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Protein

Phosphoserine phosphatase, chloroplastic

Gene

PSP

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

Functioni

Catalyzes the last step in the plastidial phosphorylated pathway of serine biosynthesis (PPSB). The reaction mechanism proceeds via the formation of a phosphoryl-enzyme intermediates. Required for embryo, pollen and root development. May be required preferentially for serine biosynthesis in non-photosynthetic tissues.2 Publications

Catalytic activityi

O-phospho-L(or D)-serine + H2O = L(or D)-serine + phosphate.

Cofactori

Mg2+By similarityNote: Binds 1 Mg2+ ion per subunit.By similarity

Kineticsi

Approximately 60% inhibition of PSP activity by 10 mM serine was observed.

  1. KM=3.5 mM for 3-phosphoserine (at 30 degrees Celsius and pH 7.5)1 Publication

    Pathwayi: L-serine biosynthesis

    This protein is involved in step 3 of the subpathway that synthesizes L-serine from 3-phospho-D-glycerate.
    Proteins known to be involved in the 3 steps of the subpathway in this organism are:
    1. D-3-phosphoglycerate dehydrogenase 2, chloroplastic (PGDH2), D-3-phosphoglycerate dehydrogenase 1, chloroplastic (PGDH1), D-3-phosphoglycerate dehydrogenase 3, chloroplastic (PGDH3)
    2. Phosphoserine aminotransferase 1, chloroplastic (PSAT1), Phosphoserine aminotransferase 2, chloroplastic (PSAT2)
    3. Phosphoserine phosphatase, chloroplastic (PSP)
    This subpathway is part of the pathway L-serine biosynthesis, which is itself part of Amino-acid biosynthesis.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes L-serine from 3-phospho-D-glycerate, the pathway L-serine biosynthesis and in Amino-acid biosynthesis.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei89 – 891NucleophileBy similarity
    Metal bindingi89 – 891MagnesiumBy similarity
    Active sitei91 – 911Proton donorBy similarity
    Metal bindingi91 – 911Magnesium; via carbonyl oxygenBy similarity
    Binding sitei98 – 981SubstrateBy similarity
    Binding sitei134 – 1341SubstrateBy similarity
    Binding sitei227 – 2271SubstrateBy similarity
    Metal bindingi248 – 2481MagnesiumBy similarity

    GO - Molecular functioni

    • calcium ion binding Source: UniProtKB
    • magnesium ion binding Source: UniProtKB
    • phosphoserine phosphatase activity Source: TAIR

    GO - Biological processi

    • dephosphorylation Source: GOC
    • embryo development ending in seed dormancy Source: TAIR
    • L-serine biosynthetic process Source: TAIR
    • L-serine metabolic process Source: UniProtKB
    • pollen development Source: TAIR
    • root development Source: TAIR
    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Amino-acid biosynthesis, Serine biosynthesis

    Keywords - Ligandi

    Magnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciARA:AT1G18640-MONOMER.
    MetaCyc:AT1G18640-MONOMER.
    BRENDAi3.1.3.3. 399.
    ReactomeiR-ATH-977347. Serine biosynthesis.
    UniPathwayiUPA00135; UER00198.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Phosphoserine phosphatase, chloroplastic (EC:3.1.3.3)
    Short name:
    PSP
    Short name:
    PSPase
    Alternative name(s):
    O-phosphoserine phosphohydrolase
    Gene namesi
    Name:PSP
    Synonyms:PSP1
    Ordered Locus Names:At1g18640
    ORF Names:F26I16.2
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    Proteomesi
    • UP000006548 Componenti: Chromosome 1

    Organism-specific databases

    TAIRiAT1G18640.

    Subcellular locationi

    GO - Cellular componenti

    • chloroplast Source: TAIR
    Complete GO annotation...

    Keywords - Cellular componenti

    Chloroplast, Plastid

    Pathology & Biotechi

    Disruption phenotypei

    Embryo lethal when homozygous.2 Publications

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transit peptidei1 – 6262ChloroplastSequence analysisAdd
    BLAST
    Chaini63 – 295233Phosphoserine phosphatase, chloroplasticPRO_0000032375Add
    BLAST

    Proteomic databases

    PaxDbiO82796.
    PRIDEiO82796.

    Expressioni

    Tissue specificityi

    Ubiquitous. Mainly expressed in shoot and root meristems, vasculature, pollen, anthers, carpels and seeds.1 Publication

    Inductioni

    Up-regulated in aerial parts by 8 hours exposure to darkness, whereas longer exposure down-regulate expression in both roots and aerial parts.1 Publication

    Gene expression databases

    GenevisibleiO82796. AT.

    Interactioni

    Protein-protein interaction databases

    BioGridi23684. 1 interaction.
    IntActiO82796. 1 interaction.
    STRINGi3702.AT1G18640.2.

    Structurei

    3D structure databases

    ProteinModelPortaliO82796.
    SMRiO82796. Positions 42-295.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni178 – 1792Substrate bindingBy similarity

    Sequence similaritiesi

    Belongs to the SerB family.Curated

    Keywords - Domaini

    Transit peptide

    Phylogenomic databases

    eggNOGiKOG1615. Eukaryota.
    COG0560. LUCA.
    HOGENOMiHOG000231116.
    InParanoidiO82796.
    KOiK01079.
    OMAiGHEGNIV.
    PhylomeDBiO82796.

    Family and domain databases

    Gene3Di1.10.150.210. 1 hit.
    3.40.50.1000. 2 hits.
    InterProiIPR023214. HAD-like_dom.
    IPR006383. HAD-SF_hydro_IB_PSP-like.
    IPR023190. Pser_Pase_dom_2.
    [Graphical view]
    SUPFAMiSSF56784. SSF56784. 1 hit.
    TIGRFAMsiTIGR01488. HAD-SF-IB. 1 hit.

    Sequencei

    Sequence statusi: Complete.

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

    O82796-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MEALTTSRVV PVQVPCRKLS SLFANFSCLE LRRYPCRGLV SIMNHPKLLR
    60 70 80 90 100
    PVTASVQPHE LSTLGHEGNI VPSKEILDLW RSVEAVCFDV DSTVCVDEGI
    110 120 130 140 150
    DELAEFCGAG KAVAEWTARA MGGSVPFEEA LAARLSLFKP SLSKVEEYLD
    160 170 180 190 200
    KRPPRLSPGI EELVKKLRAN NIDVYLISGG FRQMINPVAS ILGIPRENIF
    210 220 230 240 250
    ANNLLFGNSG EFLGFDENEP TSRSGGKAKA VQQIRKGRLY KTMAMIGDGA
    260 270 280 290
    TDLEARKPGG ADLFICYAGV QLREAVAANA DWLIFKFESL INSLD
    Length:295
    Mass (Da):32,318
    Last modified:April 26, 2005 - v2
    Checksum:iF14C95E636F7745E
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti266 – 2661C → S in BAA33806 (PubMed:10196182).Curated
    Sequence conflicti266 – 2661C → S in BAA33807 (PubMed:10196182).Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB018408 mRNA. Translation: BAA33806.1.
    AB018409 Genomic DNA. Translation: BAA33807.1.
    AC026238 Genomic DNA. Translation: AAF98410.1.
    CP002684 Genomic DNA. Translation: AEE29738.1.
    AY065351 mRNA. Translation: AAL38792.1.
    AY096687 mRNA. Translation: AAM20321.1.
    AY087385 mRNA. Translation: AAM64935.1.
    PIRiB86320.
    T51362.
    RefSeqiNP_973858.1. NM_202129.2.
    UniGeneiAt.356.
    At.41785.

    Genome annotation databases

    EnsemblPlantsiAT1G18640.2; AT1G18640.2; AT1G18640.
    GeneIDi838445.
    GrameneiAT1G18640.2; AT1G18640.2; AT1G18640.
    KEGGiath:AT1G18640.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AB018408 mRNA. Translation: BAA33806.1.
    AB018409 Genomic DNA. Translation: BAA33807.1.
    AC026238 Genomic DNA. Translation: AAF98410.1.
    CP002684 Genomic DNA. Translation: AEE29738.1.
    AY065351 mRNA. Translation: AAL38792.1.
    AY096687 mRNA. Translation: AAM20321.1.
    AY087385 mRNA. Translation: AAM64935.1.
    PIRiB86320.
    T51362.
    RefSeqiNP_973858.1. NM_202129.2.
    UniGeneiAt.356.
    At.41785.

    3D structure databases

    ProteinModelPortaliO82796.
    SMRiO82796. Positions 42-295.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi23684. 1 interaction.
    IntActiO82796. 1 interaction.
    STRINGi3702.AT1G18640.2.

    Proteomic databases

    PaxDbiO82796.
    PRIDEiO82796.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblPlantsiAT1G18640.2; AT1G18640.2; AT1G18640.
    GeneIDi838445.
    GrameneiAT1G18640.2; AT1G18640.2; AT1G18640.
    KEGGiath:AT1G18640.

    Organism-specific databases

    TAIRiAT1G18640.

    Phylogenomic databases

    eggNOGiKOG1615. Eukaryota.
    COG0560. LUCA.
    HOGENOMiHOG000231116.
    InParanoidiO82796.
    KOiK01079.
    OMAiGHEGNIV.
    PhylomeDBiO82796.

    Enzyme and pathway databases

    UniPathwayiUPA00135; UER00198.
    BioCyciARA:AT1G18640-MONOMER.
    MetaCyc:AT1G18640-MONOMER.
    BRENDAi3.1.3.3. 399.
    ReactomeiR-ATH-977347. Serine biosynthesis.

    Miscellaneous databases

    PROiO82796.

    Gene expression databases

    GenevisibleiO82796. AT.

    Family and domain databases

    Gene3Di1.10.150.210. 1 hit.
    3.40.50.1000. 2 hits.
    InterProiIPR023214. HAD-like_dom.
    IPR006383. HAD-SF_hydro_IB_PSP-like.
    IPR023190. Pser_Pase_dom_2.
    [Graphical view]
    SUPFAMiSSF56784. SSF56784. 1 hit.
    TIGRFAMsiTIGR01488. HAD-SF-IB. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Plastidic pathway of serine biosynthesis. Molecular cloning and expression of 3-phosphoserine phosphatase from Arabidopsis thaliana."
      Ho C.-L., Noji M., Saito K.
      J. Biol. Chem. 274:11007-11012(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA], FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, SUBCELLULAR LOCATION.
    2. "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana."
      Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K.
      , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W.
      Nature 408:816-820(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Columbia.
    3. The Arabidopsis Information Resource (TAIR)
      Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
      Cited for: GENOME REANNOTATION.
      Strain: cv. Columbia.
    4. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
      Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
      , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
      Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: cv. Columbia.
    5. "Full-length cDNA from Arabidopsis thaliana."
      Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B., Feldmann K.A.
      Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    6. "The phosphorylated pathway of serine biosynthesis is essential both for male gametophyte and embryo development and for root growth in Arabidopsis."
      Cascales-Minana B., Munoz-Bertomeu J., Flores-Tornero M., Anoman A.D., Pertusa J., Alaiz M., Osorio S., Fernie A.R., Segura J., Ros R.
      Plant Cell 25:2084-2101(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, TISSUE SPECIFICITY, INDUCTION, SUBCELLULAR LOCATION, DISRUPTION PHENOTYPE.
      Strain: cv. Columbia.
    7. "Arabidopsis phosphoglycerate dehydrogenase1 of the phosphoserine pathway is essential for development and required for ammonium assimilation and tryptophan biosynthesis."
      Benstein R.M., Ludewig K., Wulfert S., Wittek S., Gigolashvili T., Frerigmann H., Gierth M., Fluegge U.I., Krueger S.
      Plant Cell 25:5011-5029(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: DISRUPTION PHENOTYPE.
      Strain: cv. Columbia.

    Entry informationi

    Entry nameiSERC_ARATH
    AccessioniPrimary (citable) accession number: O82796
    Secondary accession number(s): Q9FZ85
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 26, 2005
    Last sequence update: April 26, 2005
    Last modified: February 17, 2016
    This is version 115 of the entry and version 2 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.