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P51884

- LUM_HUMAN

UniProt

P51884 - LUM_HUMAN

Protein

Lumican

Gene

LUM

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 2 (23 Jan 2002)
      Previous versions | rss
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    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. positive regulation of transcription from RNA polymerase II promoter Source: Ensembl
    10. response to growth factor Source: Ensembl
    11. response to organic cyclic compound Source: Ensembl
    12. small molecule metabolic process Source: Reactome
    13. visual perception Source: ProtInc

    Enzyme and pathway databases

    ReactomeiREACT_121120. Keratan sulfate biosynthesis.
    REACT_121313. Keratan sulfate degradation.
    REACT_13552. Integrin cell surface interactions.
    REACT_163906. ECM proteoglycans.

    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: 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: UniProt
    4. fibrillar collagen trimer Source: UniProtKB
    5. Golgi lumen Source: Reactome
    6. lysosomal lumen Source: Reactome
    7. proteinaceous extracellular matrix Source: ProtInc

    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

    Protein-protein interaction databases

    BioGridi110238. 3 interactions.
    IntActiP51884. 2 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.
    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

    MSLSAFTLFL ALIGGTSGQY YDYDFPLSIY GQSSPNCAPE CNCPESYPSA    50
    MYCDELKLKS VPMVPPGIKY LYLRNNQIDH IDEKAFENVT DLQWLILDHN 100
    LLENSKIKGR VFSKLKQLKK LHINHNNLTE SVGPLPKSLE DLQLTHNKIT 150
    KLGSFEGLVN LTFIHLQHNR LKEDAVSAAF KGLKSLEYLD LSFNQIARLP 200
    SGLPVSLLTL YLDNNKISNI PDEYFKRFNA LQYLRLSHNE LADSGIPGNS 250
    FNVSSLVELD LSYNKLKNIP TVNENLENYY LEVNQLEKFD IKSFCKILGP 300
    LSYSKIKHLR LDGNRISETS LPPDMYECLR VANEVTLN 338
    Length:338
    Mass (Da):38,429
    Last modified:January 23, 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:
    EMBL
    GenBank
    DDBJ
    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:
    EMBL
    GenBank
    DDBJ
    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 .
    CCDSi CCDS9038.1.
    RefSeqi NP_002336.1. NM_002345.3.
    UniGenei Hs.406475.

    3D structure databases

    ProteinModelPortali P51884.
    SMRi P51884. Positions 37-329.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 110238. 3 interactions.
    IntActi P51884. 2 interactions.
    MINTi MINT-1422554.
    STRINGi 9606.ENSP00000266718.

    PTM databases

    PhosphoSitei P51884.

    Polymorphism databases

    DMDMi 20141464.

    Proteomic databases

    MaxQBi P51884.
    PaxDbi P51884.
    PeptideAtlasi P51884.
    PRIDEi P51884.

    Protocols and materials databases

    DNASUi 4060.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000266718 ; ENSP00000266718 ; ENSG00000139329 .
    GeneIDi 4060.
    KEGGi hsa:4060.
    UCSCi uc001tbm.3. human.

    Organism-specific databases

    CTDi 4060.
    GeneCardsi GC12M091430.
    HGNCi HGNC:6724. LUM.
    HPAi CAB022193.
    HPA001522.
    MIMi 600616. gene.
    neXtProti NX_P51884.
    PharmGKBi PA30486.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi COG4886.
    HOGENOMi HOG000234447.
    HOVERGENi HBG108061.
    InParanoidi P51884.
    KOi K08122.
    OMAi KKLHINY.
    OrthoDBi EOG75F4DF.
    PhylomeDBi P51884.
    TreeFami TF334562.

    Enzyme and pathway databases

    Reactomei REACT_121120. Keratan sulfate biosynthesis.
    REACT_121313. Keratan sulfate degradation.
    REACT_13552. Integrin cell surface interactions.
    REACT_163906. ECM proteoglycans.

    Miscellaneous databases

    ChiTaRSi LUM. human.
    GeneWikii LUM.
    GenomeRNAii 4060.
    NextBioi 15912.
    PMAP-CutDB P51884.
    PROi P51884.
    SOURCEi Search...

    Gene expression databases

    Bgeei P51884.
    CleanExi HS_LUM.
    Genevestigatori P51884.

    Family and domain databases

    InterProi IPR001611. Leu-rich_rpt.
    IPR003591. Leu-rich_rpt_typical-subtyp.
    IPR000372. LRR-contain_N.
    IPR027219. Lumican.
    [Graphical view ]
    PANTHERi PTHR24371:SF54. PTHR24371:SF54. 1 hit.
    Pfami PF13855. LRR_8. 3 hits.
    PF01462. LRRNT. 1 hit.
    [Graphical view ]
    SMARTi SM00369. LRR_TYP. 1 hit.
    SM00013. LRRNT. 1 hit.
    [Graphical view ]
    PROSITEi PS51450. LRR. 10 hits.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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(1995) [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(1995) [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 (MAY-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(2004) [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(2004) [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(2004) [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(2004) [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(2005) [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(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: GLYCOSYLATION [LARGE SCALE ANALYSIS] AT ASN-88; ASN-127; ASN-160 AND ASN-252.
      Tissue: Liver.
    11. "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(2011) [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: October 1, 1996
    Last sequence update: January 23, 2002
    Last modified: October 1, 2014
    This is version 143 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