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

Gene ID: 834090, updated on 7-Sep-2023

Summary

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Gene symbol
CLC-A
Gene description
chloride channel A
Primary source
Araport:AT5G40890
Locus tag
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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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. 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
  2. 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
  3. 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
  4. 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
  5. Residues important for nitrate/proton coupling in plant and mammalian CLC transporters. Bergsdorf EY, et al. J Biol Chem, 2009 Apr 24. PMID 19261613, Free PMC Article

See all (14) 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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