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Protein

Inositol-phosphate phosphatase

Gene

VTC4

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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-phosphate phosphatase (VTC4), 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
    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Ligandi

    Lithium, Magnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciMetaCyc: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-RKQ9M8S8.
    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

    TAIRiAT3G02870.

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: TAIR
    • plasma membrane Source: TAIR
    Complete GO annotation...

    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.

    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

    Belongs to the inositol monophosphatase family.Curated

    Phylogenomic databases

    eggNOGiKOG2951. Eukaryota.
    COG0483. LUCA.
    HOGENOMiHOG000282238.
    InParanoidiQ9M8S8.
    KOiK10047.
    OMAiGDPWKEC.
    OrthoDBiEOG09360J4S.
    PhylomeDBiQ9M8S8.

    Family and domain databases

    CDDicd01639. IMPase. 1 hit.
    InterProiIPR033942. IMPase.
    IPR020583. Inositol_monoP_metal-BS.
    IPR020552. Inositol_monoPase_Li-sen.
    IPR000760. Inositol_monophosphatase-like.
    IPR020550. Inositol_monophosphatase_CS.
    [Graphical view]
    PANTHERiPTHR20854. PTHR20854. 1 hit.
    PfamiPF00459. Inositol_P. 1 hit.
    [Graphical view]
    PRINTSiPR00377. IMPHPHTASES.
    PR00378. LIIMPHPHTASE.
    PROSITEiPS00629. IMP_1. 1 hit.
    PS00630. IMP_2. 1 hit.
    [Graphical view]

    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.
    KEGGiath:AT3G02870.

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    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.

    3D structure databases

    ProteinModelPortaliQ9M8S8.
    SMRiQ9M8S8.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi3702.AT3G02870.1.

    Proteomic databases

    PaxDbiQ9M8S8.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

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

    Organism-specific databases

    TAIRiAT3G02870.

    Phylogenomic databases

    eggNOGiKOG2951. Eukaryota.
    COG0483. LUCA.
    HOGENOMiHOG000282238.
    InParanoidiQ9M8S8.
    KOiK10047.
    OMAiGDPWKEC.
    OrthoDBiEOG09360J4S.
    PhylomeDBiQ9M8S8.

    Enzyme and pathway databases

    UniPathwayiUPA00823; UER00788.
    BioCyciMetaCyc: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-RKQ9M8S8.

    Miscellaneous databases

    PROiQ9M8S8.

    Gene expression databases

    ExpressionAtlasiQ9M8S8. baseline and differential.
    GenevisibleiQ9M8S8. AT.

    Family and domain databases

    CDDicd01639. IMPase. 1 hit.
    InterProiIPR033942. IMPase.
    IPR020583. Inositol_monoP_metal-BS.
    IPR020552. Inositol_monoPase_Li-sen.
    IPR000760. Inositol_monophosphatase-like.
    IPR020550. Inositol_monophosphatase_CS.
    [Graphical view]
    PANTHERiPTHR20854. PTHR20854. 1 hit.
    PfamiPF00459. Inositol_P. 1 hit.
    [Graphical view]
    PRINTSiPR00377. IMPHPHTASES.
    PR00378. LIIMPHPHTASE.
    PROSITEiPS00629. IMP_1. 1 hit.
    PS00630. IMP_2. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiVTC4_ARATH
    AccessioniPrimary (citable) accession number: Q9M8S8
    Secondary accession number(s): Q8LE95
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: September 22, 2009
    Last sequence update: October 1, 2000
    Last modified: November 30, 2016
    This is version 102 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Arabidopsis thaliana
      Arabidopsis thaliana: entries and gene names
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    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.