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O43679 (LDB2_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 111. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length373 AA.
Sequence statusComplete.
Protein existenceEvidence 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.

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 keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 373373LIM domain-binding protein 2
PRO_0000084387

Regions

Region298 – 33639LIM-binding domain (LID) By similarity

Natural variations

Alternative sequence1 – 2424Missing in isoform 3.
VSP_027825
Alternative sequence296 – 2972Missing in isoform 3.
VSP_027828
Alternative sequence298 – 33134DVMVV…QYDAA → GLGAIPNCSLNPGRDGDLCH STAVTPSGQFKEKH in isoform 2.
VSP_027826
Alternative sequence332 – 37342Missing in isoform 2.
VSP_027827

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 (a) (CLIM1a) [UniParc].

Last modified June 1, 1998. Version 1.
Checksum: E86387BA027F383A

FASTA37342,793
        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 

« Hide

Isoform 2 (b) (CLIM1b) [UniParc].

Checksum: F1FFE930C99FB3F8
Show »

FASTA33138,005
Isoform 3 [UniParc].

Checksum: B46DD3274FC5AFF2
Show »

FASTA34739,740

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 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.
CCDSCCDS3420.1. [O43679-1]
CCDS47031.1. [O43679-2]
RefSeqNP_001124306.1. NM_001130834.1. [O43679-2]
NP_001281.1. NM_001290.3. [O43679-1]
UniGeneHs.714330.

3D structure databases

ProteinModelPortalO43679.
SMRO43679. Positions 298-325.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid114535. 4 interactions.
DIPDIP-24262N.
IntActO43679. 2 interactions.
MINTMINT-233497.
STRING9606.ENSP00000306772.

PTM databases

PhosphoSiteO43679.

Proteomic databases

PaxDbO43679.
PRIDEO43679.

Protocols and materials databases

DNASU9079.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000304523; ENSP00000306772; ENSG00000169744. [O43679-1]
ENST00000441778; ENSP00000392089; ENSG00000169744. [O43679-2]
GeneID9079.
KEGGhsa:9079.
UCSCuc003goz.3. human. [O43679-1]
uc003gpa.3. human. [O43679-2]

Organism-specific databases

CTD9079.
GeneCardsGC04M016445.
HGNCHGNC:6533. LDB2.
HPACAB017544.
MIM603450. gene.
neXtProtNX_O43679.
PharmGKBPA30317.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG282114.
HOGENOMHOG000030908.
HOVERGENHBG000135.
InParanoidO43679.
OMAYQSSEMA.
PhylomeDBO43679.
TreeFamTF319923.

Gene expression databases

ArrayExpressO43679.
BgeeO43679.
CleanExHS_LDB2.
GenevestigatorO43679.

Family and domain databases

InterProIPR029005. LIM-bd/SEUSS.
IPR002691. LIM-dom-bd.
[Graphical view]
PANTHERPTHR10378. PTHR10378. 1 hit.
PfamPF01803. LIM_bind. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSLDB2. human.
GeneWikiLDB2.
GenomeRNAi9079.
NextBio34017.
PROO43679.
SOURCESearch...

Entry information

Entry nameLDB2_HUMAN
AccessionPrimary (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: July 9, 2014
This is version 111 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny 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

SIMILARITY comments

Index of protein domains and families

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human chromosome 4

Human chromosome 4: entries, gene names and cross-references to MIM