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LDB1 (LIM domain binding 1)

Written2006-11Takeshi Setogawa, Testu Akiyama
Laboratory of Molecular and Genetic Information, Institute for Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan

(Note : for Links provided by Atlas : click)

Identity

Alias (NCBI)CLIM2
NLI
HGNC (Hugo) LDB1
HGNC Alias symbNLI
CLIM2
HGNC Alias namecarboxy terminal LIM domain protein 2
LocusID (NCBI) 8861
Atlas_Id 41135
Location 10q24.32  [Link to chromosome band 10q24]
Location_base_pair Starts at 102106489 and ends at 102115002 bp from pter ( according to GRCh38/hg38-Dec_2013)  [Mapping LDB1.png]
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
LDB1 (10q24.32)::LDB1 (10q24.32)PRICKLE4 (6p21.1)::LDB1 (10q24.32)

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 Peutz Jeghers 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

Note
  
Entity Oral squamous cell carcinoma
Oncogenesis LDB1 and LMO4 are frequently detected in less-differentiated and metastasized squamous carcinoma, and overexpressed at the carcinoma invasive front.
  

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, Carrière C, Ostendorff HP, Andersen B, Rosenfeld MG
Genes & development. 1997 ; 11 (11) : 1370-1380.
PMID 9192866
 
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
 
Functional analysis of the nuclear LIM domain interactor NLI.
Jurata LW, Gill GN
Molecular and cellular biology. 1997 ; 17 (10) : 5688-5698.
PMID 9315627
 
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
 
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
 

Citation

This paper should be referenced as such :
Akiyama, T ; Setogawa, T
LDB1 (LIM domain binding 1)
Atlas Genet Cytogenet Oncol Haematol. 2007;11(3):167-168.
Free journal version : [ pdf ]   [ DOI ]


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 2 ]
  del(11)(p12p13) LMO2
TAL1 (1p32) deletion in lymphoid malignancies


External links

 

Nomenclature
HGNC (Hugo)LDB1   6532
Cards
AtlasLDB1ID41135ch10q24
Entrez_Gene (NCBI)LDB1    LIM domain binding 1
AliasesCLIM-2; CLIM2; LDB-1; NLI
GeneCards (Weizmann)LDB1
Ensembl hg19 (Hinxton)ENSG00000198728 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000198728 [Gene_View]  ENSG00000198728 [Sequence]  chr10:102106489-102115002 [Contig_View]  LDB1 [Vega]
ICGC DataPortalENSG00000198728
TCGA cBioPortalLDB1
AceView (NCBI)LDB1
Genatlas (Paris)LDB1
SOURCE (Princeton)LDB1
Genetics Home Reference (NIH)LDB1
Genomic and cartography
GoldenPath hg38 (UCSC)LDB1  -     chr10:102106489-102115002 -  10q24.32   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)LDB1  -     10q24.32   [Description]    (hg19-Feb_2009)
GoldenPathLDB1 - 10q24.32 [CytoView hg19]  LDB1 - 10q24.32 [CytoView hg38]
ImmunoBaseENSG00000198728
Genome Data Viewer NCBILDB1 [Mapview hg19]  
OMIM603451   
Gene and transcription
Genbank (Entrez)AB016485 AB250384 AF064491 AF068652 AK300588
RefSeq transcript (Entrez)NM_001113407 NM_001321612 NM_003893
Consensus coding sequences : CCDS (NCBI)LDB1
Gene ExpressionLDB1 [ NCBI-GEO ]   LDB1 [ EBI - ARRAY_EXPRESS ]   LDB1 [ SEEK ]   LDB1 [ MEM ]
Gene Expression Viewer (FireBrowse)LDB1 [ Firebrowse - Broad ]
GenevisibleExpression of LDB1 in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)8861
GTEX Portal (Tissue expression)LDB1
Human Protein AtlasENSG00000198728-LDB1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ86U70   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ86U70  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ86U70
PhosPhoSitePlusQ86U70
Domaine pattern : Prosite (Expaxy)LID (PS51957)   
Domains : Interpro (EBI)LDB1    LID    LIM-bd/SEUSS   
Domain families : Pfam (Sanger)LID (PF17916)    LIM_bind (PF01803)   
Domain families : Pfam (NCBI)pfam17916    pfam01803   
Conserved Domain (NCBI)LDB1
PDB (RSDB)2XJY    2XJZ    2YPA    6TYD   
PDB Europe2XJY    2XJZ    2YPA    6TYD   
PDB (PDBSum)2XJY    2XJZ    2YPA    6TYD   
PDB (IMB)2XJY    2XJZ    2YPA    6TYD   
Structural Biology KnowledgeBase2XJY    2XJZ    2YPA    6TYD   
SCOP (Structural Classification of Proteins)2XJY    2XJZ    2YPA    6TYD   
CATH (Classification of proteins structures)2XJY    2XJZ    2YPA    6TYD   
SuperfamilyQ86U70
AlphaFold pdb e-kbQ86U70   
Human Protein Atlas [tissue]ENSG00000198728-LDB1 [tissue]
HPRD09144
Protein Interaction databases
DIP (DOE-UCLA)Q86U70
IntAct (EBI)Q86U70
BioGRIDLDB1
STRING (EMBL)LDB1
ZODIACLDB1
Ontologies - Pathways
QuickGOQ86U70
Ontology : AmiGOnegative regulation of transcription by RNA polymerase II  chromatin  transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery  gastrulation with mouth forming second  hair follicle development  DNA binding  chromatin binding  transcription coregulator activity  protein binding  nucleus  nucleus  nucleoplasm  transcription regulator complex  transcription regulator complex  regulation of transcription, DNA-templated  transcription by RNA polymerase II  multicellular organism development  nervous system development  anterior/posterior axis specification  epithelial structure maintenance  Wnt signaling pathway  enzyme binding  cerebellar Purkinje cell differentiation  cellular component assembly  neuron differentiation  LIM domain binding  LIM domain binding  LIM domain binding  regulation of cell migration  cell leading edge  protein-containing complex  regulation of transcription elongation from RNA polymerase II promoter  somatic stem cell population maintenance  protein homodimerization activity  regulation of kinase activity  protein self-association  histone H3-K4 acetylation  negative regulation of erythrocyte differentiation  positive regulation of cell adhesion  negative regulation of transcription, DNA-templated  positive regulation of transcription by RNA polymerase II  positive regulation of transcription by RNA polymerase II  positive regulation of transcription by RNA polymerase II  positive regulation of hemoglobin biosynthetic process  mesendoderm development  regulation of focal adhesion assembly  RNA polymerase II-specific DNA-binding transcription factor binding  RNA polymerase II-specific DNA-binding transcription factor binding  DNA-binding transcription factor binding  regulation of hematopoietic stem cell differentiation  beta-catenin-TCF complex  
Ontology : EGO-EBInegative regulation of transcription by RNA polymerase II  chromatin  transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery  gastrulation with mouth forming second  hair follicle development  DNA binding  chromatin binding  transcription coregulator activity  protein binding  nucleus  nucleus  nucleoplasm  transcription regulator complex  transcription regulator complex  regulation of transcription, DNA-templated  transcription by RNA polymerase II  multicellular organism development  nervous system development  anterior/posterior axis specification  epithelial structure maintenance  Wnt signaling pathway  enzyme binding  cerebellar Purkinje cell differentiation  cellular component assembly  neuron differentiation  LIM domain binding  LIM domain binding  LIM domain binding  regulation of cell migration  cell leading edge  protein-containing complex  regulation of transcription elongation from RNA polymerase II promoter  somatic stem cell population maintenance  protein homodimerization activity  regulation of kinase activity  protein self-association  histone H3-K4 acetylation  negative regulation of erythrocyte differentiation  positive regulation of cell adhesion  negative regulation of transcription, DNA-templated  positive regulation of transcription by RNA polymerase II  positive regulation of transcription by RNA polymerase II  positive regulation of transcription by RNA polymerase II  positive regulation of hemoglobin biosynthetic process  mesendoderm development  regulation of focal adhesion assembly  RNA polymerase II-specific DNA-binding transcription factor binding  RNA polymerase II-specific DNA-binding transcription factor binding  DNA-binding transcription factor binding  regulation of hematopoietic stem cell differentiation  beta-catenin-TCF complex  
Pathways : BIOCARTAMulti-step Regulation of Transcription by Pitx2 [Genes]   
Pathways : KEGGTranscriptional misregulation in cancer   
REACTOMEQ86U70 [protein]
REACTOME PathwaysR-HSA-9010553 [pathway]   
NDEx NetworkLDB1
Atlas of Cancer Signalling NetworkLDB1
Wikipedia pathwaysLDB1
Orthology - Evolution
OrthoDB8861
GeneTree (enSembl)ENSG00000198728
Phylogenetic Trees/Animal Genes : TreeFamLDB1
Homologs : HomoloGeneLDB1
Homology/Alignments : Family Browser (UCSC)LDB1
Gene fusions - Rearrangements
Fusion : QuiverLDB1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerLDB1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)LDB1
dbVarLDB1
ClinVarLDB1
MonarchLDB1
1000_GenomesLDB1 
Exome Variant ServerLDB1
GNOMAD BrowserENSG00000198728
Varsome BrowserLDB1
ACMGLDB1 variants
VarityQ86U70
Genomic Variants (DGV)LDB1 [DGVbeta]
DECIPHERLDB1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisLDB1 
Mutations
ICGC Data PortalLDB1 
TCGA Data PortalLDB1 
Broad Tumor PortalLDB1
OASIS PortalLDB1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICLDB1  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DLDB1
Mutations and Diseases : HGMDLDB1
LOVD (Leiden Open Variation Database)[gene] [transcripts] [variants]
BioMutaLDB1
DgiDB (Drug Gene Interaction Database)LDB1
DoCM (Curated mutations)LDB1
CIViC (Clinical Interpretations of Variants in Cancer)LDB1
NCG (London)LDB1
Cancer3DLDB1
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM603451   
Orphanet
DisGeNETLDB1
MedgenLDB1
Genetic Testing Registry LDB1
NextProtQ86U70 [Medical]
GENETestsLDB1
Target ValidationLDB1
Huge Navigator LDB1 [HugePedia]
ClinGenLDB1
Clinical trials, drugs, therapy
MyCancerGenomeLDB1
Protein Interactions : CTDLDB1
Pharm GKB GenePA30316
PharosQ86U70
Clinical trialLDB1
Miscellaneous
canSAR (ICR)LDB1
HarmonizomeLDB1
DataMed IndexLDB1
Probes
Litterature
PubMed73 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
EVEXLDB1
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Fri Oct 8 21:21:10 CEST 2021

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