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Protein

LIM and senescent cell antigen-like-containing domain protein 2

Gene

LIMS2

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Adapter protein in a cytoplasmic complex linking beta-integrins to the actin cytoskeleton, bridges the complex to cell surface receptor tyrosine kinases and growth factor receptors. Plays a role in modulating cell spreading and migration.1 Publication

GO - Molecular functioni

GO - Biological processi

Keywordsi

LigandMetal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-HSA-446353 Cell-extracellular matrix interactions

Names & Taxonomyi

Protein namesi
Recommended name:
LIM and senescent cell antigen-like-containing domain protein 2
Alternative name(s):
LIM-like protein 2
Particularly interesting new Cys-His protein 2
Short name:
PINCH-2
Gene namesi
Name:LIMS2
Synonyms:PINCH2
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 2

Organism-specific databases

EuPathDBiHostDB:ENSG00000072163.18
HGNCiHGNC:16084 LIMS2
MIMi607908 gene
neXtProtiNX_Q7Z4I7

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

Cell junction, Cell membrane, Membrane, Nucleus

Pathology & Biotechi

Involvement in diseasei

Limb-girdle muscular dystrophy 2W (LGMD2W)1 Publication
The disease may be caused by mutations affecting the gene represented in this entry.
Disease descriptionA form of autosomal recessive limb-girdle muscular dystrophy, a degenerative myopathy characterized by slowly progressive wasting and weakness of the proximal muscles of arms and legs around the pelvic or shoulder girdles, elevated creatine kinase levels and dystrophic features on muscle biopsy. LGMD2W is characterized by childhood-onset of weakness progressing to a severe quadriparesis. Additionally, patients have biventricular cardiac dysfunction due to dilated cardiomyopathy.
See also OMIM:616827
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_07652792N → K in LGMD2W; unknown pathological significance. 1 PublicationCorresponds to variant dbSNP:rs754385302Ensembl.1
Natural variantiVAR_07652897P → L in LGMD2W; unknown pathological significance. 1 PublicationCorresponds to variant dbSNP:rs768056213Ensembl.1
Natural variantiVAR_076529323L → P in LGMD2W; unknown pathological significance. 1 PublicationCorresponds to variant dbSNP:rs869025562Ensembl.1

Keywords - Diseasei

Disease mutation, Limb-girdle muscular dystrophy

Organism-specific databases

DisGeNETi55679
MalaCardsiLIMS2
MIMi616827 phenotype
OpenTargetsiENSG00000072163
Orphaneti466801 Autosomal recessive limb-girdle muscular dystrophy type 2W
PharmGKBiPA30390

Polymorphism and mutation databases

BioMutaiLIMS2
DMDMi74750091

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002660111 – 341LIM and senescent cell antigen-like-containing domain protein 2Add BLAST341

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei327PhosphothreonineCombined sources1
Modified residuei328PhosphoserineCombined sources1
Isoform 2 (identifier: Q7Z4I7-2)
Modified residuei22PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ7Z4I7
MaxQBiQ7Z4I7
PaxDbiQ7Z4I7
PeptideAtlasiQ7Z4I7
PRIDEiQ7Z4I7
ProteomicsDBi69192
69193 [Q7Z4I7-2]
69194 [Q7Z4I7-3]

PTM databases

iPTMnetiQ7Z4I7
PhosphoSitePlusiQ7Z4I7

Expressioni

Gene expression databases

BgeeiENSG00000072163 Expressed in 190 organ(s), highest expression level in fundus of stomach
CleanExiHS_LIMS2
ExpressionAtlasiQ7Z4I7 baseline and differential
GenevisibleiQ7Z4I7 HS

Organism-specific databases

HPAiHPA058340

Interactioni

Subunit structurei

Interacts with TGFB1I1 (By similarity). Interacts with integrin-linked protein kinase 1 (ILK) via the first LIM domain, and in competition with LIMS1. Part of the heterotrimeric IPP complex composed of integrin-linked kinase (ILK), LIMS1 or LIMS2, and PARVA.By similarity2 Publications

Binary interactionsi

Protein-protein interaction databases

BioGridi120808, 14 interactors
IntActiQ7Z4I7, 13 interactors
MINTiQ7Z4I7
STRINGi9606.ENSP00000326888

Structurei

Secondary structure

1341
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliQ7Z4I7
SMRiQ7Z4I7
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ7Z4I7

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini13 – 74LIM zinc-binding 1PROSITE-ProRule annotationAdd BLAST62
Domaini76 – 133LIM zinc-binding 2PROSITE-ProRule annotationAdd BLAST58
Domaini138 – 195LIM zinc-binding 3PROSITE-ProRule annotationAdd BLAST58
Domaini196 – 255LIM zinc-binding 4PROSITE-ProRule annotationAdd BLAST60
Domaini256 – 315LIM zinc-binding 5PROSITE-ProRule annotationAdd BLAST60

Keywords - Domaini

LIM domain, Repeat

Phylogenomic databases

eggNOGiKOG2272 Eukaryota
ENOG410XP46 LUCA
GeneTreeiENSGT00760000118910
HOGENOMiHOG000253950
HOVERGENiHBG000053
InParanoidiQ7Z4I7
OMAiDHFSCTH
OrthoDBiEOG091G08K3
PhylomeDBiQ7Z4I7
TreeFamiTF314113

Family and domain databases

InterProiView protein in InterPro
IPR017351 PINCH
IPR001781 Znf_LIM
PANTHERiPTHR24210 PTHR24210, 1 hit
PfamiView protein in Pfam
PF00412 LIM, 5 hits
PIRSFiPIRSF038003 PINCH, 1 hit
SMARTiView protein in SMART
SM00132 LIM, 5 hits
PROSITEiView protein in PROSITE
PS00478 LIM_DOMAIN_1, 4 hits
PS50023 LIM_DOMAIN_2, 5 hits

Sequences (5+)i

Sequence statusi: Complete.

This entry describes 5 isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 5 described isoforms and 2 potential isoforms that are computationally mapped.Show allAlign All

Isoform 1 (identifier: Q7Z4I7-1) [UniParc]FASTAAdd to basket
Also known as: LIM-like protein 2B

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
MTGSNMSDAL ANAVCQRCQA RFSPAERIVN SNGELYHEHC FVCAQCFRPF
60 70 80 90 100
PEGLFYEFEG RKYCEHDFQM LFAPCCGSCG EFIIGRVIKA MNNNWHPGCF
110 120 130 140 150
RCELCDVELA DLGFVKNAGR HLCRPCHNRE KAKGLGKYIC QRCHLVIDEQ
160 170 180 190 200
PLMFRSDAYH PDHFNCTHCG KELTAEAREL KGELYCLPCH DKMGVPICGA
210 220 230 240 250
CRRPIEGRVV NALGKQWHVE HFVCAKCEKP FLGHRHYEKK GLAYCETHYN
260 270 280 290 300
QLFGDVCYNC SHVIEGDVVS ALNKAWCVSC FSCSTCNSKL TLKNKFVEFD
310 320 330 340
MKPVCKRCYE KFPLELKKRL KKLSELTSRK AQPKATDLNS A
Length:341
Mass (Da):38,916
Last modified:October 1, 2003 - v1
Checksum:iEEA8D74C309D9C8A
GO
Isoform 2 (identifier: Q7Z4I7-2) [UniParc]FASTAAdd to basket
Also known as: LIM-like protein 2A

The sequence of this isoform differs from the canonical sequence as follows:
     1-4: MTGS → MAARLGALAASGLYRRRQHRQSPPPATG

Show »
Length:365
Mass (Da):41,512
Checksum:i3B8E1C98AFB2B698
GO
Isoform 3 (identifier: Q7Z4I7-3) [UniParc]FASTAAdd to basket
Also known as: LIM-like protein 2C

The sequence of this isoform differs from the canonical sequence as follows:
     1-5: Missing.

Show »
Length:336
Mass (Da):38,426
Checksum:i27F7EA97B557804D
GO
Isoform 4 (identifier: Q7Z4I7-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-152: Missing.

Show »
Length:189
Mass (Da):21,615
Checksum:i896862131C240B5B
GO
Isoform 5 (identifier: Q7Z4I7-5) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     3-3: G → GRKRKWGETGTGSGAAPAAALRW

Note: No experimental confirmation available.
Show »
Length:363
Mass (Da):41,226
Checksum:iD0F6B8B3618F20FF
GO

Computationally mapped potential isoform sequencesi

There are 2 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
H0Y592H0Y592_HUMAN
LIM and senescent cell antigen-like...
LIMS2
169Annotation score:
F8WEF3F8WEF3_HUMAN
LIM and senescent cell antigen-like...
LIMS2
60Annotation score:

Sequence cautioni

The sequence AAM77350 differs from that shown. Reason: Frameshift at position 331.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti111D → G in BAG60013 (PubMed:14702039).Curated1
Sequence conflicti294N → D in AAM97589 (PubMed:12167643).Curated1
Sequence conflicti294N → D in BAB14047 (PubMed:15815621).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_07652792N → K in LGMD2W; unknown pathological significance. 1 PublicationCorresponds to variant dbSNP:rs754385302Ensembl.1
Natural variantiVAR_07652897P → L in LGMD2W; unknown pathological significance. 1 PublicationCorresponds to variant dbSNP:rs768056213Ensembl.1
Natural variantiVAR_076529323L → P in LGMD2W; unknown pathological significance. 1 PublicationCorresponds to variant dbSNP:rs869025562Ensembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0455391 – 152Missing in isoform 4. 2 PublicationsAdd BLAST152
Alternative sequenceiVSP_0219161 – 5Missing in isoform 3. 2 Publications5
Alternative sequenceiVSP_0219171 – 4MTGS → MAARLGALAASGLYRRRQHR QSPPPATG in isoform 2. 1 Publication4
Alternative sequenceiVSP_0460783G → GRKRKWGETGTGSGAAPAAA LRW in isoform 5. 1 Publication1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF484961 mRNA Translation: AAM97589.1
AF520987 mRNA Translation: AAM77350.1 Frameshift.
AF527764 mRNA Translation: AAQ09011.1
AF527765 mRNA Translation: AAQ09012.1
AF527766 mRNA Translation: AAQ09013.1
AF527770 mRNA Translation: AAQ09017.1
AK022470 mRNA Translation: BAB14047.1
AK297645 mRNA Translation: BAG60013.1
BX458594 mRNA No translation available.
AC010976 Genomic DNA No translation available.
AC074114 Genomic DNA No translation available.
BC065816 mRNA Translation: AAH65816.1
CCDSiCCDS2147.1 [Q7Z4I7-2]
CCDS54394.1 [Q7Z4I7-3]
CCDS54395.1 [Q7Z4I7-1]
CCDS54396.1 [Q7Z4I7-5]
CCDS58725.1 [Q7Z4I7-4]
RefSeqiNP_001129509.2, NM_001136037.2 [Q7Z4I7-5]
NP_001154875.1, NM_001161403.1 [Q7Z4I7-1]
NP_001154876.1, NM_001161404.1 [Q7Z4I7-3]
NP_001243471.1, NM_001256542.1 [Q7Z4I7-4]
NP_060450.2, NM_017980.4 [Q7Z4I7-2]
UniGeneiHs.469881

Genome annotation databases

EnsembliENST00000324938; ENSP00000326888; ENSG00000072163 [Q7Z4I7-2]
ENST00000355119; ENSP00000347240; ENSG00000072163 [Q7Z4I7-1]
ENST00000409254; ENSP00000386907; ENSG00000072163 [Q7Z4I7-4]
ENST00000409286; ENSP00000386252; ENSG00000072163 [Q7Z4I7-4]
ENST00000409455; ENSP00000386383; ENSG00000072163 [Q7Z4I7-3]
ENST00000409754; ENSP00000386345; ENSG00000072163 [Q7Z4I7-4]
ENST00000409808; ENSP00000386637; ENSG00000072163 [Q7Z4I7-3]
ENST00000410011; ENSP00000387002; ENSG00000072163 [Q7Z4I7-3]
ENST00000410038; ENSP00000386570; ENSG00000072163 [Q7Z4I7-4]
ENST00000545738; ENSP00000443794; ENSG00000072163 [Q7Z4I7-5]
GeneIDi55679
KEGGihsa:55679
UCSCiuc002tov.4 human [Q7Z4I7-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF484961 mRNA Translation: AAM97589.1
AF520987 mRNA Translation: AAM77350.1 Frameshift.
AF527764 mRNA Translation: AAQ09011.1
AF527765 mRNA Translation: AAQ09012.1
AF527766 mRNA Translation: AAQ09013.1
AF527770 mRNA Translation: AAQ09017.1
AK022470 mRNA Translation: BAB14047.1
AK297645 mRNA Translation: BAG60013.1
BX458594 mRNA No translation available.
AC010976 Genomic DNA No translation available.
AC074114 Genomic DNA No translation available.
BC065816 mRNA Translation: AAH65816.1
CCDSiCCDS2147.1 [Q7Z4I7-2]
CCDS54394.1 [Q7Z4I7-3]
CCDS54395.1 [Q7Z4I7-1]
CCDS54396.1 [Q7Z4I7-5]
CCDS58725.1 [Q7Z4I7-4]
RefSeqiNP_001129509.2, NM_001136037.2 [Q7Z4I7-5]
NP_001154875.1, NM_001161403.1 [Q7Z4I7-1]
NP_001154876.1, NM_001161404.1 [Q7Z4I7-3]
NP_001243471.1, NM_001256542.1 [Q7Z4I7-4]
NP_060450.2, NM_017980.4 [Q7Z4I7-2]
UniGeneiHs.469881

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3IXEX-ray1.90B11-73[»]
ProteinModelPortaliQ7Z4I7
SMRiQ7Z4I7
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi120808, 14 interactors
IntActiQ7Z4I7, 13 interactors
MINTiQ7Z4I7
STRINGi9606.ENSP00000326888

PTM databases

iPTMnetiQ7Z4I7
PhosphoSitePlusiQ7Z4I7

Polymorphism and mutation databases

BioMutaiLIMS2
DMDMi74750091

Proteomic databases

EPDiQ7Z4I7
MaxQBiQ7Z4I7
PaxDbiQ7Z4I7
PeptideAtlasiQ7Z4I7
PRIDEiQ7Z4I7
ProteomicsDBi69192
69193 [Q7Z4I7-2]
69194 [Q7Z4I7-3]

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000324938; ENSP00000326888; ENSG00000072163 [Q7Z4I7-2]
ENST00000355119; ENSP00000347240; ENSG00000072163 [Q7Z4I7-1]
ENST00000409254; ENSP00000386907; ENSG00000072163 [Q7Z4I7-4]
ENST00000409286; ENSP00000386252; ENSG00000072163 [Q7Z4I7-4]
ENST00000409455; ENSP00000386383; ENSG00000072163 [Q7Z4I7-3]
ENST00000409754; ENSP00000386345; ENSG00000072163 [Q7Z4I7-4]
ENST00000409808; ENSP00000386637; ENSG00000072163 [Q7Z4I7-3]
ENST00000410011; ENSP00000387002; ENSG00000072163 [Q7Z4I7-3]
ENST00000410038; ENSP00000386570; ENSG00000072163 [Q7Z4I7-4]
ENST00000545738; ENSP00000443794; ENSG00000072163 [Q7Z4I7-5]
GeneIDi55679
KEGGihsa:55679
UCSCiuc002tov.4 human [Q7Z4I7-1]

Organism-specific databases

CTDi55679
DisGeNETi55679
EuPathDBiHostDB:ENSG00000072163.18
GeneCardsiLIMS2
HGNCiHGNC:16084 LIMS2
HPAiHPA058340
MalaCardsiLIMS2
MIMi607908 gene
616827 phenotype
neXtProtiNX_Q7Z4I7
OpenTargetsiENSG00000072163
Orphaneti466801 Autosomal recessive limb-girdle muscular dystrophy type 2W
PharmGKBiPA30390
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2272 Eukaryota
ENOG410XP46 LUCA
GeneTreeiENSGT00760000118910
HOGENOMiHOG000253950
HOVERGENiHBG000053
InParanoidiQ7Z4I7
OMAiDHFSCTH
OrthoDBiEOG091G08K3
PhylomeDBiQ7Z4I7
TreeFamiTF314113

Enzyme and pathway databases

ReactomeiR-HSA-446353 Cell-extracellular matrix interactions

Miscellaneous databases

ChiTaRSiLIMS2 human
EvolutionaryTraceiQ7Z4I7
GenomeRNAii55679
PROiPR:Q7Z4I7
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000072163 Expressed in 190 organ(s), highest expression level in fundus of stomach
CleanExiHS_LIMS2
ExpressionAtlasiQ7Z4I7 baseline and differential
GenevisibleiQ7Z4I7 HS

Family and domain databases

InterProiView protein in InterPro
IPR017351 PINCH
IPR001781 Znf_LIM
PANTHERiPTHR24210 PTHR24210, 1 hit
PfamiView protein in Pfam
PF00412 LIM, 5 hits
PIRSFiPIRSF038003 PINCH, 1 hit
SMARTiView protein in SMART
SM00132 LIM, 5 hits
PROSITEiView protein in PROSITE
PS00478 LIM_DOMAIN_1, 4 hits
PS50023 LIM_DOMAIN_2, 5 hits
ProtoNetiSearch...

Entry informationi

Entry nameiLIMS2_HUMAN
AccessioniPrimary (citable) accession number: Q7Z4I7
Secondary accession number(s): A6NLH0
, B4DMV1, F5H6E6, Q7Z4I2, Q7Z4I6, Q7Z4I8, Q8NFE7, Q9HA13
Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 12, 2006
Last sequence update: October 1, 2003
Last modified: November 7, 2018
This is version 129 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 2
    Human chromosome 2: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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