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    SKD1 AAA-type ATPase family protein [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 817306, updated on 18-Sep-2024

    Summary

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    Official Symbol
    SKD1
    Official Full Name
    AAA-type ATPase family protein
    Primary source
    TAIR:AT2G27600
    Locus tag
    AT2G27600
    See related
    Araport:AT2G27600
    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
    ATSKD1; F10A12.27; F10A12_27; SUPPRESSOR OF K+ TRANSPORT GROWTH DEFECT1; VACUOLAR PROTEIN SORTING 4; VPS4
    Summary
    Encodes a SKD1 (Suppressor of K+ Transport Growth Defect1) homolog. Localized to the cytoplasm and to multivesicular endosomes. Involved in multivesicular endosome function.
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    Genomic context

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    See SKD1 in Genome Data Viewer
    Location:
    chromosome: 2
    Exon count:
    8
    Sequence:
    Chromosome: 2; NC_003071.7 (11780896..11783992)

    Chromosome 2 - NC_003071.7Genomic Context describing neighboring genes Neighboring gene A20/AN1-like zinc finger family protein Neighboring gene S-adenosyl-L-methionine-dependent methyltransferases superfamily protein Neighboring gene Tetratricopeptide repeat (TPR)-like superfamily protein Neighboring gene Ubiquitin carboxyl-terminal hydrolase-related protein Neighboring gene Ubiquitin carboxyl-terminal hydrolase-related protein

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003071.7

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Suppressor of K+ transport growth defect 1 (SKD1) interacts with RING-type ubiquitin ligase and sucrose non-fermenting 1-related protein kinase (SnRK1) in the halophyte ice plant. Chiang CP, et al. J Exp Bot, 2013 May. PMID 23580756, Free PMC Article
    2. Seeds of Arabidopsis plants expressing dominant-negative AtSKD1 under control of the GL2 promoter show a transparent testa phenotype and a mucilage defect. Shahriari M, et al. Plant Signal Behav, 2010 Oct. PMID 20930567, Free PMC Article
    3. A novel endosomal sorting complex required for transport (ESCRT) component in Arabidopsis thaliana controls cell expansion and development. Reyes FC, et al. J Biol Chem, 2014 Feb 21. PMID 24385429, Free PMC Article
    4. The Arabidopsis AAA ATPase SKD1 is involved in multivesicular endosome function and interacts with its positive regulator LYST-INTERACTING PROTEIN5. Haas TJ, et al. Plant Cell, 2007 Apr. PMID 17468262, Free PMC Article
    5. Arabidopsis LIP5, a positive regulator of multivesicular body biogenesis, is a critical target of pathogen-responsive MAPK cascade in plant basal defense. Wang F, et al. PLoS Pathog, 2014 Jul. PMID 25010425, Free PMC Article

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Seeds of the dominant-negative AtSKD1 under control of GS2 promoter display a transparent testa phenotype caused by a lack of proanthocyanidin (PA) and do not possess seed coat mucilage.
      Title: Seeds of Arabidopsis plants expressing dominant-negative AtSKD1 under control of the GL2 promoter show a transparent testa phenotype and a mucilage defect.
    2. Dominant-negative AtSKD1 induces vacuolar defects in Arabidopsis trichomes and specifically inhibits vacuolar trafficking.
      Title: The AAA-type ATPase AtSKD1 contributes to vacuolar maintenance of Arabidopsis thaliana.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    NM_128319.4

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within endosome organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in potassium ion homeostasis TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in sodium ion homeostasis TAS
    Traceable Author Statement
    more info
    		 PubMed 
    acts_upstream_of_or_within trichome branching IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within vacuole organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within vesicle-mediated transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm ISM
    Inferred from Sequence Model
    more info
    		  
    located_in cytoplasmic stress granule IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in multivesicular body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in peroxisome HDA PubMed 
    located_in plasmodesma HDA PubMed 

    General protein information

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    Preferred Names
    AAA-type ATPase family protein
    NP_180328.1
    • SUPPRESSOR OF K+ TRANSPORT GROWTH DEFECT1 (SKD1); FUNCTIONS IN: nucleoside-triphosphatase activity, nucleotide binding, ATP binding; INVOLVED IN: vesicle-mediated transport, endosome organization; LOCATED IN: cytoplasm, multivesicular body; EXPRESSED IN: 24 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: ATPase, AAA+ type, core (InterPro:IPR003593), ATPase, AAA-type, core (InterPro:IPR003959), ATPase, AAA-type, conserved site (InterPro:IPR003960), Vps4 oligomerisation, C-terminal (InterPro:IPR015415), MIT (InterPro:IPR007330); BEST Arabidopsis thaliana protein match is: P-loop containing nucleoside triphosphate hydrolases superfamily protein (TAIR:AT1G80350.1); Has 30691 Blast hits to 28172 proteins in 3117 species: Archae - 1476; Bacteria - 10868; Metazoa - 5113; Fungi - 3519; Plants - 2854; Viruses - 27; Other Eukaryotes - 6834 (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_003071.7 Reference assembly

      Range
      11780896..11783992
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_128319.4 → NP_180328.1  AAA-type ATPase family protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_180328.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q8LAK9, Q9ZNT0
      UniProtKB/TrEMBL
      A0A178VQU8, A0A5S9X287
      Conserved Domains (4) summary
      cd02678
      Location:4 → 78
      MIT_VPS4; MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in intracellular protein transport proteins of the AAA-ATPase family. The molecular function of the MIT domain is unclear.
      pfam09336
      Location:368 → 432
      Vps4_C; Vps4 C terminal oligomerization domain
      pfam17862
      Location:323 → 358
      AAA_lid_3; AAA+ lid domain
      cd19521
      Location:126 → 296
      RecA-like_VPS4; ATPase domain of vacuolar protein sorting-associated protein 4
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9ZNT0.1

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