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Protein

Protein NRT1/ PTR FAMILY 6.3

Gene

NPF6.3

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Dual affinity nitrate transporter. Involved in proton-dependent nitrate uptake and in the regulation of the nitrate transporter NRT2.1. Acts also as a nitrate sensor that trigger a specific signaling pathway stimulating lateral root growth and seed germination. The uptake activity is not required for sensor function. Displays an auxin transport facilitation inhibited by high nitrate concentration. Required to prevent auxin accumulation in preemerged lateral root primordia and young lateral roots when external nitrate concentration is low or null. May be involved in the basipetal transport of auxin out of the lateral root tips. Acts as a bidirectional transporter involved in root-to-shoot nitrate translocation. Recognizes specifically nitrate and chlorate, but not nitrite, alanine, sulfate, phosphate or the di-peptide Ala-Ala.11 Publications

Kineticsi

  1. KM=49 µM for nitrate (for the high-affinity phase, in the presence of 250 µM nitrate at pH 5.5)1 Publication
  2. KM=4 mM for nitrate (for the low-affinity phase, in the presence of 10 mM nitrate at pH 5.5)1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei356Substrate1
    Binding sitei360Substrate1

    GO - Molecular functioni

    • nitrate transmembrane transporter activity Source: TAIR
    • symporter activity Source: UniProtKB-KW

    GO - Biological processi

    • auxin-activated signaling pathway Source: UniProtKB-KW
    • nitrate assimilation Source: UniProtKB-KW
    • nitrate transport Source: TAIR
    • oligopeptide transport Source: InterPro
    • response to herbicide Source: UniProtKB-KW
    • response to nitrate Source: TAIR
    • response to water deprivation Source: TAIR
    Complete GO annotation...

    Keywords - Biological processi

    Auxin signaling pathway, Herbicide resistance, Nitrate assimilation, Symport, Transport

    Protein family/group databases

    TCDBi2.A.17.3.1. the proton-dependent oligopeptide transporter (pot/ptr) family.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Protein NRT1/ PTR FAMILY 6.3
    Short name:
    AtNPF6.3
    Alternative name(s):
    Nitrate transporter 1.1
    Short name:
    AtNRT1
    Nitrate/chlorate transporter
    Protein CHLORINA 1
    Gene namesi
    Name:NPF6.3
    Synonyms:CHL1, NRT1, NRT1.1
    Ordered Locus Names:At1g12110
    ORF Names:F12F1.1, T28K15_13
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    Proteomesi
    • UP000006548 Componenti: Chromosome 1

    Organism-specific databases

    TAIRiAT1G12110.

    Subcellular locationi

    Topology

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Transmembranei46 – 66HelicalSequence analysisAdd BLAST21
    Transmembranei77 – 97HelicalSequence analysisAdd BLAST21
    Transmembranei102 – 122HelicalSequence analysisAdd BLAST21
    Transmembranei143 – 163HelicalSequence analysisAdd BLAST21
    Transmembranei193 – 213HelicalSequence analysisAdd BLAST21
    Transmembranei219 – 239HelicalSequence analysisAdd BLAST21
    Transmembranei342 – 362HelicalSequence analysisAdd BLAST21
    Transmembranei374 – 394HelicalSequence analysisAdd BLAST21
    Transmembranei423 – 443HelicalSequence analysisAdd BLAST21
    Transmembranei460 – 480HelicalSequence analysisAdd BLAST21
    Transmembranei501 – 521HelicalSequence analysisAdd BLAST21
    Transmembranei542 – 562HelicalSequence analysisAdd BLAST21

    GO - Cellular componenti

    • integral component of membrane Source: UniProtKB-KW
    • plasma membrane Source: TAIR
    Complete GO annotation...

    Keywords - Cellular componenti

    Membrane

    Pathology & Biotechi

    Disruption phenotypei

    Altered development of nascent organs. Reduced stomatal opening and reduced transpiration rates in the light resulting in enhanced drought tolerance. Slower translocation of nitrate to the leaves.3 Publications

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi28T → A: No effect on phosphorylation and on nitrate transport. 1 Publication1
    Mutagenesisi41E → A: Loss of the transporter activity. 1 Publication1
    Mutagenesisi44E → A: Loss of the transporter activity. 1 Publication1
    Mutagenesisi45R → A: Loss of the transporter activity. 2 Publications1
    Mutagenesisi101T → A: Loss of phosphorylation and 91% reduction of high-affinity nitrate transport, but no effect on the nitrate binding. 2 Publications1
    Mutagenesisi101T → D: Loss of low-affinity nitrate transport. 2 Publications1
    Mutagenesisi130C → A: 90% reduction of the transporter activity. 1 Publication1
    Mutagenesisi164K → A: 90% reduction of the transporter activity. 2 Publications1
    Mutagenesisi356H → A: Loss of the transporter activity. 2 Publications1
    Mutagenesisi476E → A: 80% reduction of the transporter activity. 1 Publication1
    Mutagenesisi492P → L in chl1-9; loss of high- and low-affinity nitrate transport, but no effect on nitrate sensing. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00000643161 – 590Protein NRT1/ PTR FAMILY 6.3Add BLAST590

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei101Phosphothreonine; by CIPK231 Publication1

    Post-translational modificationi

    Acts as a high-affinity nitrate transporter when phosphorylated and as a low-affinity transporter when dephosphorylated. Forms homodimer when unphosphorylated and monomer when phosphorylated. Low nitrogen concentration in the medium stimulates phosphorylation. Phosphorylation also regulates the nitrate signaling.2 Publications

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    PaxDbiQ05085.
    PRIDEiQ05085.

    PTM databases

    iPTMnetiQ05085.

    Expressioni

    Tissue specificityi

    Expressed in the stele in lateral root primordia before emergence and in the tip of primary and emerged lateral roots. Detected in emerging and immature leaves, guard cells, flower buds, style, stigma, anthers and pollen grains. Not detected in the shoot apical meristem.4 Publications

    Developmental stagei

    Expressed in the columella root cap at day 1 after germination. At day 3, detected in the root meristematic region and at day 5, expressed throughout the root tip.1 Publication

    Inductioni

    By nitrate and auxin.4 Publications

    Gene expression databases

    GenevisibleiQ05085. AT.

    Interactioni

    Subunit structurei

    Monomer and homodimer. The dimer has the 2 monomers in the same orientation. Interacts with CIPK23.3 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    CIPK23Q93VD33EBI-2463703,EBI-974277

    Protein-protein interaction databases

    BioGridi23003. 21 interactors.
    IntActiQ05085. 1 interactor.
    STRINGi3702.AT1G12110.1.

    Structurei

    Secondary structure

    1590
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi18 – 20Combined sources3
    Beta strandi25 – 29Combined sources5
    Helixi33 – 37Combined sources5
    Helixi39 – 53Combined sources15
    Helixi56 – 61Combined sources6
    Helixi67 – 94Combined sources28
    Helixi98 – 121Combined sources24
    Turni132 – 134Combined sources3
    Helixi143 – 171Combined sources29
    Helixi172 – 174Combined sources3
    Helixi182 – 184Combined sources3
    Helixi185 – 204Combined sources20
    Helixi207 – 214Combined sources8
    Helixi217 – 236Combined sources20
    Helixi237 – 241Combined sources5
    Helixi251 – 261Combined sources11
    Beta strandi277 – 279Combined sources3
    Helixi330 – 340Combined sources11
    Helixi343 – 347Combined sources5
    Helixi350 – 360Combined sources11
    Helixi362 – 369Combined sources8
    Helixi381 – 385Combined sources5
    Helixi386 – 401Combined sources16
    Helixi403 – 407Combined sources5
    Turni408 – 410Combined sources3
    Beta strandi414 – 417Combined sources4
    Helixi419 – 448Combined sources30
    Helixi462 – 465Combined sources4
    Helixi466 – 490Combined sources25
    Helixi497 – 525Combined sources29
    Turni526 – 528Combined sources3
    Helixi536 – 538Combined sources3
    Helixi542 – 569Combined sources28
    Turni572 – 574Combined sources3

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    4OH3X-ray3.25A/B1-590[»]
    5A2NX-ray3.70A/B1-590[»]
    5A2OX-ray3.71A/B1-590[»]
    ProteinModelPortaliQ05085.
    SMRiQ05085.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Keywords - Domaini

    Transmembrane, Transmembrane helix

    Phylogenomic databases

    eggNOGiKOG1237. Eukaryota.
    COG3104. LUCA.
    HOGENOMiHOG000237400.
    InParanoidiQ05085.
    OMAiKMVGMLP.
    OrthoDBiEOG0936064U.
    PhylomeDBiQ05085.

    Family and domain databases

    InterProiIPR020846. MFS_dom.
    IPR000109. POT_fam.
    IPR018456. PTR2_symporter_CS.
    [Graphical view]
    PANTHERiPTHR11654. PTHR11654. 1 hit.
    PfamiPF00854. PTR2. 1 hit.
    [Graphical view]
    SUPFAMiSSF103473. SSF103473. 2 hits.
    PROSITEiPS01022. PTR2_1. 1 hit.
    PS01023. PTR2_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q05085-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSLPETKSDD ILLDAWDFQG RPADRSKTGG WASAAMILCI EAVERLTTLG
    60 70 80 90 100
    IGVNLVTYLT GTMHLGNATA ANTVTNFLGT SFMLCLLGGF IADTFLGRYL
    110 120 130 140 150
    TIAIFAAIQA TGVSILTLST IIPGLRPPRC NPTTSSHCEQ ASGIQLTVLY
    160 170 180 190 200
    LALYLTALGT GGVKASVSGF GSDQFDETEP KERSKMTYFF NRFFFCINVG
    210 220 230 240 250
    SLLAVTVLVY VQDDVGRKWG YGICAFAIVL ALSVFLAGTN RYRFKKLIGS
    260 270 280 290 300
    PMTQVAAVIV AAWRNRKLEL PADPSYLYDV DDIIAAEGSM KGKQKLPHTE
    310 320 330 340 350
    QFRSLDKAAI RDQEAGVTSN VFNKWTLSTL TDVEEVKQIV RMLPIWATCI
    360 370 380 390 400
    LFWTVHAQLT TLSVAQSETL DRSIGSFEIP PASMAVFYVG GLLLTTAVYD
    410 420 430 440 450
    RVAIRLCKKL FNYPHGLRPL QRIGLGLFFG SMAMAVAALV ELKRLRTAHA
    460 470 480 490 500
    HGPTVKTLPL GFYLLIPQYL IVGIGEALIY TGQLDFFLRE CPKGMKGMST
    510 520 530 540 550
    GLLLSTLALG FFFSSVLVTI VEKFTGKAHP WIADDLNKGR LYNFYWLVAV
    560 570 580 590
    LVALNFLIFL VFSKWYVYKE KRLAEVGIEL DDEPSIPMGH
    Length:590
    Mass (Da):64,922
    Last modified:June 1, 1994 - v1
    Checksum:i78D3E660AAF90D47
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    L10357 mRNA. Translation: AAA32770.1.
    AC002131 Genomic DNA. Translation: AAC17604.1.
    CP002684 Genomic DNA. Translation: AEE28838.1.
    BT002016 mRNA. Translation: AAN72027.1.
    BT008783 mRNA. Translation: AAP68222.1.
    AK317498 mRNA. Translation: BAH20163.1.
    PIRiA45772.
    RefSeqiNP_563899.1. NM_101083.4.
    UniGeneiAt.19624.

    Genome annotation databases

    EnsemblPlantsiAT1G12110.1; AT1G12110.1; AT1G12110.
    GeneIDi837763.
    GrameneiAT1G12110.1; AT1G12110.1; AT1G12110.
    KEGGiath:AT1G12110.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    L10357 mRNA. Translation: AAA32770.1.
    AC002131 Genomic DNA. Translation: AAC17604.1.
    CP002684 Genomic DNA. Translation: AEE28838.1.
    BT002016 mRNA. Translation: AAN72027.1.
    BT008783 mRNA. Translation: AAP68222.1.
    AK317498 mRNA. Translation: BAH20163.1.
    PIRiA45772.
    RefSeqiNP_563899.1. NM_101083.4.
    UniGeneiAt.19624.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    4OH3X-ray3.25A/B1-590[»]
    5A2NX-ray3.70A/B1-590[»]
    5A2OX-ray3.71A/B1-590[»]
    ProteinModelPortaliQ05085.
    SMRiQ05085.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi23003. 21 interactors.
    IntActiQ05085. 1 interactor.
    STRINGi3702.AT1G12110.1.

    Protein family/group databases

    TCDBi2.A.17.3.1. the proton-dependent oligopeptide transporter (pot/ptr) family.

    PTM databases

    iPTMnetiQ05085.

    Proteomic databases

    PaxDbiQ05085.
    PRIDEiQ05085.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblPlantsiAT1G12110.1; AT1G12110.1; AT1G12110.
    GeneIDi837763.
    GrameneiAT1G12110.1; AT1G12110.1; AT1G12110.
    KEGGiath:AT1G12110.

    Organism-specific databases

    TAIRiAT1G12110.

    Phylogenomic databases

    eggNOGiKOG1237. Eukaryota.
    COG3104. LUCA.
    HOGENOMiHOG000237400.
    InParanoidiQ05085.
    OMAiKMVGMLP.
    OrthoDBiEOG0936064U.
    PhylomeDBiQ05085.

    Miscellaneous databases

    PROiQ05085.

    Gene expression databases

    GenevisibleiQ05085. AT.

    Family and domain databases

    InterProiIPR020846. MFS_dom.
    IPR000109. POT_fam.
    IPR018456. PTR2_symporter_CS.
    [Graphical view]
    PANTHERiPTHR11654. PTHR11654. 1 hit.
    PfamiPF00854. PTR2. 1 hit.
    [Graphical view]
    SUPFAMiSSF103473. SSF103473. 2 hits.
    PROSITEiPS01022. PTR2_1. 1 hit.
    PS01023. PTR2_2. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiPTR7_ARATH
    AccessioniPrimary (citable) accession number: Q05085
    Secondary accession number(s): B9DHE6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 1, 1994
    Last sequence update: June 1, 1994
    Last modified: November 30, 2016
    This is version 117 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    When mutated confers resistance to the herbicide chlorate.
    The kinase CIPK23 is a negative regulator of the high-affinity response, while the kinase CIPK8 is a positive regulator of the low-affinity response. Thr-101 is not the direct target of CIPK8.

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Arabidopsis thaliana
      Arabidopsis thaliana: entries and gene names
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.