P18827 (SDC1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Syndecan-1
Short name=SYND1

Alternative name(s):
CD_antigen=CD138

Gene names

Name:	SDC1
Synonyms:	SDC

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	310 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Cell surface proteoglycan that bears both heparan sulfate and chondroitin sulfate and that links the cytoskeleton to the interstitial matrix.
Subunit structure	Interacts with CDCP1. Ref.9
Subcellular location	Membrane; Single-pass type I membrane protein. Secreted. Note: Shedding of the ectodomain produces a soluble form.
Post-translational modification	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.
Sequence similarities	Belongs to the syndecan proteoglycan family.

Ontologies

Keywords
Cellular component	Membrane Secreted
Coding sequence diversity	Polymorphism
Domain	Signal Transmembrane Transmembrane helix
PTM	Glycoprotein Heparan sulfate Proteoglycan
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	Sertoli cell development Inferred from electronic annotation. Source: Compara canonical Wnt receptor signaling pathway Inferred from electronic annotation. Source: Compara carbohydrate metabolic process Traceable author statement. Source: Reactome chondroitin sulfate metabolic process Traceable author statement. Source: Reactome glycosaminoglycan biosynthetic process Traceable author statement. Source: Reactome glycosaminoglycan catabolic process Traceable author statement. Source: Reactome lipid metabolic process Traceable author statement. Source: Reactome lipoprotein metabolic process Traceable author statement. Source: Reactome myoblast development Inferred from sequence or structural similarity. Source: UniProtKB odontogenesis Inferred from electronic annotation. Source: Compara response to cAMP Inferred from electronic annotation. Source: Compara response to calcium ion Inferred from electronic annotation. Source: Compara response to glucocorticoid stimulus Inferred from electronic annotation. Source: Compara response to hydrogen peroxide Inferred from electronic annotation. Source: Compara response to toxin Inferred from electronic annotation. Source: Compara striated muscle cell development Inferred from expression pattern PubMed 9566955. Source: UniProtKB ureteric bud development Inferred from electronic annotation. Source: Compara wound healing Inferred from electronic annotation. Source: Compara
Cellular_component	Golgi lumen Traceable author statement. Source: Reactome external side of plasma membrane Inferred from electronic annotation. Source: Compara extracellular region Inferred from electronic annotation. Source: UniProtKB-SubCell focal adhesion Inferred from direct assay. Source: HPA integral to plasma membrane Traceable author statement Ref.2. Source: ProtInc lysosomal lumen Traceable author statement. Source: Reactome protein complex Inferred from electronic annotation. Source: Compara
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Signal peptide	1 – 22	22	Potential
	Chain	23 – 310	288	Syndecan-1		PRO_0000033499
Regions
	Topological domain	23 – 254	232	Extracellular Potential
	Transmembrane	255 – 275	21	Helical; Potential
	Topological domain	276 – 310	35	Cytoplasmic Potential
Sites
	Site	242 – 243	2	Cleavage By similarity
Amino acid modifications
	Glycosylation	37	1	O-linked (Xyl...) (chondroitin sulfate) By similarity
	Glycosylation	43	1	N-linked (GlcNAc...) Potential
	Glycosylation	45	1	O-linked (Xyl...) (heparan sulfate) By similarity
	Glycosylation	47	1	O-linked (Xyl...) (heparan sulfate) By similarity
	Glycosylation	206	1	O-linked (Xyl...) (chondroitin sulfate) By similarity
	Glycosylation	216	1	O-linked (Xyl...) (chondroitin sulfate) By similarity
Natural variations
	Natural variant	76	1	T → M. Corresponds to variant rs2230922 [ dbSNP | Ensembl ].		VAR_052242
	Natural variant	136	1	L → Q. Ref.1 Ref.2 Ref.3 Ref.5 Ref.6 Ref.7 Corresponds to variant rs10205485 [ dbSNP | Ensembl ].		VAR_052243
Experimental info
	Sequence conflict	19	1	P → L in AAA60605. Ref.2
	Sequence conflict	259	1	G → V in AAH08765. Ref.6

Sequences

	Sequence		Length	Mass (Da)
	P18827 [UniParc]. Last modified May 5, 2009. Version 3. Checksum: 8E9EF4A57F5FDBD0	FASTA	310	32,462
	10 20 30 40 50 60 MRRAALWLWL CALALSLQPA LPQIVATNLP PEDQDGSGDD SDNFSGSGAG ALQDITLSQQ 70 80 90 100 110 120 TPSTWKDTQL LTAIPTSPEP TGLEATAAST STLPAGEGPK EGEAVVLPEV EPGLTAREQE 130 140 150 160 170 180 ATPRPRETTQ LPTTHLASTT TATTAQEPAT SHPHRDMQPG HHETSTPAGP SQADLHTPHT 190 200 210 220 230 240 EDGGPSATER AAEDGASSQL PAAEGSGEQD FTFETSGENT AVVAVEPDRR NQSPVDQGAT 250 260 270 280 290 300 GASQGLLDRK EVLGGVIAGG LVGLIFAVCL VGFMLYRMKK KDEGSYSLEE PKQANGGAYQ 310 KPTKQEEFYA

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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]	Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C. Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases 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]	"Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
+	Additional computationally mapped references.

Web resources

Atlas of Genetics and Cytogenetics in Oncology and Haematology

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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.

IPI

IPI00002441.

PIR

A41776.

RefSeq

NP_001006947.1. NM_001006946.1.
NP_002988.3. NM_002997.4.

UniGene

Hs.224607.
Hs.665958.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
4GVC	X-ray	1.54	B	303-310	[»]
4GVD	X-ray	1.85	C/D	303-310	[»]

ProteinModelPortal

P18827.

SMR

P18827. Positions 277-310.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-1123N.

IntAct

P18827. 1 interaction.

STRING

9606.ENSP00000254351.

PTM databases

PhosphoSite

P18827.

Polymorphism databases

DMDM

229463011.

Proteomic databases

PaxDb

P18827.

PRIDE

P18827.

Protocols and materials databases

DNASU

6382.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000254351; ENSP00000254351; ENSG00000115884.
ENST00000381150; ENSP00000370542; ENSG00000115884.

GeneID

6382.

KEGG

hsa:6382.

UCSC

uc002rdo.1. human.

Organism-specific databases

CTD

6382.

GeneCards

GC02M020400.

H-InvDB

HIX0161948.

HGNC

HGNC:10658. SDC1.

HPA

CAB002424.
HPA006185.

MIM

186355. gene.

neXtProt

NX_P18827.

PharmGKB

PA35588.

GenAtlas

Search...

Phylogenomic databases

eggNOG

NOG86393.

HOGENOM

HOG000133092.

HOVERGEN

HBG017783.

InParanoid

P18827.

KO

K06257.

OMA

KQANGGA.

OrthoDB

EOG46DM3T.

PhylomeDB

P18827.

Enzyme and pathway databases

Pathway_Interaction_DB

arf6_traffickingpathway. Arf6 trafficking events.
avb3_integrin_pathway. Integrins in angiogenesis.
syndecan_pathway. Proteogylcan syndecan-mediated signaling events.
syndecan_1_pathway. Syndecan-1-mediated signaling events.

Reactome

REACT_111217. Metabolism.
REACT_116125. Disease.

Gene expression databases

ArrayExpress

P18827.

Bgee

P18827.

CleanEx

HS_SDC1.

Genevestigator

P18827.

GermOnline

ENSG00000115884. Homo sapiens.

Family and domain databases

InterPro

IPR003585. Neurexin-like.
IPR001050. Syndecan.
[Graphical view]

PANTHER

PTHR10915. PTHR10915. 1 hit.

Pfam

PF01034. Syndecan. 1 hit.
[Graphical view]

SMART

SM00294. 4.1m. 1 hit.
[Graphical view]

PROSITE

PS00964. SYNDECAN. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

ChiTaRS

SDC1. human.

GenomeRNAi

6382.

NextBio

24782.

PMAP-CutDB

P18827.

SOURCE

Search...

Entry information

Entry name

SDC1_HUMAN

Accession

Primary (citable) accession number: P18827
Secondary accession number(s): D6W523 , Q53QV0, Q546D3, Q96HB7

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1990
Last sequence update:	May 5, 2009
Last modified:	May 1, 2013
This is version 129 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.