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    PPDK pyruvate orthophosphate dikinase [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 827226, updated on 18-Sep-2024

    Summary

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    Official Symbol
    PPDK
    Official Full Name
    pyruvate orthophosphate dikinase
    Primary source
    TAIR:AT4G15530
    Locus tag
    AT4G15530
    See related
    Araport:AT4G15530
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Arabidopsis thaliana (ecotype: Columbia)
    Lineage
    Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
    Also known as
    DL3805C; FCAALL.325; pyruvate orthophosphate dikinase
    Summary
    Encodes a dual-targeted protein believed to act as a pyruvate, orthophosphate dikinase. These enzymes are normally associated with C4 photosynthesis which does not occur in Arabidopsis. However, PPDK may play a role in remobilizing nitrogen during leaf senescence in Arabidopsis. The product of the long transcript (.1 gene model) was shown to be targeted to the chloroplast, whereas the shorter transcript (no targeting sequence) accumulates in the cytosol. The two proteins were also found to be expressed in slightly different tissues.
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    Genomic context

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    See PPDK in Genome Data Viewer
    Location:
    chromosome: 4
    Exon count:
    19
    Sequence:
    Chromosome: 4; NC_003075.7 (8864615..8870979, complement)

    Chromosome 4 - NC_003075.7Genomic Context describing neighboring genes Neighboring gene ncRNA Neighboring gene Photosystem II reaction center PsbP family protein Neighboring gene tRNA/rRNA methyltransferase (SpoU) family protein Neighboring gene EamA-like transporter family Neighboring gene PH-response transcription factor Neighboring gene indole-3-acetate beta-D-glucosyltransferase

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003075.7

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Cytosolic pyruvate,orthophosphate dikinase functions in nitrogen remobilization during leaf senescence and limits individual seed growth and nitrogen content. Taylor L, et al. Plant J, 2010 May 1. PMID 20202167
    2. The Arabidopsis PPDK gene is transcribed from two promoters to produce differentially expressed transcripts responsible for cytosolic and plastidic proteins. Parsley K, et al. Plant Mol Biol, 2006 Oct. PMID 16915520
    3. Arabidopsis uses two gluconeogenic gateways for organic acids to fuel seedling establishment. Eastmond PJ, et al. Nat Commun, 2015 Apr 10. PMID 25858700, Free PMC Article
    4. Reticulate leaves and stunted roots are independent phenotypes pointing at opposite roles of the phosphoenolpyruvate/phosphate translocator defective in cue1 in the plastids of both organs. Staehr P, et al. Front Plant Sci, 2014. PMID 24782872, Free PMC Article
    5. The pyruvate, orthophosphate dikinase regulatory proteins of Arabidopsis are both bifunctional and interact with the catalytic and nucleotide-binding domains of pyruvate, orthophosphate dikinase. Astley HM, et al. Plant J, 2011 Dec. PMID 21883547

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Arabidopsis uses two gluconeogenic gateways for organic acids to fuel seedling establishment, one is via PCK1, and a second via PPDK.
      Title: Arabidopsis uses two gluconeogenic gateways for organic acids to fuel seedling establishment.
    2. Over-expression of PPDK during senescence increases nitrogen remobilization from senescing leaves and increases seed size and seed nitrogen content.
      Title: Cytosolic pyruvate,orthophosphate dikinase functions in nitrogen remobilization during leaf senescence and limits individual seed growth and nitrogen content.
    3. In cotyledons pyruvate orthophosphate dikinase may be important in supplying phosphoenol pyruvate to gluconeogenesis, and in ageing leaves it allows remobilisation of nitrogen to supply reproductive tissue [pyruvate orthophosphate dikinase] [PPDK]
      Title: The Arabidopsis PPDK gene is transcribed from two promoters to produce differentially expressed transcripts responsible for cytosolic and plastidic proteins.
    Submit: New GeneRIF Correction

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    NM_001036570.1
    NM_001084926.1
    NM_001084927.2
    NM_001125515.1
    NM_001341051.1
    NM_117643.4
    NM_179060.4

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables pyruvate, phosphate dikinase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables pyruvate, phosphate dikinase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in pyruvate metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in chloroplast HDA PubMed 
    located_in chloroplast IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in chloroplast ISM
    Inferred from Sequence Model
    more info
    		  
    located_in chloroplast stroma HDA PubMed 
    located_in cytosol HDA PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    NOT located_in cytosol RCA
    inferred from Reviewed Computational Analysis
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    pyruvate orthophosphate dikinase
    NP_001031647.1
    • pyruvate orthophosphate dikinase (PPDK); FUNCTIONS IN: kinase activity, pyruvate, phosphate dikinase activity; INVOLVED IN: phosphorylation, response to absence of light; LOCATED IN: cytosol, nucleus, chloroplast; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 11 growth stages; CONTAINS InterPro DOMAIN/s: PEP-utilising enzyme, mobile domain (InterPro:IPR008279), ATP-grasp fold, subdomain 1 (InterPro:IPR013815), Pyruvate, phosphate dikinase (InterPro:IPR010121), Pyruvate/Phosphoenolpyruvate kinase, catalytic core (InterPro:IPR015813), Pyruvate phosphate dikinase, PEP/pyruvate-binding (InterPro:IPR002192), PEP-utilising enzyme, mobile region, conserved site (InterPro:IPR018274), ATP-grasp fold, subdomain 2 (InterPro:IPR013816), PEP-utilising enzyme (InterPro:IPR000121); Has 35333 Blast hits to 34131 proteins in 2444 species: Archae - 798; Bacteria - 22429; Metazoa - 974; Fungi - 991; Plants - 531; Viruses - 0; Other Eukaryotes - 9610 (source: NCBI BLink).
    NP_001078395.1
    • pyruvate orthophosphate dikinase (PPDK); FUNCTIONS IN: kinase activity, pyruvate, phosphate dikinase activity; INVOLVED IN: phosphorylation, response to absence of light; LOCATED IN: cytosol, nucleus, chloroplast; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 11 growth stages; CONTAINS InterPro DOMAIN/s: PEP-utilising enzyme, mobile domain (InterPro:IPR008279), ATP-grasp fold, subdomain 1 (InterPro:IPR013815), Pyruvate, phosphate dikinase (InterPro:IPR010121), Pyruvate/Phosphoenolpyruvate kinase, catalytic core (InterPro:IPR015813), Pyruvate phosphate dikinase, PEP/pyruvate-binding (InterPro:IPR002192), PEP-utilising enzyme, mobile region, conserved site (InterPro:IPR018274), ATP-grasp fold, subdomain 2 (InterPro:IPR013816), PEP-utilising enzyme (InterPro:IPR000121); Has 15226 Blast hits to 15137 proteins in 2575 species: Archae - 291; Bacteria - 9909; Metazoa - 12; Fungi - 19; Plants - 160; Viruses - 0; Other Eukaryotes - 4835 (source: NCBI BLink).
    NP_001078396.1
    • pyruvate orthophosphate dikinase (PPDK); FUNCTIONS IN: kinase activity, pyruvate, phosphate dikinase activity; INVOLVED IN: phosphorylation, response to absence of light; LOCATED IN: cytosol, nucleus, chloroplast; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 11 growth stages; CONTAINS InterPro DOMAIN/s: PEP-utilising enzyme, mobile domain (InterPro:IPR008279), Pyruvate, phosphate dikinase (InterPro:IPR010121), ATP-grasp fold, subdomain 1 (InterPro:IPR013815), Pyruvate phosphate dikinase, PEP/pyruvate-binding (InterPro:IPR002192), Pyruvate/Phosphoenolpyruvate kinase, catalytic core (InterPro:IPR015813), PEP-utilising enzyme, mobile region, conserved site (InterPro:IPR018274), ATP-grasp fold, subdomain 2 (InterPro:IPR013816), PEP-utilising enzyme (InterPro:IPR000121); Has 15119 Blast hits to 15038 proteins in 2560 species: Archae - 291; Bacteria - 9841; Metazoa - 12; Fungi - 19; Plants - 125; Viruses - 0; Other Eukaryotes - 4831 (source: NCBI BLink).
    NP_001118987.1
    • pyruvate orthophosphate dikinase (PPDK); FUNCTIONS IN: kinase activity, pyruvate, phosphate dikinase activity; INVOLVED IN: phosphorylation, response to absence of light; LOCATED IN: cytosol, nucleus, chloroplast; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 11 growth stages; CONTAINS InterPro DOMAIN/s: Pyruvate phosphate dikinase, PEP/pyruvate-binding (InterPro:IPR002192), PEP-utilising enzyme, mobile domain (InterPro:IPR008279), Pyruvate/Phosphoenolpyruvate kinase, catalytic core (InterPro:IPR015813), PEP-utilising enzyme, mobile region, conserved site (InterPro:IPR018274), ATP-grasp fold, subdomain 2 (InterPro:IPR013816), PEP-utilising enzyme (InterPro:IPR000121), ATP-grasp fold, subdomain 1 (InterPro:IPR013815), Pyruvate, phosphate dikinase (InterPro:IPR010121); Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; Bacteria - 1396; Metazoa - 17338; Fungi - 3422; Plants - 5037; Viruses - 0; Other Eukaryotes - 2996 (source: NCBI BLink).
    NP_193288.2
    • pyruvate orthophosphate dikinase (PPDK); FUNCTIONS IN: kinase activity, pyruvate, phosphate dikinase activity; INVOLVED IN: phosphorylation, response to absence of light; LOCATED IN: cytosol, nucleus, chloroplast; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 11 growth stages; CONTAINS InterPro DOMAIN/s: PEP-utilising enzyme, mobile domain (InterPro:IPR008279), ATP-grasp fold, subdomain 1 (InterPro:IPR013815), Pyruvate, phosphate dikinase (InterPro:IPR010121), Pyruvate/Phosphoenolpyruvate kinase, catalytic core (InterPro:IPR015813), Pyruvate phosphate dikinase, PEP/pyruvate-binding (InterPro:IPR002192), PEP-utilising enzyme, mobile region, conserved site (InterPro:IPR018274), ATP-grasp fold, subdomain 2 (InterPro:IPR013816), PEP-utilising enzyme (InterPro:IPR000121); Has 15214 Blast hits to 15125 proteins in 2575 species: Archae - 291; Bacteria - 9898; Metazoa - 12; Fungi - 19; Plants - 160; Viruses - 0; Other Eukaryotes - 4834 (source: NCBI BLink).
    NP_849391.2
    • pyruvate orthophosphate dikinase (PPDK); FUNCTIONS IN: kinase activity, pyruvate, phosphate dikinase activity; INVOLVED IN: phosphorylation, response to absence of light; LOCATED IN: cytosol, nucleus, chloroplast stroma, chloroplast; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 11 growth stages; CONTAINS InterPro DOMAIN/s: PEP-utilising enzyme, mobile domain (InterPro:IPR008279), ATP-grasp fold, subdomain 1 (InterPro:IPR013815), Pyruvate, phosphate dikinase (InterPro:IPR010121), Pyruvate/Phosphoenolpyruvate kinase, catalytic core (InterPro:IPR015813), Pyruvate phosphate dikinase, PEP/pyruvate-binding (InterPro:IPR002192), PEP-utilising enzyme, mobile region, conserved site (InterPro:IPR018274), ATP-grasp fold, subdomain 2 (InterPro:IPR013816), PEP-utilising enzyme (InterPro:IPR000121); Has 15301 Blast hits to 15212 proteins in 2599 species: Archae - 294; Bacteria - 9981; Metazoa - 12; Fungi - 19; Plants - 160; Viruses - 0; Other Eukaryotes - 4835 (source: NCBI BLink).

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference assembly

    Genomic

    1. NC_003075.7 Reference assembly

      Range
      8864615..8870979 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_117643.4 → NP_193288.2  pyruvate orthophosphate dikinase [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178UZQ3, B9DHM5
      Conserved Domains (4) summary
      PRK09279
      Location:1 → 871
      PRK09279; pyruvate phosphate dikinase; Provisional
      pfam00391
      Location:426 → 505
      PEP-utilizers; PEP-utilizing enzyme, mobile domain
      pfam01326
      Location:23 → 359
      PPDK_N; Pyruvate phosphate dikinase, PEP/pyruvate binding domain
      pfam02896
      Location:517 → 872
      PEP-utilizers_C; PEP-utilizing enzyme, TIM barrel domain

    2. NM_179060.4 → NP_849391.2  pyruvate orthophosphate dikinase [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A5S9XSP5, A0A654FPJ2
      Conserved Domains (1) summary
      PRK09279
      Location:84 → 952
      PRK09279; pyruvate phosphate dikinase; Provisional

    3. NM_001084926.1 → NP_001078395.1  pyruvate orthophosphate dikinase [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A5S9XSP5, A0A654FPJ2
      Conserved Domains (1) summary
      PRK09279
      Location:84 → 952
      PRK09279; pyruvate phosphate dikinase; Provisional

    4. NM_001036570.1 → NP_001031647.1  pyruvate orthophosphate dikinase [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178UZQ3
      Conserved Domains (4) summary
      PRK09279
      Location:1 → 853
      PRK09279; pyruvate phosphate dikinase; Provisional
      pfam00391
      Location:408 → 487
      PEP-utilizers; PEP-utilizing enzyme, mobile domain
      pfam01326
      Location:5 → 341
      PPDK_N; Pyruvate phosphate dikinase, PEP/pyruvate binding domain
      pfam02896
      Location:499 → 854
      PEP-utilizers_C; PEP-utilizing enzyme, TIM barrel domain

    5. NM_001084927.2 → NP_001078396.1  pyruvate orthophosphate dikinase [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      B9DGK5, O23404, Q27GJ5, Q2V3I1, Q3EA16
      UniProtKB/TrEMBL
      A0A5S9XSP5
      Conserved Domains (4) summary
      PRK09279
      Location:91 → 959
      PRK09279; pyruvate phosphate dikinase; Provisional
      pfam00391
      Location:514 → 593
      PEP-utilizers; PEP-utilizing enzyme, mobile domain
      pfam01326
      Location:111 → 447
      PPDK_N; Pyruvate phosphate dikinase, PEP/pyruvate binding domain
      pfam02896
      Location:605 → 960
      PEP-utilizers_C; PEP-utilizing enzyme, TIM barrel domain

    6. NM_001125515.1 → NP_001118987.1  pyruvate orthophosphate dikinase [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      B9DGK5, O23404, Q27GJ5, Q2V3I1, Q3EA16
      UniProtKB/TrEMBL
      A0A5S9XSP5
      Conserved Domains (4) summary
      PRK09279
      Location:91 → 959
      PRK09279; pyruvate phosphate dikinase; Provisional
      pfam00391
      Location:514 → 593
      PEP-utilizers; PEP-utilizing enzyme, mobile domain
      pfam01326
      Location:111 → 447
      PPDK_N; Pyruvate phosphate dikinase, PEP/pyruvate binding domain
      pfam02896
      Location:605 → 960
      PEP-utilizers_C; PEP-utilizing enzyme, TIM barrel domain

    7. NM_001341051.1 → NP_001328869.1  pyruvate orthophosphate dikinase [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A178UZQ3
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O23404.2

    Gene LinkOut

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