family and domain databases

    Gene3Di3.20.20.60. 1 hit.
    3.30.1490.20. 2 hits.
    3.30.470.20. 1 hit.
    3.50.30.10. 1 hit.
    InterProiIPR013815. ATP_grasp_subdomain_1.
    IPR013816. ATP_grasp_subdomain_2.
    IPR008279. PEP-util_enz_mobile_dom.
    IPR018274. PEP_util_AS.
    IPR000121. PEP_util_C.
    IPR023151. PEP_util_CS.
    IPR002192. PPDK_PEP-bd.
    IPR010121. Pyruvate_phosphate_dikinase.
    IPR015813. Pyrv/PenolPyrv_Kinase-like_dom.
    [Graphical view]
    PANTHERiPTHR22931:SF9. PTHR22931:SF9. 1 hit.
    PfamiPF00391. PEP-utilizers. 1 hit.
    PF02896. PEP-utilizers_C. 1 hit.
    PF01326. PPDK_N. 3 hits.
    [Graphical view]
    PIRSFiPIRSF000853. PPDK. 1 hit.
    SUPFAMiSSF51621. SSF51621. 1 hit.
    SSF52009. SSF52009. 1 hit.
    TIGRFAMsiTIGR01828. pyru_phos_dikin. 1 hit.
    PROSITEiPS00742. PEP_ENZYMES_2. 1 hit.
    PS00370. PEP_ENZYMES_PHOS_SITE. 1 hit.
    [Graphical view]

    Sequences (4)i

    Sequence statusi: Complete.

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

    This entry describes 4 isoformsi produced by alternative promoter usage and alternative splicing. AlignAdd to basket

    Note: One additional alternative promoter may be used. According to EST data.
    Isoform 1 (identifier: O23404-1) [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
    MLYIRKKMTS MIVKTTPELF KGNGVFRTDH LGENRMVSRS NRLGDGSNRF
    60 70 80 90 100
    PRTGTIHCQR LSIAKTGLHR ETKARAILSP VSDPAASIAQ KRVFTFGKGR
    110 120 130 140 150
    SEGNKGMKSL LGGKGANLAE MASIGLSVPP GLTISTEACQ QYQIAGKKLP
    160 170 180 190 200
    EGLWEEILEG LSFIERDIGA SLADPSKPLL LSVRSGAAIS MPGMMDTVLN
    210 220 230 240 250
    LGLNDQVVVG LAAKSGERFA YDSFRRFLDM FGDVVMGIPH AKFEEKLERM
    260 270 280 290 300
    KERKGVKNDT DLSAADLKEL VEQYKSVYLE AKGQEFPSDP KKQLELAIEA
    310 320 330 340 350
    VFDSWDSPRA NKYRSINQIT GLKGTAVNIQ CMVFGNMGDT SGTGVLFTRN
    360 370 380 390 400
    PSTGEKKLYG EFLVNAQGED VVAGIRTPED LDTMKRFMPE AYAELVENCN
    410 420 430 440 450
    ILERHYKDMM DIEFTVQEER LWMLQCRAGK RTGKGAVKIA VDMVGEGLVE
    460 470 480 490 500
    KSSAIKMVEP QHLDQLLHPQ FHDPSGYREK VVAKGLPASP GAAVGQVVFT
    510 520 530 540 550
    AEEAEAWHSQ GKTVILVRTE TSPDDVGGMH AAEGILTARG GMTSHAAVVA
    560 570 580 590 600
    RGWGKCCIAG CSEIRVDENH KVLLIGDLTI NEGEWISMNG STGEVILGKQ
    610 620 630 640 650
    ALAPPALSPD LETFMSWADA IRRLKVMANA DTPEDAIAAR KNGAQGIGLC
    660 670 680 690 700
    RTEHMFFGAD RIKAVRKMIM AVTTEQRKAS LDILLPYQRS DFEGIFRAMD
    710 720 730 740 750
    GLPVTIRLLD PPLHEFLPEG DLDNIVHELA EETGVKEDEV LSRIEKLSEV
    760 770 780 790 800
    NPMLGFRGCR LGISYPELTE MQARAIFEAA ASMQDQGVTV IPEIMVPLVG
    810 820 830 840 850
    TPQELGHQVD VIRKVAKKVF AEKGHTVSYK VGTMIEIPRA ALIADEIAKE
    860 870 880 890 900
    AEFFSFGTND LTQMTFGYSR DDVGKFLPIY LAKGILQHDP FEVLDQQGVG
    910 920 930 940 950
    QLIKMATEKG RAARPSLKVG ICGEHGGDPS SVGFFAEAGL DYVSCSPFRV
    960
    PIARLAAAQV VVA
    Note: Translation of the sequence shown in PubMed:16915520 was N-terminally extended.
    Length:963
    Mass (Da):105,138
    Last modified:July 1, 2008 - v2
    Checksum:i239263180A836FE2
    GO
    Isoform 2 (identifier: O23404-2) [UniParc]FASTAAdd to basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-88: Missing.
         89-91: AQK → MMQ

    Note: Produced by alternative promoter usage. Cytoplasmic.
    Show »
    Length:875
    Mass (Da):95,393
    Checksum:iF8929AE2403188EA
    GO
    Isoform 3 (identifier: O23404-3) [UniParc]FASTAAdd to basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-7: Missing.

    Note: Produced by alternative splicing of isoform 1. Derived from EST data. No experimental confirmation available.
    Show »
    Length:956
    Mass (Da):104,205
    Checksum:i42BDE83BC6B979FF
    GO
    Isoform 4 (identifier: O23404-4) [UniParc]FASTAAdd to basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-106: Missing.

    Note: Produced by alternative splicing of isoform 1. Derived from EST data. No experimental confirmation available.
    Show »
    Length:857
    Mass (Da):93,380
    Checksum:iA843A22058F89E7E
    GO

    Sequence cautioni

    The sequence CAB10331 differs from that shown. Reason: Erroneous gene model prediction.Curated
    The sequence CAB78595 differs from that shown. Reason: Erroneous gene model prediction.Curated

    Alternative sequence

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Alternative sequenceiVSP_0346031 – 106Missing in isoform 4. CuratedAdd BLAST106
    Alternative sequenceiVSP_0346041 – 88Missing in isoform 2. 1 PublicationAdd BLAST88
    Alternative sequenceiVSP_0346051 – 7Missing in isoform 3. 1 Publication7
    Alternative sequenceiVSP_03460689 – 91AQK → MMQ in isoform 2. 1 Publication3

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    Z97339 Genomic DNA. Translation: CAB10331.1. Sequence problems.
    AL161541 Genomic DNA. Translation: CAB78595.1. Sequence problems.
    CP002687 Genomic DNA. Translation: AEE83616.1.
    CP002687 Genomic DNA. Translation: AEE83617.1.
    CP002687 Genomic DNA. Translation: AEE83618.1.
    CP002687 Genomic DNA. Translation: AEE83619.1.
    CP002687 Genomic DNA. Translation: AEE83620.1.
    CP002687 Genomic DNA. Translation: AEE83621.1.
    AK317187 mRNA. Translation: BAH19872.1.
    PIRiA71420.
    RefSeqiNP_001031647.1. NM_001036570.1. [O23404-4]
    NP_001078395.1. NM_001084926.1. [O23404-3]
    NP_001078396.1. NM_001084927.2. [O23404-1]
    NP_001118987.1. NM_001125515.1. [O23404-1]
    NP_193288.2. NM_117643.4. [O23404-2]
    NP_849391.2. NM_179060.4. [O23404-3]
    UniGeneiAt.23286.
    At.44851.

    Genome annotation databases

    EnsemblPlantsiAT4G15530.5; AT4G15530.5; AT4G15530. [O23404-1]
    AT4G15530.6; AT4G15530.6; AT4G15530. [O23404-1]
    GeneIDi827226.
    GrameneiAT4G15530.5; AT4G15530.5; AT4G15530.
    AT4G15530.6; AT4G15530.6; AT4G15530.
    KEGGiath:AT4G15530.

    Keywords - Coding sequence diversityi

    Alternative promoter usage, Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    Z97339 Genomic DNA. Translation: CAB10331.1. Sequence problems.
    AL161541 Genomic DNA. Translation: CAB78595.1. Sequence problems.
    CP002687 Genomic DNA. Translation: AEE83616.1.
    CP002687 Genomic DNA. Translation: AEE83617.1.
    CP002687 Genomic DNA. Translation: AEE83618.1.
    CP002687 Genomic DNA. Translation: AEE83619.1.
    CP002687 Genomic DNA. Translation: AEE83620.1.
    CP002687 Genomic DNA. Translation: AEE83621.1.
    AK317187 mRNA. Translation: BAH19872.1.
    PIRiA71420.
    RefSeqiNP_001031647.1. NM_001036570.1. [O23404-4]
    NP_001078395.1. NM_001084926.1. [O23404-3]
    NP_001078396.1. NM_001084927.2. [O23404-1]
    NP_001118987.1. NM_001125515.1. [O23404-1]
    NP_193288.2. NM_117643.4. [O23404-2]
    NP_849391.2. NM_179060.4. [O23404-3]
    UniGeneiAt.23286.
    At.44851.

    3D structure databases

    ProteinModelPortaliO23404.
    SMRiO23404.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi12523. 4 interactors.
    STRINGi3702.AT4G15530.5.

    PTM databases

    iPTMnetiO23404.

    Proteomic databases

    PaxDbiO23404.
    PRIDEiO23404.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblPlantsiAT4G15530.5; AT4G15530.5; AT4G15530. [O23404-1]
    AT4G15530.6; AT4G15530.6; AT4G15530. [O23404-1]
    GeneIDi827226.
    GrameneiAT4G15530.5; AT4G15530.5; AT4G15530.
    AT4G15530.6; AT4G15530.6; AT4G15530.
    KEGGiath:AT4G15530.

    Organism-specific databases

    TAIRiAT4G15530.

    Phylogenomic databases

    eggNOGiENOG410IIM3. Eukaryota.
    COG0574. LUCA.
    HOGENOMiHOG000039664.
    InParanoidiO23404.
    KOiK01006.
    OMAiVRRETNP.
    OrthoDBiEOG0936014R.
    PhylomeDBiO23404.

    Enzyme and pathway databases

    BioCyciARA:AT4G15530-MONOMER.
    BRENDAi2.7.11.32. 399.

    Miscellaneous databases

    PROiO23404.

    Gene expression databases

    ExpressionAtlasiO23404. baseline and differential.
    GenevisibleiO23404. AT.

    Family and domain databases

    Gene3Di3.20.20.60. 1 hit.
    3.30.1490.20. 2 hits.
    3.30.470.20. 1 hit.
    3.50.30.10. 1 hit.
    InterProiIPR013815. ATP_grasp_subdomain_1.
    IPR013816. ATP_grasp_subdomain_2.
    IPR008279. PEP-util_enz_mobile_dom.
    IPR018274. PEP_util_AS.
    IPR000121. PEP_util_C.
    IPR023151. PEP_util_CS.
    IPR002192. PPDK_PEP-bd.
    IPR010121. Pyruvate_phosphate_dikinase.
    IPR015813. Pyrv/PenolPyrv_Kinase-like_dom.
    [Graphical view]
    PANTHERiPTHR22931:SF9. PTHR22931:SF9. 1 hit.
    PfamiPF00391. PEP-utilizers. 1 hit.
    PF02896. PEP-utilizers_C. 1 hit.
    PF01326. PPDK_N. 3 hits.
    [Graphical view]
    PIRSFiPIRSF000853. PPDK. 1 hit.
    SUPFAMiSSF51621. SSF51621. 1 hit.
    SSF52009. SSF52009. 1 hit.
    TIGRFAMsiTIGR01828. pyru_phos_dikin. 1 hit.
    PROSITEiPS00742. PEP_ENZYMES_2. 1 hit.
    PS00370. PEP_ENZYMES_PHOS_SITE. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiPPDK1_ARATH
    AccessioniPrimary (citable) accession number: O23404
    Secondary accession number(s): B9DGK5
    , Q27GJ5, Q2V3I1, Q3EA16
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 1, 2008
    Last sequence update: July 1, 2008
    Last modified: November 30, 2016
    This is version 126 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    The reaction takes place in three steps, mediated by a phosphocarrier histidine residue located on the surface of the central domain. The two first partial reactions are catalyzed at an active site located on the N-terminal domain, and the third partial reaction is catalyzed at an active site located on the C-terminal domain. For catalytic turnover, the central domain swivels from the concave surface of the N-terminal domain to that of the C-terminal domain.By similarity

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Arabidopsis thaliana
      Arabidopsis thaliana: entries and gene names
    2. SIMILARITY comments
      Index of protein domains and families

    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.