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LDB1 (LIM domain binding 1)

Identity

Other namesCLIM2
NLI
HGNC (Hugo) LDB1
LocusID (NCBI) 8861
Location 10q24.32
Location_base_pair Starts at 103867325 and ends at 103880210 bp from pter ( according to hg19-Feb_2009)  [Mapping]

DNA/RNA

Description 7kb; 11exons
Transcription 2292 nucleotides mRNA

Protein

Description 375 amino acids; 42.8 kDa protein
Expression Widely expressed
Localisation Nuclear
Function LDB1 is a nuclear protein that contains an N-terminal dimerization domain and a C-terminal LIM interaction domain (LID). LDB1 binds to LIM-homeodomain (LIM-HD) and LIM-only (LMO) proteins. It acts as an adaptor protein that mediates interactions between different classes of transcription factors and their cofactors. LDB1 forms a complex with LKB1, LMO4, and GATA-6. The tumor suppressor LKB1is mutated in Peutz­Jeghers syndrome and various sporadic cancers. A complex containing LDB1, LKB1, LMO4, and GATA-6 induces cyclin-dependent kinase inhibitor p21 expression. Targeted deletion of the Ldb1 gene in mice displays multiple developmental defects that reveal a requirement of Ldb1 gene during normal development.

Implicated in

Entity Oral squamous cell carcinoma
Oncogenesis LDB1 and are frequently detected in less-differentiated and metastasized squamous carcinoma, and overexpressed at the carcinoma invasive front. END_ENTITY
  

External links

Nomenclature
HGNC (Hugo)LDB1   6532
Entrez_Gene (NCBI)LDB1  8861  LIM domain binding 1
Cards
AtlasLDB1ID41135ch10q24
GeneCards (Weizmann)LDB1
Ensembl (Hinxton)ENSG00000198728 [Gene_View]  chr10:103867325-103880210 [Contig_View]  LDB1 [Vega]
AceView (NCBI)LDB1
Genatlas (Paris)LDB1
SOURCE (Stanford)NM_001113407 NM_003893
Genomic and cartography
GoldenPath (UCSC)LDB1  -  10q24.32   chr10:103867325-103880210 -  10q24-q25   [Description]    (hg19-Feb_2009)
EnsemblLDB1 - 10q24-q25 [CytoView]
Mapping of homologs : NCBILDB1 [Mapview]
OMIM603451   
Gene and transcription
Genbank (Entrez)AB016485 AB250384 AF064491 AF068652 AK300588
RefSeq transcript (SRS)NM_001113407 NM_003893
RefSeq transcript (Entrez)NM_001113407 NM_003893
RefSeq genomic (SRS)AC_000142 NC_000010 NC_018921 NT_030059 NW_001838006 NW_004078068
RefSeq genomic (Entrez)AC_000142 NC_000010 NC_018921 NT_030059 NW_001838006 NW_004078068
Consensus coding sequences : CCDS (NCBI)LDB1
Cluster EST : UnigeneHs.454418 [ SRS ] Hs.454418 [ NCBI ]
CGAP (NCI)Hs.454418
Alternative Splicing : Fast-db (Paris)GSHG0004333
Alternative Splicing GalleryENSG00000198728
Gene ExpressionLDB1 [ NCBI-GEO ]   LDB1 [ EBI - ARRAY_EXPRESS ]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ86U70 (SRS) Q86U70 (Uniprot)
NextProtQ86U70
With graphics : InterProQ86U70
Splice isoforms : SwissVarQ86U70(Swissvar)
Domains : Interpro (SRS)LIM-dom-bd   
Domains : Interpro (EBI)LIM-dom-bd   
Related proteins : CluSTrQ86U70
Domain families : Pfam (SRS)
Domain families : Pfam (Sanger)
Domain families : Pfam (NCBI)
DMDM8861
Blocks (Seattle)Q86U70
PDB (SRS)2XJY    2XJZ   
PDB (PDBSum)2XJY    2XJZ   
PDB (IMB)2XJY    2XJZ   
PDB (RSDB)2XJY    2XJZ   
Human Protein AtlasENSG00000198728
HPRD09144
IPIIPI00856078   IPI00428954   IPI00760574   
Protein Interaction databases
DIP (DOE-UCLA)Q86U70
IntAct (EBI)Q86U70
FunCoupENSG00000198728
REACTOMELDB1
Protein Interaction Database8861
BioGRIDLDB1
InParanoidQ86U70
Interologous Interaction database Q86U70
IntegromeDBLDB1
Polymorphism : SNP, mutations, diseases
SNP Single Nucleotide Polymorphism (NCBI)LDB1
SNP (GeneSNP Utah)LDB1
SNP : HGBaseLDB1
Genetic variants : HAPMAPLDB1
Somatic Mutations in Cancer : COSMICLDB1 
CONAN: Copy Number AnalysisLDB1 
Mutations and Diseases : HGMDLDB1
OMIM603451   
GENETests603451   
Disease Genetic AssociationLDB1
Huge Navigator LDB1 [HugePedia]  LDB1 [HugeCancerGEM]
Genomic VariantsLDB1  LDB1 [DGVbeta]
ClinVarLDB1
snp3D : Map Gene to Disease8861
General knowledge
Homologs : HomoloGeneLDB1
Homology/Alignments : Family Browser (UCSC)LDB1
Phylogenetic Trees/Animal Genes : TreeFamLDB1
Chemical/Protein Interactions : CTD8861
Chemical/Pharm GKB GenePA30316
Clinical trialLDB1
Cancer Resource (Charite)ENSG00000198728
Ontology : AmiGOnuclear chromatin  transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery  RNA polymerase II activating transcription factor binding  enhancer sequence-specific DNA binding  gastrulation with mouth forming second  hair follicle development  chromatin binding  transcription corepressor activity  nucleus  transcription factor complex  cell-cell junction  transcription, DNA-dependent  regulation of transcription, DNA-dependent  transcription from RNA polymerase II promoter  multicellular organismal development  anterior/posterior axis specification  epithelial structure maintenance  Wnt receptor signaling pathway  enzyme binding  cerebellar Purkinje cell differentiation  cellular component assembly  neuron differentiation  LIM domain binding  LIM domain binding  regulation of DNA-dependent transcription, elongation  somatic stem cell maintenance  protein homodimerization activity  protein complex  protein self-association  histone H3-K4 acetylation  negative regulation of erythrocyte differentiation  positive regulation of cell adhesion  negative regulation of transcription, DNA-dependent  positive regulation of transcription from RNA polymerase II promoter  positive regulation of transcription from RNA polymerase II promoter  positive regulation of hemoglobin biosynthetic process  head development  
Ontology : EGO-EBInuclear chromatin  transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery  RNA polymerase II activating transcription factor binding  enhancer sequence-specific DNA binding  gastrulation with mouth forming second  hair follicle development  chromatin binding  transcription corepressor activity  nucleus  transcription factor complex  cell-cell junction  transcription, DNA-dependent  regulation of transcription, DNA-dependent  transcription from RNA polymerase II promoter  multicellular organismal development  anterior/posterior axis specification  epithelial structure maintenance  Wnt receptor signaling pathway  enzyme binding  cerebellar Purkinje cell differentiation  cellular component assembly  neuron differentiation  LIM domain binding  LIM domain binding  regulation of DNA-dependent transcription, elongation  somatic stem cell maintenance  protein homodimerization activity  protein complex  protein self-association  histone H3-K4 acetylation  negative regulation of erythrocyte differentiation  positive regulation of cell adhesion  negative regulation of transcription, DNA-dependent  positive regulation of transcription from RNA polymerase II promoter  positive regulation of transcription from RNA polymerase II promoter  positive regulation of hemoglobin biosynthetic process  head development  
Pathways : BIOCARTAMulti-step Regulation of Transcription by Pitx2 [Genes]   
Other databases
Probes
Litterature
PubMed47 Pubmed reference(s) in Entrez
PubGeneLDB1
iHOPLDB1

Bibliography

Interactions of the LIM-domain-binding factor Ldb1 with LIM homeodomain proteins.
Agulnick AD, Taira M, Breen JJ, Tanaka T, Dawid IB, Westphal H
Nature. 1996 ; 384 (6606) : 270-272.
PMID 8918878
 
A family of LIM domain-associated cofactors confer transcriptional synergism between LIM and Otx homeodomain proteins.
Bach I, Carriˆ®re C, Ostendorff HP, Andersen B, Rosenfeld MG
Genes & development. 1997 ; 11 (11) : 1370-1380.
PMID 9192866
 
Functional analysis of the nuclear LIM domain interactor NLI.
Jurata LW, Gill GN
Molecular and cellular biology. 1997 ; 17 (10) : 5688-5698.
PMID 9315627
 
The LIM-domain binding protein Ldb1 and its partner LMO2 act as negative regulators of erythroid differentiation.
Visvader JE, Mao X, Fujiwara Y, Hahm K, Orkin SH
Proceedings of the National Academy of Sciences of the United States of America. 1997 ; 94 (25) : 13707-13712.
PMID 9391090
 
Ssdp proteins interact with the LIM-domain-binding protein Ldb1 to regulate development.
Chen L, Segal D, Hukriede NA, Podtelejnikov AV, Bayarsaihan D, Kennison JA, Ogryzko VV, Dawid IB, Westphal H
Proceedings of the National Academy of Sciences of the United States of America. 2002 ; 99 (22) : 14320-14325.
PMID 12381786
 
LIM-domain-binding protein 1: a multifunctional cofactor that interacts with diverse proteins.
Matthews JM, Visvader JE
EMBO reports. 2003 ; 4 (12) : 1132-1137.
PMID 14647207
 
The LIM-only protein, LMO4, and the LIM domain-binding protein, LDB1, expression in squamous cell carcinomas of the oral cavity.
Mizunuma H, Miyazawa J, Sanada K, Imai K
British journal of cancer. 2003 ; 88 (10) : 1543-1548.
PMID 12771919
 
Functional ablation of the mouse Ldb1 gene results in severe patterning defects during gastrulation.
Mukhopadhyay M, Teufel A, Yamashita T, Agulnick AD, Chen L, Downs KM, Schindler A, Grinberg A, Huang SP, Dorward D, Westphal H
Development (Cambridge, England). 2003 ; 130 (3) : 495-505.
PMID 12490556
 
The tumor suppressor LKB1 induces p21 expression in collaboration with LMO4, GATA-6, and Ldb1.
Setogawa T, Shinozaki-Yabana S, Masuda T, Matsuura K, Akiyama T
Biochemical and biophysical research communications. 2006 ; 343 (4) : 1186-1190.
PMID 16580634
 
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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Contributor(s)

Written11-2006Takeshi Setogawa, Testu Akiyama

Citation

This paper should be referenced as such :
Setogawa T, Akiyama T . LDB1 (LIM domain binding 1). Atlas Genet Cytogenet Oncol Haematol. November 2006 .
URL : http://AtlasGeneticsOncology.org/Genes/LDB1ID41135ch10q24.html

This paper is referenced by INIST as such :
http://documents.irevues.inist.fr/bitstream/2042/38429/1/11-2006-LDB1ID41135ch10q24.pdf   [ Bibliographic record ]

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indexed on : Fri Jun 14 16:52:59 CEST 2013
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