O43679 (LDB2_HUMAN) 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

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

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 By similarity.
Subcellular location	Nucleus Ref.4.
Post-translational modification	Ubiquitinated by RLIM/RNF12, leading to its degradation by the proteasome By similarity.
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 electronic annotation. Source: Compara hair follicle development Inferred from electronic annotation. Source: Compara positive regulation of cellular component biogenesis Inferred from electronic annotation. Source: Compara positive regulation of transcription from RNA polymerase II promoter Inferred from electronic annotation. Source: Compara somatic stem cell maintenance Inferred from electronic annotation. Source: Compara
Cellular_component	nucleus Inferred from direct assay Ref.4. Source: UniProtKB transcription factor complex Inferred from electronic annotation. Source: Compara
Molecular_function	LIM domain binding Inferred from sequence or structural similarity. Source: UniProtKB transcription cofactor activity Traceable author statement PubMed 9880598. Source: ProtInc
Complete GO annotation...

Alternative products

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

Isoform 1 (identifier: O43679-1)

Also known as: a; CLIM1a;

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: O43679-2)

Also known as: b; CLIM1b;

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: O43679-3)

The sequence of this isoform differs from the canonical sequence as follows:
     1-24: Missing.
     296-297: Missing.

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_0000084387
Regions
	Region	298 – 336	39	LIM-binding domain (LID) By similarity
Natural variations
	Alternative sequence	1 – 24	24	Missing in isoform 3.		VSP_027825
	Alternative sequence	296 – 297	2	Missing in isoform 3.		VSP_027828
	Alternative sequence	298 – 331	34	DVMVV…QYDAA → GLGAIPNCSLNPGRDGDLCH STAVTPSGQFKEKH in isoform 2.		VSP_027826
	Alternative sequence	332 – 373	42	Missing in isoform 2.		VSP_027827

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 (a) (CLIM1a) [UniParc]. Last modified June 1, 1998. Version 1. Checksum: E86387BA027F383A	FASTA	373	42,793
	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 DQCTMVTQHG 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 SAGNNANSTG SKKKTTAANL SLSSQVPDVM 310 320 330 340 350 360 VVGEPTLMGG EFGDEDERLI TRLENTQYDA ANGMDDEEDF NNSPALGNNS PWNSKPPATQ 370 ETKSENPPPQ ASQ
	Isoform 2 (b) (CLIM1b) [UniParc]. Checksum: F1FFE930C99FB3F8	FASTA	331	38,005
	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 DQCTMVTQHG 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 SAGNNANSTG SKKKTTAANL SLSSQVPGLG 310 320 330 AIPNCSLNPG RDGDLCHSTA VTPSGQFKEK H
	Isoform 3 [UniParc]. Checksum: B46DD3274FC5AFF2	FASTA	347	39,740
	10 20 30 40 50 60 MVQPEYRIYE MNKRLQSRTE DSDNLWWDAF ATEFFEDDAT LTLSFCLEDG PKRYTIGRTL 70 80 90 100 110 120 IPRYFSTVFE GGVTDLYYIL KHSKESYHNS SITVDCDQCT MVTQHGKPMF TKVCTEGRLI 130 140 150 160 170 180 LEFTFDDLMR IKTWHFTIRQ YRELVPRSIL AMHAQDPQVL DQLSKNITRM GLTNFTLNYL 190 200 210 220 230 240 RLCVILEPMQ ELMSRHKTYN LSPRDCLKTC LFQKWQRMVA PPAEPTRQPT TKRRKRKNST 250 260 270 280 290 300 SSTSNSSAGN NANSTGSKKK TTAANLSLSS QDVMVVGEPT LMGGEFGDED ERLITRLENT 310 320 330 340 QYDAANGMDD EEDFNNSPAL GNNSPWNSKP PATQETKSEN PPPQASQ

References

	« Hide 'large scale' referencesShow '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 1).
[2]	"Cloning and identification of LDB1 cDNA." Zhou Y., Du G.W., Wang J.H., Yuan J.G., Qiang B.Q. Submitted (MAR-1998) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3).
[3]	"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] (ISOFORMS 1 AND 2). Tissue: Brain.
[4]	"Selection system for genes encoding nuclear-targeted proteins." Ueki N., Oda T., Kondo M., Yano K., Noguchi T., Muramatsu M.-A. Nat. Biotechnol. 16:1338-1342(1998) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), SUBCELLULAR LOCATION. Tissue: Fetal brain.
[5]	"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). Tissue: Lung.
[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]	"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].
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AF068651 mRNA. Translation: AAC77817.1. AF052389 mRNA. Translation: AAC13274.1. AF064492 mRNA. Translation: AAC28342.1. AF064493 mRNA. Translation: AAC28343.1. AF047337 mRNA. Translation: AAC83552.1. BC034019 mRNA. Translation: AAH34019.1.
IPI	IPI00014634. IPI00790687. IPI00855748.
RefSeq	NP_001124306.1. NM_001130834.1. NP_001281.1. NM_001290.3.
UniGene	Hs.714330.
3D structure databases
ProteinModelPortal	O43679.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-24262N.
IntAct	O43679. 1 interaction.
MINT	MINT-233497.
STRING	9606.ENSP00000306772.
PTM databases
PhosphoSite	O43679.
Proteomic databases
PaxDb	O43679.
PRIDE	O43679.
Protocols and materials databases
DNASU	9079.
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENST00000304523; ENSP00000306772; ENSG00000169744. ENST00000441778; ENSP00000392089; ENSG00000169744.
GeneID	9079.
KEGG	hsa:9079.
UCSC	uc003goz.3. human. uc003gpa.3. human. uc003gpb.3. human.
Organism-specific databases
CTD	9079.
GeneCards	GC04M016445.
HGNC	HGNC:6533. LDB2.
HPA	CAB017544.
MIM	603450. gene.
neXtProt	NX_O43679.
PharmGKB	PA30317.
GenAtlas	Search...
Phylogenomic databases
eggNOG	NOG282114.
HOGENOM	HOG000030908.
HOVERGEN	HBG000135.
InParanoid	O43679.
OMA	LGNSSPW.
OrthoDB	EOG4XWFXV.
PhylomeDB	O43679.
Gene expression databases
ArrayExpress	O43679.
Bgee	O43679.
CleanEx	HS_LDB2.
Genevestigator	O43679.
GermOnline	ENSG00000169744. Homo sapiens.
Family and domain databases
InterPro	IPR002691. LIM-dom-bd. [Graphical view]
PANTHER	PTHR10378. PTHR10378. 1 hit.
ProtoNet	Search...
Other
ChiTaRS	LDB2. human.
GenomeRNAi	9079.
NextBio	34017.
SOURCE	Search...

Entry information

Entry name

LDB2_HUMAN

Accession

Primary (citable) accession number: O43679
Secondary accession number(s): O60619, O75480

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 5, 2005
Last sequence update:	June 1, 1998
Last modified:	May 1, 2013
This is version 101 of the entry and version 1 of the sequence. [Complete history]

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.