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P70662 (LDB1_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 123. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
LIM domain-binding protein 1

Short name=LDB-1
Alternative name(s):
Carboxyl-terminal LIM domain-binding protein 2
Short name=CLIM-2
LIM domain-binding factor CLIM2
Short name=mLdb1
Nuclear LIM interactor
Gene names
Name:Ldb1
Synonyms:Nli
OrganismMus musculus (Mouse) [Reference proteome]
Taxonomic identifier10090 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus

Protein attributes

Sequence length411 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Binds to the LIM domain of a wide variety of LIM domain-containing transcription factors. May regulate the transcriptional activity of LIM-containing proteins by determining specific partner interactions. Plays a role in the development of interneurons and motor neurons in cooperation with LHX3 and ISL1. Acts synergistically with LHX1/LIM1 in axis formation and activation of gene expression. Acts with LMO2 in the regulation of red blood cell development, maintaining erythroid precursors in an immature state. Ref.1 Ref.2 Ref.3 Ref.4 Ref.6 Ref.8 Ref.12

Subunit structure

Interacts with ESR1 By similarity. Forms homodimers and heterodimers. Interacts with and activates LHX1/LIM1. Interacts with the LIM domains of ISL1 and LMO2. Can assemble in a complex with LMO2 and TAL1/SCL but does not interact with TAL1/SCL directly. Strongly interacts with the LIM2 domain of LMX1A and more weakly with the LIM1 domain. Homodimerization is not required for, and does not effect, LMX1A-binding. Component of a nuclear TAL-1 complex composed at least of CBFA2T3, LDB1, TAL1 and TCF3. Interacts with LHX6 and LHX9. At neuronal promoters, forms a complex with LHX3 involved in the specification of interneurons, in motor neurons, it is displaced by ISL1 to form a ternary complex in which ISL1 contacts both LHX3 and LDB1. Ref.1 Ref.4 Ref.8 Ref.9 Ref.10 Ref.11 Ref.12 Ref.13 Ref.14

Subcellular location

Nucleus Ref.2 Ref.4 Ref.8.

Tissue specificity

Expression overlaps that of LIM domain-containing proteins. Expressed widely in the embryo with highest expression in several regions of the brain the central nervous system ganglia. Also expressed in fetal liver, lung, kidney, thymus and olfactory epithelium. Expressed in multiple adult tissues including heart, brain, liver, kidney, testis, lung and muscle and a diverse range of neuronal cell types, with expression highest in the pituitary gland and skin. Expressed in both embryonic and adult hemopoietic cells, including the erythroid lineage. Ref.1 Ref.3 Ref.4 Ref.6

Domain

The dimerization domain is located in the N-terminus. Ref.8 Ref.9

Post-translational modification

Ubiquitinated by RLIM/RNF12, leading to its degradation by the proteasome. Ref.13

Sequence similarities

Belongs to the LDB family.

Ontologies

Keywords
   Cellular componentNucleus
   Coding sequence diversityAlternative splicing
   Molecular functionDevelopmental protein
   PTMAcetylation
Ubl conjugation
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processWnt signaling pathway

Inferred from mutant phenotype PubMed 12490556. Source: MGI

anterior/posterior axis specification

Inferred from mutant phenotype PubMed 12490556. Source: MGI

cellular component assembly

Inferred from genetic interaction PubMed 17991461. Source: MGI

cerebellar Purkinje cell differentiation

Inferred from mutant phenotype PubMed 17664423. Source: MGI

cerebellum development

Inferred from mutant phenotype PubMed 17664423. Source: MGI

epithelial structure maintenance

Inferred from genetic interaction PubMed 17991461. Source: MGI

gastrulation with mouth forming second

Inferred from mutant phenotype PubMed 12490556. Source: MGI

hair follicle development

Inferred from genetic interaction PubMed 17991461. Source: MGI

head development

Inferred from genetic interaction PubMed 15857913. Source: UniProtKB

histone H3-K4 acetylation

Inferred from mutant phenotype PubMed 20570862. Source: BHF-UCL

negative regulation of erythrocyte differentiation

Inferred from mutant phenotype Ref.4. Source: UniProtKB

negative regulation of transcription, DNA-templated

Inferred from electronic annotation. Source: Ensembl

neuron differentiation

Inferred from expression pattern Ref.2. Source: UniProtKB

positive regulation of cell adhesion

Inferred from genetic interaction PubMed 17991461. Source: MGI

positive regulation of hemoglobin biosynthetic process

Inferred from mutant phenotype PubMed 20570862. Source: BHF-UCL

positive regulation of transcription from RNA polymerase II promoter

Inferred from mutant phenotype PubMed 20570862. Source: BHF-UCL

primitive erythrocyte differentiation

Traceable author statement PubMed 20570862. Source: BHF-UCL

regulation of DNA-templated transcription, elongation

Inferred from mutant phenotype PubMed 20570862. Source: BHF-UCL

somatic stem cell maintenance

Inferred from genetic interaction PubMed 17991461. Source: MGI

transcription from RNA polymerase II promoter

Inferred from direct assay PubMed 15857913. Source: UniProtKB

transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery

Inferred from mutant phenotype PubMed 20570862. Source: BHF-UCL

   Cellular_componentnuclear chromatin

Inferred from electronic annotation. Source: Ensembl

nucleus

Inferred from direct assay Ref.2Ref.4. Source: UniProtKB

protein complex

Inferred from direct assay PubMed 15857913. Source: UniProtKB

transcription factor complex

Inferred from electronic annotation. Source: Ensembl

   Molecular_functionLIM domain binding

Inferred from direct assay Ref.2Ref.8. Source: UniProtKB

chromatin binding

Inferred from direct assay PubMed 18550854PubMed 19011221. Source: MGI

enhancer sequence-specific DNA binding

Inferred from direct assay PubMed 19323994. Source: MGI

enzyme binding

Inferred from physical interaction Ref.13. Source: UniProtKB

protein binding

Inferred from physical interaction Ref.10Ref.4. Source: UniProtKB

protein homodimerization activity

Inferred from direct assay Ref.8Ref.9. Source: UniProtKB

protein self-association

Inferred from physical interaction PubMed 19323994. Source: MGI

transcription cofactor activity

Inferred from electronic annotation. Source: InterPro

transcription factor binding transcription factor activity

Inferred from physical interaction PubMed 17991461Ref.1Ref.3. Source: MGI

Complete GO annotation...

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: P70662-1)

Also known as: Visvader-a;

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Isoform 2 (identifier: P70662-2)

Also known as: Tran-b;

The sequence of this isoform differs from the canonical sequence as follows:
     2-36: Missing.
     336-355: DVMVVGEPTLMGGEFGDEDE → VSISAFFSSGLPHCSPLTPV
     356-411: Missing.
Note: Due to intron retention. Lacks LIM-binding domain. Lacks ability to activate LIM domain-dependent transcription.
Isoform 3 (identifier: P70662-3)

Also known as: Tran-a;

The sequence of this isoform differs from the canonical sequence as follows:
     2-36: Missing.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed By similarity
Chain2 – 411410LIM domain-binding protein 1
PRO_0000084385

Regions

Region336 – 37439LIM-binding domain (LID)

Amino acid modifications

Modified residue21N-acetylserine By similarity

Natural variations

Alternative sequence2 – 3635Missing in isoform 2 and isoform 3.
VSP_027833
Alternative sequence336 – 35520DVMVV…GDEDE → VSISAFFSSGLPHCSPLTPV in isoform 2.
VSP_027834
Alternative sequence356 – 41156Missing in isoform 2.
VSP_027835

Experimental info

Sequence conflict2621Y → C in AAB96885. Ref.3
Sequence conflict3341V → A in AAB96885. Ref.3
Sequence conflict389 – 3902PW → QR in AAB96885. Ref.3

Secondary structure

............................ 411
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 (Visvader-a) [UniParc].

Last modified September 11, 2007. Version 2.
Checksum: 47C53DFA23044580

FASTA41146,503
        10         20         30         40         50         60 
MSVGCACPGC SSKSFKLYSP KEPPNGNAFP PFHPGTMLDR DVGPTPMYPP TYLEPGIGRH 

        70         80         90        100        110        120 
TPYGNQTDYR IFELNKRLQN WTEECDNLWW DAFTTEFFED DAMLTITFCL EDGPKRYTIG 

       130        140        150        160        170        180 
RTLIPRYFRS IFEGGATELY YVLKHPKEAF HSNFVSLDCD QGSMVTQHGK PMFTQVCVEG 

       190        200        210        220        230        240 
RLYLEFMFDD MMRIKTWHFS IRQHRELIPR SILAMHAQDP QMLDQLSKNI TRCGLSNSTL 

       250        260        270        280        290        300 
NYLRLCVILE PMQELMSRHK TYSLSPRDCL KTCLFQKWQR MVAPPAEPAR QQPSKRRKRK 

       310        320        330        340        350        360 
MSGGSTMSSG GGNTNNSNSK KKSPASTFAL SSQVPDVMVV GEPTLMGGEF GDEDERLITR 

       370        380        390        400        410 
LENTQFDAAN GIDDEDSFNN SPALGANSPW NSKPPSSQES KSENPTSQAS Q 

« Hide

Isoform 2 (Tran-b) [UniParc].

Checksum: AE90F933828A17BC
Show »

FASTA32036,798
Isoform 3 (Tran-a) [UniParc].

Checksum: FDE13F1E9984E4EA
Show »

FASTA37642,910

References

« Hide 'large scale' references
[1]"Interactions of the LIM-domain-binding factor Ldb1 with LIM homeodomain proteins."
Agulnick A.D., Taira M., Breen J.J., Tanaka T., Dawid I.B., Westphal H.
Nature 384:270-272(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3), FUNCTION, INTERACTION WITH LHX1, TISSUE SPECIFICITY.
Strain: Swiss Webster.
Tissue: Embryo.
[2]"Nuclear LIM interactor, a rhombotin and LIM homeodomain interacting protein, is expressed early in neuronal development."
Jurata L.W., Kenny D.A., Gill G.N.
Proc. Natl. Acad. Sci. U.S.A. 93:11693-11698(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3), FUNCTION, SUBCELLULAR LOCATION.
Tissue: Embryo.
[3]"A family of LIM domain-associated cofactors confer transcriptional synergism between LIM and Otx homeodomain proteins."
Bach I., Carriere C., Ostendorff H.P., Andersen B., Rosenfeld M.G.
Genes Dev. 11:1370-1380(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3), FUNCTION, TISSUE SPECIFICITY.
Tissue: Embryonic head.
[4]"The LIM-domain binding protein Ldb1 and its partner LMO2 act as negative regulators of erythroid differentiation."
Visvader J.E., Mao X., Fujiwara Y., Hahm K., Orkin S.H.
Proc. Natl. Acad. Sci. U.S.A. 94:13707-13712(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, INTERACTION WITH LMO2, IDENTIFICATION IN A COMPLEX WITH LMO2 AND TAL1.
Tissue: Yolk sac.
[5]"Genomic structure and chromosomal localization of the mouse LIM domain-binding protein 1 gene, Ldb1."
Yamashita T., Agulnick A.D., Copeland N.G., Gilbert D.J., Jenkins N.A., Westphal H.
Genomics 48:87-92(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: 129/Sv.
[6]"Spliced isoforms of LIM-domain-binding protein (CLIM/NLI/Ldb) lacking the LIM-interaction domain."
Tran Y.H., Xu Z., Kato A., Mistry A.C., Goya Y., Taira M., Brandt S.J., Hirose S.
J. Biochem. 140:105-119(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), FUNCTION, ALTERNATIVE SPLICING, TISSUE SPECIFICITY.
Tissue: Heart.
[7]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3).
Strain: FVB/N.
Tissue: Mammary gland.
[8]"Functional analysis of the nuclear LIM domain interactor NLI."
Jurata L.W., Gill G.N.
Mol. Cell. Biol. 17:5688-5698(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH ISL1; LMO2 AND LMX1A, HOMODIMERIZATION, SUBCELLULAR LOCATION, IDENTIFICATION OF LIM-BINDING DOMAIN.
[9]"Interactions between LIM domains and the LIM domain-binding protein Ldb1."
Breen J.J., Agulnick A.D., Westphal H., Dawid I.B.
J. Biol. Chem. 273:4712-4717(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH LHX1, DOMAIN, HOMODIMERIZATION.
[10]"A brain region-specific gene product Lhx6.1 interacts with Ldb1 through tandem LIM-domains."
Kimura N., Ueno M., Nakashima K., Taga T.
J. Biochem. 126:180-187(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH LHX6.
Tissue: Fetal brain.
[11]"Characterization of Lhx9, a novel LIM/homeobox gene expressed by the pioneer neurons in the mouse cerebral cortex."
Bertuzzi S., Porter F.D., Pitts A., Kumar M., Agulnick A., Wassif C., Westphal H.
Mech. Dev. 81:193-198(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH LHX9.
[12]"LIM factor Lhx3 contributes to the specification of motor neuron and interneuron identity through cell-type-specific protein-protein interactions."
Thaler J.P., Lee S.K., Jurata L.W., Gill G.N., Pfaff S.L.
Cell 110:237-249(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH LHX3 AND ISL1.
[13]"Ubiquitination-dependent cofactor exchange on LIM homeodomain transcription factors."
Ostendorff H.P., Peirano R.I., Peters M.A., Schluter A., Bossenz M., Scheffner M., Bach I.
Nature 416:99-103(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH RLIM, UBIQUITINATION.
[14]"ETO2 coordinates cellular proliferation and differentiation during erythropoiesis."
Goardon N., Lambert J.A., Rodriguez P., Nissaire P., Herblot S., Thibault P., Dumenil D., Strouboulis J., Romeo P.-H., Hoang T.
EMBO J. 25:357-366(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION IN A NUCLEAR TAL-1 COMPLEX.
[15]"Structural basis for the recognition of ldb1 by the N-terminal LIM domains of LMO2 and LMO4."
Deane J.E., Mackay J.P., Kwan A.H.Y., Sum E.Y.M., Visvader J.E., Matthews J.M.
EMBO J. 22:2224-2233(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 336-375 IN COMPLEXES WITH LMO2 AND LMO4.
[16]"Tandem LIM domains provide synergistic binding in the LMO4:Ldb1 complex."
Deane J.E., Ryan D.P., Sunde M., Maher M.J., Guss J.M., Visvader J.E., Matthews J.M.
EMBO J. 23:3589-3598(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.3 ANGSTROMS) OF 336-375 IN COMPLEX WITH LMO4.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U70375 mRNA. Translation: AAC52933.1.
U69270 mRNA. Translation: AAC52887.1.
U89488 mRNA. Translation: AAB96885.1.
AF030333 mRNA. Translation: AAB94131.1.
AF024524 Genomic DNA. Translation: AAC40064.1.
AB250383 mRNA. Translation: BAE95401.1.
BC013624 mRNA. Translation: AAH13624.1.
CCDSCCDS29870.1. [P70662-3]
CCDS50455.1. [P70662-1]
RefSeqNP_001106879.1. NM_001113408.1. [P70662-1]
NP_034827.1. NM_010697.1.
UniGeneMm.327442.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1J2ONMR-A336-375[»]
1M3VNMR-A336-375[»]
1RUTX-ray1.30X336-375[»]
2JTNNMR-A331-375[»]
2L6YNMR-B336-348[»]
2L6ZNMR-C336-348[»]
2LXDNMR-A336-375[»]
4JCJX-ray3.00A/B/C336-366[»]
ProteinModelPortalP70662.
SMRP70662. Positions 336-363.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid201125. 27 interactions.
IntActP70662. 6 interactions.
MINTMINT-2779250.

PTM databases

PhosphoSiteP70662.

Proteomic databases

PaxDbP70662.
PRIDEP70662.

Protocols and materials databases

DNASU16825.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSMUST00000026252; ENSMUSP00000026252; ENSMUSG00000025223.
ENSMUST00000056931; ENSMUSP00000053680; ENSMUSG00000025223.
ENSMUST00000137771; ENSMUSP00000114667; ENSMUSG00000025223.
ENSMUST00000156585; ENSMUSP00000118546; ENSMUSG00000025223. [P70662-1]
GeneID16825.
KEGGmmu:16825.
UCSCuc008hrz.1. mouse. [P70662-1]
uc008hsa.1. mouse. [P70662-2]

Organism-specific databases

CTD8861.
MGIMGI:894762. Ldb1.

Phylogenomic databases

eggNOGNOG282114.
GeneTreeENSGT00390000005639.
HOGENOMHOG000030908.
HOVERGENHBG000135.
InParanoidP70662.
KOK15617.
OMAGSNSPWN.
PhylomeDBP70662.
TreeFamTF319923.

Gene expression databases

ArrayExpressP70662.
BgeeP70662.
CleanExMM_LDB1.
GenevestigatorP70662.

Family and domain databases

InterProIPR029005. LIM-bd/SEUSS.
IPR002691. LIM-dom-bd.
[Graphical view]
PANTHERPTHR10378. PTHR10378. 1 hit.
PfamPF01803. LIM_bind. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSLDB1. mouse.
EvolutionaryTraceP70662.
NextBio290724.
PROP70662.
SOURCESearch...

Entry information

Entry nameLDB1_MOUSE
AccessionPrimary (citable) accession number: P70662
Secondary accession number(s): O55204, Q1EQX2, Q71V68
Entry history
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: September 11, 2007
Last modified: July 9, 2014
This is version 123 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MGD cross-references

Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot