LIMD1_BOVIN
ID LIMD1_BOVIN Reviewed; 674 AA.
AC G5E5X0;
DT 18-APR-2012, integrated into UniProtKB/Swiss-Prot.
DT 14-DEC-2011, sequence version 1.
DT 03-AUG-2022, entry version 58.
DE RecName: Full=LIM domain-containing protein 1;
GN Name=LIMD1;
OS Bos taurus (Bovine).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Laurasiatheria; Artiodactyla; Ruminantia; Pecora; Bovidae;
OC Bovinae; Bos.
OX NCBI_TaxID=9913;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Hereford;
RX PubMed=19393038; DOI=10.1186/gb-2009-10-4-r42;
RA Zimin A.V., Delcher A.L., Florea L., Kelley D.R., Schatz M.C., Puiu D.,
RA Hanrahan F., Pertea G., Van Tassell C.P., Sonstegard T.S., Marcais G.,
RA Roberts M., Subramanian P., Yorke J.A., Salzberg S.L.;
RT "A whole-genome assembly of the domestic cow, Bos taurus.";
RL Genome Biol. 10:R42.01-R42.10(2009).
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; DAAA02054514; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; DAAA02054515; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; DAAA02054516; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; DAAA02054517; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; DAAA02054518; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR RefSeq; NP_001180092.1; NM_001193163.1.
DR AlphaFoldDB; G5E5X0; -.
DR STRING; 9913.ENSBTAP00000036851; -.
DR iPTMnet; G5E5X0; -.
DR PaxDb; G5E5X0; -.
DR PRIDE; G5E5X0; -.
DR Ensembl; ENSBTAT00000037007; ENSBTAP00000036851; ENSBTAG00000026097.
DR GeneID; 617525; -.
DR KEGG; bta:617525; -.
DR CTD; 8994; -.
DR VEuPathDB; HostDB:ENSBTAG00000026097; -.
DR VGNC; VGNC:30888; LIMD1.
DR eggNOG; KOG1701; Eukaryota.
DR GeneTree; ENSGT00940000159019; -.
DR HOGENOM; CLU_001357_11_1_1; -.
DR InParanoid; G5E5X0; -.
DR OMA; SKLTMDG; -.
DR OrthoDB; 326249at2759; -.
DR TreeFam; TF320310; -.
DR Reactome; R-BTA-1234176; Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha.
DR Proteomes; UP000009136; Chromosome 22.
DR Bgee; ENSBTAG00000026097; Expressed in cardiac ventricle and 103 other tissues.
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; IBA:GO_Central.
DR GO; GO:0005886; C:plasma membrane; IEA:Ensembl.
DR GO; GO:0016442; C:RISC complex; IEA:Ensembl.
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; IEA:Ensembl.
DR GO; GO:0007010; P:cytoskeleton organization; IBA:GO_Central.
DR GO; GO:0035195; P:miRNA-mediated gene silencing; IEA:Ensembl.
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; IEA:Ensembl.
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; IEA:Ensembl.
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 3: Inferred from homology;
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..674
FT /note="LIM domain-containing protein 1"
FT /id="PRO_0000416960"
FT DOMAIN 468..529
FT /note="LIM zinc-binding 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00125"
FT DOMAIN 533..593
FT /note="LIM zinc-binding 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00125"
FT DOMAIN 594..662
FT /note="LIM zinc-binding 3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00125"
FT REGION 54..136
FT /note="Mediates nuclear export"
FT /evidence="ECO:0000250"
FT REGION 73..109
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 142..165
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 188..259
FT /note="Interaction with EGLN1/PHD2"
FT /evidence="ECO:0000250"
FT REGION 204..388
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 402..440
FT /note="Interaction with RB1"
FT /evidence="ECO:0000250"
FT REGION 470..674
FT /note="Necessary for nuclear localization"
FT /evidence="ECO:0000250"
FT COMPBIAS 145..159
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 234..250
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 259..274
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 287..321
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 338..356
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 147
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9UGP4"
FT MOD_RES 235
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9UGP4"
FT MOD_RES 241
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:B5DEH0"
FT MOD_RES 271
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9UGP4"
FT MOD_RES 276
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9UGP4"
FT MOD_RES 314
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:B5DEH0"
FT MOD_RES 422
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q9UGP4"
SQ SEQUENCE 674 AA; 71885 MW; 7455F78244E7C95E CRC64;
MDKYDDLGLE ASKFIEDLNM YEASKDGLFR VDKGAGNNPE FEETRRVFAT KMAKIHLQQQ
QQQQLLQEET LPRASRGPIN GGARLGPPAH REAGGGSKLA ADGAAKPPLA ASTVAPGTTI
TVAPGQPSYP PQEQRAKLYV RGSRQGSQDC GSKESMVNSE MSAFHRPGPC EDPSCLTHGD
YYDNLSLAGP KWADDPGVSP GIRLGVGSGW SGTPGSDPLL SKPSRDPHLY HQQLSAGSGR
SLQSGQDGGP GGGNSEKPAG VWTTASSQRV SPGLPSAGPE NGALPRSAQP RTPSFSAPLA
LNRPSQGSLP RTNSGVGSEV SGTMPKPTVD PQPWFQDGPK SYLSSSAPSS SPASMDHMQA
GALPGLGPKP GSTDPGIGPK LSPNSLVHPV MSTLPELSCK EGASSWASDG SLGPVLPETP
SSPRVRLPCQ TLIPGPELGP TAAELKLEAL TQRLEREMDA HPKADYFGAC VKCSKGVFGA
GQACQAMGNL YHDACFTCAA CSRKLRGKAF YFVNGKVFCE EDFLYSGFQQ SADRCFLCGH
LIMDMILQAL GKSYHPGCFR CVICNECLDG VPFTVDSENK IYCVRDYHKV LAPKCAACGL
PILPPEGSDE TIRVVSMDRD YHVECYHCED CGLELNDEDG HRCYPLEDHL FCHSCHVKRL
EKGPSPAALR QHHF
