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P78330

- SERB_HUMAN

UniProt

P78330 - SERB_HUMAN

Protein

Phosphoserine phosphatase

Gene

PSPH

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 137 (01 Oct 2014)
      Sequence version 2 (26 Apr 2005)
      Previous versions | rss
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    Functioni

    Catalyzes the last step in the biosynthesis of serine from carbohydrates. The reaction mechanism proceeds via the formation of a phosphoryl-enzyme intermediates.1 Publication

    Catalytic activityi

    O-phospho-L(or D)-serine + H2O = L(or D)-serine + phosphate.3 Publications

    Cofactori

    Binds 1 magnesium ion per subunit.1 Publication

    Enzyme regulationi

    Inhibited by calcium ions.1 Publication

    Pathwayi

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei20 – 201Nucleophile
    Metal bindingi20 – 201Magnesium
    Active sitei22 – 221Proton donor
    Metal bindingi22 – 221Magnesium; via carbonyl oxygen
    Binding sitei29 – 291Substrate
    Binding sitei65 – 651Substrate
    Binding sitei158 – 1581Substrate
    Metal bindingi179 – 1791Magnesium

    GO - Molecular functioni

    1. calcium ion binding Source: UniProtKB
    2. magnesium ion binding Source: UniProtKB
    3. phosphoserine phosphatase activity Source: UniProtKB
    4. protein homodimerization activity Source: UniProtKB

    GO - Biological processi

    1. cellular amino acid biosynthetic process Source: Reactome
    2. cellular nitrogen compound metabolic process Source: Reactome
    3. dephosphorylation Source: GOC
    4. L-serine biosynthetic process Source: RefGenome
    5. L-serine metabolic process Source: UniProtKB
    6. response to mechanical stimulus Source: Ensembl
    7. response to nutrient levels Source: Ensembl
    8. response to testosterone Source: Ensembl
    9. small molecule metabolic process Source: Reactome

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Amino-acid biosynthesis, Serine biosynthesis

    Keywords - Ligandi

    Magnesium, Metal-binding

    Enzyme and pathway databases

    BioCyciMetaCyc:HS07370-MONOMER.
    ReactomeiREACT_115789. Serine biosynthesis.
    UniPathwayiUPA00135; UER00198.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Phosphoserine phosphatase (EC:3.1.3.3)
    Short name:
    PSP
    Short name:
    PSPase
    Alternative name(s):
    L-3-phosphoserine phosphatase
    O-phosphoserine phosphohydrolase
    Gene namesi
    Name:PSPH
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 7

    Organism-specific databases

    HGNCiHGNC:9577. PSPH.

    Subcellular locationi

    GO - Cellular componenti

    1. cytoplasm Source: RefGenome
    2. cytosol Source: Reactome
    3. neuron projection Source: Ensembl

    Pathology & Biotechi

    Involvement in diseasei

    Phosphoserine phosphatase deficiency (PSPHD) [MIM:614023]: A disorder that results in pre- and postnatal growth retardation, moderate psychomotor retardation and facial features suggestive of Williams syndrome.1 Publication
    Note: The disease is caused by mutations affecting the gene represented in this entry.
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti32 – 321D → N in PSPHD. 1 Publication
    Corresponds to variant rs28933976 [ dbSNP | Ensembl ].
    VAR_022378
    Natural varianti52 – 521M → T in PSPHD. 1 Publication
    VAR_022379

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi23 – 231S → A: Reduces activity by about 50%. 1 Publication
    Mutagenesisi23 – 231S → T: Reduces activity by about 80%. 1 Publication
    Mutagenesisi29 – 291E → D: Reduces activity by about 95%. 1 Publication
    Mutagenesisi29 – 291E → Q: Loss of activity. 1 Publication
    Mutagenesisi65 – 651R → A or K: Loss of activity. 1 Publication
    Mutagenesisi133 – 1331N → A: Reduces activity by about 75%. 1 Publication
    Mutagenesisi182 – 1821T → S: Reduces activity by about 99%. 1 Publication
    Mutagenesisi182 – 1821T → V: Reduces activity by about 25%. 1 Publication
    Mutagenesisi202 – 2021R → A: Reduces activity by about 99%. 1 Publication
    Mutagenesisi202 – 2021R → K: Reduces activity by about 95%. 1 Publication

    Keywords - Diseasei

    Disease mutation

    Organism-specific databases

    MIMi614023. phenotype.
    Orphaneti79350. 3-phosphoserine phosphatase deficiency.
    PharmGKBiPA33928.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 225225Phosphoserine phosphatasePRO_0000156879Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei1 – 11N-acetylmethionine1 Publication

    Keywords - PTMi

    Acetylation, Phosphoprotein

    Proteomic databases

    MaxQBiP78330.
    PaxDbiP78330.
    PeptideAtlasiP78330.
    PRIDEiP78330.

    PTM databases

    PhosphoSiteiP78330.

    Expressioni

    Gene expression databases

    ArrayExpressiP78330.
    BgeeiP78330.
    CleanExiHS_PSPH.
    GenevestigatoriP78330.

    Organism-specific databases

    HPAiHPA020376.
    HPA029515.

    Interactioni

    Subunit structurei

    Homodimer.3 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    ASF1BQ9NVP21EBI-1042956,EBI-1055650
    PRPSAP1Q145581EBI-1042956,EBI-724449
    STYXL1Q9Y6J81EBI-1042956,EBI-1044511

    Protein-protein interaction databases

    BioGridi111695. 6 interactions.
    IntActiP78330. 1 interaction.
    STRINGi9606.ENSP00000275605.

    Structurei

    Secondary structure

    1
    225
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi6 – 138
    Beta strandi15 – 206
    Turni23 – 253
    Beta strandi26 – 283
    Helixi30 – 378
    Turni41 – 433
    Turni45 – 473
    Turni49 – 524
    Helixi58 – 6912
    Helixi73 – 8210
    Helixi91 – 10010
    Beta strandi104 – 1129
    Helixi113 – 12210
    Helixi127 – 1293
    Beta strandi130 – 1334
    Beta strandi135 – 1373
    Beta strandi143 – 1464
    Beta strandi148 – 1503
    Helixi151 – 1533
    Helixi157 – 16913
    Beta strandi174 – 1807
    Helixi181 – 1844
    Turni185 – 1895
    Beta strandi190 – 1967
    Helixi203 – 2086
    Beta strandi210 – 2145
    Helixi216 – 2194
    Helixi221 – 2244

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1L8LX-ray2.51A/B1-225[»]
    1L8OX-ray2.80A/B1-225[»]
    1NNLX-ray1.53A/B1-225[»]
    ProteinModelPortaliP78330.
    SMRiP78330. Positions 4-225.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP78330.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni109 – 1102Substrate binding

    Sequence similaritiesi

    Belongs to the SerB family.Curated

    Phylogenomic databases

    eggNOGiCOG0560.
    HOGENOMiHOG000231116.
    HOVERGENiHBG057486.
    InParanoidiP78330.
    KOiK01079.
    OMAiYAGFDES.
    OrthoDBiEOG7CRTQD.
    PhylomeDBiP78330.
    TreeFamiTF315024.

    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.
    IPR004469. SerB.
    [Graphical view]
    PfamiPF00702. Hydrolase. 1 hit.
    [Graphical view]
    SUPFAMiSSF56784. SSF56784. 1 hit.
    TIGRFAMsiTIGR01488. HAD-SF-IB. 1 hit.
    TIGR00338. serB. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P78330-1 [UniParc]FASTAAdd to Basket

    « Hide

    MVSHSELRKL FYSADAVCFD VDSTVIREEG IDELAKICGV EDAVSEMTRR    50
    AMGGAVPFKA ALTERLALIQ PSREQVQRLI AEQPPHLTPG IRELVSRLQE 100
    RNVQVFLISG GFRSIVEHVA SKLNIPATNV FANRLKFYFN GEYAGFDETQ 150
    PTAESGGKGK VIKLLKEKFH FKKIIMIGDG ATDMEACPPA DAFIGFGGNV 200
    IRQQVKDNAK WYITDFVELL GELEE 225
    Length:225
    Mass (Da):25,008
    Last modified:April 26, 2005 - v2
    Checksum:iBD5D72697747FA30
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti2 – 21V → I in CAA71318. (PubMed:9188776)Curated

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti32 – 321D → N in PSPHD. 1 Publication
    Corresponds to variant rs28933976 [ dbSNP | Ensembl ].
    VAR_022378
    Natural varianti52 – 521M → T in PSPHD. 1 Publication
    VAR_022379

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Y10275 mRNA. Translation: CAA71318.1.
    AK315235 mRNA. Translation: BAG37662.1.
    BX537439 mRNA. Translation: CAD97681.1.
    CH471140 Genomic DNA. Translation: EAX07968.1.
    BC063614 mRNA. Translation: AAH63614.1.
    CCDSiCCDS5522.1.
    RefSeqiNP_004568.2. NM_004577.3.
    XP_005271830.1. XM_005271773.1.
    XP_005271831.1. XM_005271774.1.
    XP_005271832.1. XM_005271775.1.
    XP_005271833.1. XM_005271776.1.
    XP_005271834.1. XM_005271777.2.
    XP_006715823.1. XM_006715760.1.
    UniGeneiHs.512656.

    Genome annotation databases

    EnsembliENST00000275605; ENSP00000275605; ENSG00000146733.
    ENST00000395471; ENSP00000378854; ENSG00000146733.
    ENST00000437355; ENSP00000401639; ENSG00000146733.
    GeneIDi5723.
    KEGGihsa:5723.
    UCSCiuc003trh.3. human.

    Polymorphism databases

    DMDMi62906870.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Y10275 mRNA. Translation: CAA71318.1 .
    AK315235 mRNA. Translation: BAG37662.1 .
    BX537439 mRNA. Translation: CAD97681.1 .
    CH471140 Genomic DNA. Translation: EAX07968.1 .
    BC063614 mRNA. Translation: AAH63614.1 .
    CCDSi CCDS5522.1.
    RefSeqi NP_004568.2. NM_004577.3.
    XP_005271830.1. XM_005271773.1.
    XP_005271831.1. XM_005271774.1.
    XP_005271832.1. XM_005271775.1.
    XP_005271833.1. XM_005271776.1.
    XP_005271834.1. XM_005271777.2.
    XP_006715823.1. XM_006715760.1.
    UniGenei Hs.512656.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1L8L X-ray 2.51 A/B 1-225 [» ]
    1L8O X-ray 2.80 A/B 1-225 [» ]
    1NNL X-ray 1.53 A/B 1-225 [» ]
    ProteinModelPortali P78330.
    SMRi P78330. Positions 4-225.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 111695. 6 interactions.
    IntActi P78330. 1 interaction.
    STRINGi 9606.ENSP00000275605.

    PTM databases

    PhosphoSitei P78330.

    Polymorphism databases

    DMDMi 62906870.

    Proteomic databases

    MaxQBi P78330.
    PaxDbi P78330.
    PeptideAtlasi P78330.
    PRIDEi P78330.

    Protocols and materials databases

    DNASUi 5723.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000275605 ; ENSP00000275605 ; ENSG00000146733 .
    ENST00000395471 ; ENSP00000378854 ; ENSG00000146733 .
    ENST00000437355 ; ENSP00000401639 ; ENSG00000146733 .
    GeneIDi 5723.
    KEGGi hsa:5723.
    UCSCi uc003trh.3. human.

    Organism-specific databases

    CTDi 5723.
    GeneCardsi GC07M056046.
    HGNCi HGNC:9577. PSPH.
    HPAi HPA020376.
    HPA029515.
    MIMi 172480. gene.
    614023. phenotype.
    neXtProti NX_P78330.
    Orphaneti 79350. 3-phosphoserine phosphatase deficiency.
    PharmGKBi PA33928.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi COG0560.
    HOGENOMi HOG000231116.
    HOVERGENi HBG057486.
    InParanoidi P78330.
    KOi K01079.
    OMAi YAGFDES.
    OrthoDBi EOG7CRTQD.
    PhylomeDBi P78330.
    TreeFami TF315024.

    Enzyme and pathway databases

    UniPathwayi UPA00135 ; UER00198 .
    BioCyci MetaCyc:HS07370-MONOMER.
    Reactomei REACT_115789. Serine biosynthesis.

    Miscellaneous databases

    ChiTaRSi PSPH. human.
    EvolutionaryTracei P78330.
    GeneWikii PSPH.
    GenomeRNAii 5723.
    NextBioi 22244.
    PROi P78330.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi P78330.
    Bgeei P78330.
    CleanExi HS_PSPH.
    Genevestigatori P78330.

    Family and domain databases

    Gene3Di 1.10.150.210. 1 hit.
    3.40.50.1000. 2 hits.
    InterProi IPR023214. HAD-like_dom.
    IPR006383. HAD-SF_hydro_IB_PSP-like.
    IPR023190. Pser_Pase_dom_2.
    IPR004469. SerB.
    [Graphical view ]
    Pfami PF00702. Hydrolase. 1 hit.
    [Graphical view ]
    SUPFAMi SSF56784. SSF56784. 1 hit.
    TIGRFAMsi TIGR01488. HAD-SF-IB. 1 hit.
    TIGR00338. serB. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Human L-3-phosphoserine phosphatase: sequence, expression and evidence for a phosphoenzyme intermediate."
      Collet J.-F., Gerin I., Rider M.H., Veiga-Da-Cunha M., Van Schaftingen E.
      FEBS Lett. 408:281-284(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    2. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
      Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
      , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
      Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Tissue: Kidney.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Tissue: Endometrial tumor.
    4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    5. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
      The MGC Project Team
      Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    6. "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
      Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
      Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    7. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    8. "Molecular basis for the local conformational rearrangement of human phosphoserine phosphatase."
      Kim H.Y., Heo Y.S., Kim J.H., Park M.H., Moon J., Kim E., Kwon D., Yoon J., Shin D., Jeong E.J., Park S.Y., Lee T.G., Jeon Y.H., Ro S., Cho J.M., Hwang K.Y.
      J. Biol. Chem. 277:46651-46658(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.51 ANGSTROMS) OF 3-225 IN COMPLEXES WITH INHIBITOR 2-AMINO-3-PHOSPHONOPROPIONIC ACID; SERINE AND PHOSPHATE ION, SUBUNIT, CATALYTIC ACTIVITY, ACTIVE SITE, MUTAGENESIS OF SER-23; GLU-29; ARG-65; ASN-133; THR-182 AND ARG-202.
    9. "High-resolution structure of human phosphoserine phosphatase in open conformation."
      Peeraer Y., Rabijns A., Verboven C., Collet J.F., Van Schaftingen E., De Ranter C.
      Acta Crystallogr. D 59:971-977(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.53 ANGSTROMS) OF 3-225 IN COMPLEX WITH CALCIUM IONS, FUNCTION, CATALYTIC ACTIVITY, ACTIVE SITE, SUBUNIT.
    10. "How calcium inhibits the magnesium-dependent enzyme human phosphoserine phosphatase."
      Peeraer Y., Rabijns A., Collet J.F., Van Schaftingen E., De Ranter C.
      Eur. J. Biochem. 271:3421-3427(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.53 ANGSTROMS) OF 3-225 IN COMPLEX WITH CALCIUM IONS, COFACTOR, CATALYTIC ACTIVITY, ENZYME REGULATION.
    11. Cited for: VARIANTS PSPHD ASN-32 AND THR-52.

    Entry informationi

    Entry nameiSERB_HUMAN
    AccessioniPrimary (citable) accession number: P78330
    Secondary accession number(s): B2RCR5, Q7Z3S5
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 30, 2000
    Last sequence update: April 26, 2005
    Last modified: October 1, 2014
    This is version 137 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program
    DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Human chromosome 7
      Human chromosome 7: entries, gene names and cross-references to MIM
    2. Human entries with polymorphisms or disease mutations
      List of human entries with polymorphisms or disease mutations
    3. Human polymorphisms and disease mutations
      Index of human polymorphisms and disease mutations
    4. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    5. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    6. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    7. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3