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    VAR1 FtsH extracellular protease family [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 834232, updated on 18-Sep-2024

    Summary

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    Official Symbol
    VAR1
    Official Full Name
    FtsH extracellular protease family
    Primary source
    TAIR:AT5G42270
    Locus tag
    AT5G42270
    See related
    Araport:AT5G42270
    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
    FTSH5; K5J14.13; K5J14_13; VARIEGATED 1
    Summary
    VAR1 contains a conserved motif for ATPase and a metalloprotease characteristic to FtsH proteins, and is targeted into chloroplasts. A VAR1-fusion protein synthesized in vitro exhibited ATPase activity and partial metalloprotease activity. This protein is located to the thylakoid membrane and forms a complex with VAR2. FtsH1 (VAR1) and FtsH5 are interchangeable in thylakoid membranes. Phosphorylation of this protein is dependent on calcium.
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    Genomic context

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    See VAR1 in Genome Data Viewer
    Location:
    chromosome: 5
    Exon count:
    5
    Sequence:
    Chromosome: 5; NC_003076.8 (16902475..16905294)

    Chromosome 5 - NC_003076.8Genomic Context describing neighboring genes Neighboring gene beta glucosidase 12 Neighboring gene miscRNA Neighboring gene Cysteine/Histidine-rich C1 domain family protein Neighboring gene transcription activator-like protein Neighboring gene ubiquitin-like protein 5 Neighboring gene Pentatricopeptide repeat (PPR-like) superfamily protein Neighboring gene Zn-dependent exopeptidases superfamily 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. The VAR1 locus of Arabidopsis encodes a chloroplastic FtsH and is responsible for leaf variegation in the mutant alleles. Sakamoto W, et al. Genes Cells, 2002 Aug. PMID 12167156
    2. FtsH2 and FtsH5: two homologous subunits use different integration mechanisms leading to the same thylakoid multimeric complex. Rodrigues RA, et al. Plant J, 2011 Feb. PMID 21214651, Free PMC Article
    3. Thylakoid-Bound FtsH Proteins Facilitate Proper Biosynthesis of Photosystem I. Järvi S, et al. Plant Physiol, 2016 Jun. PMID 27208291, Free PMC Article
    4. A chloroplast-targeted DnaJ protein AtJ8 is negatively regulated by light and has rapid turnover in darkness. Chen KM, et al. J Plant Physiol, 2011 Oct 15. PMID 21592617
    5. The hetero-hexameric nature of a chloroplast AAA+ FtsH protease contributes to its thermodynamic stability. Moldavski O, et al. PLoS One, 2012. PMID 22558304, Free PMC Article

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. the thylakoid membrane-bound FtsH5 and FtsH2 have dual functions in the maintenance of photosynthetic complexes.
      Title: Thylakoid-Bound FtsH Proteins Facilitate Proper Biosynthesis of Photosystem I.
    2. The AtJ8 protein was found to be nearly missing from the var1 mutant, which lacks the FTSH5 protease. AtJ8 is expressed mainly in darkness, is prone to a rapid turnover but is partially stabilized by the FTSH proteases.
      Title: A chloroplast-targeted DnaJ protein AtJ8 is negatively regulated by light and has rapid turnover in darkness.
    3. To gain structural information of the possible complexes, the Arabidopsis FtsH2 (type B) and FtsH5 (type A) were modeled.
      Title: The hetero-hexameric nature of a chloroplast AAA+ FtsH protease contributes to its thermodynamic stability.
    4. The Sec pathway integrates FtsH5 into thylakoids.
      Title: FtsH2 and FtsH5: two homologous subunits use different integration mechanisms leading to the same thylakoid multimeric complex.
    5. The effect of FtsHs in D1 degradation was investigated in Arabidopsis (Arabidopsis thaliana) mutants lacking FtsH2 (yellow variegated2 [var2]) or FtsH5 (var1).
      Title: The variegated mutants lacking chloroplastic FtsHs are defective in D1 degradation and accumulate reactive oxygen species.
    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_123592.4

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables ATP hydrolysis activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables ATP-dependent peptidase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP-dependent peptidase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    enables mRNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables metalloendopeptidase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within PSII associated light-harvesting complex II catabolic process TAS
    Traceable Author Statement
    more info
    		 PubMed 
    acts_upstream_of_or_within photoinhibition IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within photosystem I assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within protein catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chloroplast HDA PubMed 
    located_in chloroplast IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in chloroplast ISM
    Inferred from Sequence Model
    more info
    		  
    located_in chloroplast envelope HDA PubMed 
    located_in chloroplast thylakoid HDA PubMed 
    located_in chloroplast thylakoid membrane HDA PubMed 
    located_in chloroplast thylakoid membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plastid HDA PubMed 
    located_in thylakoid HDA PubMed 

    General protein information

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    Preferred Names
    FtsH extracellular protease family
    NP_568604.1
    • VARIEGATED 1 (VAR1); FUNCTIONS IN: metallopeptidase activity, ATP-dependent peptidase activity, ATPase activity; INVOLVED IN: photoinhibition, PSII associated light-harvesting complex II catabolic process, protein catabolic process; LOCATED IN: thylakoid, chloroplast thylakoid membrane, chloroplast, chloroplast envelope; EXPRESSED IN: 24 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Peptidase M41, FtsH (InterPro:IPR005936), ATPase, AAA-type, core (InterPro:IPR003959), ATPase, AAA+ type, core (InterPro:IPR003593), ATPase, AAA-type, conserved site (InterPro:IPR003960), Peptidase M41 (InterPro:IPR000642); BEST Arabidopsis thaliana protein match is: FTSH protease 1 (TAIR:AT1G50250.1); 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
      16902475..16905294
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_123592.4 → NP_568604.1  FtsH extracellular protease family [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_568604.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q9FH02
      UniProtKB/TrEMBL
      A0A178U8J6, A0A5S9YAJ7
      Conserved Domains (1) summary
      TIGR01241
      Location:192 → 694
      FtsH_fam; ATP-dependent metalloprotease FtsH
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9FH02.1

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