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    ISA3 isoamylase 3 [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 826481, updated on 7-Sep-2023

    Summary

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    Gene symbol
    ISA3
    Gene description
    isoamylase 3
    Primary source
    Araport:AT4G09020
    Locus tag
    AT4G09020
    See related
    TAIR:AT4G09020
    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
    ATISA3; F23J3.50; F23J3_50; isoamylase 3
    Summary
    Encodes an isoamylase-like protein. Mutant studies show that the gene is strongly involved in starch breakdown. A GUS-protein fusion product was shown to localize to the surface of chloroplastic structures reminiscent of starch granules. In the mutants, the chloroplastic alpha-amylase AMY3 is upregulated.
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    Genomic context

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    See ISA3 in Genome Data Viewer
    Location:
    chromosome: 4
    Exon count:
    24
    Sequence:
    Chromosome: 4; NC_003075.7 (5783909..5789100)

    Chromosome 4 - NC_003075.7Genomic Context describing neighboring genes Neighboring gene ascorbate peroxidase 4 Neighboring gene ncRNA Neighboring gene Mitochondrial ribosomal protein L27 Neighboring gene uncharacterized protein Neighboring gene arabinogalactan protein 10 Neighboring gene RNA-binding (RRM/RBD/RNP motifs) family protein

    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. Evidence for distinct mechanisms of starch granule breakdown in plants. Delatte T, et al. J Biol Chem, 2006 Apr 28. PMID 16495218
    2. Starch granule biosynthesis in Arabidopsis is abolished by removal of all debranching enzymes but restored by the subsequent removal of an endoamylase. Streb S, et al. Plant Cell, 2008 Dec. PMID 19074683, Free PMC Article
    3. Further evidence for the mandatory nature of polysaccharide debranching for the aggregation of semicrystalline starch and for overlapping functions of debranching enzymes in Arabidopsis leaves. Wattebled F, et al. Plant Physiol, 2008 Nov. PMID 18815382, Free PMC Article
    4. The debate on the pathway of starch synthesis: a closer look at low-starch mutants lacking plastidial phosphoglucomutase supports the chloroplast-localized pathway. Streb S, et al. Plant Physiol, 2009 Dec. PMID 19776162, Free PMC Article
    5. The oligomeric stromal proteome of Arabidopsis thaliana chloroplasts. Peltier JB, et al. Mol Cell Proteomics, 2006 Jan. PMID 16207701

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Data propose that ISA3 function in normal amylopectin synthesis by promoting amylopectin crystallization but conclude that they are not mandatory for starch granule synthesis.
      Title: Starch granule biosynthesis in Arabidopsis is abolished by removal of all debranching enzymes but restored by the subsequent removal of an endoamylase.
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    Pathways from PubChem

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    General gene information

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    Markers

    Homology

    NM_116971.6

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables isoamylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in starch catabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within starch catabolic process 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 starch grain IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in chloroplast stroma HDA PubMed 

    General protein information

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    Preferred Names
    isoamylase 3
    NP_192641.2
    • isoamylase 3 (ISA3); FUNCTIONS IN: isoamylase activity, alpha-amylase activity; INVOLVED IN: carbohydrate metabolic process, starch catabolic process; LOCATED IN: chloroplast, chloroplast stroma, chloroplast starch grain; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Glycosyl hydrolase, family 13, all-beta (InterPro:IPR013780), Immunoglobulin-like fold (InterPro:IPR013783), Glycoside hydrolase, family 13, N-terminal (InterPro:IPR004193), Immunoglobulin E-set (InterPro:IPR014756), Glycoside hydrolase, catalytic core (InterPro:IPR017853), Glycoside hydrolase, subgroup, catalytic core (InterPro:IPR013781), Glycosyl hydrolase, family 13, catalytic domain (InterPro:IPR006047); BEST Arabidopsis thaliana protein match is: isoamylase 1 (TAIR:AT2G39930.1); 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).

    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
      5783909..5789100
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_116971.6 → NP_192641.2  isoamylase 3 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_192641.2

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q8RWW6, Q9M0S5
      UniProtKB/TrEMBL
      A0A178V6J6
      Conserved Domains (3) summary
      cd02856
      Location:91 → 240
      E_set_GDE_Isoamylase_N; N-terminal Early set domain associated with the catalytic domain of Glycogen debranching enzyme and bacterial isoamylase (also called glycogen 6-glucanohydrolase)
      cd11326
      Location:220 → 659
      AmyAc_Glg_debranch; Alpha amylase catalytic domain found in glycogen debranching enzymes
      COG1523
      Location:78 → 739
      PulA; Pullulanase/glycogen debranching enzyme [Carbohydrate transport and metabolism]
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9M0S5.2

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