LDB1

Identity

Other names	CLIM2
	NLI
HGNC	LDB1
Location	10q24
Location_base_pair	Starts at 103857315 and ends at 103870200 bp from pter ( according to hg18-Mar_2006).

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	LDB1   6532
Entrez_Gene	LDB1  8861  LIM domain binding 1
	Cards
Atlas	LDB1ID41135ch10q24
GeneCards	LDB1
Ensembl	LDB1 [Search_View]   ENSG00000198728 [Gene_View]
Genatlas	LDB1
GeneLynx	LDB1
eGenome	LDB1
euGene	8861
	Genomic and cartography
GoldenPath	LDB1  -  10q24   chr10:103857315-103870200 -  10q24-q25   [Description]    (hg18-Mar_2006)
Ensembl	LDB1 - 10q24-q25 [CytoView]
NCBI	Mapview
OMIM	Disease map [OMIM]
HomoloGene	LDB1
	Gene and transcription
Genbank	AB016485 [ ENTREZ ]
Genbank	AB250384 [ ENTREZ ]
Genbank	AF064491 [ ENTREZ ]
Genbank	AF068652 [ ENTREZ ]
Genbank	AK308481 [ ENTREZ ]
RefSeq	NM_001113407 [ SRS ]    NM_001113407 [ ENTREZ ]
RefSeq	NM_003893 [ SRS ]    NM_003893 [ ENTREZ ]
RefSeq	AC_000053 [ SRS ]    AC_000053 [ ENTREZ ]
RefSeq	AC_000142 [ SRS ]    AC_000142 [ ENTREZ ]
RefSeq	NC_000010 [ SRS ]    NC_000010 [ ENTREZ ]
RefSeq	NT_030059 [ SRS ]    NT_030059 [ ENTREZ ]
RefSeq	NW_001838006 [ SRS ]    NW_001838006 [ ENTREZ ]
RefSeq	NW_924884 [ SRS ]    NW_924884 [ ENTREZ ]
AceView	LDB1 AceView - NCBI
Unigene	Hs.709666 [ SRS ]    Hs.709666 [ NCBI ]     HS709666 [ spliceNest ]
Fast-db	16569 (alternative variants)
	Protein : pattern, domain, 3D structure
SwissProt	Q86U70 [ SRS]    Q86U70 [ EXPASY ]     Q86U70 [ INTERPRO ]     Q86U70 [ UNIPROT ]
Interpro	IPR002691 LIM_bd [ SRS ]    IPR002691 LIM_bd [ EBI ]
CluSTr	Q86U70
Pfam	PF01803 LIM_bind [ SRS ]    PF01803 LIM_bind [ Sanger ]    pfam01803 [ NCBI-CDD ]
Blocks	Q86U70
HPRD	09144
	Protein Interaction databases
DIP	Q86U70
IntAct	Q86U70
	Polymorphism : SNP, mutations, diseases
OMIM	603451    [ map ]
GENECLINICS	603451
SNP	LDB1 [dbSNP-NCBI]
SNP	NM_001113407 [SNP-NCI]
SNP	NM_003893 [SNP-NCI]
SNP	LDB1 [GeneSNPs - Utah]  LDB1] [HGBASE - SRS]
HAPMAP	LDB1 [HAPMAP]
COSMIC	LDB1 [Somatic mutation (COSMIC-CGP-Sanger)]
HGMD	LDB1
	General knowledge
Family Browser	LDB1 [UCSC Family Browser]
SOURCE	NM_001113407
SOURCE	NM_003893
SMD	Hs.709666
SAGE	Hs.709666
GO	transcription corepressor activity [Amigo]  transcription corepressor activity
GO	nucleus [Amigo]  nucleus
GO	multicellular organismal development [Amigo]  multicellular organismal development
GO	neuron differentiation [Amigo]  neuron differentiation
GO	LIM domain binding [Amigo]  LIM domain binding
GO	LIM domain binding [Amigo]  LIM domain binding
GO	protein homodimerization activity [Amigo]  protein homodimerization activity
GO	protein complex [Amigo]  protein complex
GO	negative regulation of erythrocyte differentiation [Amigo]  negative regulation of erythrocyte differentiation
GO	negative regulation of transcription, DNA-dependent [Amigo]  negative regulation of transcription, DNA-dependent
GO	negative regulation of transcription, DNA-dependent [Amigo]  negative regulation of transcription, DNA-dependent
BIOCARTA	Multi-step Regulation of Transcription by Pitx2    [Genes]
PubGene	LDB1
TreeFam	LDB1
CTD	8861 [Comparative ToxicoGenomics Database]
	Other databases
	Probes
Probe	LDB1 Related clones (RZPD - Berlin)
	PubMed
PubMed	29 Pubmed reference(s) in Entrez

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 articles	automatic search in PubMed
Last year publications	automatic search in PubMed

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Contributor(s)

Written	11-2006	Takeshi Setogawa, Testu Akiyama

Citation

This paper should be referenced as such :

Setogawa T, Akiyama T . LDB1. Atlas Genet Cytogenet Oncol Haematol. November 2006 . URL : http://AtlasGeneticsOncology.org/Genes/LDB1ID41135ch10q24.html

© Atlas of Genetics and Cytogenetics in Oncology and Haematology

indexed on : Tue Oct 14 21:21:10 2008