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Q9H400

- LIME1_HUMAN

UniProt

Q9H400 - LIME1_HUMAN

Protein

Lck-interacting transmembrane adapter 1

Gene

LIME1

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 104 (01 Oct 2014)
      Sequence version 1 (01 Mar 2001)
      Previous versions | rss
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    Functioni

    Involved in BCR (B-cell antigen receptor)-mediated signaling in B-cells and TCR (T-cell antigen receptor)-mediated T-cell signaling in T-cells. In absence of TCR signaling, may be involved in CD4-mediated inhibition of T-cell activation. Couples activation of these receptors and their associated kinases with distal intracellular events such as calcium mobilization or MAPK activation through the recruitment of PLCG2, GRB2, GRAP2, and other signaling molecules.1 Publication

    GO - Biological processi

    1. B cell receptor signaling pathway Source: InterPro
    2. T cell receptor signaling pathway Source: InterPro

    Keywords - Biological processi

    Adaptive immunity, Immunity

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Lck-interacting transmembrane adapter 1
    Short name:
    Lck-interacting membrane protein
    Alternative name(s):
    Lck-interacting molecule
    Gene namesi
    Name:LIME1
    Synonyms:LIME
    ORF Names:LP8067
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 20

    Organism-specific databases

    HGNCiHGNC:26016. LIME1.

    Subcellular locationi

    Cell membrane 2 Publications; Single-pass type III membrane protein 2 Publications
    Note: Present in lipid rafts. Recruited to the immunological synapse upon conjugation of T-cell with antigen-presenting cell.

    GO - Cellular componenti

    1. extracellular space Source: UniProt
    2. integral component of membrane Source: UniProtKB-KW
    3. plasma membrane Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cell membrane, Membrane

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi145 – 1451Y → F: No change in binding to LCK, CSK or FYN. 1 Publication
    Mutagenesisi167 – 1671Y → F: Abolishes binding to CSK. 1 Publication
    Mutagenesisi200 – 2001Y → F: Reduces binding to CSK. 1 Publication
    Mutagenesisi235 – 2351Y → F: No change in binding to LCK, CSK or FYN. 1 Publication
    Mutagenesisi254 – 2541Y → F: Abolishes binding to LCK and reduces binding to FYN. 1 Publication

    Organism-specific databases

    PharmGKBiPA142671551.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 295295Lck-interacting transmembrane adapter 1PRO_0000083332Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Lipidationi28 – 281S-palmitoyl cysteine1 Publication
    Lipidationi31 – 311S-palmitoyl cysteine1 Publication
    Modified residuei167 – 1671Phosphotyrosine2 Publications
    Modified residuei200 – 2001Phosphotyrosine2 Publications
    Modified residuei254 – 2541Phosphotyrosine; by LCK2 Publications

    Post-translational modificationi

    Palmitoylation of Cys-28 and Cys-31 is required for raft targeting.1 Publication
    Phosphorylated on tyrosines upon TCR activation and/or CD4 coreceptor stimulation, or upon BCR stimulation; which leads to the recruitment of SH2-containing proteins.2 Publications

    Keywords - PTMi

    Lipoprotein, Palmitate, Phosphoprotein

    Proteomic databases

    MaxQBiQ9H400.
    PaxDbiQ9H400.
    PRIDEiQ9H400.

    PTM databases

    PhosphoSiteiQ9H400.

    Expressioni

    Tissue specificityi

    Expressed in peripheral blood lymphocytes, lymphoid tissues, and liver. Present in T-cells and plasma cells, and in various hematopoietic cell lines (at protein level).3 Publications

    Gene expression databases

    BgeeiQ9H400.
    CleanExiHS_LIME1.
    GenevestigatoriQ9H400.

    Organism-specific databases

    HPAiCAB015363.

    Interactioni

    Subunit structurei

    When phosphorylated in response to BCR activation, interacts with LYN, PIK3R1, PLCG2, and GRB2 By similarity. When phosphorylated in response to TCR stimulation and/or CD4 co-stimulation, interacts with LCK, CSK, FYN, PTPN11/SHP2, GRB2, PIK3R1 and GRAP2.By similarity2 Publications

    Protein-protein interaction databases

    IntActiQ9H400. 1 interaction.
    STRINGi9606.ENSP00000309521.

    Structurei

    3D structure databases

    ProteinModelPortaliQ9H400.
    ModBaseiSearch...
    MobiDBiSearch...

    Topological domain

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Topological domaini1 – 66ExtracellularSequence Analysis
    Topological domaini28 – 295268CytoplasmicSequence AnalysisAdd
    BLAST

    Transmembrane

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transmembranei7 – 2721Helical; Signal-anchor for type III membrane proteinSequence AnalysisAdd
    BLAST

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni145 – 1484Interaction with GRB2By similarity
    Regioni167 – 1704Interaction with CSK
    Regioni200 – 2034Interaction with CSK
    Regioni235 – 2384Interaction with LCK and PIK3R1By similarity
    Regioni254 – 2574Interaction with LCK, PLCG2 and PIK3R1By similarity

    Keywords - Domaini

    Signal-anchor, Transmembrane, Transmembrane helix

    Phylogenomic databases

    eggNOGiNOG77780.
    HOGENOMiHOG000231956.
    HOVERGENiHBG080499.
    InParanoidiQ9H400.
    OMAiVAEYACI.
    OrthoDBiEOG780RNR.
    PhylomeDBiQ9H400.
    TreeFamiTF337416.

    Family and domain databases

    InterProiIPR026072. Lime1.
    [Graphical view]
    PfamiPF15332. LIME1. 1 hit.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q9H400-1) [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

    MGLPVSWAPP ALWVLGCCAL LLSLWALCTA CRRPEDAVAP RKRARRQRAR    50
    LQGSATAAEA SLLRRTHLCS LSKSDTRLHE LHRGPRSSRA LRPASMDLLR 100
    PHWLEVSRDI TGPQAAPSAF PHQELPRALP AAAATAGCAG LEATYSNVGL 150
    AALPGVSLAA SPVVAEYARV QKRKGTHRSP QEPQQGKTEV TPAAQVDVLY 200
    SRVCKPKRRD PGPTTDPLDP KGQGAILALA GDLAYQTLPL RALDVDSGPL 250
    ENVYESIREL GDPAGRSSTC GAGTPPASSC PSLGRGWRPL PASLP 295
    Length:295
    Mass (Da):31,288
    Last modified:March 1, 2001 - v1
    Checksum:iD85ACE978F2DC99E
    GO
    Isoform 2 (identifier: Q9H400-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-95: Missing.

    Show »
    Length:200
    Mass (Da):20,841
    Checksum:i44A69D6E2379BCB3
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti246 – 2461D → G in BAA91148. (PubMed:14702039)Curated

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti211 – 2111P → L.
    Corresponds to variant rs1151625 [ dbSNP | Ensembl ].
    VAR_053918

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei1 – 9595Missing in isoform 2. 1 PublicationVSP_016642Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AY203957 mRNA. Translation: AAP34480.1.
    AK000413 mRNA. Translation: BAA91148.1.
    AL121845 Genomic DNA. Translation: CAC03671.1.
    AL121845 Genomic DNA. Translation: CAI21882.1.
    CH471077 Genomic DNA. Translation: EAW75213.1.
    CH471077 Genomic DNA. Translation: EAW75214.1.
    CH471077 Genomic DNA. Translation: EAW75215.1.
    CH471077 Genomic DNA. Translation: EAW75216.1.
    CH471077 Genomic DNA. Translation: EAW75217.1.
    CH471077 Genomic DNA. Translation: EAW75218.1.
    BC017016 mRNA. Translation: AAH17016.1.
    CCDSiCCDS13536.1. [Q9H400-1]
    RefSeqiNP_060276.2. NM_017806.2. [Q9H400-1]
    UniGeneiHs.233220.

    Genome annotation databases

    EnsembliENST00000309546; ENSP00000309521; ENSG00000203896. [Q9H400-1]
    GeneIDi54923.
    KEGGihsa:54923.
    UCSCiuc002ygp.4. human. [Q9H400-1]

    Polymorphism databases

    DMDMi74752630.

    Keywords - Coding sequence diversityi

    Alternative splicing, Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AY203957 mRNA. Translation: AAP34480.1 .
    AK000413 mRNA. Translation: BAA91148.1 .
    AL121845 Genomic DNA. Translation: CAC03671.1 .
    AL121845 Genomic DNA. Translation: CAI21882.1 .
    CH471077 Genomic DNA. Translation: EAW75213.1 .
    CH471077 Genomic DNA. Translation: EAW75214.1 .
    CH471077 Genomic DNA. Translation: EAW75215.1 .
    CH471077 Genomic DNA. Translation: EAW75216.1 .
    CH471077 Genomic DNA. Translation: EAW75217.1 .
    CH471077 Genomic DNA. Translation: EAW75218.1 .
    BC017016 mRNA. Translation: AAH17016.1 .
    CCDSi CCDS13536.1. [Q9H400-1 ]
    RefSeqi NP_060276.2. NM_017806.2. [Q9H400-1 ]
    UniGenei Hs.233220.

    3D structure databases

    ProteinModelPortali Q9H400.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi Q9H400. 1 interaction.
    STRINGi 9606.ENSP00000309521.

    PTM databases

    PhosphoSitei Q9H400.

    Polymorphism databases

    DMDMi 74752630.

    Proteomic databases

    MaxQBi Q9H400.
    PaxDbi Q9H400.
    PRIDEi Q9H400.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000309546 ; ENSP00000309521 ; ENSG00000203896 . [Q9H400-1 ]
    GeneIDi 54923.
    KEGGi hsa:54923.
    UCSCi uc002ygp.4. human. [Q9H400-1 ]

    Organism-specific databases

    CTDi 54923.
    GeneCardsi GC20P062366.
    HGNCi HGNC:26016. LIME1.
    HPAi CAB015363.
    MIMi 609809. gene.
    neXtProti NX_Q9H400.
    PharmGKBi PA142671551.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi NOG77780.
    HOGENOMi HOG000231956.
    HOVERGENi HBG080499.
    InParanoidi Q9H400.
    OMAi VAEYACI.
    OrthoDBi EOG780RNR.
    PhylomeDBi Q9H400.
    TreeFami TF337416.

    Miscellaneous databases

    GeneWikii LIME1.
    GenomeRNAii 54923.
    NextBioi 58007.
    PROi Q9H400.
    SOURCEi Search...

    Gene expression databases

    Bgeei Q9H400.
    CleanExi HS_LIME1.
    Genevestigatori Q9H400.

    Family and domain databases

    InterProi IPR026072. Lime1.
    [Graphical view ]
    Pfami PF15332. LIME1. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "LIME: a new membrane raft-associated adaptor protein involved in CD4 and CD8 coreceptor signaling."
      Brdickova N., Brdicka T., Angelisova P., Horvath O., Spicka J., Hilgert I., Paces J., Simeoni L., Kliche S., Merten C., Schraven B., Horejsi V.
      J. Exp. Med. 198:1453-1462(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), TISSUE SPECIFICITY, SUBCELLULAR LOCATION, INTERACTION WITH LCK AND CSK, PHOSPHORYLATION AT TYR-167; TYR-200 AND TYR-254, PALMITOYLATION AT CYS-28 AND CYS-31, MUTAGENESIS OF TYR-145; TYR-167; TYR-200; TYR-235 AND TYR-254, FUNCTION.
    2. "LIME, a novel transmembrane adaptor protein, associates with p56lck and mediates T cell activation."
      Hur E.M., Son M., Lee O.-H., Choi Y.B., Park C., Lee H., Yun Y.
      J. Exp. Med. 198:1463-1473(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), INTERACTION WITH LCK, PHOSPHORYLATION, TISSUE SPECIFICITY, SUBCELLULAR LOCATION.
    3. "Large-scale cDNA transfection screening for genes related to cancer development and progression."
      Wan D., Gong Y., Qin W., Zhang P., Li J., Wei L., Zhou X., Li H., Qiu X., Zhong F., He L., Yu J., Yao G., Jiang H., Qian L., Yu Y., Shu H., Chen X.
      , Xu H., Guo M., Pan Z., Chen Y., Ge C., Yang S., Gu J.
      Proc. Natl. Acad. Sci. U.S.A. 101:15724-15729(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
    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] (ISOFORM 1).
    5. "The DNA sequence and comparative analysis of human chromosome 20."
      Deloukas P., Matthews L.H., Ashurst J.L., Burton J., Gilbert J.G.R., Jones M., Stavrides G., Almeida J.P., Babbage A.K., Bagguley C.L., Bailey J., Barlow K.F., Bates K.N., Beard L.M., Beare D.M., Beasley O.P., Bird C.P., Blakey S.E.
      , Bridgeman A.M., Brown A.J., Buck D., Burrill W.D., Butler A.P., Carder C., Carter N.P., Chapman J.C., Clamp M., Clark G., Clark L.N., Clark S.Y., Clee C.M., Clegg S., Cobley V.E., Collier R.E., Connor R.E., Corby N.R., Coulson A., Coville G.J., Deadman R., Dhami P.D., Dunn M., Ellington A.G., Frankland J.A., Fraser A., French L., Garner P., Grafham D.V., Griffiths C., Griffiths M.N.D., Gwilliam R., Hall R.E., Hammond S., Harley J.L., Heath P.D., Ho S., Holden J.L., Howden P.J., Huckle E., Hunt A.R., Hunt S.E., Jekosch K., Johnson C.M., Johnson D., Kay M.P., Kimberley A.M., King A., Knights A., Laird G.K., Lawlor S., Lehvaeslaiho M.H., Leversha M.A., Lloyd C., Lloyd D.M., Lovell J.D., Marsh V.L., Martin S.L., McConnachie L.J., McLay K., McMurray A.A., Milne S.A., Mistry D., Moore M.J.F., Mullikin J.C., Nickerson T., Oliver K., Parker A., Patel R., Pearce T.A.V., Peck A.I., Phillimore B.J.C.T., Prathalingam S.R., Plumb R.W., Ramsay H., Rice C.M., Ross M.T., Scott C.E., Sehra H.K., Shownkeen R., Sims S., Skuce C.D., Smith M.L., Soderlund C., Steward C.A., Sulston J.E., Swann R.M., Sycamore N., Taylor R., Tee L., Thomas D.W., Thorpe A., Tracey A., Tromans A.C., Vaudin M., Wall M., Wallis J.M., Whitehead S.L., Whittaker P., Willey D.L., Williams L., Williams S.A., Wilming L., Wray P.W., Hubbard T., Durbin R.M., Bentley D.R., Beck S., Rogers J.
      Nature 414:865-871(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    6. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    7. "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] (ISOFORM 1).
      Tissue: Colon.
    8. Cited for: TISSUE SPECIFICITY.

    Entry informationi

    Entry nameiLIME1_HUMAN
    AccessioniPrimary (citable) accession number: Q9H400
    Secondary accession number(s): E1P5K5
    , E1P5K6, Q5JWJ2, Q6XYB3, Q9NX69
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 20, 2005
    Last sequence update: March 1, 2001
    Last modified: October 1, 2014
    This is version 104 of the entry and version 1 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, 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

    External Data

    Dasty 3