Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Lck-interacting transmembrane adapter 1

Gene

LIME1

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

Complete GO annotation...

Keywords - Biological processi

Adaptive immunity, Immunity

Enzyme and pathway databases

BioCyciZFISH:ENSG00000179189-MONOMER.

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

HGNCiHGNC:26016. LIME1.

Subcellular locationi

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

GO - Cellular componenti

  • extracellular space Source: UniProtKB
  • integral component of membrane Source: UniProtKB-KW
  • plasma membrane Source: UniProtKB-SubCell
Complete GO annotation...

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 residuei167Phosphotyrosine1 Publication1
Modified residuei200Phosphotyrosine1 Publication1
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.

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.
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

Protein-protein interaction databases

BioGridi120264. 3 interactors.
IntActiQ9H400. 1 interactor.
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

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. AlignAdd to basket

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

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 rs1151625dbSNPEnsembl.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. 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_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

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. 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_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. 3 interactors.
IntActiQ9H400. 1 interactor.
STRINGi9606.ENSP00000309521.

PTM databases

iPTMnetiQ9H400.
PhosphoSitePlusiQ9H400.
SwissPalmiQ9H400.

Polymorphism and mutation databases

BioMutaiLIME1.
DMDMi74752630.

Proteomic databases

EPDiQ9H400.
MaxQBiQ9H400.
PaxDbiQ9H400.
PeptideAtlasiQ9H400.
PRIDEiQ9H400.

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.
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.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000179189-MONOMER.

Miscellaneous databases

GeneWikiiLIME1.
GenomeRNAii54923.
PROiQ9H400.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000203896.
CleanExiHS_LIME1.
ExpressionAtlasiQ9H400. baseline and differential.
GenevisibleiQ9H400. HS.

Family and domain databases

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

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: November 2, 2016
This is version 122 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.