O55203 (LDB2_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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 names

Name:	Ldb2
Synonyms:	Clim1

Organism

Mus musculus (Mouse) [Reference proteome]

Taxonomic identifier

10090 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Mus › Mus

Protein attributes

Sequence length	373 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.
Subunit structure	Interacts with LHX9. Ref.4 Ref.5
Subcellular location	Nucleus Probable.
Post-translational modification	Ubiquitinated by RLIM/RNF12, leading to its degradation by the proteasome. Ref.5
Sequence similarities	Belongs to the LDB family.

Ontologies

Keywords
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing
PTM	Ubl conjugation
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	epithelial structure maintenance Inferred from genetic interaction PubMed 17991461. Source: MGI hair follicle development Inferred from genetic interaction PubMed 17991461. Source: MGI positive regulation of cellular component biogenesis Inferred from genetic interaction PubMed 17991461. Source: MGI positive regulation of transcription from RNA polymerase II promoter Inferred from genetic interaction PubMed 10431247Ref.1. Source: MGI somatic stem cell maintenance Inferred from genetic interaction PubMed 17991461. Source: MGI
Cellular_component	transcription factor complex Inferred from direct assay Ref.1. Source: MGI
Molecular_function	LIM domain binding Inferred from sequence or structural similarity. Source: UniProtKB transcription cofactor activity Inferred from electronic annotation. Source: InterPro transcription factor binding transcription factor activity Inferred from physical interaction Ref.1. Source: MGI
Complete GO annotation...

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: O55203-1)

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.

Isoform 2 (identifier: O55203-2)

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.

Isoform 3 (identifier: O55203-3)

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.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 373	373	LIM domain-binding protein 2		PRO_0000084388
Regions
	Region	298 – 336	39	LIM-binding domain (LID) By similarity
Natural variations
	Alternative sequence	296 – 297	2	Missing in isoform 3.		VSP_027829
	Alternative sequence	298 – 331	34	DVMVV…QYDAA → GLGAIPNCSLNPGRDGDLCH STAVTPSGQFKEKH in isoform 2 and isoform 3.		VSP_014369
	Alternative sequence	332 – 373	42	Missing in isoform 2 and isoform 3.		VSP_014370
Experimental info
	Sequence conflict	272	1	A → G in AAB96884. Ref.1
	Sequence conflict	272	1	A → G in AAB96886. Ref.1
	Sequence conflict	279	1	A → S in AAB96884. Ref.1
	Sequence conflict	279	1	A → S in AAB96886. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 (CLIM-1a) [UniParc]. Last modified September 11, 2007. Version 2. Checksum: 0748DBAEB5586AB4	FASTA	373	42,691
	10 20 30 40 50 60 MSSTPHDPFY SSPFGPFYRR HTPYMVQPEY RIYEMNKRLQ SRTEDSDNLW WDAFATEFFE 70 80 90 100 110 120 DDATLTLSFC LEDGPKRYTI GRTLIPRYFS TVFEGGVTDL YYILKHSKES YHNSSITVDC 130 140 150 160 170 180 DQCAMVTQHG KPMFTKVCTE GRLILEFTFD DLMRIKTWHF TIRQYRELVP RSILAMHAQD 190 200 210 220 230 240 PQVLDQLSKN ITRMGLTNFT LNYLRLCVIL EPMQELMSRH KTYNLSPRDC LKTCLFQKWQ 250 260 270 280 290 300 RMVAPPAEPT RQPTTKRRKR KNSTSSTSNS SAGNTTNSAG SKKKTPAASL SLATQVPDVM 310 320 330 340 350 360 VVGEPTLMGG EFGDEDERLI TRLENTQYDA ANGMDDEEDF NNSPALGNNS PWNSKPPATQ 370 ETKSENAPPQ ASQ
	Isoform 2 (CLIM-1b) [UniParc]. Checksum: A4A4131EEF631544	FASTA	331	37,929
	10 20 30 40 50 60 MSSTPHDPFY SSPFGPFYRR HTPYMVQPEY RIYEMNKRLQ SRTEDSDNLW WDAFATEFFE 70 80 90 100 110 120 DDATLTLSFC LEDGPKRYTI GRTLIPRYFS TVFEGGVTDL YYILKHSKES YHNSSITVDC 130 140 150 160 170 180 DQCAMVTQHG KPMFTKVCTE GRLILEFTFD DLMRIKTWHF TIRQYRELVP RSILAMHAQD 190 200 210 220 230 240 PQVLDQLSKN ITRMGLTNFT LNYLRLCVIL EPMQELMSRH KTYNLSPRDC LKTCLFQKWQ 250 260 270 280 290 300 RMVAPPAEPT RQPTTKRRKR KNSTSSTSNS SAGNTTNSAG SKKKTPAASL SLATQVPGLG 310 320 330 AIPNCSLNPG RDGDLCHSTA VTPSGQFKEK H
	Isoform 3 [UniParc]. Checksum: 2F09D73318CEA63A	FASTA	329	37,733
	10 20 30 40 50 60 MSSTPHDPFY SSPFGPFYRR HTPYMVQPEY RIYEMNKRLQ SRTEDSDNLW WDAFATEFFE 70 80 90 100 110 120 DDATLTLSFC LEDGPKRYTI GRTLIPRYFS TVFEGGVTDL YYILKHSKES YHNSSITVDC 130 140 150 160 170 180 DQCAMVTQHG KPMFTKVCTE GRLILEFTFD DLMRIKTWHF TIRQYRELVP RSILAMHAQD 190 200 210 220 230 240 PQVLDQLSKN ITRMGLTNFT LNYLRLCVIL EPMQELMSRH KTYNLSPRDC LKTCLFQKWQ 250 260 270 280 290 300 RMVAPPAEPT RQPTTKRRKR KNSTSSTSNS SAGNTTNSAG SKKKTPAASL SLATQGLGAI 310 320 PNCSLNPGRD GDLCHSTAVT PSGQFKEKH

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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/6. 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.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	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.
IPI	IPI00116609. IPI00607962. IPI00798495.
RefSeq	NP_001070866.1. NM_001077398.1. NP_034828.3. NM_010698.3.
UniGene	Mm.25785.
3D structure databases
ProteinModelPortal	O55203.
SMR	O55203. Positions 298-325.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-46444N.
PTM databases
PhosphoSite	O55203.
Proteomic databases
PaxDb	O55203.
PRIDE	O55203.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENSMUST00000070748; ENSMUSP00000067737; ENSMUSG00000039706.
GeneID	16826.
KEGG	mmu:16826.
UCSC	uc008xis.1. mouse. uc008xit.1. mouse. uc008xiu.1. mouse.
Organism-specific databases
CTD	9079.
MGI	MGI:894670. Ldb2.
Phylogenomic databases
eggNOG	NOG282114.
GeneTree	ENSGT00390000005639.
HOGENOM	HOG000030908.
HOVERGEN	HBG000135.
InParanoid	O55203.
OMA	LGNSSPW.
OrthoDB	EOG4XWFXV.
Gene expression databases
Bgee	O55203.
CleanEx	MM_LDB2.
Genevestigator	O55203.
GermOnline	ENSMUSG00000039706. Mus musculus.
Family and domain databases
InterPro	IPR002691. LIM-dom-bd. [Graphical view]
PANTHER	PTHR10378. PTHR10378. 1 hit.
ProtoNet	Search...
Other
ChiTaRS	LDB2. mouse.
NextBio	290728.
SOURCE	Search...

Entry information

Entry name

LDB2_MOUSE

Accession

Primary (citable) accession number: O55203
Secondary accession number(s): O55205, Q3UHY1, Q6AXE6

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 5, 2005
Last sequence update:	September 11, 2007
Last modified:	April 3, 2013
This is version 86 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program