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Protein

Lumican

Gene

LUM

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

GO - Molecular functioni

  1. collagen binding Source: UniProtKB
  2. extracellular matrix structural constituent Source: UniProtKB

GO - Biological processi

  1. carbohydrate metabolic process Source: Reactome
  2. cartilage development Source: Ensembl
  3. collagen fibril organization Source: UniProtKB
  4. extracellular matrix organization Source: Reactome
  5. glycosaminoglycan metabolic process Source: Reactome
  6. keratan sulfate biosynthetic process Source: Reactome
  7. keratan sulfate catabolic process Source: Reactome
  8. keratan sulfate metabolic process Source: Reactome
  9. pathogenesis Source: Reactome
  10. positive regulation of transcription from RNA polymerase II promoter Source: Ensembl
  11. response to growth factor Source: Ensembl
  12. response to organic cyclic compound Source: Ensembl
  13. small molecule metabolic process Source: Reactome
  14. visual perception Source: ProtInc
Complete GO annotation...

Enzyme and pathway databases

ReactomeiREACT_121120. Keratan sulfate biosynthesis.
REACT_121313. Keratan sulfate degradation.
REACT_13552. Integrin cell surface interactions.
REACT_163906. ECM proteoglycans.
REACT_268431. Defective B4GALT1 causes B4GALT1-CDG (CDG-2d).
REACT_268786. Defective CHST6 causes MCDC1.

Names & Taxonomyi

Protein namesi
Recommended name:
Lumican
Alternative name(s):
Keratan sulfate proteoglycan lumican
Short name:
KSPG lumican
Gene namesi
Name:LUM
Synonyms:LDC, SLRR2D
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 12

Organism-specific databases

HGNCiHGNC:6724. LUM.

Subcellular locationi

GO - Cellular componenti

  1. extracellular region Source: UniProtKB
  2. extracellular space Source: BHF-UCL
  3. extracellular vesicular exosome Source: UniProtKB
  4. fibrillar collagen trimer Source: UniProtKB
  5. Golgi lumen Source: Reactome
  6. lysosomal lumen Source: Reactome
  7. proteinaceous extracellular matrix Source: ProtInc
Complete GO annotation...

Keywords - Cellular componenti

Extracellular matrix, Secreted

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA30486.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 1818Add
BLAST
Chaini19 – 338320LumicanPRO_0000032733Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei19 – 191Pyrrolidone carboxylic acid1 Publication
Modified residuei20 – 201SulfotyrosineBy similarity
Modified residuei21 – 211SulfotyrosineBy similarity
Modified residuei23 – 231SulfotyrosineBy similarity
Modified residuei30 – 301SulfotyrosineBy similarity
Glycosylationi88 – 881N-linked (GlcNAc...) (keratan sulfate)3 Publications
Glycosylationi127 – 1271N-linked (GlcNAc...) (keratan sulfate)Sequence Analysis
Glycosylationi160 – 1601N-linked (GlcNAc...) (keratan sulfate)3 Publications
Glycosylationi252 – 2521N-linked (GlcNAc...) (keratan sulfate)Sequence Analysis
Disulfide bondi295 ↔ 328By similarity

Post-translational modificationi

Sulfated on tyrosine residue(s).1 Publication

Keywords - PTMi

Disulfide bond, Glycoprotein, Proteoglycan, Pyrrolidone carboxylic acid, Sulfation

Proteomic databases

MaxQBiP51884.
PaxDbiP51884.
PeptideAtlasiP51884.
PRIDEiP51884.

PTM databases

PhosphoSiteiP51884.

Miscellaneous databases

PMAP-CutDBP51884.

Expressioni

Tissue specificityi

Cornea and other tissues.

Developmental stagei

Present in the extracellular matrix of human articular cartilage at all ages, although its abundance is far greater in the adult. In the adult cartilage lumican exists predominantly in a glycoprotein form lacking keratan sulfate, whereas the juvenile form of the molecule is a proteoglycan.

Gene expression databases

BgeeiP51884.
CleanExiHS_LUM.
GenevestigatoriP51884.

Organism-specific databases

HPAiCAB022193.
HPA001522.

Interactioni

Subunit structurei

Binds to laminin.By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
MMP14P502812EBI-725780,EBI-992788

Protein-protein interaction databases

BioGridi110238. 4 interactions.
IntActiP51884. 3 interactions.
MINTiMINT-1422554.
STRINGi9606.ENSP00000266718.

Structurei

3D structure databases

ProteinModelPortaliP51884.
SMRiP51884. Positions 37-329.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini28 – 6639LRRNTAdd
BLAST
Repeati67 – 8822LRR 1Add
BLAST
Repeati91 – 11424LRR 2Add
BLAST
Repeati117 – 13721LRR 3Add
BLAST
Repeati138 – 15922LRR 4Add
BLAST
Repeati160 – 18122LRR 5Add
BLAST
Repeati185 – 20521LRR 6Add
BLAST
Repeati206 – 22722LRR 7Add
BLAST
Repeati230 – 25324LRR 8Add
BLAST
Repeati255 – 27622LRR 9Add
BLAST
Repeati277 – 29620LRR 10Add
BLAST
Repeati305 – 32622LRR 11Add
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi37 – 5317Cys-richAdd
BLAST

Sequence similaritiesi

Contains 11 LRR (leucine-rich) repeats.Curated
Contains 1 LRRNT domain.Curated

Keywords - Domaini

Leucine-rich repeat, Repeat, Signal

Phylogenomic databases

eggNOGiCOG4886.
GeneTreeiENSGT00760000118969.
HOGENOMiHOG000234447.
HOVERGENiHBG108061.
InParanoidiP51884.
KOiK08122.
OMAiKKLHINY.
OrthoDBiEOG75F4DF.
PhylomeDBiP51884.
TreeFamiTF334562.

Family and domain databases

InterProiIPR001611. Leu-rich_rpt.
IPR003591. Leu-rich_rpt_typical-subtyp.
IPR000372. LRR-contain_N.
IPR027219. Lumican.
[Graphical view]
PANTHERiPTHR24371:SF54. PTHR24371:SF54. 1 hit.
PfamiPF13855. LRR_8. 3 hits.
PF01462. LRRNT. 1 hit.
[Graphical view]
SMARTiSM00369. LRR_TYP. 1 hit.
SM00013. LRRNT. 1 hit.
[Graphical view]
PROSITEiPS51450. LRR. 10 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

P51884-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSLSAFTLFL ALIGGTSGQY YDYDFPLSIY GQSSPNCAPE CNCPESYPSA
60 70 80 90 100
MYCDELKLKS VPMVPPGIKY LYLRNNQIDH IDEKAFENVT DLQWLILDHN
110 120 130 140 150
LLENSKIKGR VFSKLKQLKK LHINHNNLTE SVGPLPKSLE DLQLTHNKIT
160 170 180 190 200
KLGSFEGLVN LTFIHLQHNR LKEDAVSAAF KGLKSLEYLD LSFNQIARLP
210 220 230 240 250
SGLPVSLLTL YLDNNKISNI PDEYFKRFNA LQYLRLSHNE LADSGIPGNS
260 270 280 290 300
FNVSSLVELD LSYNKLKNIP TVNENLENYY LEVNQLEKFD IKSFCKILGP
310 320 330
LSYSKIKHLR LDGNRISETS LPPDMYECLR VANEVTLN
Length:338
Mass (Da):38,429
Last modified:January 22, 2002 - v2
Checksum:i905D2EBD370CC59D
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti27 – 271L → P in AAA85268 (PubMed:7665616).Curated
Sequence conflicti101 – 1011L → V in AAA85268 (PubMed:7665616).Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti199 – 1991L → P Found in patients with amyotrophic lateral sclerosis. 1 Publication
Corresponds to variant rs147975710 [ dbSNP | Ensembl ].
VAR_065763

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U18728 mRNA. Translation: AAA85268.1.
U21128 mRNA. Translation: AAA91639.1.
BT006707 mRNA. Translation: AAP35353.1.
AK312682 mRNA. Translation: BAG35562.1.
CH471054 Genomic DNA. Translation: EAW97449.1.
BC007038 mRNA. Translation: AAH07038.1.
BC035997 mRNA. Translation: AAH35997.1.
CCDSiCCDS9038.1.
RefSeqiNP_002336.1. NM_002345.3.
UniGeneiHs.406475.

Genome annotation databases

EnsembliENST00000266718; ENSP00000266718; ENSG00000139329.
GeneIDi4060.
KEGGihsa:4060.
UCSCiuc001tbm.3. human.

Polymorphism databases

DMDMi20141464.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U18728 mRNA. Translation: AAA85268.1.
U21128 mRNA. Translation: AAA91639.1.
BT006707 mRNA. Translation: AAP35353.1.
AK312682 mRNA. Translation: BAG35562.1.
CH471054 Genomic DNA. Translation: EAW97449.1.
BC007038 mRNA. Translation: AAH07038.1.
BC035997 mRNA. Translation: AAH35997.1.
CCDSiCCDS9038.1.
RefSeqiNP_002336.1. NM_002345.3.
UniGeneiHs.406475.

3D structure databases

ProteinModelPortaliP51884.
SMRiP51884. Positions 37-329.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi110238. 4 interactions.
IntActiP51884. 3 interactions.
MINTiMINT-1422554.
STRINGi9606.ENSP00000266718.

PTM databases

PhosphoSiteiP51884.

Polymorphism databases

DMDMi20141464.

Proteomic databases

MaxQBiP51884.
PaxDbiP51884.
PeptideAtlasiP51884.
PRIDEiP51884.

Protocols and materials databases

DNASUi4060.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000266718; ENSP00000266718; ENSG00000139329.
GeneIDi4060.
KEGGihsa:4060.
UCSCiuc001tbm.3. human.

Organism-specific databases

CTDi4060.
GeneCardsiGC12M091430.
HGNCiHGNC:6724. LUM.
HPAiCAB022193.
HPA001522.
MIMi600616. gene.
neXtProtiNX_P51884.
PharmGKBiPA30486.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiCOG4886.
GeneTreeiENSGT00760000118969.
HOGENOMiHOG000234447.
HOVERGENiHBG108061.
InParanoidiP51884.
KOiK08122.
OMAiKKLHINY.
OrthoDBiEOG75F4DF.
PhylomeDBiP51884.
TreeFamiTF334562.

Enzyme and pathway databases

ReactomeiREACT_121120. Keratan sulfate biosynthesis.
REACT_121313. Keratan sulfate degradation.
REACT_13552. Integrin cell surface interactions.
REACT_163906. ECM proteoglycans.
REACT_268431. Defective B4GALT1 causes B4GALT1-CDG (CDG-2d).
REACT_268786. Defective CHST6 causes MCDC1.

Miscellaneous databases

ChiTaRSiLUM. human.
GeneWikiiLUM.
GenomeRNAii4060.
NextBioi15912.
PMAP-CutDBP51884.
PROiP51884.
SOURCEiSearch...

Gene expression databases

BgeeiP51884.
CleanExiHS_LUM.
GenevestigatoriP51884.

Family and domain databases

InterProiIPR001611. Leu-rich_rpt.
IPR003591. Leu-rich_rpt_typical-subtyp.
IPR000372. LRR-contain_N.
IPR027219. Lumican.
[Graphical view]
PANTHERiPTHR24371:SF54. PTHR24371:SF54. 1 hit.
PfamiPF13855. LRR_8. 3 hits.
PF01462. LRRNT. 1 hit.
[Graphical view]
SMARTiSM00369. LRR_TYP. 1 hit.
SM00013. LRRNT. 1 hit.
[Graphical view]
PROSITEiPS51450. LRR. 10 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The human lumican gene. Organization, chromosomal location, and expression in articular cartilage."
    Grover J., Chen X.-N., Korenberg J.R., Roughley P.J.
    J. Biol. Chem. 270:21942-21949(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Tissue: Cartilage, Intestine and Placenta.
  2. "Primary structure of human lumican (keratan sulfate proteoglycan) and localization of the gene (LUM) to chromosome 12q21.3-q22."
    Chakravarti S., Stallings R.L., Sundar-Raj N., Cornuet P.K., Hassell J.R.
    Genomics 27:481-488(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], PARTIAL PROTEIN SEQUENCE.
    Tissue: Cornea.
  3. "Cloning of human full-length CDSs in BD Creator(TM) system donor vector."
    Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S., Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y., Phelan M., Farmer A.
    Submitted (APR-2003) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
  4. "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(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
  5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  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(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Lung and Prostate.
  7. "Identification of tyrosine sulfation in extracellular leucine-rich repeat proteins using mass spectrometry."
    Onnerfjord P., Heathfield T.F., Heinegaard D.
    J. Biol. Chem. 279:26-33(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: SULFATION, PYROGLUTAMATE FORMATION AT GLN-19, IDENTIFICATION BY MASS SPECTROMETRY.
  8. "Screening for N-glycosylated proteins by liquid chromatography mass spectrometry."
    Bunkenborg J., Pilch B.J., Podtelejnikov A.V., Wisniewski J.R.
    Proteomics 4:454-465(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: GLYCOSYLATION [LARGE SCALE ANALYSIS] AT ASN-88 AND ASN-160.
    Tissue: Plasma.
  9. "Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry."
    Liu T., Qian W.-J., Gritsenko M.A., Camp D.G. II, Monroe M.E., Moore R.J., Smith R.D.
    J. Proteome Res. 4:2070-2080(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: GLYCOSYLATION [LARGE SCALE ANALYSIS] AT ASN-88; ASN-127; ASN-160 AND ASN-252.
    Tissue: Plasma.
  10. "Glycoproteomics analysis of human liver tissue by combination of multiple enzyme digestion and hydrazide chemistry."
    Chen R., Jiang X., Sun D., Han G., Wang F., Ye M., Wang L., Zou H.
    J. Proteome Res. 8:651-661(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: GLYCOSYLATION [LARGE SCALE ANALYSIS] AT ASN-88; ASN-127; ASN-160 AND ASN-252.
    Tissue: Liver.
  11. "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome."
    Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D., Wang L., Ye M., Zou H.
    J. Proteomics 96:253-262(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Liver.
  12. "Resequencing of 29 candidate genes in patients with familial and sporadic amyotrophic lateral sclerosis."
    Daoud H., Valdmanis P.N., Gros-Louis F., Belzil V., Spiegelman D., Henrion E., Diallo O., Desjarlais A., Gauthier J., Camu W., Dion P.A., Rouleau G.A.
    Arch. Neurol. 68:587-593(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: VARIANT PRO-199.

Entry informationi

Entry nameiLUM_HUMAN
AccessioniPrimary (citable) accession number: P51884
Secondary accession number(s): B2R6R5, Q96QM7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 30, 1996
Last sequence update: January 22, 2002
Last modified: March 31, 2015
This is version 148 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, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 12
    Human chromosome 12: 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.