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O43679

- LDB2_HUMAN

UniProt

O43679 - LDB2_HUMAN

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Protein

LIM domain-binding protein 2

Gene

LDB2

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 4 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

  1. LIM domain binding Source: UniProtKB
  2. transcription cofactor activity Source: ProtInc

GO - Biological processi

  1. epithelial structure maintenance Source: Ensembl
  2. hair follicle development Source: Ensembl
  3. positive regulation of cellular component biogenesis Source: Ensembl
  4. positive regulation of transcription from RNA polymerase II promoter Source: Ensembl
  5. somatic stem cell maintenance Source: Ensembl
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
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 4

Organism-specific databases

HGNCiHGNC:6533. LDB2.

Subcellular locationi

Nucleus 1 Publication

GO - Cellular componenti

  1. nucleus Source: UniProtKB
  2. transcription factor complex Source: Ensembl
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA30317.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 373373LIM domain-binding protein 2PRO_0000084387Add
BLAST

Post-translational modificationi

Ubiquitinated by RLIM/RNF12, leading to its degradation by the proteasome.By similarity

Keywords - PTMi

Ubl conjugation

Proteomic databases

PaxDbiO43679.
PRIDEiO43679.

PTM databases

PhosphoSiteiO43679.

Expressioni

Gene expression databases

BgeeiO43679.
CleanExiHS_LDB2.
ExpressionAtlasiO43679. baseline.
GenevestigatoriO43679.

Organism-specific databases

HPAiCAB017544.

Interactioni

Subunit structurei

Interacts with LHX9.By similarity

Protein-protein interaction databases

BioGridi114535. 4 interactions.
DIPiDIP-24262N.
IntActiO43679. 2 interactions.
MINTiMINT-233497.
STRINGi9606.ENSP00000306772.

Structurei

3D structure databases

ProteinModelPortaliO43679.
SMRiO43679. 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

eggNOGiNOG282114.
GeneTreeiENSGT00390000005639.
HOGENOMiHOG000030908.
HOVERGENiHBG000135.
InParanoidiO43679.
OMAiYQSSEMA.
PhylomeDBiO43679.
TreeFamiTF319923.

Family and domain databases

InterProiIPR029005. LIM-bd/SEUSS.
IPR002691. LIM-dom-bd.
[Graphical view]
PANTHERiPTHR10378. PTHR10378. 1 hit.
PfamiPF01803. LIM_bind. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. Align

Isoform 1 (identifier: O43679) [UniParc]FASTAAdd to Basket

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.

« 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 DQCTMVTQHG 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 SAGNNANSTG SKKKTTAANL SLSSQVPDVM
310 320 330 340 350
VVGEPTLMGG EFGDEDERLI TRLENTQYDA ANGMDDEEDF NNSPALGNNS
360 370
PWNSKPPATQ ETKSENPPPQ ASQ
Length:373
Mass (Da):42,793
Last modified:June 1, 1998 - v1
Checksum:iE86387BA027F383A
GO
Isoform 2 (identifier: O43679-2) [UniParc]FASTAAdd to Basket

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.

Show »
Length:331
Mass (Da):38,005
Checksum:iF1FFE930C99FB3F8
GO
Isoform 3 (identifier: O43679-3) [UniParc]FASTAAdd to Basket

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

Show »
Length:347
Mass (Da):39,740
Checksum:iB46DD3274FC5AFF2
GO

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 2424Missing in isoform 3. 1 PublicationVSP_027825Add
BLAST
Alternative sequencei296 – 2972Missing in isoform 3. 1 PublicationVSP_027828
Alternative sequencei298 – 33134DVMVV…QYDAA → GLGAIPNCSLNPGRDGDLCH STAVTPSGQFKEKH in isoform 2. 1 PublicationVSP_027826Add
BLAST
Alternative sequencei332 – 37342Missing in isoform 2. 1 PublicationVSP_027827Add
BLAST

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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.
CCDSiCCDS3420.1. [O43679-1]
CCDS47031.1. [O43679-2]
RefSeqiNP_001124306.1. NM_001130834.1. [O43679-2]
NP_001281.1. NM_001290.3. [O43679-1]
UniGeneiHs.714330.

Genome annotation databases

EnsembliENST00000304523; ENSP00000306772; ENSG00000169744. [O43679-1]
ENST00000441778; ENSP00000392089; ENSG00000169744. [O43679-2]
GeneIDi9079.
KEGGihsa:9079.
UCSCiuc003goz.3. human. [O43679-1]
uc003gpa.3. human. [O43679-2]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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 .
CCDSi CCDS3420.1. [O43679-1 ]
CCDS47031.1. [O43679-2 ]
RefSeqi NP_001124306.1. NM_001130834.1. [O43679-2 ]
NP_001281.1. NM_001290.3. [O43679-1 ]
UniGenei Hs.714330.

3D structure databases

ProteinModelPortali O43679.
SMRi O43679. Positions 298-325.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 114535. 4 interactions.
DIPi DIP-24262N.
IntActi O43679. 2 interactions.
MINTi MINT-233497.
STRINGi 9606.ENSP00000306772.

PTM databases

PhosphoSitei O43679.

Proteomic databases

PaxDbi O43679.
PRIDEi O43679.

Protocols and materials databases

DNASUi 9079.
Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000304523 ; ENSP00000306772 ; ENSG00000169744 . [O43679-1 ]
ENST00000441778 ; ENSP00000392089 ; ENSG00000169744 . [O43679-2 ]
GeneIDi 9079.
KEGGi hsa:9079.
UCSCi uc003goz.3. human. [O43679-1 ]
uc003gpa.3. human. [O43679-2 ]

Organism-specific databases

CTDi 9079.
GeneCardsi GC04M016445.
HGNCi HGNC:6533. LDB2.
HPAi CAB017544.
MIMi 603450. gene.
neXtProti NX_O43679.
PharmGKBi PA30317.
GenAtlasi Search...

Phylogenomic databases

eggNOGi NOG282114.
GeneTreei ENSGT00390000005639.
HOGENOMi HOG000030908.
HOVERGENi HBG000135.
InParanoidi O43679.
OMAi YQSSEMA.
PhylomeDBi O43679.
TreeFami TF319923.

Miscellaneous databases

ChiTaRSi LDB2. human.
GeneWikii LDB2.
GenomeRNAii 9079.
NextBioi 34017.
PROi O43679.
SOURCEi Search...

Gene expression databases

Bgeei O43679.
CleanExi HS_LDB2.
ExpressionAtlasi O43679. baseline.
Genevestigatori O43679.

Family and domain databases

InterProi IPR029005. LIM-bd/SEUSS.
IPR002691. LIM-dom-bd.
[Graphical view ]
PANTHERi PTHR10378. PTHR10378. 1 hit.
Pfami PF01803. LIM_bind. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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].

Entry informationi

Entry nameiLDB2_HUMAN
AccessioniPrimary (citable) accession number: O43679
Secondary accession number(s): O60619, O75480
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 5, 2005
Last sequence update: June 1, 1998
Last modified: October 29, 2014
This is version 113 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (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.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 4
    Human chromosome 4: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3