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Protein

LIM domain-containing protein 1

Gene

Limd1

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Adapter or scaffold protein which participates in the assembly of numerous protein complexes and is involved in several cellular processes such as cell fate determination, cytoskeletal organization, repression of gene transcription, cell-cell adhesion, cell differentiation, proliferation and migration. Positively regulates microRNA (miRNA)-mediated gene silencing and is essential for P-body formation and integrity. Acts as a hypoxic regulator by bridging an association between the prolyl hydroxylases and VHL enabling efficient degradation of HIF1A. Acts as a transcriptional corepressor for SNAI1- and SNAI2/SLUG-dependent repression of E-cadherin transcription. Negatively regulates the Hippo signaling pathway and antagonizes phosphorylation of YAP1. Inhibits E2F-mediated transcription, and suppresses the expression of the majority of genes with E2F1-responsive elements. Regulates osteoblast development, function, differentiation and stress osteoclastogenesis. Enhances the ability of TRAF6 to activate adapter protein complex 1 (AP-1) and negatively regulates the canonical Wnt receptor signaling pathway in osteoblasts. May act as a tumor suppressor by inhibiting cell proliferation.2 Publications

GO - Molecular functioni

  • transcription corepressor activity Source: UniProtKB
  • zinc ion binding Source: InterPro

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Repressor

Keywords - Biological processi

RNA-mediated gene silencing, Transcription, Transcription regulation

Keywords - Ligandi

Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
LIM domain-containing protein 1
Gene namesi
Name:Limd1
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 9

Organism-specific databases

MGIiMGI:1352502. Limd1.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell junction, Cytoplasm, Nucleus

Pathology & Biotechi

Keywords - Diseasei

Tumor suppressor

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 668668LIM domain-containing protein 1PRO_0000075802Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei139 – 1391PhosphoserineBy similarity
Modified residuei228 – 2281PhosphoserineBy similarity
Modified residuei235 – 2351PhosphoserineBy similarity
Modified residuei273 – 2731PhosphoserineBy similarity
Modified residuei296 – 2961PhosphoserineBy similarity
Modified residuei308 – 3081PhosphoserineBy similarity
Modified residuei413 – 4131PhosphoserineCombined sources

Post-translational modificationi

Phosphorylated during mitosis.By similarity

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ9QXD8.
MaxQBiQ9QXD8.
PaxDbiQ9QXD8.
PeptideAtlasiQ9QXD8.
PRIDEiQ9QXD8.

PTM databases

iPTMnetiQ9QXD8.
PhosphoSiteiQ9QXD8.

Expressioni

Tissue specificityi

Ubiquitous.1 Publication

Inductioni

Up-regulated during osteoclast differentiation.2 Publications

Gene expression databases

BgeeiENSMUSG00000025239.
CleanExiMM_LIMD1.
GenevisibleiQ9QXD8. MM.

Interactioni

Subunit structurei

Interacts with SQSTM1 and RB1. Interacts with EIF4E, AGO1, AGO2, DCP2, DDX6, LATS1, LATS2, EGLN1/PHD2, EGLN2/PHD1 and EGLN3/PHD3. Interacts (via LIM zinc-binding 2) with VHL. Found in a complex composed of LIMD1, VHL, EGLN1/PHD2, TCEB2 AND CUL2 (By similarity). Interacts (via LIM domains) with SNAI1 (via SNAG domain), SNAI2/SLUG (via SNAG domain) and SCRT1 (via SNAG domain). Found in a complex with TRAF6, PRKCZ and SQSTM1. Interacts (via LIM domains) with TRAF6.By similarity2 Publications

Protein-protein interaction databases

BioGridi205887. 3 interactions.
DIPiDIP-38453N.
IntActiQ9QXD8. 5 interactions.
MINTiMINT-4100414.
STRINGi10090.ENSMUSP00000026269.

Structurei

3D structure databases

ProteinModelPortaliQ9QXD8.
SMRiQ9QXD8. Positions 462-650.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini462 – 52362LIM zinc-binding 1PROSITE-ProRule annotationAdd
BLAST
Domaini527 – 58761LIM zinc-binding 2PROSITE-ProRule annotationAdd
BLAST
Domaini587 – 65670LIM zinc-binding 3PROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni54 – 12875Mediates nuclear exportBy similarityAdd
BLAST
Regioni181 – 25676Interaction with EGLN1/PHD2By similarityAdd
BLAST
Regioni396 – 43439Interaction with RB1By similarityAdd
BLAST
Regioni464 – 668205Necessary for nuclear localizationBy similarityAdd
BLAST

Sequence similaritiesi

Belongs to the zyxin/ajuba family.Curated
Contains 3 LIM zinc-binding domains.PROSITE-ProRule annotation

Keywords - Domaini

LIM domain, Repeat

Phylogenomic databases

eggNOGiKOG1701. Eukaryota.
ENOG410Y3GP. LUCA.
GeneTreeiENSGT00760000119039.
HOGENOMiHOG000072700.
HOVERGENiHBG052327.
InParanoidiQ9QXD8.
KOiK16682.
OMAiCHACHLK.
OrthoDBiEOG091G057U.
PhylomeDBiQ9QXD8.
TreeFamiTF320310.

Family and domain databases

Gene3Di2.10.110.10. 3 hits.
InterProiIPR028734. LIMD1.
IPR001781. Znf_LIM.
[Graphical view]
PANTHERiPTHR24219:SF3. PTHR24219:SF3. 1 hit.
PfamiPF00412. LIM. 3 hits.
[Graphical view]
SMARTiSM00132. LIM. 3 hits.
[Graphical view]
PROSITEiPS00478. LIM_DOMAIN_1. 2 hits.
PS50023. LIM_DOMAIN_2. 3 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9QXD8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDKYDDLGLE ASKFIEDLNM YEASKDGLFR VDKGAGNNPE FEETRRVFAT
60 70 80 90 100
KMAKIHLQQQ QQQQLLQEEA LPRAGRSPVN GGNRQGASGK LAADGAAKPP
110 120 130 140 150
LAVPTVAPGL ATTTAAAQPS YPSQEQRIRP SAHGARPGSQ NCGSREGPVS
160 170 180 190 200
SQRPALHGLS PSCEDPSCLT HGDYYDNFSL ASPQWGDKPE GCPSVSLGVG
210 220 230 240 250
SGWPGCPGND STLPKSCGDH HPYQPQLSTV CSGRSFESGI SGQDGGIGGH
260 270 280 290 300
SSEKPTGLWS TASSQRVNLG FSSMGLENGT SAQPKGTTVS APMVPSSASQ
310 320 330 340 350
GACPKRDSGL GYEASGRVFK PLVDTQPWLQ DGPKSYLSVS APLSSTAGKD
360 370 380 390 400
STQPGMTTGL DPKFGCVESG TSPKPSPTSN VHPVMSTPSE LSCKESSPSW
410 420 430 440 450
STDSSLEPVL PGSPTPSRVR LPCQTLAPGP ELGPSTAELK LEALTQRLER
460 470 480 490 500
EMDAHPKADY FGSCVKCSKG VFGAGQACQA MGDLYHDACF TCAACSRKLR
510 520 530 540 550
GKAFYFVNGK VFCEEDFLYS GFQQSADRCF LCGHLIMDMI LQALGKSYHP
560 570 580 590 600
GCFRCVICNE CLDGVPFTVD SENKIYCVRD YHKVLAPKCA ACGLPILPPE
610 620 630 640 650
GSDETIRVVS MDRDYHVECY HCEDCGLELN DEDGHRCYPL EDHLFCHSCH
660
VKRLEKGPSP APLHQHHF
Length:668
Mass (Da):71,422
Last modified:May 24, 2004 - v2
Checksum:i68C05A7BADEBDC92
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti17 – 171D → E in BAC32988 (PubMed:16141072).Curated
Sequence conflicti331 – 3311D → N in AAH56449 (PubMed:15489334).Curated
Sequence conflicti487 – 4871D → N in BAC32988 (PubMed:16141072).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ132409 mRNA. Translation: CAB63700.1.
AK004806 mRNA. Translation: BAB23578.1.
AK047198 mRNA. Translation: BAC32988.1.
BC056449 mRNA. Translation: AAH56449.1.
CCDSiCCDS23660.1.
RefSeqiNP_038888.2. NM_013860.2.
UniGeneiMm.10987.

Genome annotation databases

EnsembliENSMUST00000026269; ENSMUSP00000026269; ENSMUSG00000025239.
GeneIDi29806.
KEGGimmu:29806.
UCSCiuc009sge.2. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ132409 mRNA. Translation: CAB63700.1.
AK004806 mRNA. Translation: BAB23578.1.
AK047198 mRNA. Translation: BAC32988.1.
BC056449 mRNA. Translation: AAH56449.1.
CCDSiCCDS23660.1.
RefSeqiNP_038888.2. NM_013860.2.
UniGeneiMm.10987.

3D structure databases

ProteinModelPortaliQ9QXD8.
SMRiQ9QXD8. Positions 462-650.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi205887. 3 interactions.
DIPiDIP-38453N.
IntActiQ9QXD8. 5 interactions.
MINTiMINT-4100414.
STRINGi10090.ENSMUSP00000026269.

PTM databases

iPTMnetiQ9QXD8.
PhosphoSiteiQ9QXD8.

Proteomic databases

EPDiQ9QXD8.
MaxQBiQ9QXD8.
PaxDbiQ9QXD8.
PeptideAtlasiQ9QXD8.
PRIDEiQ9QXD8.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000026269; ENSMUSP00000026269; ENSMUSG00000025239.
GeneIDi29806.
KEGGimmu:29806.
UCSCiuc009sge.2. mouse.

Organism-specific databases

CTDi8994.
MGIiMGI:1352502. Limd1.

Phylogenomic databases

eggNOGiKOG1701. Eukaryota.
ENOG410Y3GP. LUCA.
GeneTreeiENSGT00760000119039.
HOGENOMiHOG000072700.
HOVERGENiHBG052327.
InParanoidiQ9QXD8.
KOiK16682.
OMAiCHACHLK.
OrthoDBiEOG091G057U.
PhylomeDBiQ9QXD8.
TreeFamiTF320310.

Miscellaneous databases

ChiTaRSiLimd1. mouse.
PROiQ9QXD8.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000025239.
CleanExiMM_LIMD1.
GenevisibleiQ9QXD8. MM.

Family and domain databases

Gene3Di2.10.110.10. 3 hits.
InterProiIPR028734. LIMD1.
IPR001781. Znf_LIM.
[Graphical view]
PANTHERiPTHR24219:SF3. PTHR24219:SF3. 1 hit.
PfamiPF00412. LIM. 3 hits.
[Graphical view]
SMARTiSM00132. LIM. 3 hits.
[Graphical view]
PROSITEiPS00478. LIM_DOMAIN_1. 2 hits.
PS50023. LIM_DOMAIN_2. 3 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiLIMD1_MOUSE
AccessioniPrimary (citable) accession number: Q9QXD8
Secondary accession number(s): Q8C8G4, Q9CW55
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 24, 2004
Last sequence update: May 24, 2004
Last modified: September 7, 2016
This is version 122 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

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.