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Protein

LIM domain-binding protein 2

Gene

LDB2

Organism
Homo sapiens (Human)
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: Ensembl
  • LIM domain binding Source: UniProtKB
  • transcription cofactor activity Source: ProtInc

GO - Biological processi

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
Proteomesi
  • UP000005640 Componenti: Chromosome 4

Organism-specific databases

HGNCiHGNC:6533. LDB2.

Subcellular locationi

GO - Cellular componenti

  • cell leading edge Source: UniProtKB
  • nucleolus Source: HPA
  • nucleus Source: UniProtKB
  • plasma membrane Source: HPA
  • transcription factor complex Source: Ensembl

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi9079.
OpenTargetsiENSG00000169744.
PharmGKBiPA30317.

Polymorphism and mutation databases

BioMutaiLDB2.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000843871 – 373LIM domain-binding protein 2Add BLAST373

Post-translational modificationi

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

Keywords - PTMi

Ubl conjugation

Proteomic databases

MaxQBiO43679.
PaxDbiO43679.
PeptideAtlasiO43679.
PRIDEiO43679.

PTM databases

iPTMnetiO43679.
PhosphoSitePlusiO43679.

Expressioni

Gene expression databases

BgeeiENSG00000169744.
CleanExiHS_LDB2.
ExpressionAtlasiO43679. baseline and differential.
GenevisibleiO43679. HS.

Organism-specific databases

HPAiCAB017544.
HPA068634.

Interactioni

Subunit structurei

Interacts with LHX9 (By similarity). Interacts with SLK; leading to negatively regulate SLK kinase activity (By similarity).By similarity

Binary interactionsi

Show more details

GO - Molecular functioni

Protein-protein interaction databases

BioGridi114535. 11 interactors.
DIPiDIP-24262N.
DIP-41215N.
IntActiO43679. 19 interactors.
MINTiMINT-233497.
STRINGi9606.ENSP00000306772.

Structurei

3D structure databases

ProteinModelPortaliO43679.
SMRiO43679.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni298 – 336LIM-binding domain (LID)By similarityAdd BLAST39

Sequence similaritiesi

Belongs to the LDB family.Curated

Phylogenomic databases

eggNOGiKOG2181. Eukaryota.
ENOG410YZVH. LUCA.
GeneTreeiENSGT00390000005639.
HOGENOMiHOG000030908.
HOVERGENiHBG000135.
InParanoidiO43679.
OMAiNSSPWNS.
OrthoDBiEOG091G0A0P.
PhylomeDBiO43679.
TreeFamiTF319923.

Family and domain databases

InterProiView protein in InterPro
IPR030174. LDB2.
IPR029005. LIM-bd/SEUSS.
PANTHERiPTHR10378. PTHR10378. 1 hit.
PTHR10378:SF13. PTHR10378:SF13. 1 hit.
PfamiView protein in Pfam
PF01803. LIM_bind. 2 hits.

Sequences (3)i

Sequence statusi: Complete.

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

Isoform 1 (identifier: O43679-1) [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)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0278251 – 24Missing in isoform 3. 1 PublicationAdd BLAST24
Alternative sequenceiVSP_027828296 – 297Missing in isoform 3. 1 Publication2
Alternative sequenceiVSP_027826298 – 331DVMVV…QYDAA → GLGAIPNCSLNPGRDGDLCH STAVTPSGQFKEKH in isoform 2. 1 PublicationAdd BLAST34
Alternative sequenceiVSP_027827332 – 373Missing in isoform 2. 1 PublicationAdd BLAST42

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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_001130834.2. [O43679-2]
NP_001281.1. NM_001290.4. [O43679-1]
UniGeneiHs.714330.

Genome annotation databases

EnsembliENST00000304523; ENSP00000306772; ENSG00000169744. [O43679-1]
ENST00000441778; ENSP00000392089; ENSG00000169744. [O43679-2]
GeneIDi9079.
KEGGihsa:9079.
UCSCiuc003goz.5. human. [O43679-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiLDB2_HUMAN
AccessioniPrimary (citable) accession number: O43679
Secondary accession number(s): O60619, O75480
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 5, 2005
Last sequence update: June 1, 1998
Last modified: August 30, 2017
This is version 137 of the entry and version 1 of the sequence. See 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