Human Gene LIMK2 (uc003akh.3) Description and Page Index
  Description: Homo sapiens LIM domain kinase 2 (LIMK2), transcript variant 2a, mRNA.
RefSeq Summary (NM_005569): There are approximately 40 known eukaryotic LIM proteins, so named for the LIM domains they contain. LIM domains are highly conserved cysteine-rich structures containing 2 zinc fingers. Although zinc fingers usually function by binding to DNA or RNA, the LIM motif probably mediates protein-protein interactions. LIM kinase-1 and LIM kinase-2 belong to a small subfamily with a unique combination of 2 N-terminal LIM motifs and a C-terminal protein kinase domain. The protein encoded by this gene is phosphorylated and activated by ROCK, a downstream effector of Rho, and the encoded protein, in turn, phosphorylates cofilin, inhibiting its actin-depolymerizing activity. It is thought that this pathway contributes to Rho-induced reorganization of the actin cytoskeleton. At least three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr22:31,608,250-31,676,066 Size: 67,817 Total Exon Count: 16 Strand: +
Coding Region
   Position: hg19 chr22:31,608,395-31,674,427 Size: 66,033 Coding Exon Count: 16 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-15

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr22:31,608,250-31,676,066)mRNA (may differ from genome)Protein (638 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: LIMK2_HUMAN
DESCRIPTION: RecName: Full=LIM domain kinase 2; Short=LIMK-2; EC=2.7.11.1;
FUNCTION: Displays serine/threonine-specific phosphorylation of myelin basic protein and histone (MBP) in vitro.
CATALYTIC ACTIVITY: ATP + a protein = ADP + a phosphoprotein.
SUBUNIT: Binds ROCK1 and LKAP. Interacts with PARD3. Interacts with NISCH (By similarity).
SUBCELLULAR LOCATION: Isoform LIMK2a: Cytoplasm. Nucleus. Note=Isoform LIMK2a is distributed in the cytoplasm and the nucleus.
SUBCELLULAR LOCATION: Isoform LIMK2b: Cytoplasm. Nucleus. Note=Isoform LIMK2b occurs mainly in the cytoplasm and is scarcely translocated to the nucleus.
TISSUE SPECIFICITY: Highest expression in the placenta; moderate level in liver, lung, kidney, and pancreas. LIMK2a is found to be more abundant then LIMK2b in liver, colon, stomach, and spleen, while in brain, kidney, and placenta LIMK2b is the dominant form. In adult lung, both LIMK2a and LIMK2b is nearly equally observed.
PTM: Phosphorylated on serine and/or threonine residues by ROCK1.
SIMILARITY: Belongs to the protein kinase superfamily. TKL Ser/Thr protein kinase family.
SIMILARITY: Contains 2 LIM zinc-binding domains.
SIMILARITY: Contains 1 PDZ (DHR) domain.
SIMILARITY: Contains 1 protein kinase domain.
SEQUENCE CAUTION: Sequence=AAB54055.1; Type=Erroneous gene model prediction;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): LIMK2
CDC HuGE Published Literature: LIMK2
Positive Disease Associations: Diabetic Nephropathies
Related Studies:
  1. Diabetic Nephropathies
    Caitrin W McDonough et al. Kidney international 2011, A genome-wide association study for diabetic nephropathy genes in African Americans., Kidney international. [PubMed 21150874]

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 66.71 RPKM in Whole Blood
Total median expression: 705.50 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -67.70145-0.467 Picture PostScript Text
3' UTR -613.881639-0.375 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011009 - Kinase-like_dom
IPR001478 - PDZ
IPR000719 - Prot_kinase_cat_dom
IPR017441 - Protein_kinase_ATP_BS
IPR001245 - Ser-Thr/Tyr_kinase_cat_dom
IPR001781 - Znf_LIM

Pfam Domains:
PF00069 - Protein kinase domain
PF00412 - LIM domain
PF00595 - PDZ domain (Also known as DHR or GLGF)
PF06293 - Lipopolysaccharide kinase (Kdo/WaaP) family
PF07714 - Protein tyrosine kinase

SCOP Domains:
50156 - PDZ domain-like
56112 - Protein kinase-like (PK-like)
57716 - Glucocorticoid receptor-like (DNA-binding domain)

Protein Data Bank (PDB) 3-D Structure
MuPIT help

1X6A
- NMR MuPIT


ModBase Predicted Comparative 3D Structure on P53671
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
 Gene Details    
 Gene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0004871 signal transducer activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0016740 transferase activity
GO:0046872 metal ion binding
GO:0046982 protein heterodimerization activity

Biological Process:
GO:0006468 protein phosphorylation
GO:0007283 spermatogenesis
GO:0016310 phosphorylation
GO:0035556 intracellular signal transduction
GO:0060322 head development
GO:0061303 cornea development in camera-type eye

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005801 cis-Golgi network


-  Descriptions from all associated GenBank mRNAs
  AK302553 - Homo sapiens cDNA FLJ53448 complete cds, highly similar to LIM domain kinase 2 (EC 2.7.11.1).
JA482221 - Sequence 204 from Patent WO2011072091.
JE980513 - Sequence 204 from Patent EP2862929.
AK093554 - Homo sapiens cDNA FLJ36235 fis, clone THYMU2001325, highly similar to LIM domain kinase 2 (EC 2.7.11.1).
AX748198 - Sequence 1723 from Patent EP1308459.
AK291640 - Homo sapiens cDNA FLJ76874 complete cds, highly similar to Homo sapiens LIM domain kinase 2 (LIMK2), transcript variant 2a,mRNA.
D45906 - Homo sapiens mRNA for LIMK-2, complete cds.
JD179981 - Sequence 161005 from Patent EP1572962.
JD407292 - Sequence 388316 from Patent EP1572962.
JD462450 - Sequence 443474 from Patent EP1572962.
JD547183 - Sequence 528207 from Patent EP1572962.
JD389318 - Sequence 370342 from Patent EP1572962.
CR456513 - Homo sapiens LIMK2 full length open reading frame (ORF) cDNA clone (cDNA clone C22ORF:pGEM.LIMK2).
CU013400 - Homo sapiens LIMK2, mRNA (cDNA clone IMAGE:100000274), complete cds, without stop codon, in Gateway system.
CU013112 - Homo sapiens LIMK2, mRNA (cDNA clone IMAGE:100000370), complete cds, with stop codon, in Gateway system.
AB587469 - Synthetic construct DNA, clone: pF1KB8450, Homo sapiens LIMK2 gene for LIM domain kinase 2, without stop codon, in Flexi system.
AB451396 - Homo sapiens LIMK2 mRNA for LIM domain kinase 2 isoform 2a, partial cds, clone: FLJ08094AAAF.
AB451269 - Homo sapiens LIMK2 mRNA for LIM domain kinase 2 isoform 2a, complete cds, clone: FLJ08094AAAN.
AK299112 - Homo sapiens cDNA FLJ53457 complete cds, highly similar to LIM domain kinase 2 (EC 2.7.11.1).
JA482220 - Sequence 203 from Patent WO2011072091.
JE980512 - Sequence 203 from Patent EP2862929.
JA482222 - Sequence 205 from Patent WO2011072091.
JE980514 - Sequence 205 from Patent EP2862929.
AK314391 - Homo sapiens cDNA, FLJ95165, highly similar to Homo sapiens LIM domain kinase 2 (LIMK2), transcript variant 2b,mRNA.
AK293774 - Homo sapiens cDNA FLJ55959 complete cds, highly similar to LIM domain kinase 2 (EC 2.7.11.1).
AL117466 - Homo sapiens mRNA; cDNA DKFZp586K0922 (from clone DKFZp586K0922).
D85527 - Homo sapiens LIMK2b mRNA, partial cds.
BC013051 - Homo sapiens LIM domain kinase 2, mRNA (cDNA clone MGC:8917 IMAGE:3861412), complete cds.
KJ891550 - Synthetic construct Homo sapiens clone ccsbBroadEn_00944 LIMK2 gene, encodes complete protein.
KJ905224 - Synthetic construct Homo sapiens clone ccsbBroadEn_14690 LIMK2 gene, encodes complete protein.
AM393090 - Synthetic construct Homo sapiens clone IMAGE:100001806 for hypothetical protein (LIMK2 gene).
JD020553 - Sequence 1577 from Patent EP1572962.
JD031137 - Sequence 12161 from Patent EP1572962.
JD026097 - Sequence 7121 from Patent EP1572962.
JD032624 - Sequence 13648 from Patent EP1572962.
AK092838 - Homo sapiens cDNA FLJ35519 fis, clone SPLEN2001176.
JD420326 - Sequence 401350 from Patent EP1572962.
JD397977 - Sequence 379001 from Patent EP1572962.
JD143238 - Sequence 124262 from Patent EP1572962.
JD251131 - Sequence 232155 from Patent EP1572962.
JD313569 - Sequence 294593 from Patent EP1572962.
JD393230 - Sequence 374254 from Patent EP1572962.
JD365458 - Sequence 346482 from Patent EP1572962.
JD519780 - Sequence 500804 from Patent EP1572962.
DQ586206 - Homo sapiens piRNA piR-53318, complete sequence.
JD514354 - Sequence 495378 from Patent EP1572962.
JD362800 - Sequence 343824 from Patent EP1572962.
JD073802 - Sequence 54826 from Patent EP1572962.
JD228892 - Sequence 209916 from Patent EP1572962.
JD448876 - Sequence 429900 from Patent EP1572962.
JD165891 - Sequence 146915 from Patent EP1572962.
JD066509 - Sequence 47533 from Patent EP1572962.
JD180756 - Sequence 161780 from Patent EP1572962.
JD421767 - Sequence 402791 from Patent EP1572962.
DQ585689 - Homo sapiens piRNA piR-52801, complete sequence.
JD286482 - Sequence 267506 from Patent EP1572962.
JD246163 - Sequence 227187 from Patent EP1572962.
JD279038 - Sequence 260062 from Patent EP1572962.
JD532739 - Sequence 513763 from Patent EP1572962.
JD265539 - Sequence 246563 from Patent EP1572962.
JD415130 - Sequence 396154 from Patent EP1572962.
JD396972 - Sequence 377996 from Patent EP1572962.
DQ594610 - Homo sapiens piRNA piR-60722, complete sequence.
JD183006 - Sequence 164030 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04360 - Axon guidance
hsa04666 - Fc gamma R-mediated phagocytosis
hsa04810 - Regulation of actin cytoskeleton

Reactome (by CSHL, EBI, and GO)

Protein P53671 (Reactome details) participates in the following event(s):

R-HSA-419087 LIM kinase phosphorylation by ROCK
R-HSA-3928577 ROCK phosphorylates LIMK1,2
R-HSA-3928608 LIMK phosphorylates CFL1, inactivating it
R-HSA-416572 Sema4D induced cell migration and growth-cone collapse
R-HSA-5627117 RHO GTPases Activate ROCKs
R-HSA-3928662 EPHB-mediated forward signaling
R-HSA-400685 Sema4D in semaphorin signaling
R-HSA-195258 RHO GTPase Effectors
R-HSA-2682334 EPH-Ephrin signaling
R-HSA-373755 Semaphorin interactions
R-HSA-194315 Signaling by Rho GTPases
R-HSA-422475 Axon guidance
R-HSA-162582 Signal Transduction
R-HSA-1266738 Developmental Biology

-  Other Names for This Gene
  Alternate Gene Symbols: A8K6H5, LIMK2_HUMAN, NM_005569, NP_005560, P53671, Q7KZ80, Q7L3H5, Q96E10, Q99464, Q9UFU0
UCSC ID: uc003akh.3
RefSeq Accession: NM_005569
Protein: P53671 (aka LIMK2_HUMAN or LIK2_HUMAN)
CCDS: CCDS13891.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_005569.3
exon count: 16CDS single in 3' UTR: no RNA size: 3701
ORF size: 1917CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3701.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.