LDB2_HUMAN
ID LDB2_HUMAN Reviewed; 373 AA.
AC O43679; O60619; O75480;
DT 05-JUL-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-1998, sequence version 1.
DT 03-AUG-2022, entry version 168.
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 Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
RX PubMed=9799849; DOI=10.1007/s003359900899;
RA Semina E.V., Altherr M.R., Murray J.C.;
RT "Cloning and chromosomal localization of two novel human genes encoding
RT LIM-domain binding factors CLIM1 and CLIM2/LDB1/NLI.";
RL Mamm. Genome 9:921-924(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3).
RA Zhou Y., Du G.W., Wang J.H., Yuan J.G., Qiang B.Q.;
RT "Cloning and identification of LDB1 cDNA.";
RL Submitted (MAR-1998) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2).
RC TISSUE=Brain;
RA Phillips J.C., Goldman D.A., Wiggs J.L.;
RT "Cloning, characterization, and physical mapping of the human homologs of
RT the mouse C-LIM gene.";
RL Submitted (MAY-1998) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), AND SUBCELLULAR
RP LOCATION.
RC TISSUE=Fetal brain;
RX PubMed=9853615; DOI=10.1038/4315;
RA Ueki N., Oda T., Kondo M., Yano K., Noguchi T., Muramatsu M.-A.;
RT "Selection system for genes encoding nuclear-targeted proteins.";
RL Nat. Biotechnol. 16:1338-1342(1998).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC TISSUE=Lung;
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 [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 IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21406692; DOI=10.1126/scisignal.2001570;
RA Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T.,
RA Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.;
RT "System-wide temporal characterization of the proteome and phosphoproteome
RT of human embryonic stem cell differentiation.";
RL Sci. Signal. 4:RS3-RS3(2011).
CC -!- FUNCTION: Binds to the LIM domain of a wide variety of LIM domain-
CC containing transcription factors.
CC -!- SUBUNIT: Interacts with LHX9 (By similarity). Interacts with SLK;
CC leading to negatively regulate SLK kinase activity (By similarity).
CC {ECO:0000250|UniProtKB:O55203}.
CC -!- INTERACTION:
CC O43679; Q9NWQ9: C14orf119; NbExp=3; IntAct=EBI-2865580, EBI-725606;
CC O43679; O15182: CETN3; NbExp=3; IntAct=EBI-2865580, EBI-712959;
CC O43679; Q9BY27: DGCR6L; NbExp=3; IntAct=EBI-2865580, EBI-742953;
CC O43679; Q9H6Z9: EGLN3; NbExp=3; IntAct=EBI-2865580, EBI-1175354;
CC O43679; Q7L775: EPM2AIP1; NbExp=3; IntAct=EBI-2865580, EBI-6255981;
CC O43679; Q86VI1: EXOC3L1; NbExp=3; IntAct=EBI-2865580, EBI-2813180;
CC O43679; Q9BVM4: GGACT; NbExp=3; IntAct=EBI-2865580, EBI-10299852;
CC O43679; Q8WUI4-6: HDAC7; NbExp=3; IntAct=EBI-2865580, EBI-12094670;
CC O43679; Q68G74: LHX8; NbExp=5; IntAct=EBI-2865580, EBI-8474075;
CC O43679; P25800: LMO1; NbExp=3; IntAct=EBI-2865580, EBI-8639312;
CC O43679; P25791-3: LMO2; NbExp=5; IntAct=EBI-2865580, EBI-11959475;
CC O43679; Q8TAP4-4: LMO3; NbExp=5; IntAct=EBI-2865580, EBI-11742507;
CC O43679; P61968: LMO4; NbExp=6; IntAct=EBI-2865580, EBI-2798728;
CC O43679; Q8TBB1: LNX1; NbExp=3; IntAct=EBI-2865580, EBI-739832;
CC O43679; Q969H8: MYDGF; NbExp=3; IntAct=EBI-2865580, EBI-718622;
CC O43679; Q96HA8: NTAQ1; NbExp=3; IntAct=EBI-2865580, EBI-741158;
CC O43679; P20618: PSMB1; NbExp=3; IntAct=EBI-2865580, EBI-372273;
CC O43679; O00560: SDCBP; NbExp=3; IntAct=EBI-2865580, EBI-727004;
CC O43679; Q96GM5: SMARCD1; NbExp=3; IntAct=EBI-2865580, EBI-358489;
CC O43679; Q9BWW4: SSBP3; NbExp=4; IntAct=EBI-2865580, EBI-2902395;
CC O43679; Q99598: TSNAX; NbExp=4; IntAct=EBI-2865580, EBI-742638;
CC O43679; Q6DKK2: TTC19; NbExp=3; IntAct=EBI-2865580, EBI-948354;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:9853615}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=3;
CC Name=1; Synonyms=a, CLIM1a;
CC IsoId=O43679-1; Sequence=Displayed;
CC Name=2; Synonyms=b, CLIM1b;
CC IsoId=O43679-2; Sequence=VSP_027826, VSP_027827;
CC Name=3;
CC IsoId=O43679-3; Sequence=VSP_027825, VSP_027828;
CC -!- PTM: Ubiquitinated by RLIM/RNF12, leading to its degradation by the
CC proteasome. {ECO:0000250|UniProtKB:O55203}.
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; AF068651; AAC77817.1; -; mRNA.
DR EMBL; AF052389; AAC13274.1; -; mRNA.
DR EMBL; AF064492; AAC28342.1; -; mRNA.
DR EMBL; AF064493; AAC28343.1; -; mRNA.
DR EMBL; AF047337; AAC83552.1; -; mRNA.
DR EMBL; BC034019; AAH34019.1; -; mRNA.
DR CCDS; CCDS3420.1; -. [O43679-1]
DR CCDS; CCDS47031.1; -. [O43679-2]
DR RefSeq; NP_001124306.1; NM_001130834.2. [O43679-2]
DR RefSeq; NP_001281.1; NM_001290.4. [O43679-1]
DR AlphaFoldDB; O43679; -.
DR SMR; O43679; -.
DR BioGRID; 114535; 28.
DR DIP; DIP-24262N; -.
DR DIP; DIP-41215N; -.
DR IntAct; O43679; 30.
DR MINT; O43679; -.
DR STRING; 9606.ENSP00000306772; -.
DR iPTMnet; O43679; -.
DR MetOSite; O43679; -.
DR PhosphoSitePlus; O43679; -.
DR BioMuta; LDB2; -.
DR EPD; O43679; -.
DR jPOST; O43679; -.
DR MassIVE; O43679; -.
DR MaxQB; O43679; -.
DR PaxDb; O43679; -.
DR PeptideAtlas; O43679; -.
DR PRIDE; O43679; -.
DR ProteomicsDB; 49107; -. [O43679-1]
DR ProteomicsDB; 49108; -. [O43679-2]
DR ProteomicsDB; 49109; -. [O43679-3]
DR Antibodypedia; 4310; 238 antibodies from 27 providers.
DR DNASU; 9079; -.
DR Ensembl; ENST00000304523.10; ENSP00000306772.5; ENSG00000169744.13. [O43679-1]
DR Ensembl; ENST00000441778.6; ENSP00000392089.2; ENSG00000169744.13. [O43679-2]
DR GeneID; 9079; -.
DR KEGG; hsa:9079; -.
DR MANE-Select; ENST00000304523.10; ENSP00000306772.5; NM_001290.5; NP_001281.1.
DR UCSC; uc003goz.5; human. [O43679-1]
DR CTD; 9079; -.
DR DisGeNET; 9079; -.
DR GeneCards; LDB2; -.
DR HGNC; HGNC:6533; LDB2.
DR HPA; ENSG00000169744; Low tissue specificity.
DR MIM; 603450; gene.
DR neXtProt; NX_O43679; -.
DR OpenTargets; ENSG00000169744; -.
DR PharmGKB; PA30317; -.
DR VEuPathDB; HostDB:ENSG00000169744; -.
DR eggNOG; KOG2181; Eukaryota.
DR GeneTree; ENSGT00390000005639; -.
DR InParanoid; O43679; -.
DR OMA; PWNSKPA; -.
DR OrthoDB; 849287at2759; -.
DR PhylomeDB; O43679; -.
DR TreeFam; TF319923; -.
DR PathwayCommons; O43679; -.
DR SignaLink; O43679; -.
DR BioGRID-ORCS; 9079; 6 hits in 1072 CRISPR screens.
DR ChiTaRS; LDB2; human.
DR GeneWiki; LDB2; -.
DR GenomeRNAi; 9079; -.
DR Pharos; O43679; Tbio.
DR PRO; PR:O43679; -.
DR Proteomes; UP000005640; Chromosome 4.
DR RNAct; O43679; protein.
DR Bgee; ENSG00000169744; Expressed in right lung and 190 other tissues.
DR ExpressionAtlas; O43679; baseline and differential.
DR Genevisible; O43679; HS.
DR GO; GO:0031252; C:cell leading edge; ISS:UniProtKB.
DR GO; GO:0005730; C:nucleolus; IDA:HPA.
DR GO; GO:0005654; C:nucleoplasm; IDA:HPA.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0005886; C:plasma membrane; IDA:HPA.
DR GO; GO:0005667; C:transcription regulator complex; IBA:GO_Central.
DR GO; GO:0019899; F:enzyme binding; IEA:Ensembl.
DR GO; GO:0030274; F:LIM domain binding; ISS:UniProtKB.
DR GO; GO:0003712; F:transcription coregulator activity; TAS:ProtInc.
DR GO; GO:0044085; P:cellular component biogenesis; IEA:Ensembl.
DR GO; GO:0010669; P:epithelial structure maintenance; IEA:Ensembl.
DR GO; GO:0001942; P:hair follicle development; IEA:Ensembl.
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; IEA:Ensembl.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR GO; GO:0030334; P:regulation of cell migration; ISS:UniProtKB.
DR GO; GO:0043549; P:regulation of kinase activity; ISS:UniProtKB.
DR GO; GO:0035019; P:somatic stem cell population maintenance; IEA:Ensembl.
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_0000084387"
FT DOMAIN 298..337
FT /note="LIM interaction domain (LID)"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01302"
FT REGION 244..291
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..291
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 1..24
FT /note="Missing (in isoform 3)"
FT /evidence="ECO:0000303|Ref.2"
FT /id="VSP_027825"
FT VAR_SEQ 296..297
FT /note="Missing (in isoform 3)"
FT /evidence="ECO:0000303|Ref.2"
FT /id="VSP_027828"
FT VAR_SEQ 298..331
FT /note="DVMVVGEPTLMGGEFGDEDERLITRLENTQYDAA -> GLGAIPNCSLNPGR
FT DGDLCHSTAVTPSGQFKEKH (in isoform 2)"
FT /evidence="ECO:0000303|Ref.3"
FT /id="VSP_027826"
FT VAR_SEQ 332..373
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|Ref.3"
FT /id="VSP_027827"
SQ SEQUENCE 373 AA; 42793 MW; E86387BA027F383A CRC64;
MSSTPHDPFY SSPFGPFYRR HTPYMVQPEY RIYEMNKRLQ SRTEDSDNLW WDAFATEFFE
DDATLTLSFC LEDGPKRYTI GRTLIPRYFS TVFEGGVTDL YYILKHSKES YHNSSITVDC
DQCTMVTQHG KPMFTKVCTE GRLILEFTFD DLMRIKTWHF TIRQYRELVP RSILAMHAQD
PQVLDQLSKN ITRMGLTNFT LNYLRLCVIL EPMQELMSRH KTYNLSPRDC LKTCLFQKWQ
RMVAPPAEPT RQPTTKRRKR KNSTSSTSNS SAGNNANSTG SKKKTTAANL SLSSQVPDVM
VVGEPTLMGG EFGDEDERLI TRLENTQYDA ANGMDDEEDF NNSPALGNNS PWNSKPPATQ
ETKSENPPPQ ASQ
