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Q9H400

- LIME1_HUMAN

UniProt

Q9H400 - LIME1_HUMAN

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Protein

Lck-interacting transmembrane adapter 1

Gene
LIME1, LIME, LP8067
Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

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
Complete GO annotation...

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

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 66Extracellular Reviewed prediction
Transmembranei7 – 2721Helical; Signal-anchor for type III membrane protein; Reviewed predictionAdd
BLAST
Topological domaini28 – 295268Cytoplasmic Reviewed predictionAdd
BLAST

GO - Cellular componenti

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

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 cysteine Inferred
Lipidationi31 – 311S-palmitoyl cysteine Inferred
Modified residuei167 – 1671Phosphotyrosine Inferred
Modified residuei200 – 2001Phosphotyrosine1 Publication
Modified residuei254 – 2541Phosphotyrosine; by LCK Inferred

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 GRAP2.2 Publications

Protein-protein interaction databases

IntActiQ9H400. 1 interaction.
STRINGi9606.ENSP00000309521.

Structurei

3D structure databases

ProteinModelPortaliQ9H400.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni145 – 1484Interaction with GRB2 By similarity
Regioni167 – 1704Interaction with CSK
Regioni200 – 2034Interaction with CSK
Regioni235 – 2384Interaction with LCK and PIK3R1 By similarity
Regioni254 – 2574Interaction with LCK, PLCG2 and PIK3R1 By 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

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. VSP_016642Add
BLAST

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti246 – 2461D → G in BAA91148. 1 Publication

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

« Hide 'large scale' publications
  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: July 9, 2014
This is version 103 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

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