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    IMD2 isopropylmalate dehydrogenase 2 [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 844395, updated on 18-Sep-2024

    Summary

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    Official Symbol
    IMD2
    Official Full Name
    isopropylmalate dehydrogenase 2
    Primary source
    TAIR:AT1G80560
    Locus tag
    AT1G80560
    See related
    Araport:AT1G80560
    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
    ARABIDOPSIS ISOPROPYLMALATE DEHYDROGENASE 2; ATIMD2; isopropylmalate dehydrogenase 2; T21F11.11; T21F11_11
    Summary
    The AtIMD2 is one out of 3 genes encoding the enzyme 3-isopropylmalate dehydrogenase involved in leucine biosynthesis in Arabidopsis. Its subcellular location has been targeted to plastids.
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    Genomic context

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    See IMD2 in Genome Data Viewer
    Location:
    chromosome: 1
    Exon count:
    11
    Sequence:
    Chromosome: 1; NC_003070.9 (30287763..30290299)

    Chromosome 1 - NC_003070.9Genomic Context describing neighboring genes Neighboring gene Pentatricopeptide repeat (PPR) superfamily protein Neighboring gene Isocitrate/isopropylmalate dehydrogenase family protein Neighboring gene RNI-like superfamily protein Neighboring gene Integrase-type DNA-binding 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. Structure and Mechanism of Isopropylmalate Dehydrogenase from Arabidopsis thaliana: INSIGHTS ON LEUCINE AND ALIPHATIC GLUCOSINOLATE BIOSYNTHESIS. Lee SG, et al. J Biol Chem, 2016 Jun 24. PMID 27137927, Free PMC Article
    2. Structural and functional evolution of isopropylmalate dehydrogenases in the leucine and glucosinolate pathways of Arabidopsis thaliana. He Y, et al. J Biol Chem, 2011 Aug 19. PMID 21697089, Free PMC Article
    3. Functional characterization of Arabidopsis thaliana isopropylmalate dehydrogenases reveals their important roles in gametophyte development. He Y, et al. New Phytol, 2011 Jan. PMID 20840499
    4. Cloning of cDNAs encoding isopropylmalate dehydrogenase from Arabidopsis thaliana and accumulation patterns of their transcripts. Nozawa A, et al. Biosci Biotechnol Biochem, 2005 Apr. PMID 15849421
    5. The oligomeric stromal proteome of Arabidopsis thaliana chloroplasts. Peltier JB, et al. Mol Cell Proteomics, 2006 Jan. PMID 16207701

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. the x-ray crystal structures of Arabidopsis thaliana IPMDH2 (AtIPMDH2) in complex with either isopropylmalate and Mg(2+) or NAD(+) These structures reveal conformational changes that occur upon ligand binding and provide insight on the active site of the enzyme.
      Title: Structure and Mechanism of Isopropylmalate Dehydrogenase from Arabidopsis thaliana: INSIGHTS ON LEUCINE AND ALIPHATIC GLUCOSINOLATE BIOSYNTHESIS.
    2. IPMDH2 and IPMDH3 primarily function in leucine biosynthesis, are essential for pollen development and are needed for proper embryo sac development.
      Title: Functional characterization of Arabidopsis thaliana isopropylmalate dehydrogenases reveals their important roles in gametophyte development.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    NM_106704.4

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables 3-isopropylmalate dehydrogenase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables 3-isopropylmalate dehydrogenase activity IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    enables 3-isopropylmalate dehydrogenase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables NAD+ binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables magnesium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in L-leucine biosynthetic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in L-leucine biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within L-leucine biosynthetic process IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in L-leucine biosynthetic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in embryo sac development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in pollen development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chloroplast HDA PubMed 
    located_in chloroplast ISM
    Inferred from Sequence Model
    more info
    		  
    located_in chloroplast envelope HDA PubMed 
    located_in chloroplast stroma HDA PubMed 
    located_in cytosol HDA PubMed 
    located_in plastid ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    isopropylmalate dehydrogenase 2
    NP_178171.1
    • isopropylmalate dehydrogenase 2 (IMD2); FUNCTIONS IN: 3-isopropylmalate dehydrogenase activity; INVOLVED IN: leucine biosynthetic process, metabolic process; LOCATED IN: chloroplast, chloroplast stroma, plastid, chloroplast envelope; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 14 growth stages; CONTAINS InterPro DOMAIN/s: Isopropylmalate dehydrogenase (InterPro:IPR004429), Isocitrate/isopropylmalate dehydrogenase (InterPro:IPR001804), Isocitrate/isopropylmalate dehydrogenase, conserved site (InterPro:IPR019818); BEST Arabidopsis thaliana protein match is: isopropylmalate dehydrogenase 3 (TAIR:AT1G31180.1); Has 15265 Blast hits to 15265 proteins in 2613 species: Archae - 395; Bacteria - 8292; Metazoa - 578; Fungi - 832; Plants - 243; Viruses - 0; Other Eukaryotes - 4925 (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
      30287763..30290299
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_106704.4 → NP_178171.1  isopropylmalate dehydrogenase 2 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_178171.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      P93832, Q540Z4, Q8W4P6
      UniProtKB/TrEMBL
      A0A178W3C4, A0A5S9WW30, A0A654EQQ6, Q8LEF4
      Conserved Domains (1) summary
      cl00445
      Location:1 → 405
      Iso_dh; Isocitrate/isopropylmalate dehydrogenase
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P93832.1

    Gene LinkOut

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