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Q9H400 (LIME1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 103. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Lck-interacting transmembrane adapter 1

Short name=Lck-interacting membrane protein
Alternative name(s):
Lck-interacting molecule
Gene names
Name:LIME1
Synonyms:LIME
ORF Names:LP8067
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length295 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

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. Ref.1

Subunit structure

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. Ref.1 Ref.2

Subcellular location

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. Ref.1 Ref.2

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). Ref.1 Ref.2 Ref.8

Post-translational modification

Palmitoylation of Cys-28 and Cys-31 is required for raft targeting. Ref.1

Phosphorylated on tyrosines upon TCR activation and/or CD4 coreceptor stimulation, or upon BCR stimulation; which leads to the recruitment of SH2-containing proteins. Ref.1 Ref.2

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9H400-1)

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.
Isoform 2 (identifier: Q9H400-2)

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 295295Lck-interacting transmembrane adapter 1
PRO_0000083332

Regions

Topological domain1 – 66Extracellular Potential
Transmembrane7 – 2721Helical; Signal-anchor for type III membrane protein; Potential
Topological domain28 – 295268Cytoplasmic Potential
Region145 – 1484Interaction with GRB2 By similarity
Region167 – 1704Interaction with CSK
Region200 – 2034Interaction with CSK
Region235 – 2384Interaction with LCK and PIK3R1 By similarity
Region254 – 2574Interaction with LCK, PLCG2 and PIK3R1 By similarity

Amino acid modifications

Modified residue1671Phosphotyrosine Probable
Modified residue2001Phosphotyrosine Ref.1
Modified residue2541Phosphotyrosine; by LCK Probable
Lipidation281S-palmitoyl cysteine Probable
Lipidation311S-palmitoyl cysteine Probable

Natural variations

Alternative sequence1 – 9595Missing in isoform 2.
VSP_016642
Natural variant2111P → L.
Corresponds to variant rs1151625 [ dbSNP | Ensembl ].
VAR_053918

Experimental info

Mutagenesis1451Y → F: No change in binding to LCK, CSK or FYN. Ref.1
Mutagenesis1671Y → F: Abolishes binding to CSK. Ref.1
Mutagenesis2001Y → F: Reduces binding to CSK. Ref.1
Mutagenesis2351Y → F: No change in binding to LCK, CSK or FYN. Ref.1
Mutagenesis2541Y → F: Abolishes binding to LCK and reduces binding to FYN. Ref.1
Sequence conflict2461D → G in BAA91148. Ref.4

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified March 1, 2001. Version 1.
Checksum: D85ACE978F2DC99E

FASTA29531,288
        10         20         30         40         50         60 
MGLPVSWAPP ALWVLGCCAL LLSLWALCTA CRRPEDAVAP RKRARRQRAR LQGSATAAEA 

        70         80         90        100        110        120 
SLLRRTHLCS LSKSDTRLHE LHRGPRSSRA LRPASMDLLR PHWLEVSRDI TGPQAAPSAF 

       130        140        150        160        170        180 
PHQELPRALP AAAATAGCAG LEATYSNVGL AALPGVSLAA SPVVAEYARV QKRKGTHRSP 

       190        200        210        220        230        240 
QEPQQGKTEV TPAAQVDVLY SRVCKPKRRD PGPTTDPLDP KGQGAILALA GDLAYQTLPL 

       250        260        270        280        290 
RALDVDSGPL ENVYESIREL GDPAGRSSTC GAGTPPASSC PSLGRGWRPL PASLP 

« Hide

Isoform 2 [UniParc].

Checksum: 44A69D6E2379BCB3
Show »

FASTA20020,841

References

« Hide 'large scale' references
[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. expand/collapse author list , 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. expand/collapse author list , 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. expand/collapse author list , 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]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. expand/collapse author list , 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
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]"Transmembrane adaptor molecules: a new category of lymphoid-cell markers."
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.
Blood 107:213-221(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: TISSUE SPECIFICITY.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
CCDSCCDS13536.1. [Q9H400-1]
RefSeqNP_060276.2. NM_017806.2. [Q9H400-1]
UniGeneHs.233220.

3D structure databases

ProteinModelPortalQ9H400.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

IntActQ9H400. 1 interaction.
STRING9606.ENSP00000309521.

PTM databases

PhosphoSiteQ9H400.

Polymorphism databases

DMDM74752630.

Proteomic databases

MaxQBQ9H400.
PaxDbQ9H400.
PRIDEQ9H400.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000309546; ENSP00000309521; ENSG00000203896. [Q9H400-1]
GeneID54923.
KEGGhsa:54923.
UCSCuc002ygp.4. human. [Q9H400-1]

Organism-specific databases

CTD54923.
GeneCardsGC20P062366.
HGNCHGNC:26016. LIME1.
HPACAB015363.
MIM609809. gene.
neXtProtNX_Q9H400.
PharmGKBPA142671551.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG77780.
HOGENOMHOG000231956.
HOVERGENHBG080499.
InParanoidQ9H400.
OMAVAEYACI.
OrthoDBEOG780RNR.
PhylomeDBQ9H400.
TreeFamTF337416.

Gene expression databases

BgeeQ9H400.
CleanExHS_LIME1.
GenevestigatorQ9H400.

Family and domain databases

InterProIPR026072. Lime1.
[Graphical view]
PfamPF15332. LIME1. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

GeneWikiLIME1.
GenomeRNAi54923.
NextBio58007.
PROQ9H400.
SOURCESearch...

Entry information

Entry nameLIME1_HUMAN
AccessionPrimary (citable) accession number: Q9H400
Secondary accession number(s): E1P5K5 expand/collapse secondary AC list , E1P5K6, Q5JWJ2, Q6XYB3, Q9NX69
Entry history
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 statusReviewed (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.

Relevant documents

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 20

Human chromosome 20: entries, gene names and cross-references to MIM