LDB2_MOUSE
ID LDB2_MOUSE Reviewed; 373 AA.
AC O55203; O55205; Q3UHY1; Q6AXE6;
DT 05-JUL-2005, integrated into UniProtKB/Swiss-Prot.
DT 11-SEP-2007, sequence version 2.
DT 03-AUG-2022, entry version 142.
DE RecName: Full=LIM domain-binding protein 2;
DE Short=LDB-2;
DE AltName: Full=Carboxyl-terminal LIM domain-binding protein 1;
DE Short=CLIM-1;
DE AltName: Full=LIM domain-binding factor CLIM1;
GN Name=Ldb2; Synonyms=Clim1;
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] (ISOFORMS 1 AND 2).
RX PubMed=9192866; DOI=10.1101/gad.11.11.1370;
RA Bach I., Carriere C., Ostendorff H.P., Andersen B., Rosenfeld M.G.;
RT "A family of LIM domain-associated cofactors confer transcriptional
RT synergism between LIM and Otx homeodomain proteins.";
RL Genes Dev. 11:1370-1380(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3).
RC STRAIN=C57BL/6J; TISSUE=Embryonic kidney;
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] (ISOFORM 1).
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 INTERACTION WITH LHX9.
RX PubMed=10330499; DOI=10.1016/s0925-4773(98)00233-0;
RA Bertuzzi S., Porter F.D., Pitts A., Kumar M., Agulnick A., Wassif C.,
RA Westphal H.;
RT "Characterization of Lhx9, a novel LIM/homeobox gene expressed by the
RT pioneer neurons in the mouse cerebral cortex.";
RL Mech. Dev. 81:193-198(1999).
RN [5]
RP INTERACTION WITH RLIM, AND UBIQUITINATION.
RX PubMed=11882901; DOI=10.1038/416099a;
RA Ostendorff H.P., Peirano R.I., Peters M.A., Schluter A., Bossenz M.,
RA Scheffner M., Bach I.;
RT "Ubiquitination-dependent cofactor exchange on LIM homeodomain
RT transcription factors.";
RL Nature 416:99-103(2002).
RN [6]
RP ALTERNATIVE SPLICING.
RX PubMed=16815859; DOI=10.1093/jb/mvj134;
RA Tran Y.H., Xu Z., Kato A., Mistry A.C., Goya Y., Taira M., Brandt S.J.,
RA Hirose S.;
RT "Spliced isoforms of LIM-domain-binding protein (CLIM/NLI/Ldb) lacking the
RT LIM-interaction domain.";
RL J. Biochem. 140:105-119(2006).
RN [7]
RP INTERACTION WITH SLK, SUBCELLULAR LOCATION, AND FUNCTION.
RX PubMed=19675209; DOI=10.1091/mbc.e08-07-0707;
RA Storbeck C.J., Wagner S., O'Reilly P., McKay M., Parks R.J., Westphal H.,
RA Sabourin L.A.;
RT "The Ldb1 and Ldb2 transcriptional cofactors interact with the Ste20-like
RT kinase SLK and regulate cell migration.";
RL Mol. Biol. Cell 20:4174-4182(2009).
CC -!- FUNCTION: Binds to the LIM domain of a wide variety of LIM domain-
CC containing transcription factors.
CC -!- SUBUNIT: Interacts with LHX9 (PubMed:10330499). Interacts with SLK;
CC leading to negatively regulate SLK kinase activity (PubMed:19675209).
CC {ECO:0000269|PubMed:10330499, ECO:0000269|PubMed:11882901,
CC ECO:0000269|PubMed:19675209}.
CC -!- INTERACTION:
CC O55203; Q9WTV7: Rlim; NbExp=2; IntAct=EBI-15657830, EBI-15657872;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}. Note=Colocalizes with SLK
CC at leading edges (PubMed:19675209). {ECO:0000269|PubMed:19675209}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=3;
CC Name=1; Synonyms=CLIM-1a;
CC IsoId=O55203-1; Sequence=Displayed;
CC Name=2; Synonyms=CLIM-1b;
CC IsoId=O55203-2; Sequence=VSP_014369, VSP_014370;
CC Name=3;
CC IsoId=O55203-3; Sequence=VSP_027829, VSP_014369, VSP_014370;
CC -!- PTM: Ubiquitinated by RLIM/RNF12, leading to its degradation by the
CC proteasome. {ECO:0000269|PubMed:11882901}.
CC -!- MISCELLANEOUS: [Isoform 2]: Lacks LIM-binding domain. {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the LDB family. {ECO:0000305}.
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DR EMBL; U89487; AAB96884.1; -; mRNA.
DR EMBL; U89489; AAB96886.1; -; mRNA.
DR EMBL; AK147160; BAE27725.1; -; mRNA.
DR EMBL; AK146860; BAE27488.1; -; mRNA.
DR EMBL; BC079611; AAH79611.1; -; mRNA.
DR CCDS; CCDS19271.1; -. [O55203-1]
DR CCDS; CCDS80276.1; -. [O55203-2]
DR CCDS; CCDS80278.1; -. [O55203-3]
DR RefSeq; NP_001070866.1; NM_001077398.2. [O55203-3]
DR RefSeq; NP_001273277.1; NM_001286348.1. [O55203-2]
DR RefSeq; NP_034828.3; NM_010698.4. [O55203-1]
DR RefSeq; XP_006503817.1; XM_006503754.3. [O55203-2]
DR RefSeq; XP_006503819.1; XM_006503756.3. [O55203-3]
DR AlphaFoldDB; O55203; -.
DR SMR; O55203; -.
DR BioGRID; 201126; 33.
DR DIP; DIP-46444N; -.
DR IntAct; O55203; 20.
DR STRING; 10090.ENSMUSP00000067737; -.
DR iPTMnet; O55203; -.
DR PhosphoSitePlus; O55203; -.
DR MaxQB; O55203; -.
DR PaxDb; O55203; -.
DR PeptideAtlas; O55203; -.
DR PRIDE; O55203; -.
DR ProteomicsDB; 265052; -. [O55203-1]
DR ProteomicsDB; 265053; -. [O55203-2]
DR ProteomicsDB; 265054; -. [O55203-3]
DR Antibodypedia; 4310; 238 antibodies from 27 providers.
DR DNASU; 16826; -.
DR Ensembl; ENSMUST00000070748; ENSMUSP00000067737; ENSMUSG00000039706. [O55203-1]
DR Ensembl; ENSMUST00000199256; ENSMUSP00000143775; ENSMUSG00000039706. [O55203-3]
DR Ensembl; ENSMUST00000199534; ENSMUSP00000142442; ENSMUSG00000039706. [O55203-2]
DR GeneID; 16826; -.
DR KEGG; mmu:16826; -.
DR UCSC; uc008xis.2; mouse. [O55203-3]
DR UCSC; uc008xit.2; mouse. [O55203-1]
DR UCSC; uc008xiu.2; mouse. [O55203-2]
DR CTD; 9079; -.
DR MGI; MGI:894670; Ldb2.
DR VEuPathDB; HostDB:ENSMUSG00000039706; -.
DR eggNOG; KOG2181; Eukaryota.
DR GeneTree; ENSGT00390000005639; -.
DR HOGENOM; CLU_032597_0_0_1; -.
DR InParanoid; O55203; -.
DR OMA; PWNSKPA; -.
DR OrthoDB; 849287at2759; -.
DR PhylomeDB; O55203; -.
DR TreeFam; TF319923; -.
DR BioGRID-ORCS; 16826; 2 hits in 71 CRISPR screens.
DR ChiTaRS; Ldb2; mouse.
DR PRO; PR:O55203; -.
DR Proteomes; UP000000589; Chromosome 5.
DR RNAct; O55203; protein.
DR Bgee; ENSMUSG00000039706; Expressed in embryonic brain and 227 other tissues.
DR ExpressionAtlas; O55203; baseline and differential.
DR Genevisible; O55203; MM.
DR GO; GO:0031252; C:cell leading edge; IDA:UniProtKB.
DR GO; GO:0005730; C:nucleolus; ISO:MGI.
DR GO; GO:0005654; C:nucleoplasm; ISO:MGI.
DR GO; GO:0005634; C:nucleus; ISS:UniProtKB.
DR GO; GO:0005886; C:plasma membrane; ISO:MGI.
DR GO; GO:0005667; C:transcription regulator complex; IDA:MGI.
DR GO; GO:0019899; F:enzyme binding; IPI:UniProtKB.
DR GO; GO:0030274; F:LIM domain binding; ISS:UniProtKB.
DR GO; GO:0003712; F:transcription coregulator activity; IEA:InterPro.
DR GO; GO:0044085; P:cellular component biogenesis; IGI:MGI.
DR GO; GO:0010669; P:epithelial structure maintenance; IGI:MGI.
DR GO; GO:0001942; P:hair follicle development; IGI:MGI.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR GO; GO:0007399; P:nervous system development; IBA:GO_Central.
DR GO; GO:0044089; P:positive regulation of cellular component biogenesis; IGI:MGI.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IGI:MGI.
DR GO; GO:0030334; P:regulation of cell migration; IMP:UniProtKB.
DR GO; GO:0043549; P:regulation of kinase activity; IDA:UniProtKB.
DR GO; GO:0035019; P:somatic stem cell population maintenance; IGI:MGI.
DR InterPro; IPR030174; LDB2.
DR InterPro; IPR041363; LID.
DR InterPro; IPR029005; LIM-bd/SEUSS.
DR PANTHER; PTHR10378; PTHR10378; 1.
DR PANTHER; PTHR10378:SF8; PTHR10378:SF8; 1.
DR Pfam; PF17916; LID; 1.
DR Pfam; PF01803; LIM_bind; 2.
DR PROSITE; PS51957; LID; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Nucleus; Reference proteome; Ubl conjugation.
FT CHAIN 1..373
FT /note="LIM domain-binding protein 2"
FT /id="PRO_0000084388"
FT DOMAIN 298..337
FT /note="LIM interaction domain (LID)"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01302"
FT REGION 244..287
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 327..373
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 264..287
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 342..373
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT VAR_SEQ 296..297
FT /note="Missing (in isoform 3)"
FT /evidence="ECO:0000303|PubMed:16141072"
FT /id="VSP_027829"
FT VAR_SEQ 298..331
FT /note="DVMVVGEPTLMGGEFGDEDERLITRLENTQYDAA -> GLGAIPNCSLNPGR
FT DGDLCHSTAVTPSGQFKEKH (in isoform 2 and isoform 3)"
FT /evidence="ECO:0000303|PubMed:16141072,
FT ECO:0000303|PubMed:9192866"
FT /id="VSP_014369"
FT VAR_SEQ 332..373
FT /note="Missing (in isoform 2 and isoform 3)"
FT /evidence="ECO:0000303|PubMed:16141072,
FT ECO:0000303|PubMed:9192866"
FT /id="VSP_014370"
FT CONFLICT 272
FT /note="A -> G (in Ref. 1; AAB96884/AAB96886)"
FT /evidence="ECO:0000305"
FT CONFLICT 279
FT /note="A -> S (in Ref. 1; AAB96884/AAB96886)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 373 AA; 42691 MW; 0748DBAEB5586AB4 CRC64;
MSSTPHDPFY SSPFGPFYRR HTPYMVQPEY RIYEMNKRLQ SRTEDSDNLW WDAFATEFFE
DDATLTLSFC LEDGPKRYTI GRTLIPRYFS TVFEGGVTDL YYILKHSKES YHNSSITVDC
DQCAMVTQHG KPMFTKVCTE GRLILEFTFD DLMRIKTWHF TIRQYRELVP RSILAMHAQD
PQVLDQLSKN ITRMGLTNFT LNYLRLCVIL EPMQELMSRH KTYNLSPRDC LKTCLFQKWQ
RMVAPPAEPT RQPTTKRRKR KNSTSSTSNS SAGNTTNSAG SKKKTPAASL SLATQVPDVM
VVGEPTLMGG EFGDEDERLI TRLENTQYDA ANGMDDEEDF NNSPALGNNS PWNSKPPATQ
ETKSENAPPQ ASQ
