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Lck-interacting transmembrane adapter 1 (Lck-interacting membrane protein) (Lck-interacting molecule)

 LIME1_HUMAN             Reviewed;         295 AA.
Q9H400; E1P5K5; E1P5K6; Q5JWJ2; Q6XYB3; Q9NX69;
20-DEC-2005, integrated into UniProtKB/Swiss-Prot.
01-MAR-2001, sequence version 1.
12-SEP-2018, entry version 132.
RecName: Full=Lck-interacting transmembrane adapter 1;
Short=Lck-interacting membrane protein;
AltName: Full=Lck-interacting molecule;
Name=LIME1; Synonyms=LIME; ORFNames=LP8067;
Homo sapiens (Human).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
NCBI_TaxID=9606;
[1]
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, AND
FUNCTION.
PubMed=14610046; DOI=10.1084/jem.20031484;
Brdickova N., Brdicka T., Angelisova P., Horvath O., Spicka J.,
Hilgert I., Paces J., Simeoni L., Kliche S., Merten C., Schraven B.,
Horejsi V.;
"LIME: a new membrane raft-associated adaptor protein involved in CD4
and CD8 coreceptor signaling.";
J. Exp. Med. 198:1453-1462(2003).
[2]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), INTERACTION WITH LCK,
PHOSPHORYLATION, TISSUE SPECIFICITY, AND SUBCELLULAR LOCATION.
PubMed=14610044; DOI=10.1084/jem.20030232;
Hur E.M., Son M., Lee O.-H., Choi Y.B., Park C., Lee H., Yun Y.;
"LIME, a novel transmembrane adaptor protein, associates with p56lck
and mediates T cell activation.";
J. Exp. Med. 198:1463-1473(2003).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
PubMed=15498874; DOI=10.1073/pnas.0404089101;
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.;
"Large-scale cDNA transfection screening for genes related to cancer
development and progression.";
Proc. Natl. Acad. Sci. U.S.A. 101:15724-15729(2004).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
PubMed=14702039; DOI=10.1038/ng1285;
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.;
"Complete sequencing and characterization of 21,243 full-length human
cDNAs.";
Nat. Genet. 36:40-45(2004).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
PubMed=11780052; DOI=10.1038/414865a;
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.;
"The DNA sequence and comparative analysis of human chromosome 20.";
Nature 414:865-871(2001).
[6]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
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.
[7]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
TISSUE=Colon;
PubMed=15489334; DOI=10.1101/gr.2596504;
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA
project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[8]
TISSUE SPECIFICITY.
PubMed=16160011; DOI=10.1182/blood-2005-06-2273;
Tedoldi S., Paterson J.C., Hansmann M.-L., Natkunam Y., Rudiger T.,
Angelisova P., Du M.Q., Roberton H., Roncador G., Sanchez L.,
Pozzobon M., Masir N., Barry R., Pileri S., Mason D.Y., Marafioti T.,
Horejsi V.;
"Transmembrane adaptor molecules: a new category of lymphoid-cell
markers.";
Blood 107:213-221(2006).
[9]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-256, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Liver;
PubMed=24275569; DOI=10.1016/j.jprot.2013.11.014;
Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D.,
Wang L., Ye M., Zou H.;
"An enzyme assisted RP-RPLC approach for in-depth analysis of human
liver phosphoproteome.";
J. Proteomics 96:253-262(2014).
-!- FUNCTION: 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. {ECO:0000269|PubMed:14610046}.
-!- SUBUNIT: 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. {ECO:0000250, ECO:0000269|PubMed:14610044,
ECO:0000269|PubMed:14610046}.
-!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000269|PubMed:14610044,
ECO:0000269|PubMed:14610046}; Single-pass type III membrane
protein {ECO:0000269|PubMed:14610044,
ECO:0000269|PubMed:14610046}. Note=Present in lipid rafts.
Recruited to the immunological synapse upon conjugation of T-cell
with antigen-presenting cell.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=2;
Name=1;
IsoId=Q9H400-1; Sequence=Displayed;
Name=2;
IsoId=Q9H400-2; Sequence=VSP_016642;
-!- TISSUE SPECIFICITY: 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).
{ECO:0000269|PubMed:14610044, ECO:0000269|PubMed:14610046,
ECO:0000269|PubMed:16160011}.
-!- PTM: Palmitoylation of Cys-28 and Cys-31 is required for raft
targeting. {ECO:0000269|PubMed:14610046}.
-!- PTM: Phosphorylated on tyrosines upon TCR activation and/or CD4
coreceptor stimulation, or upon BCR stimulation; which leads to
the recruitment of SH2-containing proteins.
{ECO:0000269|PubMed:14610044, ECO:0000269|PubMed:14610046}.
-----------------------------------------------------------------------
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EMBL; AY203957; AAP34480.1; -; mRNA.
EMBL; AK000413; BAA91148.1; -; mRNA.
EMBL; AL121845; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; CH471077; EAW75213.1; -; Genomic_DNA.
EMBL; CH471077; EAW75214.1; -; Genomic_DNA.
EMBL; CH471077; EAW75215.1; -; Genomic_DNA.
EMBL; CH471077; EAW75216.1; -; Genomic_DNA.
EMBL; CH471077; EAW75217.1; -; Genomic_DNA.
EMBL; CH471077; EAW75218.1; -; Genomic_DNA.
EMBL; BC017016; AAH17016.1; -; mRNA.
CCDS; CCDS13536.1; -. [Q9H400-1]
RefSeq; NP_001292583.1; NM_001305654.1.
RefSeq; NP_001292584.1; NM_001305655.1.
RefSeq; NP_060276.2; NM_017806.3. [Q9H400-1]
UniGene; Hs.233220; -.
ProteinModelPortal; Q9H400; -.
BioGrid; 120264; 4.
IntAct; Q9H400; 39.
STRING; 9606.ENSP00000309521; -.
iPTMnet; Q9H400; -.
PhosphoSitePlus; Q9H400; -.
SwissPalm; Q9H400; -.
BioMuta; LIME1; -.
DMDM; 74752630; -.
EPD; Q9H400; -.
MaxQB; Q9H400; -.
PaxDb; Q9H400; -.
PeptideAtlas; Q9H400; -.
PRIDE; Q9H400; -.
ProteomicsDB; 80775; -.
ProteomicsDB; 80776; -. [Q9H400-2]
Ensembl; ENST00000309546; ENSP00000309521; ENSG00000203896. [Q9H400-1]
GeneID; 54923; -.
KEGG; hsa:54923; -.
UCSC; uc002ygp.5; human. [Q9H400-1]
CTD; 54923; -.
EuPathDB; HostDB:ENSG00000203896.9; -.
GeneCards; LIME1; -.
HGNC; HGNC:26016; LIME1.
HPA; CAB015363; -.
MIM; 609809; gene.
neXtProt; NX_Q9H400; -.
OpenTargets; ENSG00000203896; -.
PharmGKB; PA142671551; -.
eggNOG; ENOG410J9JT; Eukaryota.
eggNOG; ENOG41114H9; LUCA.
GeneTree; ENSGT00510000050080; -.
HOGENOM; HOG000231956; -.
HOVERGEN; HBG080499; -.
InParanoid; Q9H400; -.
OMA; LYSRVCK; -.
OrthoDB; EOG091G0IKW; -.
PhylomeDB; Q9H400; -.
TreeFam; TF337416; -.
GeneWiki; LIME1; -.
GenomeRNAi; 54923; -.
PRO; PR:Q9H400; -.
Proteomes; UP000005640; Chromosome 20.
Bgee; ENSG00000203896; Expressed in 87 organ(s), highest expression level in liver.
CleanEx; HS_LIME1; -.
ExpressionAtlas; Q9H400; baseline and differential.
Genevisible; Q9H400; HS.
GO; GO:0005615; C:extracellular space; HDA:UniProtKB.
GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
GO; GO:0071008; C:U2-type post-mRNA release spliceosomal complex; IBA:GO_Central.
GO; GO:0002250; P:adaptive immune response; IEA:UniProtKB-KW.
GO; GO:0050853; P:B cell receptor signaling pathway; IEA:InterPro.
GO; GO:0000390; P:spliceosomal complex disassembly; IBA:GO_Central.
GO; GO:0050852; P:T cell receptor signaling pathway; IEA:InterPro.
InterPro; IPR026072; Lime1.
Pfam; PF15332; LIME1; 1.
1: Evidence at protein level;
Adaptive immunity; Alternative splicing; Cell membrane;
Complete proteome; Immunity; Lipoprotein; Membrane; Palmitate;
Phosphoprotein; Polymorphism; Reference proteome; Signal-anchor;
Transmembrane; Transmembrane helix.
CHAIN 1 295 Lck-interacting transmembrane adapter 1.
/FTId=PRO_0000083332.
TOPO_DOM 1 6 Extracellular. {ECO:0000255}.
TRANSMEM 7 27 Helical; Signal-anchor for type III
membrane protein. {ECO:0000255}.
TOPO_DOM 28 295 Cytoplasmic. {ECO:0000255}.
REGION 145 148 Interaction with GRB2. {ECO:0000250}.
REGION 167 170 Interaction with CSK.
{ECO:0000269|PubMed:14610046}.
REGION 200 203 Interaction with CSK.
{ECO:0000269|PubMed:14610046}.
REGION 235 238 Interaction with LCK and PIK3R1.
{ECO:0000250}.
REGION 254 257 Interaction with LCK, PLCG2 and PIK3R1.
{ECO:0000250}.
MOD_RES 145 145 Phosphotyrosine.
{ECO:0000250|UniProtKB:Q9EQR5}.
MOD_RES 167 167 Phosphotyrosine.
{ECO:0000305|PubMed:14610046}.
MOD_RES 200 200 Phosphotyrosine.
{ECO:0000269|PubMed:14610046}.
MOD_RES 235 235 Phosphotyrosine.
{ECO:0000250|UniProtKB:Q9EQR5}.
MOD_RES 254 254 Phosphotyrosine; by LCK.
{ECO:0000305|PubMed:14610046}.
MOD_RES 256 256 Phosphoserine.
{ECO:0000244|PubMed:24275569}.
LIPID 28 28 S-palmitoyl cysteine.
{ECO:0000305|PubMed:14610046}.
LIPID 31 31 S-palmitoyl cysteine.
{ECO:0000305|PubMed:14610046}.
VAR_SEQ 1 95 Missing (in isoform 2).
{ECO:0000303|PubMed:15498874}.
/FTId=VSP_016642.
VARIANT 211 211 P -> L (in dbSNP:rs1151625).
/FTId=VAR_053918.
MUTAGEN 145 145 Y->F: No change in binding to LCK, CSK or
FYN. {ECO:0000269|PubMed:14610046}.
MUTAGEN 167 167 Y->F: Abolishes binding to CSK.
{ECO:0000269|PubMed:14610046}.
MUTAGEN 200 200 Y->F: Reduces binding to CSK.
{ECO:0000269|PubMed:14610046}.
MUTAGEN 235 235 Y->F: No change in binding to LCK, CSK or
FYN. {ECO:0000269|PubMed:14610046}.
MUTAGEN 254 254 Y->F: Abolishes binding to LCK and
reduces binding to FYN.
{ECO:0000269|PubMed:14610046}.
CONFLICT 246 246 D -> G (in Ref. 4; BAA91148).
{ECO:0000305}.
SEQUENCE 295 AA; 31288 MW; D85ACE978F2DC99E CRC64;
MGLPVSWAPP ALWVLGCCAL LLSLWALCTA CRRPEDAVAP RKRARRQRAR LQGSATAAEA
SLLRRTHLCS LSKSDTRLHE LHRGPRSSRA LRPASMDLLR PHWLEVSRDI TGPQAAPSAF
PHQELPRALP AAAATAGCAG LEATYSNVGL AALPGVSLAA SPVVAEYARV QKRKGTHRSP
QEPQQGKTEV TPAAQVDVLY SRVCKPKRRD PGPTTDPLDP KGQGAILALA GDLAYQTLPL
RALDVDSGPL ENVYESIREL GDPAGRSSTC GAGTPPASSC PSLGRGWRPL PASLP


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