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    CLC-A chloride channel A [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 834090, updated on 18-Sep-2024

    Summary

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    Official Symbol
    CLC-A
    Official Full Name
    chloride channel A
    Primary source
    TAIR:AT5G40890
    Locus tag
    AT5G40890
    See related
    Araport:AT5G40890
    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
    ATCLC-A; ATCLCA; chloride channel A; CHLORIDE CHANNEL A; CHLORIDE CHANNEL-A; CLCA
    Summary
    Encodes a member of the voltage-dependent chloride channel. Also functions as a NO3-/H+ exchanger that serves to accumulate nitrate nutrient in vacuoles. Mutants homozygous for the T-DNA insertion mutation have reduced nitrate uptake capacity in high nitrate environment and exhibit hypersensitivity to chlorate.
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    Genomic context

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    See CLC-A in Genome Data Viewer
    Location:
    chromosome: 5
    Exon count:
    6
    Sequence:
    Chromosome: 5; NC_003076.8 (16381314..16385424, complement)

    Chromosome 5 - NC_003076.8Genomic Context describing neighboring genes Neighboring gene uncharacterized protein Neighboring gene uridine kinase/uracil phosphoribosyltransferase 1 Neighboring gene WD-40 repeat family protein / zfwd3 protein (ZFWD3) Neighboring gene ncRNA Neighboring gene Nucleotide-diphospho-sugar transferase family 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. Molecular mechanism underlying regulation of Arabidopsis CLCa transporter by nucleotides and phospholipids. Yang Z, et al. Nat Commun, 2023 Aug 12. PMID 37573431, Free PMC Article
    2. Cryo-EM structure of the plant nitrate transporter AtCLCa reveals characteristics of the anion-binding site and the ATP-binding pocket. He J, et al. J Biol Chem, 2023 Feb. PMID 36581207, Free PMC Article
    3. Dynamic measurement of cytosolic pH and [NO(3)(-)] uncovers the role of the vacuolar transporter AtCLCa in cytosolic pH homeostasis. Demes E, et al. Proc Natl Acad Sci U S A, 2020 Jun 30. PMID 32546525, Free PMC Article
    4. Phosphorylation of the vacuolar anion exchanger AtCLCa is required for the stomatal response to abscisic acid. Wege S, et al. Sci Signal, 2014 Jul 8. PMID 25005229
    5. ATP binding to the C terminus of the Arabidopsis thaliana nitrate/proton antiporter, AtCLCa, regulates nitrate transport into plant vacuoles. De Angeli A, et al. J Biol Chem, 2009 Sep 25. PMID 19636075, Free PMC Article

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Molecular mechanism underlying regulation of Arabidopsis CLCa transporter by nucleotides and phospholipids.
      Title: Molecular mechanism underlying regulation of Arabidopsis CLCa transporter by nucleotides and phospholipids.
    2. Cryo-EM structure of the plant nitrate transporter AtCLCa reveals characteristics of the anion-binding site and the ATP-binding pocket.
      Title: Cryo-EM structure of the plant nitrate transporter AtCLCa reveals characteristics of the anion-binding site and the ATP-binding pocket.
    3. Dynamic measurement of cytosolic pH and [NO3 (-)] uncovers the role of the vacuolar transporter AtCLCa in cytosolic pH homeostasis.
      Title: Dynamic measurement of cytosolic pH and [NO(3)(-)] uncovers the role of the vacuolar transporter AtCLCa in cytosolic pH homeostasis.
    4. Phosphorylation of Thr(38) in the amino-terminal cytoplasmic domain of AtCLCa by OST1 increased the outward anion fluxes across the vacuolar membrane, which are essential for stomatal closure.
      Title: Phosphorylation of the vacuolar anion exchanger AtCLCa is required for the stomatal response to abscisic acid.
    5. Data highlight the importance of the proline in AtCLCa for nitrate metabolism in Arabidopsis.
      Title: The proline 160 in the selectivity filter of the Arabidopsis NO(3)(-)/H(+) exchanger AtCLCa is essential for nitrate accumulation in planta.
    6. insertion mutants within the AtClCa and AtClCe genes revealed...a lower endogenous nitrate content; a higher nitrite content; a reduced nitrate influx into the root; and a decreased expression of several genes encoding nitrate transporters.
      Title: Two anion transporters AtClCa and AtClCe fulfil interconnecting but not redundant roles in nitrate assimilation pathways.
    7. Data show that ADP and AMP do not decrease the AtCLCa transport activity; nonetheless, AMP (but not ADP) competes with ATP, preventing inhibition.
      Title: ATP binding to the C terminus of the Arabidopsis thaliana nitrate/proton antiporter, AtCLCa, regulates nitrate transport into plant vacuoles.
    8. Arabidopsis thaliana CLCa (AtCLCa) is localized to an intracellular membrane, the tonoplast of the plant vacuole; direct evidence for its anion transport ability
      Title: The nitrate/proton antiporter AtCLCa mediates nitrate accumulation in plant vacuoles.
    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_001036913.2
    NM_123454.3

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables monoatomic anion channel activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables nitrate transmembrane transporter activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables voltage-gated chloride channel activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within chloride transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within nitrate transmembrane transport IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within response to nitrate IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in intracellular anatomical structure TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in nucleus ISM
    Inferred from Sequence Model
    more info
    		  

    General protein information

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    Preferred Names
    chloride channel A
    NP_001031990.1
    • chloride channel A (CLC-A); CONTAINS InterPro DOMAIN/s: Chloride channel, core (InterPro:IPR014743), Chloride channel, voltage gated (InterPro:IPR001807), Chloride channel ClC-plant (InterPro:IPR002251), Cystathionine beta-synthase, core (InterPro:IPR000644); BEST Arabidopsis thaliana protein match is: chloride channel B (TAIR:AT3G27170.1); Has 6603 Blast hits to 6339 proteins in 1710 species: Archae - 113; Bacteria - 4208; Metazoa - 956; Fungi - 346; Plants - 344; Viruses - 0; Other Eukaryotes - 636 (source: NCBI BLink).
    NP_198905.1
    • chloride channel A (CLC-A); CONTAINS InterPro DOMAIN/s: Chloride channel, core (InterPro:IPR014743), Chloride channel, voltage gated (InterPro:IPR001807), Chloride channel ClC-plant (InterPro:IPR002251), Cystathionine beta-synthase, core (InterPro:IPR000644); BEST Arabidopsis thaliana protein match is: chloride channel B (TAIR:AT3G27170.1); Has 1807 Blast hits to 1807 proteins in 277 species: Archae - 0; Bacteria - 0; Metazoa - 736; Fungi - 347; Plants - 385; Viruses - 0; Other Eukaryotes - 339 (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
      16381314..16385424 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001036913.2 → NP_001031990.1  chloride channel A [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_001031990.1

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A654G7B5, F4KIT3
      Conserved Domains (3) summary
      cd03685
      Location:1 → 444
      ClC_6_like; ClC-6-like chloride channel proteins. This CD includes ClC-6, ClC-7 and ClC-B, C, D in plants. Proteins in this family are ubiquitous in eukarotes and their functions are unclear. They are expressed in intracellular organelles membranes. This family ...
      cd04591
      Location:464 → 625
      CBS_pair_EriC_assoc_euk_bac; This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the EriC CIC-type chloride channels in eukaryotes and bacteria. These ion channels are proteins with a seemingly simple task of allowing the passive flow of ...
      pfam00654
      Location:12 → 399
      Voltage_CLC; Voltage gated chloride channel

    2. NM_123454.3 → NP_198905.1  chloride channel A [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_198905.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      O64990, P92941, Q93YS0
      UniProtKB/TrEMBL
      A0A178UNE2, A0A5S9Y9U9
      Conserved Domains (2) summary
      cd03685
      Location:55 → 576
      ClC_6_like; ClC-6-like chloride channel proteins. This CD includes ClC-6, ClC-7 and ClC-B, C, D in plants. Proteins in this family are ubiquitous in eukarotes and their functions are unclear. They are expressed in intracellular organelles membranes. This family ...
      cd04591
      Location:596 → 757
      CBS_pair_voltage-gated_CLC_euk_bac; Two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the voltage gated CLC (chloride channel) in eukaryotes and bacteria
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P92941.2

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