LIMD1_RAT
ID LIMD1_RAT Reviewed; 663 AA.
AC B5DEH0;
DT 18-APR-2012, integrated into UniProtKB/Swiss-Prot.
DT 14-OCT-2008, sequence version 1.
DT 03-AUG-2022, entry version 82.
DE RecName: Full=LIM domain-containing protein 1;
GN Name=Limd1;
OS Rattus norvegicus (Rat).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Rattus.
OX NCBI_TaxID=10116;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Brown Norway;
RX PubMed=15057822; DOI=10.1038/nature02426;
RA Gibbs R.A., Weinstock G.M., Metzker M.L., Muzny D.M., Sodergren E.J.,
RA Scherer S., Scott G., Steffen D., Worley K.C., Burch P.E., Okwuonu G.,
RA Hines S., Lewis L., Deramo C., Delgado O., Dugan-Rocha S., Miner G.,
RA Morgan M., Hawes A., Gill R., Holt R.A., Adams M.D., Amanatides P.G.,
RA Baden-Tillson H., Barnstead M., Chin S., Evans C.A., Ferriera S.,
RA Fosler C., Glodek A., Gu Z., Jennings D., Kraft C.L., Nguyen T.,
RA Pfannkoch C.M., Sitter C., Sutton G.G., Venter J.C., Woodage T., Smith D.,
RA Lee H.-M., Gustafson E., Cahill P., Kana A., Doucette-Stamm L.,
RA Weinstock K., Fechtel K., Weiss R.B., Dunn D.M., Green E.D.,
RA Blakesley R.W., Bouffard G.G., De Jong P.J., Osoegawa K., Zhu B., Marra M.,
RA Schein J., Bosdet I., Fjell C., Jones S., Krzywinski M., Mathewson C.,
RA Siddiqui A., Wye N., McPherson J., Zhao S., Fraser C.M., Shetty J.,
RA Shatsman S., Geer K., Chen Y., Abramzon S., Nierman W.C., Havlak P.H.,
RA Chen R., Durbin K.J., Egan A., Ren Y., Song X.-Z., Li B., Liu Y., Qin X.,
RA Cawley S., Cooney A.J., D'Souza L.M., Martin K., Wu J.Q.,
RA Gonzalez-Garay M.L., Jackson A.R., Kalafus K.J., McLeod M.P.,
RA Milosavljevic A., Virk D., Volkov A., Wheeler D.A., Zhang Z., Bailey J.A.,
RA Eichler E.E., Tuzun E., Birney E., Mongin E., Ureta-Vidal A., Woodwark C.,
RA Zdobnov E., Bork P., Suyama M., Torrents D., Alexandersson M., Trask B.J.,
RA Young J.M., Huang H., Wang H., Xing H., Daniels S., Gietzen D., Schmidt J.,
RA Stevens K., Vitt U., Wingrove J., Camara F., Mar Alba M., Abril J.F.,
RA Guigo R., Smit A., Dubchak I., Rubin E.M., Couronne O., Poliakov A.,
RA Huebner N., Ganten D., Goesele C., Hummel O., Kreitler T., Lee Y.-A.,
RA Monti J., Schulz H., Zimdahl H., Himmelbauer H., Lehrach H., Jacob H.J.,
RA Bromberg S., Gullings-Handley J., Jensen-Seaman M.I., Kwitek A.E.,
RA Lazar J., Pasko D., Tonellato P.J., Twigger S., Ponting C.P., Duarte J.M.,
RA Rice S., Goodstadt L., Beatson S.A., Emes R.D., Winter E.E., Webber C.,
RA Brandt P., Nyakatura G., Adetobi M., Chiaromonte F., Elnitski L.,
RA Eswara P., Hardison R.C., Hou M., Kolbe D., Makova K., Miller W.,
RA Nekrutenko A., Riemer C., Schwartz S., Taylor J., Yang S., Zhang Y.,
RA Lindpaintner K., Andrews T.D., Caccamo M., Clamp M., Clarke L., Curwen V.,
RA Durbin R.M., Eyras E., Searle S.M., Cooper G.M., Batzoglou S., Brudno M.,
RA Sidow A., Stone E.A., Payseur B.A., Bourque G., Lopez-Otin C., Puente X.S.,
RA Chakrabarti K., Chatterji S., Dewey C., Pachter L., Bray N., Yap V.B.,
RA Caspi A., Tesler G., Pevzner P.A., Haussler D., Roskin K.M., Baertsch R.,
RA Clawson H., Furey T.S., Hinrichs A.S., Karolchik D., Kent W.J.,
RA Rosenbloom K.R., Trumbower H., Weirauch M., Cooper D.N., Stenson P.D.,
RA Ma B., Brent M., Arumugam M., Shteynberg D., Copley R.R., Taylor M.S.,
RA Riethman H., Mudunuri U., Peterson J., Guyer M., Felsenfeld A., Old S.,
RA Mockrin S., Collins F.S.;
RT "Genome sequence of the Brown Norway rat yields insights into mammalian
RT evolution.";
RL Nature 428:493-521(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Brown Norway;
RA Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.;
RL Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Prostate;
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 PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-233; SER-303 AND SER-304, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22673903; DOI=10.1038/ncomms1871;
RA Lundby A., Secher A., Lage K., Nordsborg N.B., Dmytriyev A., Lundby C.,
RA Olsen J.V.;
RT "Quantitative maps of protein phosphorylation sites across 14 different rat
RT organs and tissues.";
RL Nat. Commun. 3:876-876(2012).
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 (By similarity).
CC {ECO:0000250}.
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. Found in a complex
CC with TRAF6, PRKCZ and SQSTM1. Interacts (via LIM domains) with TRAF6.
CC Interacts (via LIM domains) with SNAI1 (via SNAG domain), SNAI2/SLUG
CC (via SNAG domain) and SCRT1 (via SNAG domain) (By similarity).
CC {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}. Nucleus {ECO:0000250}.
CC Cytoplasm, P-body {ECO:0000250}. Cell junction, adherens junction
CC {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 -!- PTM: Phosphorylated during mitosis. {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the zyxin/ajuba family. {ECO:0000305}.
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DR EMBL; AABR03062206; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AABR03062956; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CH473954; EDL76759.1; -; Genomic_DNA.
DR EMBL; BC168666; AAI68666.1; -; mRNA.
DR RefSeq; NP_001106208.1; NM_001112737.2.
DR AlphaFoldDB; B5DEH0; -.
DR STRING; 10116.ENSRNOP00000006554; -.
DR iPTMnet; B5DEH0; -.
DR PhosphoSitePlus; B5DEH0; -.
DR PaxDb; B5DEH0; -.
DR PeptideAtlas; B5DEH0; -.
DR Ensembl; ENSRNOT00000006554; ENSRNOP00000006554; ENSRNOG00000004837.
DR GeneID; 316101; -.
DR KEGG; rno:316101; -.
DR UCSC; RGD:1309830; rat.
DR CTD; 8994; -.
DR RGD; 1309830; Limd1.
DR eggNOG; KOG1701; Eukaryota.
DR GeneTree; ENSGT00940000159019; -.
DR HOGENOM; CLU_001357_11_1_1; -.
DR InParanoid; B5DEH0; -.
DR OMA; SKLTMDG; -.
DR OrthoDB; 326249at2759; -.
DR PhylomeDB; B5DEH0; -.
DR TreeFam; TF320310; -.
DR Reactome; R-RNO-1234176; Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha.
DR PRO; PR:B5DEH0; -.
DR Proteomes; UP000002494; Chromosome 8.
DR Proteomes; UP000234681; Chromosome 8.
DR Bgee; ENSRNOG00000004837; Expressed in heart and 18 other tissues.
DR Genevisible; B5DEH0; RN.
DR GO; GO:0005912; C:adherens junction; ISS:UniProtKB.
DR GO; GO:0005737; C:cytoplasm; ISS:UniProtKB.
DR GO; GO:0005925; C:focal adhesion; ISS:UniProtKB.
DR GO; GO:0005654; C:nucleoplasm; IEA:Ensembl.
DR GO; GO:0005634; C:nucleus; ISS:UniProtKB.
DR GO; GO:0000932; C:P-body; ISO:RGD.
DR GO; GO:0005886; C:plasma membrane; IEA:Ensembl.
DR GO; GO:0016442; C:RISC complex; ISO:RGD.
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; ISS:UniProtKB.
DR GO; GO:0016477; P:cell migration; ISO:RGD.
DR GO; GO:0007010; P:cytoskeleton organization; ISO:RGD.
DR GO; GO:0035195; P:miRNA-mediated gene silencing; ISO:RGD.
DR GO; GO:0090090; P:negative regulation of canonical Wnt signaling pathway; ISS:UniProtKB.
DR GO; GO:0035331; P:negative regulation of hippo signaling; ISS:UniProtKB.
DR GO; GO:0045668; P:negative regulation of osteoblast differentiation; ISS:UniProtKB.
DR GO; GO:0045892; P:negative regulation of transcription, DNA-templated; ISS:UniProtKB.
DR GO; GO:0002076; P:osteoblast development; ISS:UniProtKB.
DR GO; GO:0033962; P:P-body assembly; ISO:RGD.
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; ISO:RGD.
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..663
FT /note="LIM domain-containing protein 1"
FT /id="PRO_0000416961"
FT DOMAIN 457..518
FT /note="LIM zinc-binding 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00125"
FT DOMAIN 522..582
FT /note="LIM zinc-binding 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00125"
FT DOMAIN 583..651
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..99
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 117..158
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 180..251
FT /note="Interaction with EGLN1/PHD2"
FT /evidence="ECO:0000250"
FT REGION 230..253
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 267..297
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 335..416
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 391..429
FT /note="Interaction with RB1"
FT /evidence="ECO:0000250"
FT REGION 459..663
FT /note="Necessary for nuclear localization"
FT /evidence="ECO:0000250"
FT COMPBIAS 117..148
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 335..350
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 366..406
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 227
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9UGP4"
FT MOD_RES 233
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:22673903"
FT MOD_RES 268
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9UGP4"
FT MOD_RES 291
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9UGP4"
FT MOD_RES 303
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:22673903"
FT MOD_RES 304
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:22673903"
FT MOD_RES 408
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9UGP4"
SQ SEQUENCE 663 AA; 71393 MW; E28C6B3DB3AE3629 CRC64;
MDKYDDLGLE ASKFIEDLNM YEASKDGLFR VDKGASNNPE FEETRRVFAT KMAKIHLQQQ
QQQQLLQEEA LPRAGRSPIN GGNRQGVSSK LAADGAAKPP LAVPTVAPGL ATTTMAVQSS
YPPQEQRTRP SAHGARPGSQ NCGSREGPVS SQRPALHGLG PCEDPSCLTH GDYYDNFSLA
SPQWGDKPEE SPSMSLSVGS GWPGCPGNDS LSHRSCGDSH PYHPQLSMCS GRSFESGQDS
GIGGHSSEKP TGLWSTASSQ RVNLGFSSTG LENGTPAQPK GTTVSAPMVP SSTSQGACLR
RDSSLGYEAP GRVFKPLVDT QPWLQDGPKS YLSVSAPLSS TTSKDNAQTG MTAGLDPKLG
CVESGTSPKP SPTSNVHPVM SAPSELSCKE SPPSWSTDSS LGPVLPESPT PSRVRLPCQT
LTPGPELGPS TAELKLEALT QRLEREMDAH PKADYFGACV KCSKGVFGAG QACQAMGDLY
HDACFTCAAC SRKLRGKAFY FVNGKVFCEE DFLYSGFQQS ADRCFLCGHL IMDMILQALG
KSYHPGCFRC VICNECLDGV PFTVDSENKI YCVRDYHKVL APKCAACGLP ILPPEGSDET
IRVVSMDRDY HVECYHCEDC GLELNDEDGH RCYPLEDHLF CHSCHVKRLE KGPSPASLHQ
HHF
