LDB1 (LIM domain binding 1)

2006-11-01 Takeshi Setogawa , Testu Akiyama Affiliation

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

Identity

HGNC

LDB1

LOCATION

10q24.32

LOCUSID

8861

ALIAS

CLIM-2,CLIM2,LDB-1,NLI

FUSION GENES

Show Gene Fusions

DNA/RNA

Description

7kb; 11exons

Transcription

2292 nucleotides mRNA

Proteins

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

Entity name

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.

Article Bibliography

Pubmed ID	Last Year	Title	Authors
8918878	1996	Interactions of the LIM-domain-binding factor Ldb1 with LIM homeodomain proteins.	Agulnick AD et al
9192866	1997	A family of LIM domain-associated cofactors confer transcriptional synergism between LIM and Otx homeodomain proteins.	Bach I et al
12381786	2002	Ssdp proteins interact with the LIM-domain-binding protein Ldb1 to regulate development.	Chen L et al
9315627	1997	Functional analysis of the nuclear LIM domain interactor NLI.	Jurata LW et al
14647207	2003	LIM-domain-binding protein 1: a multifunctional cofactor that interacts with diverse proteins.	Matthews JM et al
12771919	2003	The LIM-only protein, LMO4, and the LIM domain-binding protein, LDB1, expression in squamous cell carcinomas of the oral cavity.	Mizunuma H et al
12490556	2003	Functional ablation of the mouse Ldb1 gene results in severe patterning defects during gastrulation.	Mukhopadhyay M et al
16580634	2006	The tumor suppressor LKB1 induces p21 expression in collaboration with LMO4, GATA-6, and Ldb1.	Setogawa T et al
9391090	1997	The LIM-domain binding protein Ldb1 and its partner LMO2 act as negative regulators of erythroid differentiation.	Visvader JE et al

Other Information

Locus ID:

NCBI: 8861
MIM: 603451
HGNC: 6532
Ensembl: ENSG00000198728

Variants:

dbSNP: 8861
ClinVar: 8861
TCGA: ENSG00000198728
COSMIC: LDB1

RNA/Proteins

Gene ID	Transcript ID	Uniprot
ENSG00000198728	ENST00000361198	Q86U70
ENSG00000198728	ENST00000425280	Q86U70

Expression (GTEx)

100

150

200

250

Adipose - Subcutaneous

Adipose - Visceral

Adrenal Gland

Artery - Aorta

Artery - Tibial

Bladder

Brain - Amygdala

Brain - Anterior cingulate cortex

Brain - Caudate

Brain - Cerebellar Hemisphere

Brain - Cerebellum

Brain - Cortex

Brain - Frontal Cortex

Brain - Hippocampus

Brain - Hypothalamus

Brain - Nucleus accumbens

Brain - Putamen

Brain - Spinal cord

Brain - Substantia nigra

Breast - Mammary Tissue

Cells - Cultured fibroblasts

Cells - EBV - transformed lymphocytes

Cervix - Ectocervix

Cervix - Endocervix

Colon - Sigmoid

Colon - Transverse

Esophagus - Gastroesophageal Junction

Esophagus - Mucosa

Esophagus - Muscularis

Fallopian Tube

Heart - Atrial Appendage

Heart - Left Ventricle

Kidney - Cortex

Kidney - Medulla

Liver

Lung

Minor Salivary Gland

Muscle - Skeletal

Nerve - Tibial

Ovary

Pancreas

Pituitary

Prostate

Skin - Not Sun Exposed

Skin - Sun Exposed

Small Intestine - Terminal Ileum

Spleen

Stomach

Testis

Thyroid

Uterus

Vagina

Whole Blood

Pathways

Pathway	Source	External ID
Transcriptional misregulation in cancer	KEGG	ko05202
Transcriptional misregulation in cancer	KEGG	hsa05202

Protein levels (Protein atlas)

Not detected

Low

Medium

High

References

Pubmed ID	Year	Title	Citations
38695236	2024	An intricate regulatory circuit between FLI1 and GATA1/GATA2/LDB1/ERG dictates erythroid vs. megakaryocytic differentiation.	0
38695236	2024	An intricate regulatory circuit between FLI1 and GATA1/GATA2/LDB1/ERG dictates erythroid vs. megakaryocytic differentiation.	0
37573405	2023	LMO2 promotes the development of AML through interaction with transcription co-regulator LDB1.	0
37573405	2023	LMO2 promotes the development of AML through interaction with transcription co-regulator LDB1.	0
35881062	2022	The Ldb1 transcriptional co-regulator is required for establishment and maintenance of the pancreatic endocrine lineage.	2
35881062	2022	The Ldb1 transcriptional co-regulator is required for establishment and maintenance of the pancreatic endocrine lineage.	2
31892537	2020	Crystal structure of human LDB1 in complex with SSBP2.	13
32229578	2020	LDB1 Enforces Stability on Direct and Indirect Oncoprotein Partners in Leukemia.	8
31892537	2020	Crystal structure of human LDB1 in complex with SSBP2.	13
32229578	2020	LDB1 Enforces Stability on Direct and Indirect Oncoprotein Partners in Leukemia.	8
27941246	2017	LIM domain-binding 1 maintains the terminally differentiated state of pancreatic β cells.	40
27941246	2017	LIM domain-binding 1 maintains the terminally differentiated state of pancreatic β cells.	40
26598604	2016	LMO2 Oncoprotein Stability in T-Cell Leukemia Requires Direct LDB1 Binding.	7
27713177	2016	LDB1 overexpression is a negative prognostic factor in colorectal cancer.	11
26598604	2016	LMO2 Oncoprotein Stability in T-Cell Leukemia Requires Direct LDB1 Binding.	7

Citation

Takeshi Setogawa ; Testu Akiyama

LDB1 (LIM domain binding 1)

Atlas Genet Cytogenet Oncol Haematol. 2006-11-01

Online version: http://atlasgeneticsoncology.org/gene/41135/js/gene-fusions-explorer/favicon/favicon-16x16.png