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Protein

Syndecan-4

Gene

SDC4

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Cell surface proteoglycan that bears heparan sulfate. Regulates exosome biogenesis in concert with SDCBP and PDCD6IP (PubMed:22660413).1 Publication

GO - Molecular functioni

  • fibronectin binding Source: Ensembl
  • identical protein binding Source: IntAct
  • protein kinase C binding Source: Ensembl
  • thrombospondin receptor activity Source: BHF-UCL

GO - Biological processi

Enzyme and pathway databases

ReactomeiR-HSA-1971475 A tetrasaccharide linker sequence is required for GAG synthesis
R-HSA-2022928 HS-GAG biosynthesis
R-HSA-2024096 HS-GAG degradation
R-HSA-202733 Cell surface interactions at the vascular wall
R-HSA-3000170 Syndecan interactions
R-HSA-3560783 Defective B4GALT7 causes EDS, progeroid type
R-HSA-3560801 Defective B3GAT3 causes JDSSDHD
R-HSA-3656237 Defective EXT2 causes exostoses 2
R-HSA-3656253 Defective EXT1 causes exostoses 1, TRPS2 and CHDS
R-HSA-4420332 Defective B3GALT6 causes EDSP2 and SEMDJL1
R-HSA-975634 Retinoid metabolism and transport
SIGNORiP31431

Protein family/group databases

TCDBi9.A.35.1.1 the peptide translocating syndecan (syndecan) family

Names & Taxonomyi

Protein namesi
Recommended name:
Syndecan-4
Short name:
SYND4
Alternative name(s):
Amphiglycan
Ryudocan core protein
Gene namesi
Name:SDC4
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 20

Organism-specific databases

EuPathDBiHostDB:ENSG00000124145.6
HGNCiHGNC:10661 SDC4
MIMi600017 gene
neXtProtiNX_P31431

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini19 – 145ExtracellularSequence analysisAdd BLAST127
Transmembranei146 – 170HelicalSequence analysisAdd BLAST25
Topological domaini171 – 198CytoplasmicSequence analysisAdd BLAST28

Keywords - Cellular componenti

Membrane, Secreted

Pathology & Biotechi

Organism-specific databases

DisGeNETi6385
OpenTargetsiENSG00000124145
PharmGKBiPA35591

Polymorphism and mutation databases

BioMutaiSDC4
DMDMi2851418

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 18Sequence analysisAdd BLAST18
ChainiPRO_000003351119 – 198Syndecan-4Add BLAST180

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi39O-linked (Xyl...) (heparan sulfate) serineBy similarity1
Glycosylationi61O-linked (Xyl...) (heparan sulfate) serineSequence analysis1
Glycosylationi63O-linked (Xyl...) (heparan sulfate) serineSequence analysis1

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 TIMP3.1 Publication

Keywords - PTMi

Glycoprotein, Heparan sulfate, Proteoglycan

Proteomic databases

EPDiP31431
PaxDbiP31431
PeptideAtlasiP31431
PRIDEiP31431
ProteomicsDBi54789
TopDownProteomicsiP31431-1 [P31431-1]

PTM databases

iPTMnetiP31431
PhosphoSitePlusiP31431

Miscellaneous databases

PMAP-CutDBiP31431

Expressioni

Tissue specificityi

Expressed in epithelial and fibroblastic cells.1 Publication

Gene expression databases

BgeeiENSG00000124145
CleanExiHS_SDC4
GenevisibleiP31431 HS

Organism-specific databases

HPAiCAB013240
HPA005716

Interactioni

Subunit structurei

Homodimer. Interacts (via its cytoplasmic domain) with GIPC (via its PDZ domain). Interacts (via its cytoplasmic domain) with NUDT16L1 (By similarity). Interacts with CDCP1 and SDCBP.By similarity3 Publications

Binary interactionsi

Show more details

GO - Molecular functioni

  • fibronectin binding Source: Ensembl
  • identical protein binding Source: IntAct
  • protein kinase C binding Source: Ensembl

Protein-protein interaction databases

BioGridi112286, 19 interactors
DIPiDIP-29945N
ELMiP31431
IntActiP31431, 19 interactors
MINTiP31431
STRINGi9606.ENSP00000361818

Structurei

Secondary structure

1198
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi192 – 194Combined sources3
Beta strandi196 – 198Combined sources3

3D structure databases

ProteinModelPortaliP31431
SMRiP31431
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP31431

Family & Domainsi

Sequence similaritiesi

Belongs to the syndecan proteoglycan family.Curated

Keywords - Domaini

Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG410IXIG Eukaryota
ENOG4111QSA LUCA
GeneTreeiENSGT00530000063116
HOGENOMiHOG000263414
HOVERGENiHBG004501
InParanoidiP31431
KOiK16338
OMAiQEPDDFE
OrthoDBiEOG091G0OOE
PhylomeDBiP31431
TreeFamiTF320463

Family and domain databases

InterProiView protein in InterPro
IPR003585 Neurexin-like
IPR001050 Syndecan
IPR027789 Syndecan/Neurexin_dom
IPR030479 Syndecan_CS
PANTHERiPTHR10915 PTHR10915, 1 hit
PfamiView protein in Pfam
PF01034 Syndecan, 1 hit
SMARTiView protein in SMART
SM00294 4.1m, 1 hit
PROSITEiView protein in PROSITE
PS00964 SYNDECAN, 1 hit

Sequences (2)i

Sequence statusi: Complete.

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

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: P31431-1) [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
MAPARLFALL LFFVGGVAES IRETEVIDPQ DLLEGRYFSG ALPDDEDVVG
60 70 80 90 100
PGQESDDFEL SGSGDLDDLE DSMIGPEVVH PLVPLDNHIP ERAGSGSQVP
110 120 130 140 150
TEPKKLEENE VIPKRISPVE ESEDVSNKVS MSSTVQGSNI FERTEVLAAL
160 170 180 190
IVGGIVGILF AVFLILLLMY RMKKKDEGSY DLGKKPIYKK APTNEFYA
Length:198
Mass (Da):21,642
Last modified:July 15, 1998 - v2
Checksum:i8229AA2733F77A10
GO
Isoform 2 (identifier: P31431-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     149-198: ALIVGGIVGILFAVFLILLLMYRMKKKDEGSYDLGKKPIYKKAPTNEFYA → GCPEH

Note: Soluble form, lacks the transmembrane domain.
Show »
Length:153
Mass (Da):16,545
Checksum:i25AD50751A7D2642
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_02185112F → L2 PublicationsCorresponds to variant dbSNP:rs2228384Ensembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_044449149 – 198ALIVG…NEFYA → GCPEH in isoform 2. 2 PublicationsAdd BLAST50

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X67016 mRNA Translation: CAA47406.1
D13292 mRNA Translation: BAA02550.1
D79206 Genomic DNA Translation: BAA19613.1
AK312507 mRNA Translation: BAG35408.1
CR542045 mRNA Translation: CAG46842.1
CR542074 mRNA Translation: CAG46871.1
AK222695 mRNA Translation: BAD96415.1
AK223243 mRNA Translation: BAD96963.1
AL021578 Genomic DNA No translation available.
CH471077 Genomic DNA Translation: EAW75861.1
CH471077 Genomic DNA Translation: EAW75862.1
BC030805 mRNA Translation: AAH30805.1
AA151028 mRNA No translation available.
AA258502 mRNA No translation available.
CCDSiCCDS13350.1 [P31431-1]
PIRiJC1457
RefSeqiNP_002990.2, NM_002999.3 [P31431-1]
UniGeneiHs.632267

Genome annotation databases

EnsembliENST00000372733; ENSP00000361818; ENSG00000124145 [P31431-1]
GeneIDi6385
KEGGihsa:6385
UCSCiuc002xnu.4 human [P31431-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Entry informationi

Entry nameiSDC4_HUMAN
AccessioniPrimary (citable) accession number: P31431
Secondary accession number(s): O00773
, Q16833, Q53FN9, Q6FGN3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: July 15, 1998
Last modified: July 18, 2018
This is version 189 of the entry and version 2 of the sequence. See 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 20
    Human chromosome 20: 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

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