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    PGDH D-3-phosphoglycerate dehydrogenase [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 838352, updated on 18-Sep-2024

    Summary

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    Official Symbol
    PGDH
    Official Full Name
    D-3-phosphoglycerate dehydrogenase
    Primary source
    TAIR:AT1G17745
    Locus tag
    AT1G17745
    See related
    Araport:AT1G17745
    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
    3-phosphoglycerate dehydrogenase; PGDH2; phosphoglycerate dehydrogenase 2
    Summary
    encodes a 3-Phosphoglycerate dehydrogenase
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    Genomic context

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    See PGDH in Genome Data Viewer
    Location:
    chromosome: 1
    Exon count:
    4
    Sequence:
    Chromosome: 1; NC_003070.9 (6100964..6105347)

    Chromosome 1 - NC_003070.9Genomic Context describing neighboring genes Neighboring gene Protein phosphatase 2A, regulatory subunit PR55 Neighboring gene vacuolar protein sorting 46.1 Neighboring gene uncharacterized protein Neighboring gene ncRNA Neighboring gene ncRNA Neighboring gene ncRNA Neighboring gene PEP1 receptor 2 Neighboring gene Tetratricopeptide repeat (TPR)-like superfamily protein

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003070.9

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Biochemical insight into redox regulation of plastidial 3-phosphoglycerate dehydrogenase from Arabidopsis thaliana. Yoshida K, et al. J Biol Chem, 2020 Oct 30. PMID 32848019, Free PMC Article
    2. Novel regulatory mechanism of serine biosynthesis associated with 3-phosphoglycerate dehydrogenase in Arabidopsis thaliana. Okamura E, et al. Sci Rep, 2017 Jun 14. PMID 28615699, Free PMC Article
    3. Regulation of serine biosynthesis in Arabidopsis. Crucial role of plastidic 3-phosphoglycerate dehydrogenase in non-photosynthetic tissues. Ho CL, et al. J Biol Chem, 1999 Jan 1. PMID 9867856
    4. Functional characterization of the plastidial 3-phosphoglycerate dehydrogenase family in Arabidopsis. Toujani W, et al. Plant Physiol, 2013 Nov. PMID 24058165, Free PMC Article
    5. Proteomic profiling of tandem affinity purified 14-3-3 protein complexes in Arabidopsis thaliana. Chang IF, et al. Proteomics, 2009 Jun. PMID 19452453, Free PMC Article

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Biochemical insight into redox regulation of plastidial 3-phosphoglycerate dehydrogenase from Arabidopsis thaliana.
      Title: Biochemical insight into redox regulation of plastidial 3-phosphoglycerate dehydrogenase from Arabidopsis thaliana.
    2. In the present study, two Arabidopsis PGDH isoforms were inhibited by L-serine but were activated by L-amino acids such as L-homocysteine in vitro.
      Title: Novel regulatory mechanism of serine biosynthesis associated with 3-phosphoglycerate dehydrogenase in Arabidopsis thaliana.
    3. Data indicate that 3-phosphoglycerate dehydrogenases PGDH (At1g17745) and EDA9 (At4g34200) were expressed preferentially in roots while 3-PGDH (At3g19480) was expressed mainly in the aerial parts and was not expressed or very poorly in roots.
      Title: Functional characterization of the plastidial 3-phosphoglycerate dehydrogenase family in Arabidopsis.
    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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    Homology

    NM_001035984.2

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables NAD binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphoglycerate dehydrogenase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphoglycerate dehydrogenase activity IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within L-serine biosynthetic process TAS
    Traceable Author Statement
    more info
    		 PubMed 
    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 nucleus HDA PubMed 

    General protein information

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    Preferred Names
    D-3-phosphoglycerate dehydrogenase
    NP_001031061.2
    • D-3-phosphoglycerate dehydrogenase; CONTAINS InterPro DOMAIN/s: D-3-phosphoglycerate dehydrogenase (InterPro:IPR006236), D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain (InterPro:IPR006139), D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding (InterPro:IPR006140), D-3-phosphogylcerate Dehydrogenase (InterPro:IPR015508), NAD(P)-binding domain (InterPro:IPR016040), Amino acid-binding ACT (InterPro:IPR002912); BEST Arabidopsis thaliana protein match is: D-3-phosphoglycerate dehydrogenase (TAIR:AT4G34200.1).
    NP_564034.1
    • 3-phosphoglycerate dehydrogenase (PGDH); FUNCTIONS IN: phosphoglycerate dehydrogenase activity, protein binding; INVOLVED IN: L-serine biosynthetic process; LOCATED IN: cytosol, nucleus, chloroplast; EXPRESSED IN: 24 plant structures; EXPRESSED DURING: 14 growth stages; CONTAINS InterPro DOMAIN/s: D-3-phosphoglycerate dehydrogenase (InterPro:IPR006236), D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain (InterPro:IPR006139), D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding (InterPro:IPR006140), D-3-phosphogylcerate Dehydrogenase (InterPro:IPR015508), Amino acid-binding ACT (InterPro:IPR002912), NAD(P)-binding domain (InterPro:IPR016040); BEST Arabidopsis thaliana protein match is: D-3-phosphoglycerate dehydrogenase (TAIR:AT4G34200.1); Has 30450 Blast hits to 30444 proteins in 2726 species: Archae - 473; Bacteria - 18179; Metazoa - 739; Fungi - 1175; Plants - 595; Viruses - 5; Other Eukaryotes - 9284 (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_003070.9 Reference assembly

      Range
      6100964..6105347
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_101636.3 → NP_564034.1  D-3-phosphoglycerate dehydrogenase [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_564034.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      F4I918, O04130
      UniProtKB/TrEMBL
      A0A178W962, A0A5S9UYE7
      Conserved Domains (1) summary
      PRK13581
      Location:83 → 624
      PRK13581; D-3-phosphoglycerate dehydrogenase; Provisional

    2. NM_001035984.2 → NP_001031061.2  D-3-phosphoglycerate dehydrogenase [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001031061.2

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      O04130
      Conserved Domains (3) summary
      cd04902
      Location:579 → 651
      ACT_3PGDH-xct; C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH)
      PRK13581
      Location:83 → 651
      PRK13581; D-3-phosphoglycerate dehydrogenase; Provisional
      cd12173
      Location:84 → 414
      PGDH_4; Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O04130.2

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