LIMD1_MOUSE
ID LIMD1_MOUSE Reviewed; 668 AA.
AC Q9QXD8; Q8C8G4; Q9CW55;
DT 24-MAY-2004, integrated into UniProtKB/Swiss-Prot.
DT 24-MAY-2004, sequence version 2.
DT 03-AUG-2022, entry version 154.
DE RecName: Full=LIM domain-containing protein 1;
GN Name=Limd1;
OS Mus musculus (Mouse).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Mus; Mus.
OX NCBI_TaxID=10090;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], AND TISSUE SPECIFICITY.
RX PubMed=10647888; DOI=10.1007/s004399900188;
RA Kiss H., Kedra D., Yang Y., Kost-Alimova M., Kiss C., O'Brien K.P.,
RA Fransson I., Klein G., Imreh S., Dumanski J.P.;
RT "A novel gene containing LIM domains (LIMD1) is located within the common
RT eliminated region 1 (C3CER1) in 3p21.3.";
RL Hum. Genet. 105:552-559(1999).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=C57BL/6J; TISSUE=Cerebellum, and Lung;
RX PubMed=16141072; DOI=10.1126/science.1112014;
RA Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
RA Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
RA Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.,
RA Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R.,
RA Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T.,
RA Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A.,
RA Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B.,
RA Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M.,
RA Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S.,
RA Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
RA Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D.,
RA Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M.,
RA Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H.,
RA Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V.,
RA Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S.,
RA Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H.,
RA Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N.,
RA Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F.,
RA Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G.,
RA Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z.,
RA Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
RA Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
RA Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S.,
RA Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K.,
RA Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R.,
RA van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H.,
RA Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M.,
RA Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C.,
RA Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S.,
RA Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K.,
RA Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M.,
RA Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C.,
RA Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A.,
RA Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.;
RT "The transcriptional landscape of the mammalian genome.";
RL Science 309:1559-1563(2005).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=C57BL/6J; TISSUE=Brain;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [4]
RP FUNCTION, INDUCTION, AND INTERACTION WITH TRAF6.
RX PubMed=17092936; DOI=10.1074/jbc.m607399200;
RA Feng Y., Zhao H., Luderer H.F., Epple H., Faccio R., Ross F.P.,
RA Teitelbaum S.L., Longmore G.D.;
RT "The LIM protein, Limd1, regulates AP-1 activation through an interaction
RT with Traf6 to influence osteoclast development.";
RL J. Biol. Chem. 282:39-48(2007).
RN [5]
RP INTERACTION WITH SNAI1; SNAI2/SLUG AND SCRT1.
RX PubMed=18331720; DOI=10.1016/j.devcel.2008.01.005;
RA Langer E.M., Feng Y., Zhaoyuan H., Rauscher F.J. III, Kroll K.L.,
RA Longmore G.D.;
RT "Ajuba LIM proteins are snail/slug corepressors required for neural crest
RT development in Xenopus.";
RL Dev. Cell 14:424-436(2008).
RN [6]
RP FUNCTION, SUBCELLULAR LOCATION, AND INDUCTION.
RX PubMed=18657804; DOI=10.1016/j.yexcr.2008.06.003;
RA Luderer H.F., Bai S., Longmore G.D.;
RT "The LIM protein LIMD1 influences osteoblast differentiation and
RT function.";
RL Exp. Cell Res. 314:2884-2894(2008).
RN [7]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-413, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Heart, Kidney, Lung, Pancreas, Spleen, and Testis;
RX PubMed=21183079; DOI=10.1016/j.cell.2010.12.001;
RA Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R.,
RA Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.;
RT "A tissue-specific atlas of mouse protein phosphorylation and expression.";
RL Cell 143:1174-1189(2010).
CC -!- FUNCTION: Adapter or scaffold protein which participates in the
CC assembly of numerous protein complexes and is involved in several
CC cellular processes such as cell fate determination, cytoskeletal
CC organization, repression of gene transcription, cell-cell adhesion,
CC cell differentiation, proliferation and migration. Positively regulates
CC microRNA (miRNA)-mediated gene silencing and is essential for P-body
CC formation and integrity. Acts as a hypoxic regulator by bridging an
CC association between the prolyl hydroxylases and VHL enabling efficient
CC degradation of HIF1A. Acts as a transcriptional corepressor for
CC SNAI1- and SNAI2/SLUG-dependent repression of E-cadherin transcription.
CC Negatively regulates the Hippo signaling pathway and antagonizes
CC phosphorylation of YAP1. Inhibits E2F-mediated transcription, and
CC suppresses the expression of the majority of genes with E2F1-responsive
CC elements. Regulates osteoblast development, function, differentiation
CC and stress osteoclastogenesis. Enhances the ability of TRAF6 to
CC activate adapter protein complex 1 (AP-1) and negatively regulates the
CC canonical Wnt receptor signaling pathway in osteoblasts. May act as a
CC tumor suppressor by inhibiting cell proliferation.
CC {ECO:0000269|PubMed:17092936, ECO:0000269|PubMed:18657804}.
CC -!- SUBUNIT: Interacts with SQSTM1 and RB1. Interacts with EIF4E, AGO1,
CC AGO2, DCP2, DDX6, LATS1, LATS2, EGLN1/PHD2, EGLN2/PHD1 and EGLN3/PHD3.
CC Interacts (via LIM zinc-binding 2) with VHL. Found in a complex
CC composed of LIMD1, VHL, EGLN1/PHD2, ELOB and CUL2 (By similarity).
CC Interacts (via LIM domains) with SNAI1 (via SNAG domain), SNAI2/SLUG
CC (via SNAG domain) and SCRT1 (via SNAG domain). Found in a complex with
CC TRAF6, PRKCZ and SQSTM1. Interacts (via LIM domains) with TRAF6.
CC {ECO:0000250, ECO:0000269|PubMed:17092936,
CC ECO:0000269|PubMed:18331720}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:18657804}. Nucleus
CC {ECO:0000250}. Cytoplasm, P-body {ECO:0000250}. Cell junction, adherens
CC junction {ECO:0000250}. Cell junction, focal adhesion {ECO:0000250}.
CC Note=Shuttles between cytoplasm and nucleus but is localized
CC predominantly to the cytoplasm. Found in the nucleus but not nucleoli.
CC Colocalizes with VCL in the focal adhesions (By similarity).
CC {ECO:0000250}.
CC -!- TISSUE SPECIFICITY: Ubiquitous. {ECO:0000269|PubMed:10647888}.
CC -!- INDUCTION: Up-regulated during osteoclast differentiation.
CC {ECO:0000269|PubMed:17092936, ECO:0000269|PubMed:18657804}.
CC -!- PTM: Phosphorylated during mitosis. {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the zyxin/ajuba family. {ECO:0000305}.
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DR EMBL; AJ132409; CAB63700.1; -; mRNA.
DR EMBL; AK004806; BAB23578.1; -; mRNA.
DR EMBL; AK047198; BAC32988.1; -; mRNA.
DR EMBL; BC056449; AAH56449.1; -; mRNA.
DR CCDS; CCDS23660.1; -.
DR RefSeq; NP_038888.2; NM_013860.2.
DR AlphaFoldDB; Q9QXD8; -.
DR BioGRID; 205887; 4.
DR CORUM; Q9QXD8; -.
DR DIP; DIP-38453N; -.
DR IntAct; Q9QXD8; 6.
DR MINT; Q9QXD8; -.
DR STRING; 10090.ENSMUSP00000026269; -.
DR iPTMnet; Q9QXD8; -.
DR PhosphoSitePlus; Q9QXD8; -.
DR EPD; Q9QXD8; -.
DR jPOST; Q9QXD8; -.
DR MaxQB; Q9QXD8; -.
DR PaxDb; Q9QXD8; -.
DR PeptideAtlas; Q9QXD8; -.
DR PRIDE; Q9QXD8; -.
DR ProteomicsDB; 292257; -.
DR Antibodypedia; 29569; 217 antibodies from 26 providers.
DR DNASU; 29806; -.
DR Ensembl; ENSMUST00000026269; ENSMUSP00000026269; ENSMUSG00000025239.
DR GeneID; 29806; -.
DR KEGG; mmu:29806; -.
DR UCSC; uc009sge.2; mouse.
DR CTD; 8994; -.
DR MGI; MGI:1352502; Limd1.
DR VEuPathDB; HostDB:ENSMUSG00000025239; -.
DR eggNOG; KOG1701; Eukaryota.
DR GeneTree; ENSGT00940000159019; -.
DR HOGENOM; CLU_001357_11_1_1; -.
DR InParanoid; Q9QXD8; -.
DR OMA; SKLTMDG; -.
DR OrthoDB; 326249at2759; -.
DR PhylomeDB; Q9QXD8; -.
DR TreeFam; TF320310; -.
DR Reactome; R-MMU-1234176; Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha.
DR BioGRID-ORCS; 29806; 1 hit in 74 CRISPR screens.
DR ChiTaRS; Limd1; mouse.
DR PRO; PR:Q9QXD8; -.
DR Proteomes; UP000000589; Chromosome 9.
DR RNAct; Q9QXD8; protein.
DR Bgee; ENSMUSG00000025239; Expressed in saccule of membranous labyrinth and 248 other tissues.
DR ExpressionAtlas; Q9QXD8; baseline and differential.
DR Genevisible; Q9QXD8; MM.
DR GO; GO:0005912; C:adherens junction; ISS:UniProtKB.
DR GO; GO:0005737; C:cytoplasm; IDA:UniProtKB.
DR GO; GO:0005925; C:focal adhesion; ISS:UniProtKB.
DR GO; GO:0005654; C:nucleoplasm; ISO:MGI.
DR GO; GO:0005634; C:nucleus; ISS:UniProtKB.
DR GO; GO:0000932; C:P-body; ISO:MGI.
DR GO; GO:0005886; C:plasma membrane; ISO:MGI.
DR GO; GO:0016442; C:RISC complex; ISO:MGI.
DR GO; GO:0005667; C:transcription regulator complex; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0003714; F:transcription corepressor activity; IDA:UniProtKB.
DR GO; GO:0016477; P:cell migration; ISS:UniProtKB.
DR GO; GO:0007010; P:cytoskeleton organization; ISS:UniProtKB.
DR GO; GO:0035195; P:miRNA-mediated gene silencing; ISO:MGI.
DR GO; GO:0090090; P:negative regulation of canonical Wnt signaling pathway; IMP:UniProtKB.
DR GO; GO:0035331; P:negative regulation of hippo signaling; ISS:UniProtKB.
DR GO; GO:0045668; P:negative regulation of osteoblast differentiation; IMP:UniProtKB.
DR GO; GO:0045892; P:negative regulation of transcription, DNA-templated; ISS:UniProtKB.
DR GO; GO:0002076; P:osteoblast development; IMP:UniProtKB.
DR GO; GO:0033962; P:P-body assembly; ISO:MGI.
DR GO; GO:0016310; P:phosphorylation; ISS:UniProtKB.
DR GO; GO:2000637; P:positive regulation of miRNA-mediated gene silencing; ISS:UniProtKB.
DR GO; GO:0008360; P:regulation of cell shape; ISS:UniProtKB.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IBA:GO_Central.
DR GO; GO:0001666; P:response to hypoxia; ISS:UniProtKB.
DR InterPro; IPR028734; LIMD1.
DR InterPro; IPR001781; Znf_LIM.
DR PANTHER; PTHR24219:SF3; PTHR24219:SF3; 1.
DR Pfam; PF00412; LIM; 3.
DR SMART; SM00132; LIM; 3.
DR PROSITE; PS00478; LIM_DOMAIN_1; 2.
DR PROSITE; PS50023; LIM_DOMAIN_2; 3.
PE 1: Evidence at protein level;
KW Cell junction; Cytoplasm; LIM domain; Metal-binding; Nucleus;
KW Phosphoprotein; Reference proteome; Repeat; Repressor;
KW RNA-mediated gene silencing; Transcription; Transcription regulation;
KW Tumor suppressor; Zinc.
FT CHAIN 1..668
FT /note="LIM domain-containing protein 1"
FT /id="PRO_0000075802"
FT DOMAIN 462..523
FT /note="LIM zinc-binding 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00125"
FT DOMAIN 527..587
FT /note="LIM zinc-binding 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00125"
FT DOMAIN 587..656
FT /note="LIM zinc-binding 3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00125"
FT REGION 54..128
FT /note="Mediates nuclear export"
FT /evidence="ECO:0000250"
FT REGION 74..160
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 181..256
FT /note="Interaction with EGLN1/PHD2"
FT /evidence="ECO:0000250"
FT REGION 239..258
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 277..309
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 340..414
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 396..434
FT /note="Interaction with RB1"
FT /evidence="ECO:0000250"
FT REGION 464..668
FT /note="Necessary for nuclear localization"
FT /evidence="ECO:0000250"
FT COMPBIAS 111..127
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 277..303
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 340..358
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 371..411
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 139
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9UGP4"
FT MOD_RES 228
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9UGP4"
FT MOD_RES 235
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:B5DEH0"
FT MOD_RES 273
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9UGP4"
FT MOD_RES 296
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9UGP4"
FT MOD_RES 308
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:B5DEH0"
FT MOD_RES 413
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:21183079"
FT CONFLICT 17
FT /note="D -> E (in Ref. 2; BAC32988)"
FT /evidence="ECO:0000305"
FT CONFLICT 331
FT /note="D -> N (in Ref. 3; AAH56449)"
FT /evidence="ECO:0000305"
FT CONFLICT 487
FT /note="D -> N (in Ref. 2; BAC32988)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 668 AA; 71422 MW; 68C05A7BADEBDC92 CRC64;
MDKYDDLGLE ASKFIEDLNM YEASKDGLFR VDKGAGNNPE FEETRRVFAT KMAKIHLQQQ
QQQQLLQEEA LPRAGRSPVN GGNRQGASGK LAADGAAKPP LAVPTVAPGL ATTTAAAQPS
YPSQEQRIRP SAHGARPGSQ NCGSREGPVS SQRPALHGLS PSCEDPSCLT HGDYYDNFSL
ASPQWGDKPE GCPSVSLGVG SGWPGCPGND STLPKSCGDH HPYQPQLSTV CSGRSFESGI
SGQDGGIGGH SSEKPTGLWS TASSQRVNLG FSSMGLENGT SAQPKGTTVS APMVPSSASQ
GACPKRDSGL GYEASGRVFK PLVDTQPWLQ DGPKSYLSVS APLSSTAGKD STQPGMTTGL
DPKFGCVESG TSPKPSPTSN VHPVMSTPSE LSCKESSPSW STDSSLEPVL PGSPTPSRVR
LPCQTLAPGP ELGPSTAELK LEALTQRLER EMDAHPKADY FGSCVKCSKG VFGAGQACQA
MGDLYHDACF TCAACSRKLR GKAFYFVNGK VFCEEDFLYS GFQQSADRCF LCGHLIMDMI
LQALGKSYHP GCFRCVICNE CLDGVPFTVD SENKIYCVRD YHKVLAPKCA ACGLPILPPE
GSDETIRVVS MDRDYHVECY HCEDCGLELN DEDGHRCYPL EDHLFCHSCH VKRLEKGPSP
APLHQHHF
