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P18827

- SDC1_HUMAN

UniProt

P18827 - SDC1_HUMAN

Protein

Syndecan-1

Gene

SDC1

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 143 (01 Oct 2014)
      Sequence version 3 (05 May 2009)
      Previous versions | rss
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    Functioni

    Cell surface proteoglycan that bears both heparan sulfate and chondroitin sulfate and that links the cytoskeleton to the interstitial matrix.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei242 – 2432CleavageBy similarity

    GO - Molecular functioni

    1. protein binding Source: UniProtKB
    2. protein C-terminus binding Source: UniProtKB

    GO - Biological processi

    1. canonical Wnt signaling pathway Source: Ensembl
    2. carbohydrate metabolic process Source: Reactome
    3. chondroitin sulfate metabolic process Source: Reactome
    4. extracellular matrix organization Source: Reactome
    5. glycosaminoglycan biosynthetic process Source: Reactome
    6. glycosaminoglycan catabolic process Source: Reactome
    7. glycosaminoglycan metabolic process Source: Reactome
    8. inflammatory response Source: Ensembl
    9. lipoprotein metabolic process Source: Reactome
    10. myoblast development Source: UniProtKB
    11. odontogenesis Source: Ensembl
    12. phototransduction, visible light Source: Reactome
    13. response to calcium ion Source: Ensembl
    14. response to cAMP Source: Ensembl
    15. response to glucocorticoid Source: Ensembl
    16. response to hydrogen peroxide Source: Ensembl
    17. response to toxic substance Source: Ensembl
    18. retinoid metabolic process Source: Reactome
    19. Sertoli cell development Source: Ensembl
    20. small molecule metabolic process Source: Reactome
    21. striated muscle cell development Source: UniProtKB
    22. ureteric bud development Source: Ensembl
    23. wound healing Source: Ensembl

    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.
    REACT_6841. Chylomicron-mediated lipid transport.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Syndecan-1
    Short name:
    SYND1
    Alternative name(s):
    CD_antigen: CD138
    Gene namesi
    Name:SDC1
    Synonyms:SDC
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 2

    Organism-specific databases

    HGNCiHGNC:10658. SDC1.

    Subcellular locationi

    Membrane; Single-pass type I membrane protein. Secreted
    Note: Shedding of the ectodomain produces a soluble form.

    GO - Cellular componenti

    1. cytoplasm Source: HPA
    2. external side of plasma membrane Source: Ensembl
    3. extracellular vesicular exosome Source: UniProt
    4. focal adhesion Source: HPA
    5. Golgi lumen Source: Reactome
    6. integral component of plasma membrane Source: ProtInc
    7. lysosomal lumen Source: Reactome
    8. plasma membrane Source: Reactome
    9. protein complex Source: Ensembl

    Keywords - Cellular componenti

    Membrane, Secreted

    Pathology & Biotechi

    Organism-specific databases

    PharmGKBiPA35588.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 2222Sequence AnalysisAdd
    BLAST
    Chaini23 – 310288Syndecan-1PRO_0000033499Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Glycosylationi37 – 371O-linked (Xyl...) (chondroitin sulfate)By similarity
    Glycosylationi43 – 431N-linked (GlcNAc...)Sequence Analysis
    Glycosylationi45 – 451O-linked (Xyl...) (heparan sulfate)By similarity
    Glycosylationi47 – 471O-linked (Xyl...) (heparan sulfate)By similarity
    Glycosylationi206 – 2061O-linked (Xyl...) (chondroitin sulfate)By similarity
    Glycosylationi216 – 2161O-linked (Xyl...) (chondroitin sulfate)By similarity

    Post-translational modificationi

    Shedding is enhanced by a number of factors such as heparanase, thrombin or EGF. Also by stress and wound healing. PMA-mediated shedding is inhibited by TIMP3.

    Keywords - PTMi

    Glycoprotein, Heparan sulfate, Proteoglycan

    Proteomic databases

    MaxQBiP18827.
    PaxDbiP18827.
    PRIDEiP18827.

    PTM databases

    PhosphoSiteiP18827.

    Miscellaneous databases

    PMAP-CutDBP18827.

    Expressioni

    Gene expression databases

    ArrayExpressiP18827.
    BgeeiP18827.
    CleanExiHS_SDC1.
    GenevestigatoriP18827.

    Organism-specific databases

    HPAiCAB002424.
    HPA006185.

    Interactioni

    Subunit structurei

    Interacts with CDCP1. Interacts (via C-terminus) with TIAM1 (via PDZ domain).2 Publications

    Protein-protein interaction databases

    BioGridi112284. 14 interactions.
    DIPiDIP-1123N.
    IntActiP18827. 1 interaction.
    MINTiMINT-5004100.
    STRINGi9606.ENSP00000254351.

    Structurei

    Secondary structure

    1
    310
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi305 – 3095

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4GVCX-ray1.54B303-310[»]
    4GVDX-ray1.85C/D303-310[»]
    ProteinModelPortaliP18827.
    SMRiP18827. Positions 277-310.
    ModBaseiSearch...
    MobiDBiSearch...

    Topological domain

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Topological domaini23 – 254232ExtracellularSequence AnalysisAdd
    BLAST
    Topological domaini276 – 31035CytoplasmicSequence AnalysisAdd
    BLAST

    Transmembrane

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transmembranei255 – 27521HelicalSequence AnalysisAdd
    BLAST

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the syndecan proteoglycan family.Curated

    Keywords - Domaini

    Signal, Transmembrane, Transmembrane helix

    Phylogenomic databases

    eggNOGiNOG86393.
    HOGENOMiHOG000133092.
    HOVERGENiHBG017783.
    InParanoidiP18827.
    KOiK06257.
    OMAiPTKQEEF.
    OrthoDBiEOG79KPG2.
    PhylomeDBiP18827.
    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.

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

    P18827-1 [UniParc]FASTAAdd to Basket

    « Hide

    MRRAALWLWL CALALSLQPA LPQIVATNLP PEDQDGSGDD SDNFSGSGAG    50
    ALQDITLSQQ TPSTWKDTQL LTAIPTSPEP TGLEATAAST STLPAGEGPK 100
    EGEAVVLPEV EPGLTAREQE ATPRPRETTQ LPTTHLASTT TATTAQEPAT 150
    SHPHRDMQPG HHETSTPAGP SQADLHTPHT EDGGPSATER AAEDGASSQL 200
    PAAEGSGEQD FTFETSGENT AVVAVEPDRR NQSPVDQGAT GASQGLLDRK 250
    EVLGGVIAGG LVGLIFAVCL VGFMLYRMKK KDEGSYSLEE PKQANGGAYQ 300
    KPTKQEEFYA 310
    Length:310
    Mass (Da):32,462
    Last modified:May 5, 2009 - v3
    Checksum:i8E9EF4A57F5FDBD0
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti19 – 191P → L in AAA60605. (PubMed:2324102)Curated
    Sequence conflicti259 – 2591G → V in AAH08765. (PubMed:15489334)Curated

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti76 – 761T → M.
    Corresponds to variant rs2230922 [ dbSNP | Ensembl ].
    VAR_052242
    Natural varianti136 – 1361L → Q.6 Publications
    Corresponds to variant rs10205485 [ dbSNP | Ensembl ].
    VAR_052243

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X60306 mRNA. Translation: CAA42851.1.
    J05392 mRNA. Translation: AAA60605.1.
    AJ551176 mRNA. Translation: CAD80245.1.
    AC104792 Genomic DNA. Translation: AAX93151.1.
    CH471053 Genomic DNA. Translation: EAX00828.1.
    CH471053 Genomic DNA. Translation: EAX00829.1.
    CH471053 Genomic DNA. Translation: EAX00830.1.
    CH471053 Genomic DNA. Translation: EAX00831.1.
    BC008765 mRNA. Translation: AAH08765.1.
    Z48199 Genomic DNA. Translation: CAA88235.1.
    CCDSiCCDS1697.1.
    PIRiA41776.
    RefSeqiNP_001006947.1. NM_001006946.1.
    NP_002988.3. NM_002997.4.
    UniGeneiHs.224607.
    Hs.665958.

    Genome annotation databases

    EnsembliENST00000254351; ENSP00000254351; ENSG00000115884.
    ENST00000381150; ENSP00000370542; ENSG00000115884.
    GeneIDi6382.
    KEGGihsa:6382.
    UCSCiuc002rdo.1. human.

    Polymorphism databases

    DMDMi229463011.

    Keywords - Coding sequence diversityi

    Polymorphism

    Cross-referencesi

    Web resourcesi

    Atlas of Genetics and Cytogenetics in Oncology and Haematology

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X60306 mRNA. Translation: CAA42851.1 .
    J05392 mRNA. Translation: AAA60605.1 .
    AJ551176 mRNA. Translation: CAD80245.1 .
    AC104792 Genomic DNA. Translation: AAX93151.1 .
    CH471053 Genomic DNA. Translation: EAX00828.1 .
    CH471053 Genomic DNA. Translation: EAX00829.1 .
    CH471053 Genomic DNA. Translation: EAX00830.1 .
    CH471053 Genomic DNA. Translation: EAX00831.1 .
    BC008765 mRNA. Translation: AAH08765.1 .
    Z48199 Genomic DNA. Translation: CAA88235.1 .
    CCDSi CCDS1697.1.
    PIRi A41776.
    RefSeqi NP_001006947.1. NM_001006946.1.
    NP_002988.3. NM_002997.4.
    UniGenei Hs.224607.
    Hs.665958.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    4GVC X-ray 1.54 B 303-310 [» ]
    4GVD X-ray 1.85 C/D 303-310 [» ]
    ProteinModelPortali P18827.
    SMRi P18827. Positions 277-310.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 112284. 14 interactions.
    DIPi DIP-1123N.
    IntActi P18827. 1 interaction.
    MINTi MINT-5004100.
    STRINGi 9606.ENSP00000254351.

    PTM databases

    PhosphoSitei P18827.

    Polymorphism databases

    DMDMi 229463011.

    Proteomic databases

    MaxQBi P18827.
    PaxDbi P18827.
    PRIDEi P18827.

    Protocols and materials databases

    DNASUi 6382.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000254351 ; ENSP00000254351 ; ENSG00000115884 .
    ENST00000381150 ; ENSP00000370542 ; ENSG00000115884 .
    GeneIDi 6382.
    KEGGi hsa:6382.
    UCSCi uc002rdo.1. human.

    Organism-specific databases

    CTDi 6382.
    GeneCardsi GC02M020400.
    H-InvDB HIX0161948.
    HGNCi HGNC:10658. SDC1.
    HPAi CAB002424.
    HPA006185.
    MIMi 186355. gene.
    neXtProti NX_P18827.
    PharmGKBi PA35588.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi NOG86393.
    HOGENOMi HOG000133092.
    HOVERGENi HBG017783.
    InParanoidi P18827.
    KOi K06257.
    OMAi PTKQEEF.
    OrthoDBi EOG79KPG2.
    PhylomeDBi P18827.
    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.
    REACT_6841. Chylomicron-mediated lipid transport.

    Miscellaneous databases

    ChiTaRSi SDC1. human.
    GeneWikii Syndecan_1.
    GenomeRNAii 6382.
    NextBioi 24782.
    PMAP-CutDB P18827.
    PROi P18827.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi P18827.
    Bgeei P18827.
    CleanExi HS_SDC1.
    Genevestigatori P18827.

    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. "Differential expression of cell surface heparan sulfate proteoglycans in human mammary epithelial cells and lung fibroblasts."
      Lories V., Cassiman J.-J., van de Berghe H., David G.
      J. Biol. Chem. 267:1116-1122(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], VARIANT GLN-136.
      Tissue: Fibroblast.
    2. "Sequence of human syndecan indicates a novel gene family of integral membrane proteoglycans."
      Mali M., Jaakkola P., Arvilommi A.-M., Jalkanen M.
      J. Biol. Chem. 265:6884-6889(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], VARIANT GLN-136.
      Tissue: Mammary gland.
    3. "Shift of syndecan-1 expression from epithelial to stromal cells during progression of solid tumours."
      Mennerich D., Vogel A., Klaman I., Dahl E., Lichtner R.B., Rosenthal A., Pohlenz H.D., Thierauch K.H., Sommer A.
      Eur. J. Cancer 40:1373-1382(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA], VARIANT GLN-136.
    4. "Generation and annotation of the DNA sequences of human chromosomes 2 and 4."
      Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L., Du H.
      , Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K., McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C., Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S., Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H., Wilson R.K.
      Nature 434:724-731(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], VARIANT GLN-136.
    6. "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], VARIANT GLN-136.
      Tissue: Kidney.
    7. "The mapping and visual ordering of the human syndecan-1 and N-myc genes near the telomeric region of chromosome 2p."
      Kaukonen J., Alanen-Kurki L., Jalkanen M., Palotie A.
      Hum. Genet. 99:295-297(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 23-310, VARIANT GLN-136.
      Tissue: Placenta.
    8. "Regulated shedding of syndecan-1 and -4 ectodomains by thrombin and growth factor receptor activation."
      Subramanian S.V., Fitzgerald M.L., Bernfield M.
      J. Biol. Chem. 272:14713-14720(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: SHEDDING.
    9. "Adhesion signaling by a novel mitotic substrate of src kinases."
      Bhatt A.S., Erdjument-Bromage H., Tempst P., Craik C.S., Moasser M.M.
      Oncogene 24:5333-5343(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH CDCP1.
    10. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    11. "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: X-RAY CRYSTALLOGRAPHY (1.54 ANGSTROMS) OF 303-310 IN COMPLEX WITH TIAM1, INTERACTION WITH TIAM1.

    Entry informationi

    Entry nameiSDC1_HUMAN
    AccessioniPrimary (citable) accession number: P18827
    Secondary accession number(s): D6W523
    , Q53QV0, Q546D3, Q96HB7
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1990
    Last sequence update: May 5, 2009
    Last modified: October 1, 2014
    This is version 143 of the entry and version 3 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 cell differentiation molecules
      CD nomenclature of surface proteins of human leucocytes and list of entries
    2. Human chromosome 2
      Human chromosome 2: entries, gene names and cross-references to MIM
    3. Human entries with polymorphisms or disease mutations
      List of human entries with polymorphisms or disease mutations
    4. Human polymorphisms and disease mutations
      Index of human polymorphisms and disease mutations
    5. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    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