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Protein

LIM domain-binding protein 1

Gene

Ldb1

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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.7 Publications

GO - Molecular functioni

  • chromatin binding Source: MGI
  • enhancer sequence-specific DNA binding Source: MGI
  • enzyme binding Source: UniProtKB
  • LIM domain binding Source: UniProtKB
  • protein homodimerization activity Source: UniProtKB
  • protein self-association Source: MGI
  • RNA polymerase II activating transcription factor binding Source: MGI
  • transcription factor activity, transcription factor binding Source: MGI

GO - Biological processi

  • anterior/posterior axis specification Source: MGI
  • cellular component assembly Source: MGI
  • cerebellar Purkinje cell differentiation Source: MGI
  • cerebellum development Source: MGI
  • epithelial structure maintenance Source: MGI
  • gastrulation with mouth forming second Source: MGI
  • hair follicle development Source: MGI
  • head development Source: UniProtKB
  • histone H3-K4 acetylation Source: BHF-UCL
  • negative regulation of erythrocyte differentiation Source: UniProtKB
  • negative regulation of transcription, DNA-templated Source: MGI
  • neuron differentiation Source: UniProtKB
  • positive regulation of cell adhesion Source: MGI
  • positive regulation of hemoglobin biosynthetic process Source: BHF-UCL
  • positive regulation of transcription from RNA polymerase II promoter Source: BHF-UCL
  • primitive erythrocyte differentiation Source: BHF-UCL
  • regulation of cell migration Source: UniProtKB
  • regulation of DNA-templated transcription, elongation Source: BHF-UCL
  • regulation of focal adhesion assembly Source: UniProtKB
  • regulation of kinase activity Source: UniProtKB
  • somatic stem cell population maintenance Source: MGI
  • transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery Source: BHF-UCL
  • transcription from RNA polymerase II promoter Source: UniProtKB
  • Wnt signaling pathway Source: MGI
Complete GO annotation...

Keywords - Molecular functioni

Developmental protein

Names & Taxonomyi

Protein namesi
Recommended 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 namesi
Name:Ldb1
Synonyms:Nli
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 19

Organism-specific databases

MGIiMGI:894762. Ldb1.

Subcellular locationi

GO - Cellular componenti

  • cell leading edge Source: UniProtKB
  • nuclear chromatin Source: MGI
  • nucleus Source: UniProtKB
  • protein complex Source: UniProtKB
  • transcription factor complex Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedBy similarity
ChainiPRO_00000843852 – 411LIM domain-binding protein 1Add BLAST410

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylserineBy similarity1
Modified residuei61PhosphothreonineCombined sources1
Modified residuei265PhosphoserineBy similarity1
Modified residuei302PhosphoserineCombined sources1

Post-translational modificationi

Ubiquitinated by RLIM/RNF12, leading to its degradation by the proteasome.1 Publication

Keywords - PTMi

Acetylation, Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiP70662.
PaxDbiP70662.
PRIDEiP70662.

PTM databases

iPTMnetiP70662.
PhosphoSitePlusiP70662.

Expressioni

Tissue specificityi

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.4 Publications

Gene expression databases

BgeeiENSMUSG00000025223.
CleanExiMM_LDB1.
ExpressionAtlasiP70662. baseline and differential.
GenevisibleiP70662. MM.

Interactioni

Subunit structurei

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. Interacts with SLK; leading to negatively regulate SLK kinase activity (PubMed:19675209).By similarity11 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
Cbfa2t3O549722EBI-6272082,EBI-8006703
Isl1P613723EBI-6272082,EBI-7988215
Lhx3P504815EBI-6272082,EBI-7988290
Tal1P220913EBI-6272082,EBI-8006437
Tcf4Q607222EBI-6272082,EBI-310070

GO - Molecular functioni

  • enzyme binding Source: UniProtKB
  • LIM domain binding Source: UniProtKB
  • protein homodimerization activity Source: UniProtKB
  • protein self-association Source: MGI
  • RNA polymerase II activating transcription factor binding Source: MGI

Protein-protein interaction databases

BioGridi201125. 27 interactors.
DIPiDIP-42842N.
IntActiP70662. 6 interactors.
MINTiMINT-2779250.
STRINGi10090.ENSMUSP00000118546.

Structurei

Secondary structure

1411
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi336 – 344Combined sources9
Beta strandi346 – 349Combined sources4
Beta strandi355 – 357Combined sources3
Beta strandi359 – 362Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
ProteinModelPortaliP70662.
SMRiP70662.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP70662.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni336 – 374LIM-binding domain (LID)Add BLAST39

Domaini

The dimerization domain is located in the N-terminus.1 Publication

Sequence similaritiesi

Belongs to the LDB family.Curated

Phylogenomic databases

eggNOGiKOG2181. Eukaryota.
ENOG410YZVH. LUCA.
GeneTreeiENSGT00390000005639.
HOGENOMiHOG000030908.
HOVERGENiHBG000135.
InParanoidiP70662.
KOiK15617.
OMAiKMSVGCA.
OrthoDBiEOG091G0A0P.
PhylomeDBiP70662.
TreeFamiTF319923.

Sequences (3)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: P70662-1) [UniParc]FASTAAdd to basket
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.

« Hide

        10         20         30         40         50
MSVGCACPGC SSKSFKLYSP KEPPNGNAFP PFHPGTMLDR DVGPTPMYPP
60 70 80 90 100
TYLEPGIGRH TPYGNQTDYR IFELNKRLQN WTEECDNLWW DAFTTEFFED
110 120 130 140 150
DAMLTITFCL EDGPKRYTIG RTLIPRYFRS IFEGGATELY YVLKHPKEAF
160 170 180 190 200
HSNFVSLDCD QGSMVTQHGK PMFTQVCVEG RLYLEFMFDD MMRIKTWHFS
210 220 230 240 250
IRQHRELIPR SILAMHAQDP QMLDQLSKNI TRCGLSNSTL NYLRLCVILE
260 270 280 290 300
PMQELMSRHK TYSLSPRDCL KTCLFQKWQR MVAPPAEPAR QQPSKRRKRK
310 320 330 340 350
MSGGSTMSSG GGNTNNSNSK KKSPASTFAL SSQVPDVMVV GEPTLMGGEF
360 370 380 390 400
GDEDERLITR LENTQFDAAN GIDDEDSFNN SPALGANSPW NSKPPSSQES
410
KSENPTSQAS Q
Length:411
Mass (Da):46,503
Last modified:September 11, 2007 - v2
Checksum:i47C53DFA23044580
GO
Isoform 2 (identifier: P70662-2) [UniParc]FASTAAdd to basket
Also known as: Tran-b

The sequence of this isoform differs from the canonical sequence as follows:
     1-36: 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.
Show »
Length:319
Mass (Da):36,667
Checksum:i2FD1D15303732E5E
GO
Isoform 3 (identifier: P70662-3) [UniParc]FASTAAdd to basket
Also known as: Tran-a

The sequence of this isoform differs from the canonical sequence as follows:
     1-36: Missing.

Show »
Length:375
Mass (Da):42,779
Checksum:i75FACF0CA0BD2DE7
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti262Y → C in AAB96885 (PubMed:9192866).Curated1
Sequence conflicti334V → A in AAB96885 (PubMed:9192866).Curated1
Sequence conflicti389 – 390PW → QR in AAB96885 (PubMed:9192866).Curated2

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0278331 – 36Missing in isoform 2 and isoform 3. 5 PublicationsAdd BLAST36
Alternative sequenceiVSP_027834336 – 355DVMVV…GDEDE → VSISAFFSSGLPHCSPLTPV in isoform 2. 1 PublicationAdd BLAST20
Alternative sequenceiVSP_027835356 – 411Missing in isoform 2. 1 PublicationAdd BLAST56

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
CCDSiCCDS29870.1. [P70662-3]
CCDS50455.1. [P70662-1]
RefSeqiNP_001106879.1. NM_001113408.1. [P70662-1]
NP_034827.1. NM_010697.1. [P70662-3]
XP_011245459.1. XM_011247157.1. [P70662-3]
UniGeneiMm.327442.

Genome annotation databases

EnsembliENSMUST00000026252; ENSMUSP00000026252; ENSMUSG00000025223. [P70662-3]
ENSMUST00000056931; ENSMUSP00000053680; ENSMUSG00000025223. [P70662-3]
ENSMUST00000137771; ENSMUSP00000114667; ENSMUSG00000025223. [P70662-2]
ENSMUST00000156585; ENSMUSP00000118546; ENSMUSG00000025223. [P70662-1]
ENSMUST00000185355; ENSMUSP00000139562; ENSMUSG00000025223. [P70662-1]
GeneIDi16825.
KEGGimmu:16825.
UCSCiuc008hrz.1. mouse. [P70662-1]
uc008hsa.1. mouse. [P70662-2]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
CCDSiCCDS29870.1. [P70662-3]
CCDS50455.1. [P70662-1]
RefSeqiNP_001106879.1. NM_001113408.1. [P70662-1]
NP_034827.1. NM_010697.1. [P70662-3]
XP_011245459.1. XM_011247157.1. [P70662-3]
UniGeneiMm.327442.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
ProteinModelPortaliP70662.
SMRiP70662.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi201125. 27 interactors.
DIPiDIP-42842N.
IntActiP70662. 6 interactors.
MINTiMINT-2779250.
STRINGi10090.ENSMUSP00000118546.

PTM databases

iPTMnetiP70662.
PhosphoSitePlusiP70662.

Proteomic databases

MaxQBiP70662.
PaxDbiP70662.
PRIDEiP70662.

Protocols and materials databases

DNASUi16825.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000026252; ENSMUSP00000026252; ENSMUSG00000025223. [P70662-3]
ENSMUST00000056931; ENSMUSP00000053680; ENSMUSG00000025223. [P70662-3]
ENSMUST00000137771; ENSMUSP00000114667; ENSMUSG00000025223. [P70662-2]
ENSMUST00000156585; ENSMUSP00000118546; ENSMUSG00000025223. [P70662-1]
ENSMUST00000185355; ENSMUSP00000139562; ENSMUSG00000025223. [P70662-1]
GeneIDi16825.
KEGGimmu:16825.
UCSCiuc008hrz.1. mouse. [P70662-1]
uc008hsa.1. mouse. [P70662-2]

Organism-specific databases

CTDi8861.
MGIiMGI:894762. Ldb1.

Phylogenomic databases

eggNOGiKOG2181. Eukaryota.
ENOG410YZVH. LUCA.
GeneTreeiENSGT00390000005639.
HOGENOMiHOG000030908.
HOVERGENiHBG000135.
InParanoidiP70662.
KOiK15617.
OMAiKMSVGCA.
OrthoDBiEOG091G0A0P.
PhylomeDBiP70662.
TreeFamiTF319923.

Miscellaneous databases

ChiTaRSiLdb1. mouse.
EvolutionaryTraceiP70662.
PROiP70662.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000025223.
CleanExiMM_LDB1.
ExpressionAtlasiP70662. baseline and differential.
GenevisibleiP70662. MM.

Family and domain databases

ProtoNetiSearch...

Entry informationi

Entry nameiLDB1_MOUSE
AccessioniPrimary (citable) accession number: P70662
Secondary accession number(s): O55204, Q1EQX2, Q71V68
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: September 11, 2007
Last modified: November 2, 2016
This is version 143 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.