UniProtKB - Q86U70 (LDB1_HUMAN)
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Protein
LIM domain-binding protein 1
Gene
LDB1
Organism
Homo sapiens (Human)
Status
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 (By similarity).By similarity
Miscellaneous
Acts as a negative coregulator of ESR1-mediated transcription in breast cancer cells.
GO - Molecular functioni
- chromatin binding Source: Ensembl
- enhancer sequence-specific DNA binding Source: Ensembl
- enzyme binding Source: UniProtKB
- LIM domain binding Source: UniProtKB
- protein homodimerization activity Source: UniProtKB
- protein self-association Source: Ensembl
- RNA polymerase II activating transcription factor binding Source: BHF-UCL
- transcription corepressor activity Source: ProtInc
GO - Biological processi
- anterior/posterior axis specification Source: Ensembl
- cellular component assembly Source: Ensembl
- cerebellar Purkinje cell differentiation Source: Ensembl
- epithelial structure maintenance Source: Ensembl
- gastrulation with mouth forming second Source: Ensembl
- hair follicle development Source: Ensembl
- histone H3-K4 acetylation Source: BHF-UCL
- multicellular organism development Source: UniProtKB
- negative regulation of erythrocyte differentiation Source: UniProtKB
- negative regulation of transcription, DNA-templated Source: UniProtKB
- neuron differentiation Source: UniProtKB
- positive regulation of cell adhesion Source: Ensembl
- positive regulation of hemoglobin biosynthetic process Source: BHF-UCL
- positive regulation of transcription by RNA polymerase II 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 hematopoietic stem cell differentiation Source: Reactome
- regulation of kinase activity Source: UniProtKB
- regulation of transcription, DNA-templated Source: ProtInc
- somatic stem cell population maintenance Source: Ensembl
- transcription, DNA-templated Source: UniProtKB
- transcription by RNA polymerase II Source: Ensembl
- transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery Source: BHF-UCL
- Wnt signaling pathway Source: Ensembl
Keywordsi
Molecular function | Developmental protein |
Enzyme and pathway databases
Reactomei | R-HSA-8939236. RUNX1 regulates transcription of genes involved in differentiation of HSCs. R-HSA-9010553. Regulation of expression of SLITs and ROBOs. |
SIGNORi | Q86U70. |
Names & Taxonomyi
Protein namesi | Recommended name: LIM domain-binding protein 1Short name: LDB-1 Alternative name(s): Carboxyl-terminal LIM domain-binding protein 2 Short name: CLIM-2 LIM domain-binding factor CLIM2 Short name: hLdb1 Nuclear LIM interactor |
Gene namesi | Name:LDB1 Synonyms:CLIM2 |
Organismi | Homo sapiens (Human) |
Taxonomic identifieri | 9606 [NCBI] |
Taxonomic lineagei | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo |
Proteomesi |
|
Organism-specific databases
EuPathDBi | HostDB:ENSG00000198728.10. |
HGNCi | HGNC:6532. LDB1. |
MIMi | 603451. gene. |
neXtProti | NX_Q86U70. |
Pathology & Biotechi
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 245 – 249 | LCVIL → ACVAA: Abolishes interaction with ESR1. 1 Publication | 5 |
Organism-specific databases
DisGeNETi | 8861. |
OpenTargetsi | ENSG00000198728. |
PharmGKBi | PA30316. |
Polymorphism and mutation databases
BioMutai | LDB1. |
DMDMi | 158518615. |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Initiator methioninei | RemovedCombined sources | |||
ChainiPRO_0000084384 | 2 – 411 | LIM domain-binding protein 1Add BLAST | 410 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Modified residuei | 2 | N-acetylserineCombined sources | 1 | |
Modified residuei | 61 | PhosphothreonineBy similarity | 1 | |
Modified residuei | 265 | PhosphoserineCombined sources | 1 | |
Modified residuei | 302 | PhosphoserineBy similarity | 1 |
Post-translational modificationi
Ubiquitinated by RLIM/RNF12, leading to its degradation by the proteasome.By similarity
Keywords - PTMi
Acetylation, Phosphoprotein, Ubl conjugationProteomic databases
EPDi | Q86U70. |
MaxQBi | Q86U70. |
PaxDbi | Q86U70. |
PeptideAtlasi | Q86U70. |
PRIDEi | Q86U70. |
PTM databases
iPTMneti | Q86U70. |
PhosphoSitePlusi | Q86U70. |
Expressioni
Tissue specificityi
Expressed in a wide range of adult tissues including brain, heart, skeletal muscle, colon, thymus, spleen, kidney, liver, small intestine, lung and peripheral blood leukocytes.1 Publication
Gene expression databases
Bgeei | ENSG00000198728. |
CleanExi | HS_LDB1. |
Genevisiblei | Q86U70. HS. |
Organism-specific databases
HPAi | HPA034488. |
Interactioni
Subunit structurei
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 (By similarity). Interacts with ESR1. Interacts with SLK; leading to negatively regulate SLK kinase activity (By similarity).By similarity2 Publications
Binary interactionsi
GO - Molecular functioni
- enzyme binding Source: UniProtKB
- LIM domain binding Source: UniProtKB
- protein homodimerization activity Source: UniProtKB
- protein self-association Source: Ensembl
- RNA polymerase II activating transcription factor binding Source: BHF-UCL
Protein-protein interaction databases
BioGridi | 114384. 40 interactors. |
CORUMi | Q86U70. |
DIPi | DIP-31826N. |
IntActi | Q86U70. 34 interactors. |
MINTi | Q86U70. |
STRINGi | 9606.ENSP00000392466. |
Structurei
Secondary structure
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more detailsFeature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Beta strandi | 337 – 339 | Combined sources | 3 | |
Turni | 346 – 349 | Combined sources | 4 | |
Beta strandi | 355 – 357 | Combined sources | 3 | |
Beta strandi | 359 – 362 | Combined sources | 4 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
2XJY | X-ray | 2.40 | B | 334-368 | [»] | |
2XJZ | X-ray | 2.80 | I/J/K/L/M | 334-368 | [»] | |
2YPA | X-ray | 2.80 | D | 336-375 | [»] | |
ProteinModelPortali | Q86U70. | |||||
SMRi | Q86U70. | |||||
ModBasei | Search... | |||||
MobiDBi | Search... |
Miscellaneous databases
EvolutionaryTracei | Q86U70. |
Family & Domainsi
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 336 – 374 | LIM-binding domain (LID)By similarityAdd BLAST | 39 |
Domaini
The dimerization domain is located in the N-terminus.By similarity
Sequence similaritiesi
Belongs to the LDB family.Curated
Phylogenomic databases
eggNOGi | KOG2181. Eukaryota. ENOG410YZVH. LUCA. |
GeneTreei | ENSGT00390000005639. |
HOGENOMi | HOG000030908. |
HOVERGENi | HBG000135. |
InParanoidi | Q86U70. |
KOi | K15617. |
OMAi | KMSVGCA. |
OrthoDBi | EOG091G0A0P. |
PhylomeDBi | Q86U70. |
TreeFami | TF319923. |
Family and domain databases
InterProi | View protein in InterPro IPR030167. LDB1. IPR029005. LIM-bd/SEUSS. |
PANTHERi | PTHR10378. PTHR10378. 1 hit. PTHR10378:SF7. PTHR10378:SF7. 1 hit. |
Pfami | View protein in Pfam PF01803. LIM_bind. 2 hits. |
s (3)i Sequence
Sequence statusi: Complete.
: The displayed sequence is further processed into a mature form. Sequence processingi
This entry describes 3 produced by isoformsialternative splicing. AlignAdd to basket
Isoform 1 (identifier: Q86U70-1) [UniParc]FASTAAdd to basket
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.
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 MVAPPAEPTR QQPSKRRKRK
310 320 330 340 350
MSGGSTMSSG GGNTNNSNSK KKSPASTFAL SSQVPDVMVV GEPTLMGGEF
360 370 380 390 400
GDEDERLITR LENTQFDAAN GIDDEDSFNN SPALGANSPW NSKPPSSQES
410
KSENPTSQAS Q
Note: No experimental confirmation available.
Sequence cautioni
The sequence CAB45409 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated
Natural variant
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Natural variantiVAR_036366 | 299 | R → Q in a colorectal cancer sample; somatic mutation. 1 PublicationCorresponds to variant dbSNP:rs990101456Ensembl. | 1 |
Alternative sequence
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Alternative sequenceiVSP_027830 | 1 – 36 | Missing in isoform 2 and isoform 3. 7 PublicationsAdd BLAST | 36 | |
Alternative sequenceiVSP_027831 | 336 – 352 | DVMVV…GEFGD → VSISAFFSLLGCPTTHP in isoform 2. 2 PublicationsAdd BLAST | 17 | |
Alternative sequenceiVSP_027832 | 353 – 411 | Missing in isoform 2. 2 PublicationsAdd BLAST | 59 |
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AF068652 mRNA. Translation: AAC77818.1. AJ243098 Genomic DNA. Translation: CAB45409.1. Different initiation. AB016485 mRNA. Translation: BAA31991.1. AB250384 mRNA. Translation: BAE95402.1. AF064491 mRNA. Translation: AAC28341.1. BT007054 mRNA. Translation: AAP35703.1. AK300588 mRNA. Translation: BAG62286.1. AL500527 Genomic DNA. No translation available. BC000482 mRNA. Translation: AAH00482.1. BC009246 mRNA. Translation: AAH09246.1. |
CCDSi | CCDS44472.1. [Q86U70-1] CCDS7528.1. [Q86U70-2] |
RefSeqi | NP_001106878.1. NM_001113407.2. [Q86U70-1] NP_003884.1. NM_003893.4. [Q86U70-2] |
UniGenei | Hs.454418. Hs.672935. |
Genome annotation databases
Ensembli | ENST00000361198; ENSP00000354616; ENSG00000198728. [Q86U70-2] ENST00000425280; ENSP00000392466; ENSG00000198728. [Q86U70-1] |
GeneIDi | 8861. |
KEGGi | hsa:8861. |
UCSCi | uc001kuk.6. human. [Q86U70-1] |
Keywords - Coding sequence diversityi
Alternative splicing, PolymorphismSimilar proteinsi
Entry informationi
Entry namei | LDB1_HUMAN | |
Accessioni | Q86U70Primary (citable) accession number: Q86U70 Secondary accession number(s): B4DUC4 Q9UGM4 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | July 5, 2005 |
Last sequence update: | September 11, 2007 | |
Last modified: | March 28, 2018 | |
This is version 142 of the entry and version 2 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Chordata Protein Annotation Program | |
Disclaimer | Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care. |