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O75056

- SDC3_HUMAN

UniProt

O75056 - SDC3_HUMAN

Protein

Syndecan-3

Gene

SDC3

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 119 (01 Oct 2014)
      Sequence version 2 (05 Sep 2006)
      Previous versions | rss
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    Functioni

    Cell surface proteoglycan that may bear heparan sulfate By similarity. May have a role in the organization of cell shape by affecting the actin cytoskeleton, possibly by transferring signals from the cell surface in a sugar-dependent mechanism.By similarity1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei383 – 3842Cleavage of ectodomainSequence Analysis

    GO - Biological processi

    1. carbohydrate metabolic process Source: Reactome
    2. chondroitin sulfate metabolic process Source: Reactome
    3. extracellular matrix organization Source: Reactome
    4. glycosaminoglycan biosynthetic process Source: Reactome
    5. glycosaminoglycan catabolic process Source: Reactome
    6. glycosaminoglycan metabolic process Source: Reactome
    7. phototransduction, visible light Source: Reactome
    8. retinoid metabolic process Source: Reactome
    9. small molecule metabolic process Source: Reactome

    Enzyme and pathway databases

    ReactomeiREACT_120752. HS-GAG degradation.
    REACT_121248. HS-GAG biosynthesis.
    REACT_121408. A tetrasaccharide linker sequence is required for GAG synthesis.
    REACT_163942. Syndecan interactions.
    REACT_24968. Retinoid metabolism and transport.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Syndecan-3
    Short name:
    SYND3
    Gene namesi
    Name:SDC3
    Synonyms:KIAA0468
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 1

    Organism-specific databases

    HGNCiHGNC:10660. SDC3.

    Subcellular locationi

    GO - Cellular componenti

    1. Golgi lumen Source: Reactome
    2. integral component of membrane Source: UniProtKB-KW
    3. lysosomal lumen Source: Reactome
    4. membrane Source: UniProtKB
    5. plasma membrane Source: Reactome

    Keywords - Cellular componenti

    Membrane

    Pathology & Biotechi

    Organism-specific databases

    PharmGKBiPA35590.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 442442Syndecan-3PRO_0000183989Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Glycosylationi80 – 801O-linked (Xyl...) (glycosaminoglycan)Sequence Analysis
    Glycosylationi82 – 821O-linked (Xyl...) (glycosaminoglycan)Sequence Analysis
    Glycosylationi84 – 841O-linked (Xyl...) (glycosaminoglycan)Sequence Analysis
    Glycosylationi91 – 911O-linked (Xyl...) (glycosaminoglycan)Sequence Analysis
    Glycosylationi314 – 3141O-linked (Xyl...) (glycosaminoglycan)Sequence Analysis
    Glycosylationi367 – 3671O-linked (Xyl...) (glycosaminoglycan)Sequence Analysis
    Modified residuei409 – 4091Phosphotyrosine1 Publication
    Modified residuei419 – 4191Phosphotyrosine1 Publication
    Modified residuei431 – 4311Phosphotyrosine1 Publication
    Modified residuei441 – 4411Phosphotyrosine1 Publication

    Post-translational modificationi

    O-glycosylated within the Thr/Ser-rich region which could interact with lectin domains on other molecules.Curated

    Keywords - PTMi

    Glycoprotein, Heparan sulfate, Phosphoprotein, Proteoglycan

    Proteomic databases

    MaxQBiO75056.
    PaxDbiO75056.
    PRIDEiO75056.

    PTM databases

    PhosphoSiteiO75056.

    Expressioni

    Tissue specificityi

    Expressed in the nervous system, the adrenal gland, and the spleen.1 Publication

    Gene expression databases

    ArrayExpressiO75056.
    BgeeiO75056.
    CleanExiHS_SDC3.
    GenevestigatoriO75056.

    Organism-specific databases

    HPAiCAB025786.
    HPA017087.

    Interactioni

    Subunit structurei

    Interacts with TIAM1.1 Publication

    Protein-protein interaction databases

    BioGridi115027. 9 interactions.
    DIPiDIP-29944N.
    IntActiO75056. 2 interactions.
    MINTiMINT-3057059.
    STRINGi9606.ENSP00000344468.

    Structurei

    3D structure databases

    ProteinModelPortaliO75056.
    SMRiO75056. Positions 410-442.
    ModBaseiSearch...
    MobiDBiSearch...

    Topological domain

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Topological domaini1 – 387387ExtracellularSequence AnalysisAdd
    BLAST
    Topological domaini409 – 44234CytoplasmicSequence AnalysisAdd
    BLAST

    Transmembrane

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transmembranei388 – 40821HelicalSequence AnalysisAdd
    BLAST

    Family & Domainsi

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi115 – 302188Ser/Thr-rich (mucin-like)Add
    BLAST

    Sequence similaritiesi

    Belongs to the syndecan proteoglycan family.Curated

    Keywords - Domaini

    Transmembrane, Transmembrane helix

    Phylogenomic databases

    eggNOGiNOG85596.
    HOGENOMiHOG000049151.
    HOVERGENiHBG004144.
    InParanoidiO75056.
    KOiK16337.
    OMAiETAMRFS.
    PhylomeDBiO75056.
    TreeFamiTF320463.

    Family and domain databases

    InterProiIPR003585. Neurexin-like.
    IPR001050. Syndecan.
    IPR027789. Syndecan/Neurexin_dom.
    [Graphical view]
    PANTHERiPTHR10915. PTHR10915. 1 hit.
    PfamiPF01034. Syndecan. 1 hit.
    [Graphical view]
    SMARTiSM00294. 4.1m. 1 hit.
    [Graphical view]
    PROSITEiPS00964. SYNDECAN. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    O75056-1 [UniParc]FASTAAdd to Basket

    « Hide

    MKPGPPHRAG AAHGAGAGAG AAAGPGARGL LLPPLLLLLL AGRAAGAQRW    50
    RSENFERPVD LEGSGDDDSF PDDELDDLYS GSGSGYFEQE SGIETAMRFS 100
    PDVALAVSTT PAVLPTTNIQ PVGTPFEELP SERPTLEPAT SPLVVTEVPE 150
    EPSQRATTVS TTMATTAATS TGDPTVATVP ATVATATPST PAAPPFTATT 200
    AVIRTTGVRR LLPLPLTTVA TARATTPEAP SPPTTAAVLD TEAPTPRLVS 250
    TATSRPRALP RPATTQEPDI PERSTLPLGT TAPGPTEVAQ TPTPETFLTT 300
    IRDEPEVPVS GGPSGDFELP EEETTQPDTA NEVVAVGGAA AKASSPPGTL 350
    PKGARPGPGL LDNAIDSGSS AAQLPQKSIL ERKEVLVAVI VGGVVGALFA 400
    AFLVTLLIYR MKKKDEGSYT LEEPKQASVT YQKPDKQEEF YA 442
    Length:442
    Mass (Da):45,497
    Last modified:September 5, 2006 - v2
    Checksum:iD4C284CBC36A92E2
    GO

    Sequence cautioni

    The sequence BAA32313.2 differs from that shown. Reason: Intron retention.

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti208 – 2081V → I.
    Corresponds to variant rs2491132 [ dbSNP | Ensembl ].
    VAR_027251
    Natural varianti303 – 3031D → N.1 Publication
    Corresponds to variant rs4949184 [ dbSNP | Ensembl ].
    VAR_027252
    Natural varianti329 – 3291T → I.
    Corresponds to variant rs2282440 [ dbSNP | Ensembl ].
    VAR_027253

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF248634 mRNA. Translation: AAK39969.1.
    AB007937 mRNA. Translation: BAA32313.2. Sequence problems.
    AL445235 Genomic DNA. Translation: CAI22245.1.
    AL445235 Genomic DNA. Translation: CAI22250.1.
    BC013974 mRNA. No translation available.
    CCDSiCCDS30661.1.
    RefSeqiNP_055469.3. NM_014654.3.
    UniGeneiHs.158287.

    Genome annotation databases

    EnsembliENST00000339394; ENSP00000344468; ENSG00000162512.
    GeneIDi9672.
    KEGGihsa:9672.
    UCSCiuc001bse.2. human.

    Keywords - Coding sequence diversityi

    Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF248634 mRNA. Translation: AAK39969.1 .
    AB007937 mRNA. Translation: BAA32313.2 . Sequence problems.
    AL445235 Genomic DNA. Translation: CAI22245.1 .
    AL445235 Genomic DNA. Translation: CAI22250.1 .
    BC013974 mRNA. No translation available.
    CCDSi CCDS30661.1.
    RefSeqi NP_055469.3. NM_014654.3.
    UniGenei Hs.158287.

    3D structure databases

    ProteinModelPortali O75056.
    SMRi O75056. Positions 410-442.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 115027. 9 interactions.
    DIPi DIP-29944N.
    IntActi O75056. 2 interactions.
    MINTi MINT-3057059.
    STRINGi 9606.ENSP00000344468.

    PTM databases

    PhosphoSitei O75056.

    Proteomic databases

    MaxQBi O75056.
    PaxDbi O75056.
    PRIDEi O75056.

    Protocols and materials databases

    DNASUi 9672.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000339394 ; ENSP00000344468 ; ENSG00000162512 .
    GeneIDi 9672.
    KEGGi hsa:9672.
    UCSCi uc001bse.2. human.

    Organism-specific databases

    CTDi 9672.
    GeneCardsi GC01M031342.
    H-InvDB HIX0000348.
    HGNCi HGNC:10660. SDC3.
    HPAi CAB025786.
    HPA017087.
    MIMi 186357. gene.
    neXtProti NX_O75056.
    PharmGKBi PA35590.
    HUGEi Search...
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi NOG85596.
    HOGENOMi HOG000049151.
    HOVERGENi HBG004144.
    InParanoidi O75056.
    KOi K16337.
    OMAi ETAMRFS.
    PhylomeDBi O75056.
    TreeFami TF320463.

    Enzyme and pathway databases

    Reactomei REACT_120752. HS-GAG degradation.
    REACT_121248. HS-GAG biosynthesis.
    REACT_121408. A tetrasaccharide linker sequence is required for GAG synthesis.
    REACT_163942. Syndecan interactions.
    REACT_24968. Retinoid metabolism and transport.

    Miscellaneous databases

    ChiTaRSi SDC3. human.
    GeneWikii SDC3.
    GenomeRNAii 9672.
    NextBioi 36319.
    PROi O75056.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi O75056.
    Bgeei O75056.
    CleanExi HS_SDC3.
    Genevestigatori O75056.

    Family and domain databases

    InterProi IPR003585. Neurexin-like.
    IPR001050. Syndecan.
    IPR027789. Syndecan/Neurexin_dom.
    [Graphical view ]
    PANTHERi PTHR10915. PTHR10915. 1 hit.
    Pfami PF01034. Syndecan. 1 hit.
    [Graphical view ]
    SMARTi SM00294. 4.1m. 1 hit.
    [Graphical view ]
    PROSITEi PS00964. SYNDECAN. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY, VARIANT ASN-303.
    2. "Characterization of cDNA clones in size-fractionated cDNA libraries from human brain."
      Seki N., Ohira M., Nagase T., Ishikawa K., Miyajima N., Nakajima D., Nomura N., Ohara O.
      DNA Res. 4:345-349(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Tissue: Brain.
    3. "The DNA sequence and biological annotation of human chromosome 1."
      Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K.
      , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.
      Nature 441:315-321(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    4. "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].
      Tissue: Muscle.
    5. "Phosphorylation of recombinant N-syndecan (syndecan 3) core protein."
      Asundi V.K., Carey D.J.
      Biochem. Biophys. Res. Commun. 240:502-506(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: PHOSPHORYLATION AT TYR-409; TYR-419; TYR-431 AND TYR-441.
    6. "The structure of the Tiam1 PDZ domain/ phospho-syndecan1 complex reveals a ligand conformation that modulates protein dynamics."
      Liu X., Shepherd T.R., Murray A.M., Xu Z., Fuentes E.J.
      Structure 21:342-354(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH TIAM1.

    Entry informationi

    Entry nameiSDC3_HUMAN
    AccessioniPrimary (citable) accession number: O75056
    Secondary accession number(s): Q5T1Z6
    , Q5T1Z7, Q96CT3, Q96PR8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 30, 2000
    Last sequence update: September 5, 2006
    Last modified: October 1, 2014
    This is version 119 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

    Complete proteome, Reference proteome

    Documents

    1. Human chromosome 1
      Human chromosome 1: 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. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3