Q86U70 (LDB1_HUMAN) Reviewed, UniProtKB/Swiss-Prot
Last modified
May 1, 2013.
Version 99.
History...
Names·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·DocumentsCustomize order
Names·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·DocumentsCustomize orderNames and origin
| Protein names | 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=hLdb1 Nuclear LIM interactor | ||||
| Gene names |
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| Organism | Homo sapiens (Human) [Reference proteome] | ||||
| Taxonomic identifier | 9606 [NCBI] | ||||
| Taxonomic lineage | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo![]() |
Protein attributes
| Sequence length | 411 AA. |
| Sequence status | Complete. |
| Protein existence | Evidence 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. May play a role in the development of motor neurons. 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. |
| Subunit structure | 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 By similarity. Interacts with ESR1. Ref.10 |
| Subcellular location | Nucleus Probable. |
| Tissue specificity | 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. Ref.4 |
| Domain | The dimerization domain is located in the N-terminus By similarity. |
| Post-translational modification | Ubiquitinated by RLIM/RNF12, leading to its degradation by the proteasome By similarity. |
| Miscellaneous | Acts as a negative coregulator of ESR1-mediated transcription in breast cancer cells. |
| Sequence similarities | Belongs to the LDB family. |
| Sequence caution | The sequence CAB45409.1 differs from that shown. Reason: Erroneous initiation. The sequence CAH72217.1 differs from that shown. Reason: Erroneous initiation. |
Ontologies
Alternative products
| This entry describes 3 isoforms produced by alternative splicing. [Align] [Select] | ||||||
| Isoform 1 (identifier: Q86U70-1) 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. | ||||||
| Note: No experimental confirmation available. | ||||||
| Isoform 2 (identifier: Q86U70-3) Also known as: b; The sequence of this isoform differs from the canonical sequence as follows: 1-36: Missing. 336-352: DVMVVGEPTLMGGEFGD → VSISAFFSLLGCPTTHP 353-411: Missing. | ||||||
| Note: Due to intron retention. Lacks LIM-binding domain. | ||||||
| Isoform 3 (identifier: Q86U70-2) Also known as: a; The sequence of this isoform differs from the canonical sequence as follows: 1-36: Missing. |
Sequence annotation (Features)
| Feature key | Position(s) | Length | Description | Graphical view | Feature identifier | ||||||||||||
Molecule processing | |||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Chain | 1 – 411 | 411 | LIM domain-binding protein 1 | PRO_0000084384 | |||||||||||||
Regions | |||||||||||||||||
| Region | 336 – 374 | 39 | LIM-binding domain (LID) By similarity | ||||||||||||||
Natural variations | |||||||||||||||||
| Alternative sequence | 1 – 36 | 36 | Missing in isoform 2 and isoform 3. | VSP_027830 | |||||||||||||
| Alternative sequence | 336 – 352 | 17 | DVMVV…GEFGD → VSISAFFSLLGCPTTHP in isoform 2. | VSP_027831 | |||||||||||||
| Alternative sequence | 353 – 411 | 59 | Missing in isoform 2. | VSP_027832 | |||||||||||||
| Natural variant | 299 | 1 | R → Q in a colorectal cancer sample; somatic mutation. Ref.13 | VAR_036366 | |||||||||||||
Experimental info | |||||||||||||||||
| Mutagenesis | 245 – 249 | 5 | LCVIL → ACVAA: Abolishes interaction with ESR1. Ref.10 | ||||||||||||||
Secondary structure | |||||||||||||||||
Helix Strand Turn | |||||||||||||||||
| Beta strand | 337 – 339 | 3 | |||||||||||||||
| Turn | 346 – 349 | 4 | |||||||||||||||
| Beta strand | 355 – 357 | 3 | |||||||||||||||
| Beta strand | 359 – 362 | 4 | |||||||||||||||
Sequences
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References
| « Hide 'large scale' references | |
| [1] | "Cloning and chromosomal localization of two novel human genes encoding LIM-domain binding factors CLIM1 and CLIM2/LDB1/NLI." Semina E.V., Altherr M.R., Murray J.C. Mamm. Genome 9:921-924(1998) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3). Tissue: Craniofacial. |
| [2] | "Genomic structure, alternative transcripts and chromosome location of the human LIM domain binding protein gene LDB1." Drechsler M., Schumacher V., Friedrich S., Wildhardt G., Giesler S., Schroth A., Bodem J., Royer-Pokora B. Cytogenet. Cell Genet. 87:119-124(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. |
| [3] | "Isolation and chromosomal assignment of human genes encoding cofactor of LIM homeodomain proteins, CLIM1 and CLIM2." Ueki N., Seki N., Yano K., Ohira M., Saito T., Masuho Y., Muramatsu M. J. Hum. Genet. 44:112-115(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3). Tissue: Brain. |
| [4] | "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), ALTERNATIVE SPLICING, TISSUE SPECIFICITY. Tissue: Fetal brain. |
| [5] | "Cloning, characterization, and physical mapping of the human homologs of the mouse C-LIM gene." Phillips J.C., Goldman D.A., Wiggs J.L. Submitted (MAY-1998) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3). Tissue: Fetal brain. |
| [6] | "Cloning of human full-length CDSs in BD Creator(TM) system donor vector." Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S., Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y., Phelan M., Farmer A. Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3). |
| [7] | "Complete sequencing and characterization of 21,243 full-length human cDNAs." Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. Sugano S.Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2). |
| [8] | "The DNA sequence and comparative analysis of human chromosome 10." Deloukas P., Earthrowl M.E., Grafham D.V., Rubenfield M., French L., Steward C.A., Sims S.K., Jones M.C., Searle S., Scott C., Howe K., Hunt S.E., Andrews T.D., Gilbert J.G.R., Swarbreck D., Ashurst J.L., Taylor A., Battles J. Rogers J.Nature 429:375-381(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. |
| [9] | "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). Tissue: Muscle. |
| [10] | "Regulation of estrogen-dependent transcription by the LIM cofactors CLIM and RLIM in breast cancer." Johnsen S.A., Guengoer C., Prenzel T., Riethdorf S., Riethdorf L., Taniguchi-Ishigaki N., Rau T., Tursun B., Furlow J.D., Sauter G., Scheffner M., Pantel K., Gannon F., Bach I. Cancer Res. 69:128-136(2009) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH ESR1, MUTAGENESIS OF 245-LEU--LEU-249, MISCELLANEOUS. |
| [11] | "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions." Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K. Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. Tissue: Leukemic T-cell. |
| [12] | "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation." Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B. Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. |
| [13] | "The consensus coding sequences of human breast and colorectal cancers." Sjoeblom T., Jones S., Wood L.D., Parsons D.W., Lin J., Barber T.D., Mandelker D., Leary R.J., Ptak J., Silliman N., Szabo S., Buckhaults P., Farrell C., Meeh P., Markowitz S.D., Willis J., Dawson D., Willson J.K.V. Velculescu V.E.Science 314:268-274(2006) [PubMed] [Europe PMC] [Abstract] Cited for: VARIANT [LARGE SCALE ANALYSIS] GLN-299. |
| + | Additional computationally mapped references. |
Cross-references
Sequence databases | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| EMBL GenBank DDBJ | 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. Translation: CAH72217.1. Different initiation. BC000482 mRNA. Translation: AAH00482.1. BC009246 mRNA. Translation: AAH09246.1. | ||||||||||||||||||
| IPI | IPI00428954. IPI00760574. IPI00856078. | ||||||||||||||||||
| RefSeq | NP_001106878.1. NM_001113407.1. NP_003884.1. NM_003893.4. | ||||||||||||||||||
| UniGene | Hs.454418. | ||||||||||||||||||
3D structure databases | |||||||||||||||||||
| PDBe RCSB PDB PDBj |
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| ProteinModelPortal | Q86U70. | ||||||||||||||||||
| ModBase | Search... | ||||||||||||||||||
Protein-protein interaction databases | |||||||||||||||||||
| DIP | DIP-31826N. | ||||||||||||||||||
| IntAct | Q86U70. 16 interactions. | ||||||||||||||||||
| MINT | MINT-233462. | ||||||||||||||||||
| STRING | 9606.ENSP00000392466. | ||||||||||||||||||
PTM databases | |||||||||||||||||||
| PhosphoSite | Q86U70. | ||||||||||||||||||
Polymorphism databases | |||||||||||||||||||
| DMDM | 158518615. | ||||||||||||||||||
Proteomic databases | |||||||||||||||||||
| PaxDb | Q86U70. | ||||||||||||||||||
| PRIDE | Q86U70. | ||||||||||||||||||
Protocols and materials databases | |||||||||||||||||||
| DNASU | 8861. | ||||||||||||||||||
| StructuralBiologyKnowledgebase | Search... | ||||||||||||||||||
Genome annotation databases | |||||||||||||||||||
| Ensembl | ENST00000361198; ENSP00000354616; ENSG00000198728. ENST00000425280; ENSP00000392466; ENSG00000198728. | ||||||||||||||||||
| GeneID | 8861. | ||||||||||||||||||
| KEGG | hsa:8861. | ||||||||||||||||||
| UCSC | uc001kuk.4. human. uc001kul.3. human. | ||||||||||||||||||
Organism-specific databases | |||||||||||||||||||
| CTD | 8861. | ||||||||||||||||||
| GeneCards | GC10M103857. | ||||||||||||||||||
| H-InvDB | HIX0009148. | ||||||||||||||||||
| HGNC | HGNC:6532. LDB1. | ||||||||||||||||||
| HPA | HPA034488. | ||||||||||||||||||
| MIM | 603451. gene. | ||||||||||||||||||
| neXtProt | NX_Q86U70. | ||||||||||||||||||
| PharmGKB | PA30316. | ||||||||||||||||||
| GenAtlas | Search... | ||||||||||||||||||
Phylogenomic databases | |||||||||||||||||||
| eggNOG | NOG282114. | ||||||||||||||||||
| HOGENOM | HOG000030908. | ||||||||||||||||||
| HOVERGEN | HBG000135. | ||||||||||||||||||
| InParanoid | Q86U70. | ||||||||||||||||||
| KO | K15617. | ||||||||||||||||||
| OMA | GSNSPWN. | ||||||||||||||||||
| OrthoDB | EOG4XWFXV. | ||||||||||||||||||
Gene expression databases | |||||||||||||||||||
| Bgee | Q86U70. | ||||||||||||||||||
| CleanEx | HS_LDB1. | ||||||||||||||||||
| Genevestigator | Q86U70. | ||||||||||||||||||
| GermOnline | ENSG00000198728. Homo sapiens. | ||||||||||||||||||
Family and domain databases | |||||||||||||||||||
| InterPro | IPR002691. LIM-dom-bd. [Graphical view] | ||||||||||||||||||
| PANTHER | PTHR10378. PTHR10378. 1 hit. | ||||||||||||||||||
| ProtoNet | Search... | ||||||||||||||||||
Other | |||||||||||||||||||
| EvolutionaryTrace | Q86U70. | ||||||||||||||||||
| GenomeRNAi | 8861. | ||||||||||||||||||
| NextBio | 33273. | ||||||||||||||||||
| SOURCE | Search... | ||||||||||||||||||
Entry information
| Entry name | LDB1_HUMAN | ||||||||
| Accession | Primary (citable) accession number: Q86U70 Secondary accession number(s): B4DUC4 Q9UGM4 | ||||||||
| Entry history |
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| Entry status | 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. | ||||||||
Relevant documents
| Human chromosome 10 Human chromosome 10: entries, gene names and cross-references to MIM |
| Human entries with polymorphisms or disease mutations List of human entries with polymorphisms or disease mutations |
| Human polymorphisms and disease mutations Index of human polymorphisms and disease mutations |
| MIM cross-references Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot |
| PDB cross-references Index of Protein Data Bank (PDB) cross-references |
| SIMILARITY comments Index of protein domains and families |

Clusters with
