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Protein

Inositol-phosphate phosphatase

Gene

VTC4

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

Functioni

Phosphatase acting on L-galactose 1-phosphate (L-Gal 1-P), D-myoinositol 3-phosphate (D-Ins 3-P) and D-myoinositol 1-phosphate (D-Ins 1-P). Can also use beta-glycerophosphate (glycerol 2-P) and, to a lesser extent, D-galactose 1-phosphate (D-Gal 1-P), alpha-D-glucose 1-phosphate (a-D-Glc 1-P), D-manitol 1-phosphate and adenosine 2'-monophosphate as substrates. No activity with D-fructose 1-phosphate (D-Fru 1-P), fructose 1,6-bisphosphate (Fru 1,6-bisP), D-glucose 6-phosphate (D-Glc 6-P), D-alpha-glycerophosphate (glycerol 3-P), D-sorbitol 6-phosphate and D-myoinositol 2-phosphate. The C1 phosphate position in a six-member ring substrate is important for catalysis.3 Publications

Catalytic activityi

Myo-inositol phosphate + H2O = myo-inositol + phosphate.2 Publications
Beta-L-galactose 1-phosphate + H2O = L-galactose + phosphate.2 Publications

Cofactori

Mg2+1 Publication

Enzyme regulationi

Inhibited by LiCl or CaCl2. Not inhibited by ascorbate.2 Publications

Kineticsi

  1. KM=191 µM for D-myoinositol 3-phosphate1 Publication
  2. KM=107 µM for L-galactose 1-phosphate1 Publication

    pH dependencei

    Optimum pH is 7.5.1 Publication

    Pathwayi: myo-inositol biosynthesis

    This protein is involved in step 2 of the subpathway that synthesizes myo-inositol from D-glucose 6-phosphate.
    Proteins known to be involved in the 2 steps of the subpathway in this organism are:
    1. Inositol-3-phosphate synthase isozyme 1 (IPS1), Probable inositol 3-phosphate synthase isozyme 3 (IPS3), Inositol-3-phosphate synthase isozyme 2 (IPS2)
    2. Bifunctional phosphatase IMPL2, chloroplastic (HISN7), Inositol-1-monophosphatase (VTC4), Inositol-1-monophosphatase (VTC4), Inositol-phosphate phosphatase (VTC4), Inositol-1-monophosphatase (AXX17_At3g02150), Inositol-1-monophosphatase (AXX17_At1g31820), Phosphatase IMPL1, chloroplastic (IMPL1)
    This subpathway is part of the pathway myo-inositol biosynthesis, which is itself part of Polyol metabolism.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes myo-inositol from D-glucose 6-phosphate, the pathway myo-inositol biosynthesis and in Polyol metabolism.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Metal bindingi71Magnesium 1By similarity1
    Binding sitei71SubstrateBy similarity1
    Metal bindingi91Magnesium 1By similarity1
    Metal bindingi91Magnesium 2By similarity1
    Metal bindingi93Magnesium 1; via carbonyl oxygenBy similarity1
    Metal bindingi94Magnesium 2By similarity1
    Binding sitei213SubstrateBy similarity1
    Metal bindingi221Magnesium 2By similarity1
    Binding sitei221SubstrateBy similarity1

    GO - Molecular functioni

    GO - Biological processi

    • inositol biosynthetic process Source: TAIR
    • inositol phosphate dephosphorylation Source: GO_Central
    • L-ascorbic acid biosynthetic process Source: TAIR
    • phosphatidylinositol phosphorylation Source: InterPro
    • response to cold Source: TAIR
    • response to karrikin Source: TAIR
    • signal transduction Source: GO_Central

    Keywordsi

    Molecular functionHydrolase
    LigandLithium, Magnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciARA:AT3G02870-MONOMER
    MetaCyc:AT3G02870-MONOMER
    BRENDAi3.1.3.25 399
    3.1.3.93 399
    3.1.3.B9 399
    ReactomeiR-ATH-1855183 Synthesis of IP2, IP, and Ins in the cytosol
    SABIO-RKiQ9M8S8
    UniPathwayiUPA00823; UER00788

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Inositol-phosphate phosphatase (EC:3.1.3.252 Publications)
    Alternative name(s):
    L-galactose 1-phosphate phosphatase (EC:3.1.3.932 Publications)
    Myo-inositol monophosphatase
    Gene namesi
    Name:VTC4
    Synonyms:IMP
    Ordered Locus Names:At3g02870
    ORF Names:F13E7.19
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    Proteomesi
    • UP000006548 Componenti: Chromosome 3

    Organism-specific databases

    AraportiAT3G02870
    TAIRilocus:2075392 AT3G02870

    Subcellular locationi

    Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Chloroplast Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertion Graphics by Christian Stolte; Source: COMPARTMENTS

    Pathology & Biotechi

    Disruption phenotypei

    No visible phenotype, but reduced myoinositol and ascorbate levels.3 Publications

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi92P → L in vtc4-1; low levels of ascorbate. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Initiator methionineiRemovedCombined sources
    ChainiPRO_00003836792 – 271Inositol-phosphate phosphataseAdd BLAST270

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Modified residuei2N-acetylalanineCombined sources1

    Keywords - PTMi

    Acetylation

    Proteomic databases

    PaxDbiQ9M8S8
    PRIDEiQ9M8S8

    PTM databases

    iPTMnetiQ9M8S8

    Expressioni

    Tissue specificityi

    Strongly expressed in photosynthetic tissues. Expressed in pistil and seed endosperm.1 Publication

    Developmental stagei

    Detected in globular to heart stage embryos.1 Publication

    Gene expression databases

    ExpressionAtlasiQ9M8S8 baseline and differential
    GenevisibleiQ9M8S8 AT

    Interactioni

    Protein-protein interaction databases

    STRINGi3702.AT3G02870.1

    Structurei

    3D structure databases

    ProteinModelPortaliQ9M8S8
    SMRiQ9M8S8
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni93 – 96Substrate bindingBy similarity4
    Regioni194 – 196Substrate bindingBy similarity3

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiKOG2951 Eukaryota
    COG0483 LUCA
    HOGENOMiHOG000282238
    InParanoidiQ9M8S8
    KOiK10047
    OMAiNNYAEFC
    OrthoDBiEOG09360J4S
    PhylomeDBiQ9M8S8

    Family and domain databases

    CDDicd01639 IMPase, 1 hit
    InterProiView protein in InterPro
    IPR033942 IMPase
    IPR020583 Inositol_monoP_metal-BS
    IPR020552 Inositol_monoPase_Li-sen
    IPR000760 Inositol_monophosphatase-like
    IPR020550 Inositol_monophosphatase_CS
    PfamiView protein in Pfam
    PF00459 Inositol_P, 1 hit
    PRINTSiPR00377 IMPHPHTASES
    PR00378 LIIMPHPHTASE
    PROSITEiView protein in PROSITE
    PS00629 IMP_1, 1 hit
    PS00630 IMP_2, 1 hit

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    This entry describes 1 isoform i produced by alternative splicing. AlignAdd to basket

    Note: A number of isoforms are produced. According to EST sequences.
    Isoform 1 (identifier: Q9M8S8-1) [UniParc]FASTAAdd to basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

            10         20         30         40         50
    MADNDSLDQF LAAAIDAAKK AGQIIRKGFY ETKHVEHKGQ VDLVTETDKG
    60 70 80 90 100
    CEELVFNHLK QLFPNHKFIG EETTAAFGVT ELTDEPTWIV DPLDGTTNFV
    110 120 130 140 150
    HGFPFVCVSI GLTIGKVPVV GVVYNPIMEE LFTGVQGKGA FLNGKRIKVS
    160 170 180 190 200
    AQSELLTALL VTEAGTKRDK ATLDDTTNRI NSLLTKVRSL RMSGSCALDL
    210 220 230 240 250
    CGVACGRVDI FYELGFGGPW DIAAGIVIVK EAGGLIFDPS GKDLDITSQR
    260 270
    IAASNASLKE LFAEALRLTG A
    Length:271
    Mass (Da):29,121
    Last modified:October 1, 2000 - v1
    Checksum:i278584BF541B8F5F
    GO

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti5D → H in AAM62772 (Ref. 3) Curated1
    Sequence conflicti39G → S in AAM62772 (Ref. 3) Curated1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AC018363 Genomic DNA Translation: AAF26973.1
    CP002686 Genomic DNA Translation: AEE73869.1
    AY085548 mRNA Translation: AAM62772.1
    AY035150 mRNA Translation: AAK59654.1
    AY063021 mRNA Translation: AAL34195.1
    RefSeqiNP_186936.1, NM_111155.3 [Q9M8S8-1]
    UniGeneiAt.21164

    Genome annotation databases

    EnsemblPlantsiAT3G02870.1; AT3G02870.1; AT3G02870 [Q9M8S8-1]
    GeneIDi821206
    GrameneiAT3G02870.1; AT3G02870.1; AT3G02870 [Q9M8S8-1]
    KEGGiath:AT3G02870

    Keywords - Coding sequence diversityi

    Alternative splicing

    Similar proteinsi

    Entry informationi

    Entry nameiVTC4_ARATH
    AccessioniPrimary (citable) accession number: Q9M8S8
    Secondary accession number(s): Q8LE95
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: September 22, 2009
    Last sequence update: October 1, 2000
    Last modified: May 23, 2018
    This is version 115 of the entry and version 1 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

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