Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

LIM domain-binding protein 2

Gene

Ldb2

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.

GO - Molecular functioni

  • enzyme binding Source: UniProtKB
  • LIM domain binding Source: UniProtKB
  • transcription factor activity, transcription factor binding Source: MGI

GO - Biological processi

  • epithelial structure maintenance Source: MGI
  • hair follicle development Source: MGI
  • positive regulation of cellular component biogenesis Source: MGI
  • positive regulation of transcription from RNA polymerase II promoter Source: MGI
  • regulation of cell migration Source: UniProtKB
  • regulation of kinase activity Source: UniProtKB
  • somatic stem cell population maintenance Source: MGI
Complete GO annotation...

Names & Taxonomyi

Protein namesi
Recommended name:
LIM domain-binding protein 2
Short name:
LDB-2
Alternative name(s):
Carboxyl-terminal LIM domain-binding protein 1
Short name:
CLIM-1
LIM domain-binding factor CLIM1
Gene namesi
Name:Ldb2
Synonyms:Clim1
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 5

Organism-specific databases

MGIiMGI:894670. Ldb2.

Subcellular locationi

GO - Cellular componenti

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

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 373373LIM domain-binding protein 2PRO_0000084388Add
BLAST

Post-translational modificationi

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

Keywords - PTMi

Ubl conjugation

Proteomic databases

EPDiO55203.
MaxQBiO55203.
PaxDbiO55203.
PeptideAtlasiO55203.
PRIDEiO55203.

PTM databases

iPTMnetiO55203.
PhosphoSiteiO55203.

Expressioni

Gene expression databases

BgeeiO55203.
CleanExiMM_LDB2.
ExpressionAtlasiO55203. baseline and differential.
GenevisibleiO55203. MM.

Interactioni

Subunit structurei

Interacts with LHX9 (PubMed:10330499). Interacts with SLK; leading to negatively regulate SLK kinase activity (PubMed:19675209).3 Publications

GO - Molecular functioni

  • enzyme binding Source: UniProtKB
  • LIM domain binding Source: UniProtKB

Protein-protein interaction databases

BioGridi201126. 17 interactions.
DIPiDIP-46444N.
STRINGi10090.ENSMUSP00000067737.

Structurei

3D structure databases

ProteinModelPortaliO55203.
SMRiO55203. Positions 298-325.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni298 – 33639LIM-binding domain (LID)By similarityAdd
BLAST

Sequence similaritiesi

Belongs to the LDB family.Curated

Phylogenomic databases

eggNOGiKOG2181. Eukaryota.
ENOG410YZVH. LUCA.
GeneTreeiENSGT00390000005639.
HOGENOMiHOG000030908.
HOVERGENiHBG000135.
InParanoidiO55203.
OMAiLMRIRTW.
OrthoDBiEOG7DC24T.
PhylomeDBiO55203.
TreeFamiTF319923.

Family and domain databases

InterProiIPR030174. LDB2.
IPR029005. LIM-bd/SEUSS.
[Graphical view]
PANTHERiPTHR10378. PTHR10378. 1 hit.
PTHR10378:SF8. PTHR10378:SF8. 1 hit.

Sequences (3)i

Sequence statusi: Complete.

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

Isoform 1 (identifier: O55203-1) [UniParc]FASTAAdd to basket

Also known as: CLIM-1a

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
MSSTPHDPFY SSPFGPFYRR HTPYMVQPEY RIYEMNKRLQ SRTEDSDNLW
60 70 80 90 100
WDAFATEFFE DDATLTLSFC LEDGPKRYTI GRTLIPRYFS TVFEGGVTDL
110 120 130 140 150
YYILKHSKES YHNSSITVDC DQCAMVTQHG KPMFTKVCTE GRLILEFTFD
160 170 180 190 200
DLMRIKTWHF TIRQYRELVP RSILAMHAQD PQVLDQLSKN ITRMGLTNFT
210 220 230 240 250
LNYLRLCVIL EPMQELMSRH KTYNLSPRDC LKTCLFQKWQ RMVAPPAEPT
260 270 280 290 300
RQPTTKRRKR KNSTSSTSNS SAGNTTNSAG SKKKTPAASL SLATQVPDVM
310 320 330 340 350
VVGEPTLMGG EFGDEDERLI TRLENTQYDA ANGMDDEEDF NNSPALGNNS
360 370
PWNSKPPATQ ETKSENAPPQ ASQ
Length:373
Mass (Da):42,691
Last modified:September 11, 2007 - v2
Checksum:i0748DBAEB5586AB4
GO
Isoform 2 (identifier: O55203-2) [UniParc]FASTAAdd to basket

Also known as: CLIM-1b

The sequence of this isoform differs from the canonical sequence as follows:
     298-331: DVMVVGEPTLMGGEFGDEDERLITRLENTQYDAA → GLGAIPNCSLNPGRDGDLCHSTAVTPSGQFKEKH
     332-373: Missing.

Note: Lacks LIM-binding domain.
Show »
Length:331
Mass (Da):37,929
Checksum:iA4A4131EEF631544
GO
Isoform 3 (identifier: O55203-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     296-297: Missing.
     298-331: DVMVVGEPTLMGGEFGDEDERLITRLENTQYDAA → GLGAIPNCSLNPGRDGDLCHSTAVTPSGQFKEKH
     332-373: Missing.

Note: No experimental confirmation available.
Show »
Length:329
Mass (Da):37,733
Checksum:i2F09D73318CEA63A
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti272 – 2721A → G in AAB96884 (PubMed:9192866).Curated
Sequence conflicti272 – 2721A → G in AAB96886 (PubMed:9192866).Curated
Sequence conflicti279 – 2791A → S in AAB96884 (PubMed:9192866).Curated
Sequence conflicti279 – 2791A → S in AAB96886 (PubMed:9192866).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei296 – 2972Missing in isoform 3. 1 PublicationVSP_027829
Alternative sequencei298 – 33134DVMVV…QYDAA → GLGAIPNCSLNPGRDGDLCH STAVTPSGQFKEKH in isoform 2 and isoform 3. 2 PublicationsVSP_014369Add
BLAST
Alternative sequencei332 – 37342Missing in isoform 2 and isoform 3. 2 PublicationsVSP_014370Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U89487 mRNA. Translation: AAB96884.1.
U89489 mRNA. Translation: AAB96886.1.
AK147160 mRNA. Translation: BAE27725.1.
AK146860 mRNA. Translation: BAE27488.1.
BC079611 mRNA. Translation: AAH79611.1.
CCDSiCCDS19271.1. [O55203-1]
CCDS80276.1. [O55203-2]
CCDS80278.1. [O55203-3]
RefSeqiNP_001070866.1. NM_001077398.2. [O55203-3]
NP_001273277.1. NM_001286348.1. [O55203-2]
NP_034828.3. NM_010698.4. [O55203-1]
XP_006503817.1. XM_006503754.2. [O55203-2]
XP_006503819.1. XM_006503756.2. [O55203-3]
UniGeneiMm.25785.

Genome annotation databases

EnsembliENSMUST00000070748; ENSMUSP00000067737; ENSMUSG00000039706. [O55203-1]
ENSMUST00000199256; ENSMUSP00000143775; ENSMUSG00000039706. [O55203-3]
ENSMUST00000199534; ENSMUSP00000142442; ENSMUSG00000039706. [O55203-2]
GeneIDi16826.
KEGGimmu:16826.
UCSCiuc008xis.2. mouse. [O55203-3]
uc008xit.2. mouse. [O55203-1]
uc008xiu.2. mouse. [O55203-2]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U89487 mRNA. Translation: AAB96884.1.
U89489 mRNA. Translation: AAB96886.1.
AK147160 mRNA. Translation: BAE27725.1.
AK146860 mRNA. Translation: BAE27488.1.
BC079611 mRNA. Translation: AAH79611.1.
CCDSiCCDS19271.1. [O55203-1]
CCDS80276.1. [O55203-2]
CCDS80278.1. [O55203-3]
RefSeqiNP_001070866.1. NM_001077398.2. [O55203-3]
NP_001273277.1. NM_001286348.1. [O55203-2]
NP_034828.3. NM_010698.4. [O55203-1]
XP_006503817.1. XM_006503754.2. [O55203-2]
XP_006503819.1. XM_006503756.2. [O55203-3]
UniGeneiMm.25785.

3D structure databases

ProteinModelPortaliO55203.
SMRiO55203. Positions 298-325.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi201126. 17 interactions.
DIPiDIP-46444N.
STRINGi10090.ENSMUSP00000067737.

PTM databases

iPTMnetiO55203.
PhosphoSiteiO55203.

Proteomic databases

EPDiO55203.
MaxQBiO55203.
PaxDbiO55203.
PeptideAtlasiO55203.
PRIDEiO55203.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000070748; ENSMUSP00000067737; ENSMUSG00000039706. [O55203-1]
ENSMUST00000199256; ENSMUSP00000143775; ENSMUSG00000039706. [O55203-3]
ENSMUST00000199534; ENSMUSP00000142442; ENSMUSG00000039706. [O55203-2]
GeneIDi16826.
KEGGimmu:16826.
UCSCiuc008xis.2. mouse. [O55203-3]
uc008xit.2. mouse. [O55203-1]
uc008xiu.2. mouse. [O55203-2]

Organism-specific databases

CTDi9079.
MGIiMGI:894670. Ldb2.

Phylogenomic databases

eggNOGiKOG2181. Eukaryota.
ENOG410YZVH. LUCA.
GeneTreeiENSGT00390000005639.
HOGENOMiHOG000030908.
HOVERGENiHBG000135.
InParanoidiO55203.
OMAiLMRIRTW.
OrthoDBiEOG7DC24T.
PhylomeDBiO55203.
TreeFamiTF319923.

Miscellaneous databases

ChiTaRSiLdb2. mouse.
PROiO55203.
SOURCEiSearch...

Gene expression databases

BgeeiO55203.
CleanExiMM_LDB2.
ExpressionAtlasiO55203. baseline and differential.
GenevisibleiO55203. MM.

Family and domain databases

InterProiIPR030174. LDB2.
IPR029005. LIM-bd/SEUSS.
[Graphical view]
PANTHERiPTHR10378. PTHR10378. 1 hit.
PTHR10378:SF8. PTHR10378:SF8. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "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] (ISOFORMS 1 AND 2).
  2. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3).
    Strain: C57BL/6J.
    Tissue: Embryonic kidney.
  3. "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 1).
    Strain: C57BL/6J.
    Tissue: Brain.
  4. "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.
  5. "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.
  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: ALTERNATIVE SPLICING.
  7. "The Ldb1 and Ldb2 transcriptional cofactors interact with the Ste20-like kinase SLK and regulate cell migration."
    Storbeck C.J., Wagner S., O'Reilly P., McKay M., Parks R.J., Westphal H., Sabourin L.A.
    Mol. Biol. Cell 20:4174-4182(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH SLK, SUBCELLULAR LOCATION, FUNCTION.

Entry informationi

Entry nameiLDB2_MOUSE
AccessioniPrimary (citable) accession number: O55203
Secondary accession number(s): O55205, Q3UHY1, Q6AXE6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 5, 2005
Last sequence update: September 11, 2007
Last modified: July 6, 2016
This is version 111 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

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. 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.