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

LIM domain-containing protein 1

Gene

Limd1

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: -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

  • metal ion binding Source: UniProtKB-KW
  • transcription corepressor activity Source: UniProtKB

GO - Biological processi

Keywordsi

Molecular functionRepressor
Biological processRNA-mediated gene silencing, Transcription, Transcription regulation
LigandMetal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-MMU-1234176 Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha

Names & Taxonomyi

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

Organism-specific databases

MGIiMGI:1352502 Limd1

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

Keywords - Cellular componenti

Cell junction, Cytoplasm, Nucleus

Pathology & Biotechi

Keywords - Diseasei

Tumor suppressor

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000758021 – 668LIM domain-containing protein 1Add BLAST668

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei139PhosphoserineBy similarity1
Modified residuei228PhosphoserineBy similarity1
Modified residuei235PhosphoserineBy similarity1
Modified residuei273PhosphoserineBy similarity1
Modified residuei296PhosphoserineBy similarity1
Modified residuei308PhosphoserineBy similarity1
Modified residuei413PhosphoserineCombined sources1

Post-translational modificationi

Phosphorylated during mitosis.By similarity

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ9QXD8
MaxQBiQ9QXD8
PaxDbiQ9QXD8
PeptideAtlasiQ9QXD8
PRIDEiQ9QXD8

PTM databases

iPTMnetiQ9QXD8
PhosphoSitePlusiQ9QXD8

Expressioni

Tissue specificityi

Ubiquitous.1 Publication

Inductioni

Up-regulated during osteoclast differentiation.2 Publications

Gene expression databases

BgeeiENSMUSG00000025239 Expressed in 283 organ(s), highest expression level in ear vesicle
CleanExiMM_LIMD1
ExpressionAtlasiQ9QXD8 baseline and differential
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, ELOB 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 interactors
CORUMiQ9QXD8
DIPiDIP-38453N
IntActiQ9QXD8, 6 interactors
MINTiQ9QXD8
STRINGi10090.ENSMUSP00000026269

Structurei

3D structure databases

ProteinModelPortaliQ9QXD8
SMRiQ9QXD8
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini462 – 523LIM zinc-binding 1PROSITE-ProRule annotationAdd BLAST62
Domaini527 – 587LIM zinc-binding 2PROSITE-ProRule annotationAdd BLAST61
Domaini587 – 656LIM zinc-binding 3PROSITE-ProRule annotationAdd BLAST70

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni54 – 128Mediates nuclear exportBy similarityAdd BLAST75
Regioni181 – 256Interaction with EGLN1/PHD2By similarityAdd BLAST76
Regioni396 – 434Interaction with RB1By similarityAdd BLAST39
Regioni464 – 668Necessary for nuclear localizationBy similarityAdd BLAST205

Sequence similaritiesi

Belongs to the zyxin/ajuba family.Curated

Keywords - Domaini

LIM domain, Repeat

Phylogenomic databases

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

Family and domain databases

InterProiView protein in InterPro
IPR028734 LIMD1
IPR001781 Znf_LIM
PANTHERiPTHR24219:SF3 PTHR24219:SF3, 1 hit
PfamiView protein in Pfam
PF00412 LIM, 3 hits
SMARTiView protein in SMART
SM00132 LIM, 3 hits
PROSITEiView protein in PROSITE
PS00478 LIM_DOMAIN_1, 2 hits
PS50023 LIM_DOMAIN_2, 3 hits

Sequence (1+)i

Sequence statusi: Complete.

This entry has 1 described isoform and 1 potential isoform that is computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
A0A1L1SUR8A0A1L1SUR8_MOUSE
LIM domain-containing protein 1
Limd1
72Annotation score:

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti17D → E in BAC32988 (PubMed:16141072).Curated1
Sequence conflicti331D → N in AAH56449 (PubMed:15489334).Curated1
Sequence conflicti487D → N in BAC32988 (PubMed:16141072).Curated1

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

Similar proteinsi

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
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi205887, 3 interactors
CORUMiQ9QXD8
DIPiDIP-38453N
IntActiQ9QXD8, 6 interactors
MINTiQ9QXD8
STRINGi10090.ENSMUSP00000026269

PTM databases

iPTMnetiQ9QXD8
PhosphoSitePlusiQ9QXD8

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
OMAiHQPGPCE
OrthoDBiEOG091G057U
PhylomeDBiQ9QXD8
TreeFamiTF320310

Enzyme and pathway databases

ReactomeiR-MMU-1234176 Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha

Miscellaneous databases

ChiTaRSiLimd1 mouse
PROiPR:Q9QXD8
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000025239 Expressed in 283 organ(s), highest expression level in ear vesicle
CleanExiMM_LIMD1
ExpressionAtlasiQ9QXD8 baseline and differential
GenevisibleiQ9QXD8 MM

Family and domain databases

InterProiView protein in InterPro
IPR028734 LIMD1
IPR001781 Znf_LIM
PANTHERiPTHR24219:SF3 PTHR24219:SF3, 1 hit
PfamiView protein in Pfam
PF00412 LIM, 3 hits
SMARTiView protein in SMART
SM00132 LIM, 3 hits
PROSITEiView protein in PROSITE
PS00478 LIM_DOMAIN_1, 2 hits
PS50023 LIM_DOMAIN_2, 3 hits
ProtoNetiSearch...

Entry informationi

Entry nameiLIMD1_MOUSE
AccessioniPrimary (citable) accession number: Q9QXD8
Secondary accession number(s): Q8C8G4, Q9CW55
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 24, 2004
Last sequence update: May 24, 2004
Last modified: November 7, 2018
This is version 135 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

We'd like to inform you that we have updated our Privacy Notice to comply with Europe’s new General Data Protection Regulation (GDPR) that applies since 25 May 2018.

Do not show this banner again