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    VIM3 Zinc finger (C3HC4-type RING finger) family protein [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 833951, updated on 18-Sep-2024

    Summary

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    Official Symbol
    VIM3
    Official Full Name
    Zinc finger (C3HC4-type RING finger) family protein
    Primary source
    TAIR:AT5G39550
    Locus tag
    AT5G39550
    See related
    Araport:AT5G39550
    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
    MIJ24.3; MIJ24_3; ORTH1; ORTHRUS 1; VARIANT IN METHYLATION 3
    Summary
    Encodes the VIM3/ORTH1 protein that is similar to VIM1. This protein has an N-terminal PHD domain and two RING domains surrounding an SRA domain. The protein has been shown to bind to methylated cytosines of CG, CNG and CNN motifs via its SRA domain but has a preference for the former. This protein functions as an E3 ubiquitin ligase in vitro with members of the UBC8 family E2s. Either of the two RING domains present in the protein can promote ubiquitylation in vitro, but, not the PHD domain. Over-expression of ORTH1/VIM3 leads to decreased levels of FWA methylation, increased levels of FWA transcripts, and delayed flowering. Cen180 repeats are also hypomethylated in plants overexpressing this protein.
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    Genomic context

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    See VIM3 in Genome Data Viewer
    Location:
    chromosome: 5
    Exon count:
    9
    Sequence:
    Chromosome: 5; NC_003076.8 (15837178..15840678, complement)

    Chromosome 5 - NC_003076.8Genomic Context describing neighboring genes Neighboring gene pseudo Neighboring gene F-box associated ubiquitination effector family protein Neighboring gene Galactose oxidase/kelch repeat superfamily protein Neighboring gene uncharacterized protein

    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. Three SRA-domain methylcytosine-binding proteins cooperate to maintain global CpG methylation and epigenetic silencing in Arabidopsis. Woo HR, et al. PLoS Genet, 2008 Aug 15. PMID 18704160, Free PMC Article
    2. VIM proteins regulate transcription exclusively through the MET1 cytosine methylation pathway. Shook MS, et al. Epigenetics, 2014 Jul. PMID 24762702, Free PMC Article
    3. ORTH/VIM proteins that regulate DNA methylation are functional ubiquitin E3 ligases. Kraft E, et al. Plant J, 2008 Dec. PMID 18643997, Free PMC Article
    4. The SRA methyl-cytosine-binding domain links DNA and histone methylation. Johnson LM, et al. Curr Biol, 2007 Feb 20. PMID 17239600, Free PMC Article
    5. Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana. Tabata S, et al. Nature, 2000 Dec 14. PMID 11130714

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. VIM proteins function in transcriptional regulation via their roles in the MET1 DNA methylation pathway.
      Title: VIM proteins regulate transcription exclusively through the MET1 cytosine methylation pathway.
    2. ORTH proteins are ubiquitin E3 ligases that regulate DNA methylation. The ORTH1 RING domain promotes ubiquitylation, and overexpression leads to an altered flowering time because of decreased methylation of FWA.
      Title: ORTH/VIM proteins that regulate DNA methylation are functional ubiquitin E3 ligases.
    3. VIM1, VIM2, and VIM3 have overlapping functions in maintenance of global CpG methylation and epigenetic transcriptional silencing.
      Title: Three SRA-domain methylcytosine-binding proteins cooperate to maintain global CpG methylation and epigenetic silencing in Arabidopsis.
    Submit: New GeneRIF Correction

    General gene information

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    NM_123317.4

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables histone binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables methyl-CpG binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables methyl-CpNpG binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables methyl-CpNpN binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables ubiquitin-protein transferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in negative regulation of gene expression via chromosomal CpG island methylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within protein ubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein ubiquitination IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within vegetative to reproductive phase transition of meristem IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  

    General protein information

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    Preferred Names
    Zinc finger (C3HC4-type RING finger) family protein
    NP_198771.1
    • VARIANT IN METHYLATION 3 (VIM3); CONTAINS InterPro DOMAIN/s: Zinc finger, RING-type, conserved site (InterPro:IPR017907), Zinc finger, PHD-type, conserved site (InterPro:IPR019786), Zinc finger, RING-type (InterPro:IPR001841), Zinc finger, PHD-type (InterPro:IPR001965), SRA-YDG (InterPro:IPR003105), Zinc finger, C3HC4 RING-type (InterPro:IPR018957), Zinc finger, FYVE/PHD-type (InterPro:IPR011011); BEST Arabidopsis thaliana protein match is: Zinc finger (C3HC4-type RING finger) family protein (TAIR:AT1G66040.1); Has 6556 Blast hits to 5308 proteins in 497 species: Archae - 0; Bacteria - 14; Metazoa - 4783; Fungi - 431; Plants - 899; Viruses - 19; Other Eukaryotes - 410 (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
      15837178..15840678 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_123317.4 → NP_198771.1  Zinc finger (C3HC4-type RING finger) family protein [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_198771.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q67XP0, Q9FKA7
      UniProtKB/TrEMBL
      A0A654G6G1, A0A7G2FJ79
      Conserved Domains (6) summary
      PLN03208
      Location:98 → 156
      PLN03208; E3 ubiquitin-protein ligase RMA2; Provisional
      smart00249
      Location:14 → 59
      PHD; PHD zinc finger
      COG5574
      Location:448 → 519
      PEX10; RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
      cd00162
      Location:495 → 551
      RING_Ubox; RING-HC finger (C3HC4-type) [structural motif]
      pfam02182
      Location:247 → 409
      SAD_SRA; SAD/SRA domain
      cl17238
      Location:493 → 555
      RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9FKA7.1

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