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Protein

Lck-interacting transmembrane adapter 1

Gene

LIME1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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 - Molecular functioni

  • protein kinase binding Source: GO_Central

GO - Biological processi

Keywordsi

Biological processAdaptive 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
Proteomesi
  • UP000005640 Componenti: Chromosome 20

Organism-specific databases

EuPathDBiHostDB:ENSG00000203896.9
HGNCiHGNC:26016 LIME1
MIMi609809 gene
neXtProtiNX_Q9H400

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini1 – 6ExtracellularSequence analysis6
Transmembranei7 – 27Helical; Signal-anchor for type III membrane proteinSequence analysisAdd BLAST21
Topological domaini28 – 295CytoplasmicSequence analysisAdd BLAST268

Keywords - Cellular componenti

Cell membrane, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi145Y → F: No change in binding to LCK, CSK or FYN. 1 Publication1
Mutagenesisi167Y → F: Abolishes binding to CSK. 1 Publication1
Mutagenesisi200Y → F: Reduces binding to CSK. 1 Publication1
Mutagenesisi235Y → F: No change in binding to LCK, CSK or FYN. 1 Publication1
Mutagenesisi254Y → F: Abolishes binding to LCK and reduces binding to FYN. 1 Publication1

Organism-specific databases

OpenTargetsiENSG00000203896
PharmGKBiPA142671551

Polymorphism and mutation databases

BioMutaiLIME1
DMDMi74752630

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000833321 – 295Lck-interacting transmembrane adapter 1Add BLAST295

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Lipidationi28S-palmitoyl cysteine1 Publication1
Lipidationi31S-palmitoyl cysteine1 Publication1
Modified residuei145PhosphotyrosineBy similarity1
Modified residuei167Phosphotyrosine1 Publication1
Modified residuei200Phosphotyrosine1 Publication1
Modified residuei235PhosphotyrosineBy similarity1
Modified residuei254Phosphotyrosine; by LCK1 Publication1
Modified residuei256PhosphoserineCombined sources1

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

EPDiQ9H400
MaxQBiQ9H400
PaxDbiQ9H400
PeptideAtlasiQ9H400
PRIDEiQ9H400
ProteomicsDBi80775
80776 [Q9H400-2]

PTM databases

iPTMnetiQ9H400
PhosphoSitePlusiQ9H400
SwissPalmiQ9H400

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

BgeeiENSG00000203896 Expressed in 87 organ(s), highest expression level in liver
CleanExiHS_LIME1
ExpressionAtlasiQ9H400 baseline and differential
GenevisibleiQ9H400 HS

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

GO - Molecular functioni

Protein-protein interaction databases

BioGridi120264, 4 interactors
IntActiQ9H400, 39 interactors
STRINGi9606.ENSP00000309521

Structurei

3D structure databases

ProteinModelPortaliQ9H400
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni145 – 148Interaction with GRB2By similarity4
Regioni167 – 170Interaction with CSK1 Publication4
Regioni200 – 203Interaction with CSK1 Publication4
Regioni235 – 238Interaction with LCK and PIK3R1By similarity4
Regioni254 – 257Interaction with LCK, PLCG2 and PIK3R1By similarity4

Keywords - Domaini

Signal-anchor, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG410J9JT Eukaryota
ENOG41114H9 LUCA
GeneTreeiENSGT00510000050080
HOGENOMiHOG000231956
HOVERGENiHBG080499
InParanoidiQ9H400
OMAiVAEYACI
OrthoDBiEOG091G0IKW
PhylomeDBiQ9H400
TreeFamiTF337416

Family and domain databases

InterProiView protein in InterPro
IPR026072 Lime1
PfamiView protein in Pfam
PF15332 LIME1, 1 hit

Sequences (2+)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 2 described isoforms and 5 potential isoforms that are computationally mapped.Show allAlign All

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
        10         20         30         40         50
MGLPVSWAPP ALWVLGCCAL LLSLWALCTA CRRPEDAVAP RKRARRQRAR
60 70 80 90 100
LQGSATAAEA SLLRRTHLCS LSKSDTRLHE LHRGPRSSRA LRPASMDLLR
110 120 130 140 150
PHWLEVSRDI TGPQAAPSAF PHQELPRALP AAAATAGCAG LEATYSNVGL
160 170 180 190 200
AALPGVSLAA SPVVAEYARV QKRKGTHRSP QEPQQGKTEV TPAAQVDVLY
210 220 230 240 250
SRVCKPKRRD PGPTTDPLDP KGQGAILALA GDLAYQTLPL RALDVDSGPL
260 270 280 290
ENVYESIREL GDPAGRSSTC GAGTPPASSC PSLGRGWRPL PASLP
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

Computationally mapped potential isoform sequencesi

There are 5 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
A0A087WT39A0A087WT39_HUMAN
Lck-interacting transmembrane adapt...
LIME1
176Annotation score:
V9GYI1V9GYI1_HUMAN
Lck-interacting transmembrane adapt...
LIME1
131Annotation score:
A0A087WUJ1A0A087WUJ1_HUMAN
Lck-interacting transmembrane adapt...
LIME1
252Annotation score:
X6RKG5X6RKG5_HUMAN
Lck-interacting transmembrane adapt...
LIME1
106Annotation score:
A0A087WZP9A0A087WZP9_HUMAN
Lck-interacting transmembrane adapt...
LIME1
211Annotation score:

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti246D → G in BAA91148 (PubMed:14702039).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_053918211P → L. Corresponds to variant dbSNP:rs1151625Ensembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0166421 – 95Missing in isoform 2. 1 PublicationAdd BLAST95

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY203957 mRNA Translation: AAP34480.1
AK000413 mRNA Translation: BAA91148.1
AL121845 Genomic DNA No translation available.
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_001292583.1, NM_001305654.1
NP_001292584.1, NM_001305655.1
NP_060276.2, NM_017806.3 [Q9H400-1]
UniGeneiHs.233220

Genome annotation databases

EnsembliENST00000309546; ENSP00000309521; ENSG00000203896 [Q9H400-1]
GeneIDi54923
KEGGihsa:54923
UCSCiuc002ygp.5 human [Q9H400-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY203957 mRNA Translation: AAP34480.1
AK000413 mRNA Translation: BAA91148.1
AL121845 Genomic DNA No translation available.
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_001292583.1, NM_001305654.1
NP_001292584.1, NM_001305655.1
NP_060276.2, NM_017806.3 [Q9H400-1]
UniGeneiHs.233220

3D structure databases

ProteinModelPortaliQ9H400
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi120264, 4 interactors
IntActiQ9H400, 39 interactors
STRINGi9606.ENSP00000309521

PTM databases

iPTMnetiQ9H400
PhosphoSitePlusiQ9H400
SwissPalmiQ9H400

Polymorphism and mutation databases

BioMutaiLIME1
DMDMi74752630

Proteomic databases

EPDiQ9H400
MaxQBiQ9H400
PaxDbiQ9H400
PeptideAtlasiQ9H400
PRIDEiQ9H400
ProteomicsDBi80775
80776 [Q9H400-2]

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000309546; ENSP00000309521; ENSG00000203896 [Q9H400-1]
GeneIDi54923
KEGGihsa:54923
UCSCiuc002ygp.5 human [Q9H400-1]

Organism-specific databases

CTDi54923
EuPathDBiHostDB:ENSG00000203896.9
GeneCardsiLIME1
HGNCiHGNC:26016 LIME1
HPAiCAB015363
MIMi609809 gene
neXtProtiNX_Q9H400
OpenTargetsiENSG00000203896
PharmGKBiPA142671551
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410J9JT Eukaryota
ENOG41114H9 LUCA
GeneTreeiENSGT00510000050080
HOGENOMiHOG000231956
HOVERGENiHBG080499
InParanoidiQ9H400
OMAiVAEYACI
OrthoDBiEOG091G0IKW
PhylomeDBiQ9H400
TreeFamiTF337416

Miscellaneous databases

GeneWikiiLIME1
GenomeRNAii54923
PROiPR:Q9H400
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000203896 Expressed in 87 organ(s), highest expression level in liver
CleanExiHS_LIME1
ExpressionAtlasiQ9H400 baseline and differential
GenevisibleiQ9H400 HS

Family and domain databases

InterProiView protein in InterPro
IPR026072 Lime1
PfamiView protein in Pfam
PF15332 LIME1, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiLIME1_HUMAN
AccessioniPrimary (citable) accession number: Q9H400
Secondary accession number(s): E1P5K5
, E1P5K6, Q5JWJ2, Q6XYB3, Q9NX69
Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 20, 2005
Last sequence update: March 1, 2001
Last modified: November 7, 2018
This is version 133 of the entry and version 1 of the sequence. See 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 entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  2. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  3. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  4. Human chromosome 20
    Human chromosome 20: entries, gene names and cross-references to MIM
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Main funding by: National Institutes of Health

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