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    AGD5 ARF-GAP domain 5 [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 835519, updated on 18-Sep-2024

    Summary

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    Official Symbol
    AGD5
    Official Full Name
    ARF-GAP domain 5
    Primary source
    TAIR:AT5G54310
    Locus tag
    AT5G54310
    See related
    Araport:AT5G54310
    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
    ARF-GAP domain 5; AtAGD5; MDK4.13; MDK4_13; NEV; NEVERSHED
    Summary
    A member of ARF GAP domain (AGD), A thaliana has 15 members, grouped into four classes. Regulates membrane trafficking and organ separation.
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    Genomic context

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    See AGD5 in Genome Data Viewer
    Location:
    chromosome: 5
    Exon count:
    11
    Sequence:
    Chromosome: 5; NC_003076.8 (22056986..22061270, complement)

    Chromosome 5 - NC_003076.8Genomic Context describing neighboring genes Neighboring gene cytochrome c biogenesis protein family Neighboring gene cotton fiber-like protein (DUF761) Neighboring gene ncRNA Neighboring gene hypothetical protein (DUF295) Neighboring gene hypothetical protein (DUF295)

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003076.8

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Regulation of membrane trafficking and organ separation by the NEVERSHED ARF-GAP protein. Liljegren SJ, et al. Development, 2009 Jun. PMID 19429787, Free PMC Article
    2. NEVERSHED and INFLORESCENCE DEFICIENT IN ABSCISSION are differentially required for cell expansion and cell separation during floral organ abscission in Arabidopsis thaliana. Liu B, et al. J Exp Bot, 2013 Dec. PMID 23963677
    3. AGD5 is a GTPase-activating protein at the trans-Golgi network. Stefano G, et al. Plant J, 2010 Dec. PMID 21105926
    4. MTV1 and MTV4 encode plant-specific ENTH and ARF GAP proteins that mediate clathrin-dependent trafficking of vacuolar cargo from the trans-Golgi network. Sauer M, et al. Plant Cell, 2013 Jun. PMID 23771894, Free PMC Article
    5. Leaf shedding as an anti-bacterial defense in Arabidopsis cauline leaves. Patharkar OR, et al. PLoS Genet, 2017 Dec. PMID 29253890, Free PMC Article

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. IDA and NEV function during both the cell-wall loosening and the cell separation stages of the abscission process. In addition, NEV acts to inhibit premature cell expansion.
      Title: NEVERSHED and INFLORESCENCE DEFICIENT IN ABSCISSION are differentially required for cell expansion and cell separation during floral organ abscission in Arabidopsis thaliana.
    2. Data indicate that MTV1 (AT3G16270) and AGD5 (AT5G54310) Physically Interact with clathrin.
      Title: MTV1 and MTV4 encode plant-specific ENTH and ARF GAP proteins that mediate clathrin-dependent trafficking of vacuolar cargo from the trans-Golgi network.
    3. AGD5, a a GTPase-activating protein, is distributed on a sub-population of the trans-Golgi network, where it co-localises with ARF1.
      Title: AGD5 is a GTPase-activating protein at the trans-Golgi network.
    4. NEV ARF-GAP activity at the trans-Golgi network and distinct endosomal compartments is required for the proper trafficking of cargo molecules required for cell separation. [NEV]
      Title: Regulation of membrane trafficking and organ separation by the NEVERSHED ARF-GAP protein.
    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_124811.5

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables GTPase activator activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within defense response to Gram-negative bacterium IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within floral organ abscission IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in floral organ abscission IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within leaf abscission IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of cell growth IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in vesicle-mediated transport involved in floral organ abscission IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  
    located_in trans-Golgi network IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    ARF-GAP domain 5
    NP_568807.1
    • ARF-GAP domain 5 (AGD5); FUNCTIONS IN: ARF GTPase activator activity, DNA binding, zinc ion binding; INVOLVED IN: floral organ abscission, activation of ARF GTPase activity; LOCATED IN: cytosol, trans-Golgi network, endosome, nucleus; EXPRESSED IN: 23 plant structures; EXPRESSED DURING: 15 growth stages; CONTAINS InterPro DOMAIN/s: Arf GTPase activating protein (InterPro:IPR001164); BEST Arabidopsis thaliana protein match is: ARF-GAP domain 15 (TAIR:AT3G17660.1); 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_003076.8 Reference assembly

      Range
      22056986..22061270 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_124811.5 → NP_568807.1  ARF-GAP domain 5 [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_568807.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      C4NZX2, Q8L8M0, Q9FL69, Q9FVH4
      UniProtKB/TrEMBL
      A0A178UN58, A0A5S9YDY3, A0A654GB12
      Conserved Domains (2) summary
      COG5347
      Location:9 → 262
      COG5347; GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
      cd08204
      Location:19 → 117
      ArfGap; GTPase-activating protein (GAP) for the ADP ribosylation factors (ARFs)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9FL69.1

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