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Protein

LIM domain-binding protein 2

Gene

LDB2

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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
  • RNA polymerase II activating transcription factor binding Source: GO_Central
  • transcription coregulator 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

EuPathDBiHostDB:ENSG00000169744.12
HGNCiHGNC:6533 LDB2
MIMi603450 gene
neXtProtiNX_O43679

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

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

EPDiO43679
MaxQBiO43679
PaxDbiO43679
PeptideAtlasiO43679
PRIDEiO43679
ProteomicsDBi49107
49108 [O43679-2]
49109 [O43679-3]

PTM databases

iPTMnetiO43679
PhosphoSitePlusiO43679

Expressioni

Gene expression databases

BgeeiENSG00000169744 Expressed in 215 organ(s), highest expression level in forebrain
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

GO - Molecular functioni

Protein-protein interaction databases

BioGridi114535, 11 interactors
DIPiDIP-24262N
DIP-41215N
IntActiO43679, 27 interactors
MINTiO43679
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:SF8 PTHR10378:SF8, 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

This entry has 3 described isoforms and 6 potential isoforms that are computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There are 6 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
G5E9Y7G5E9Y7_HUMAN
LIM domain binding 2, isoform CRA_b
LDB2 hCG_1811661
371Annotation score:
E9PFI4E9PFI4_HUMAN
LIM domain-binding protein 2
LDB2
313Annotation score:
H0YA09H0YA09_HUMAN
LIM domain-binding protein 2
LDB2
294Annotation score:
D6RAT1D6RAT1_HUMAN
LIM domain-binding protein 2
LDB2
164Annotation score:
E7EX95E7EX95_HUMAN
LIM domain-binding protein 2
LDB2
110Annotation score:
E9PGU0E9PGU0_HUMAN
LIM domain-binding protein 2
LDB2
106Annotation score:

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

Cross-referencesi

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

3D structure databases

ProteinModelPortaliO43679
SMRiO43679
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi114535, 11 interactors
DIPiDIP-24262N
DIP-41215N
IntActiO43679, 27 interactors
MINTiO43679
STRINGi9606.ENSP00000306772

PTM databases

iPTMnetiO43679
PhosphoSitePlusiO43679

Polymorphism and mutation databases

BioMutaiLDB2

Proteomic databases

EPDiO43679
MaxQBiO43679
PaxDbiO43679
PeptideAtlasiO43679
PRIDEiO43679
ProteomicsDBi49107
49108 [O43679-2]
49109 [O43679-3]

Protocols and materials databases

DNASUi9079
Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

CTDi9079
DisGeNETi9079
EuPathDBiHostDB:ENSG00000169744.12
GeneCardsiLDB2
HGNCiHGNC:6533 LDB2
HPAiCAB017544
HPA068634
MIMi603450 gene
neXtProtiNX_O43679
OpenTargetsiENSG00000169744
PharmGKBiPA30317
GenAtlasiSearch...

Phylogenomic databases

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

Miscellaneous databases

ChiTaRSiLDB2 human
GeneWikiiLDB2
GenomeRNAii9079
PROiPR:O43679
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000169744 Expressed in 215 organ(s), highest expression level in forebrain
CleanExiHS_LDB2
ExpressionAtlasiO43679 baseline and differential
GenevisibleiO43679 HS

Family and domain databases

InterProiView protein in InterPro
IPR030174 LDB2
IPR029005 LIM-bd/SEUSS
PANTHERiPTHR10378 PTHR10378, 1 hit
PTHR10378:SF8 PTHR10378:SF8, 1 hit
PfamiView protein in Pfam
PF01803 LIM_bind, 2 hits
ProtoNetiSearch...

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: November 7, 2018
This is version 148 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. SIMILARITY comments
    Index of protein domains and families
  2. Human chromosome 4
    Human chromosome 4: entries, gene names and cross-references to MIM
  3. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
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Main funding by: National Institutes of Health

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