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PDZ and LIM domain protein 4 (LIM protein RIL) (Reversion-induced LIM protein)

 PDLI4_MOUSE             Reviewed;         330 AA.
P70271; Q5SWV2; Q8K0W4;
15-MAR-2004, integrated into UniProtKB/Swiss-Prot.
27-JUL-2011, sequence version 3.
20-JUN-2018, entry version 136.
RecName: Full=PDZ and LIM domain protein 4;
AltName: Full=LIM protein RIL;
AltName: Full=Reversion-induced LIM protein;
Name=Pdlim4; Synonyms=Ril;
Mus musculus (Mouse).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
Muroidea; Muridae; Murinae; Mus; Mus.
NCBI_TaxID=10090;
[1]
NUCLEOTIDE SEQUENCE [MRNA], PHOSPHORYLATION, AND INTERACTION WITH
PTPN13.
STRAIN=BALB/cJ; TISSUE=Brain;
PubMed=9487134; DOI=10.1091/mbc.9.3.671;
Cuppen E., Gerrits H., Pepers B., Wieringa B., Hendriks W.;
"PDZ motifs in PTP-BL and RIL bind to internal protein segments in the
LIM domain protein RIL.";
Mol. Biol. Cell 9:671-683(1998).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=C57BL/6J;
PubMed=19468303; DOI=10.1371/journal.pbio.1000112;
Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S.,
She X., Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W.,
Kapustin Y., Meric P., Maglott D., Birtle Z., Marques A.C., Graves T.,
Zhou S., Teague B., Potamousis K., Churas C., Place M., Herschleb J.,
Runnheim R., Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z.,
Lindblad-Toh K., Eichler E.E., Ponting C.P.;
"Lineage-specific biology revealed by a finished genome assembly of
the mouse.";
PLoS Biol. 7:E1000112-E1000112(2009).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.;
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases.
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
TISSUE=Lung;
PubMed=15489334; DOI=10.1101/gr.2596504;
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA
project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[5]
INTERACTION WITH TRIP6 AND PTPN13, AND MUTAGENESIS OF
326-VAL--VAL-330.
PubMed=10826496; DOI=10.1078/S0171-9335(04)70031-X;
Cuppen E., van Ham M., Wansink D.G., de Leeuw A., Wieringa B.,
Hendriks W.;
"The zyxin-related protein TRIP6 interacts with PDZ motifs in the
adaptor protein RIL and the protein tyrosine phosphatase PTP-BL.";
Eur. J. Cell Biol. 79:283-293(2000).
[6]
TISSUE SPECIFICITY.
PubMed=14729062;
Vallenius T., Scharm B., Vesikansa A., Luukko K., Schaefer R.,
Maekelae T.P.;
"The PDZ-LIM protein RIL modulates actin stress fiber turnover and
enhances the association of alpha-actinin with F-actin.";
Exp. Cell Res. 293:117-128(2004).
[7]
INTERACTION WITH PDLIM3 AND PTPN13, AND MUTAGENESIS OF GLY-261;
VAL-263; GLY-264; THR-265; ILE-266; VAL-267; LYS-272; TYR-274;
PRO-276; GLU-277; MET-280; LEU-286; ASN-287; LEU-288; ARG-291;
GLY-292; PHE-294; PHE-295; ARG-299 AND TYR-301.
PubMed=15663004;
van den Berk L.C., van Ham M.A., te Lindert M.M., Walma T., Aelen J.,
Vuister G.W., Hendriks W.J.;
"The interaction of PTP-BL PDZ domains with RIL: an enigmatic role for
the RIL LIM domain.";
Mol. Biol. Rep. 31:203-215(2004).
[8]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-111, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Brain;
PubMed=16452087; DOI=10.1074/mcp.T500041-MCP200;
Trinidad J.C., Specht C.G., Thalhammer A., Schoepfer R.,
Burlingame A.L.;
"Comprehensive identification of phosphorylation sites in postsynaptic
density preparations.";
Mol. Cell. Proteomics 5:914-922(2006).
[9]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-111, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Liver;
PubMed=17242355; DOI=10.1073/pnas.0609836104;
Villen J., Beausoleil S.A., Gerber S.A., Gygi S.P.;
"Large-scale phosphorylation analysis of mouse liver.";
Proc. Natl. Acad. Sci. U.S.A. 104:1488-1493(2007).
[10]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-107; SER-111; SER-115;
SER-118; SER-119 AND SER-124, AND IDENTIFICATION BY MASS SPECTROMETRY
[LARGE SCALE ANALYSIS].
TISSUE=Brain, Brown adipose tissue, Heart, Kidney, Liver, Lung,
Pancreas, Spleen, and Testis;
PubMed=21183079; DOI=10.1016/j.cell.2010.12.001;
Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R.,
Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.;
"A tissue-specific atlas of mouse protein phosphorylation and
expression.";
Cell 143:1174-1189(2010).
-!- FUNCTION: Suppresses SRC activation by recognizing and binding to
active SRC and facilitating PTPN13-mediated dephosphorylation of
SRC 'Tyr-419' leading to its inactivation. Inactivated SRC
dissociates from this protein allowing the initiation of a new SRC
inactivation cycle. Involved in reorganization of the actin
cytoskeleton (By similarity). In nonmuscle cells, binds to ACTN1
(alpha-actinin-1), increases the affinity of ACTN1 to F-actin
(filamentous actin), and promotes formation of actin stress
fibers. Involved in regulation of the synaptic AMPA receptor
transport in dendritic spines of hippocampal pyramidal neurons
directing the receptors toward an insertion at the postsynaptic
membrane. Links endosomal surface-internalized GRIA1-containing
AMPA receptors to the alpha-actinin/actin cytoskeleton. Increases
AMPA receptor-mediated excitatory postsynaptic currents in neurons
(By similarity). {ECO:0000250|UniProtKB:P36202,
ECO:0000250|UniProtKB:P50479}.
-!- SUBUNIT: Homodimer (By similarity). Interacts (via C-terminus only
or via combined C-terminus and LIM domain, but not LIM domain
only) with PTPN13 (via the second or fourth PDZ domains)
(PubMed:9487134, PubMed:15663004). Found in a complex with PTPN13
and TRIP6 (PubMed:10826496). Interacts (via PDZ domain) with ACTN1
and ACTN2 (via C-terminal SDL residues) (By similarity). Interacts
(via PDZ domain) with TRIP6 (via the second LIM domain or via the
third LIM domain plus C-terminus) (PubMed:10826496). Interacts
(via LIM domain) with GRIA1 (via C-terminus); this interaction as
well as the interaction with alpha-actinin is required for their
colocalization in early endosomes. Interacts with PDLIM1 (By
similarity). Forms (via LIM domain) a heterodimer with PDLIM3
(PubMed:15663004). Interacts directly with SRC (via kinase domain
and to a lesser extent the SH2 domain) (By similarity).
{ECO:0000250|UniProtKB:P36202, ECO:0000250|UniProtKB:P50479,
ECO:0000269|PubMed:10826496, ECO:0000269|PubMed:15663004,
ECO:0000269|PubMed:9487134}.
-!- INTERACTION:
Q9Z1Y4:Trip6; NbExp=2; IntAct=EBI-7288319, EBI-643879;
-!- SUBCELLULAR LOCATION: Cytoplasm, cytoskeleton
{ECO:0000250|UniProtKB:P36202}. Cell projection, dendritic spine
{ECO:0000250|UniProtKB:P36202}. Early endosome membrane
{ECO:0000250|UniProtKB:P36202}; Peripheral membrane protein
{ECO:0000250|UniProtKB:P36202}; Cytoplasmic side
{ECO:0000250|UniProtKB:P36202}. Recycling endosome membrane
{ECO:0000250|UniProtKB:P36202}; Peripheral membrane protein
{ECO:0000250|UniProtKB:P36202}; Cytoplasmic side
{ECO:0000250|UniProtKB:P36202}. Nucleus
{ECO:0000250|UniProtKB:P50479}. Cytoplasm, perinuclear region
{ECO:0000250|UniProtKB:P50479}. Cell projection, lamellipodium
{ECO:0000250|UniProtKB:P50479}. Cell junction, synapse,
synaptosome {ECO:0000250|UniProtKB:P36202}. Note=Localizes to
actin stress fibers in nonmuscle cells. Colocalizes with GRIA1 in
early endosomes. Enriched in numerous but not all spine-like
structures along dendritic branches. Colocalizes with actin and
enriched at sites containing larger amounts of actin and alpha-
actinin. Targeted efficiently to spines via its PDZ domain-
mediated interaction with the alpha-actinin/actin cytoskeletal
complex. Localizes to synaptosomes in brain (By similarity).
Colocalizes with F-actin. Colocalizes with TRIP6 at cell-cell
contacts and lamellipodia. In the cytoplasm, displays a fibrillar
pattern with characteristic thick fibers and occasional clusters.
Colocalizes with the actin stress fibers. Oxidative stress induces
redistribution from cytoskeleton to cytosol. Colocalizes with SRC
at the perinuclear region, but not at focal adhesions (By
similarity). {ECO:0000250|UniProtKB:P36202,
ECO:0000250|UniProtKB:P50479}.
-!- TISSUE SPECIFICITY: Expressed in several non-muscle tissues
including lung, brain, ovary and uterus, and especially in
epithelial cells on embryonic day 14 (E14). In the uterus, high
expression in the glandular epithelium, but absent in the simple
columnar epithelium lining the uterus cavity.
{ECO:0000269|PubMed:14729062}.
-!- PTM: Phosphorylated on tyrosine residue(s). Can be
dephosphorylated by PTPN13. {ECO:0000269|PubMed:9487134}.
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EMBL; Y08361; CAA69648.1; -; mRNA.
EMBL; AL596444; CAI25321.1; -; Genomic_DNA.
EMBL; CH466575; EDL33550.1; -; Genomic_DNA.
EMBL; BC030068; AAH30068.1; -; mRNA.
CCDS; CCDS24690.1; -.
RefSeq; NP_062290.2; NM_019417.3.
UniGene; Mm.21830; -.
ProteinModelPortal; P70271; -.
SMR; P70271; -.
BioGrid; 205965; 4.
IntAct; P70271; 3.
MINT; P70271; -.
STRING; 10090.ENSMUSP00000018755; -.
iPTMnet; P70271; -.
PhosphoSitePlus; P70271; -.
MaxQB; P70271; -.
PaxDb; P70271; -.
PeptideAtlas; P70271; -.
PRIDE; P70271; -.
Ensembl; ENSMUST00000018755; ENSMUSP00000018755; ENSMUSG00000020388.
GeneID; 30794; -.
KEGG; mmu:30794; -.
UCSC; uc007ixf.2; mouse.
CTD; 8572; -.
MGI; MGI:1353470; Pdlim4.
eggNOG; KOG1703; Eukaryota.
eggNOG; ENOG410XRD4; LUCA.
GeneTree; ENSGT00590000082980; -.
HOGENOM; HOG000290704; -.
HOVERGEN; HBG061371; -.
InParanoid; P70271; -.
OMA; HIDPEAQ; -.
OrthoDB; EOG091G0A6C; -.
TreeFam; TF106408; -.
PRO; PR:P70271; -.
Proteomes; UP000000589; Chromosome 11.
Bgee; ENSMUSG00000020388; -.
CleanEx; MM_PDLIM4; -.
ExpressionAtlas; P70271; baseline and differential.
Genevisible; P70271; MM.
GO; GO:0015629; C:actin cytoskeleton; ISO:MGI.
GO; GO:0030054; C:cell junction; IEA:UniProtKB-KW.
GO; GO:0005737; C:cytoplasm; ISO:MGI.
GO; GO:0005856; C:cytoskeleton; ISO:MGI.
GO; GO:0043197; C:dendritic spine; ISS:UniProtKB.
GO; GO:0031905; C:early endosome lumen; ISS:UniProtKB.
GO; GO:0031901; C:early endosome membrane; IEA:UniProtKB-SubCell.
GO; GO:0031941; C:filamentous actin; ISO:MGI.
GO; GO:0030027; C:lamellipodium; ISO:MGI.
GO; GO:0005634; C:nucleus; ISO:MGI.
GO; GO:0048471; C:perinuclear region of cytoplasm; ISO:MGI.
GO; GO:0045211; C:postsynaptic membrane; ISS:UniProtKB.
GO; GO:0034777; C:recycling endosome lumen; ISS:UniProtKB.
GO; GO:0055038; C:recycling endosome membrane; IEA:UniProtKB-SubCell.
GO; GO:0001725; C:stress fiber; ISO:MGI.
GO; GO:0042805; F:actinin binding; ISO:MGI.
GO; GO:0051393; F:alpha-actinin binding; ISO:MGI.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0042803; F:protein homodimerization activity; ISO:MGI.
GO; GO:0019903; F:protein phosphatase binding; IPI:UniProtKB.
GO; GO:0030036; P:actin cytoskeleton organization; ISO:MGI.
GO; GO:0031532; P:actin cytoskeleton reorganization; ISO:MGI.
GO; GO:0098976; P:excitatory chemical synaptic transmission; ISS:UniProtKB.
GO; GO:0051496; P:positive regulation of stress fiber assembly; ISO:MGI.
InterPro; IPR031847; DUF4749.
InterPro; IPR001478; PDZ.
InterPro; IPR036034; PDZ_sf.
InterPro; IPR001781; Znf_LIM.
Pfam; PF15936; DUF4749; 1.
Pfam; PF00412; LIM; 1.
Pfam; PF00595; PDZ; 1.
SMART; SM00132; LIM; 1.
SMART; SM00228; PDZ; 1.
SUPFAM; SSF50156; SSF50156; 1.
PROSITE; PS00478; LIM_DOMAIN_1; 1.
PROSITE; PS50023; LIM_DOMAIN_2; 1.
PROSITE; PS50106; PDZ; 1.
1: Evidence at protein level;
Cell junction; Cell projection; Complete proteome; Cytoplasm;
Cytoskeleton; Endosome; LIM domain; Membrane; Metal-binding; Nucleus;
Phosphoprotein; Reference proteome; Synapse; Synaptosome; Zinc.
CHAIN 1 330 PDZ and LIM domain protein 4.
/FTId=PRO_0000075874.
DOMAIN 1 84 PDZ. {ECO:0000255|PROSITE-
ProRule:PRU00143}.
DOMAIN 255 305 LIM zinc-binding. {ECO:0000255|PROSITE-
ProRule:PRU00125}.
MOD_RES 107 107 Phosphoserine.
{ECO:0000244|PubMed:21183079}.
MOD_RES 111 111 Phosphoserine.
{ECO:0000244|PubMed:16452087,
ECO:0000244|PubMed:17242355,
ECO:0000244|PubMed:21183079}.
MOD_RES 115 115 Phosphoserine.
{ECO:0000244|PubMed:21183079}.
MOD_RES 118 118 Phosphoserine.
{ECO:0000244|PubMed:21183079}.
MOD_RES 119 119 Phosphoserine.
{ECO:0000244|PubMed:21183079}.
MOD_RES 124 124 Phosphoserine.
{ECO:0000244|PubMed:21183079}.
MOD_RES 134 134 Phosphoserine.
{ECO:0000250|UniProtKB:P36202}.
MUTAGEN 261 261 G->A: No loss of interaction with PTPN13
(via PDZ domains); when associated with
A-263. {ECO:0000269|PubMed:15663004}.
MUTAGEN 263 263 V->A: No loss of interaction with PTPN13
(via PDZ domains); when associated with
A-261. {ECO:0000269|PubMed:15663004}.
MUTAGEN 264 264 G->A: No loss of interaction with PTPN13
(via PDZ domains); when associated with
A-266. {ECO:0000269|PubMed:15663004}.
MUTAGEN 265 265 T->A: No loss of interaction with PTPN13
(via PDZ domains); when associated with
A-267. {ECO:0000269|PubMed:15663004}.
MUTAGEN 266 266 I->A: No loss of interaction with PTPN13
(via PDZ domains); when associated with
A-264. {ECO:0000269|PubMed:15663004}.
MUTAGEN 267 267 V->A: No loss of interaction with PTPN13
(via PDZ domains); when associated with
A-265. {ECO:0000269|PubMed:15663004}.
MUTAGEN 272 272 K->A: No loss of interaction with PTPN13
(via PDZ domains); when associated with
A-274. {ECO:0000269|PubMed:15663004}.
MUTAGEN 274 274 Y->A: No loss of interaction with PTPN13
(via PDZ domains); when associated with
A-272. {ECO:0000269|PubMed:15663004}.
MUTAGEN 276 276 P->A: No loss of interaction with PTPN13
(via PDZ domains); when associated with
A-277. {ECO:0000269|PubMed:15663004}.
MUTAGEN 277 277 E->A: No loss of interaction with PTPN13
(via PDZ domains); when associated with
A-276. {ECO:0000269|PubMed:15663004}.
MUTAGEN 280 280 M->A: No loss of interaction with PTPN13
(via PDZ domains).
{ECO:0000269|PubMed:15663004}.
MUTAGEN 286 286 L->A: No loss of interaction with PTPN13
(via PDZ domains); when associated with
A-288. {ECO:0000269|PubMed:15663004}.
MUTAGEN 287 287 N->A: No loss of interaction with PTPN13
(via PDZ domains).
{ECO:0000269|PubMed:15663004}.
MUTAGEN 288 288 L->A: No loss of interaction with PTPN13
(via PDZ domains); when associated with
A-286. {ECO:0000269|PubMed:15663004}.
MUTAGEN 291 291 R->A: No loss of interaction with PTPN13
(via PDZ domains); when associated with
A-292. {ECO:0000269|PubMed:15663004}.
MUTAGEN 292 292 G->A: No loss of interaction with PTPN13
(via PDZ domains); when associated with
A-291. {ECO:0000269|PubMed:15663004}.
MUTAGEN 294 294 F->A: No loss of interaction with PTPN13
(via PDZ domains); when associated with
A-295. {ECO:0000269|PubMed:15663004}.
MUTAGEN 295 295 F->A: No loss of interaction with PTPN13
(via PDZ domains); when associated with
A-294. {ECO:0000269|PubMed:15663004}.
MUTAGEN 299 299 R->A: No loss of interaction with PTPN13
(via PDZ domains); when associated with
A-301. {ECO:0000269|PubMed:15663004}.
MUTAGEN 301 301 Y->A: No loss of interaction with PTPN13
(via PDZ domains); when associated with
A-299. {ECO:0000269|PubMed:15663004}.
MUTAGEN 326 330 Missing: Interaction with TRIP6.
{ECO:0000269|PubMed:10826496}.
CONFLICT 25 25 A -> L (in Ref. 1; CAA69648).
{ECO:0000305}.
CONFLICT 91 91 A -> S (in Ref. 1; CAA69648).
{ECO:0000305}.
CONFLICT 107 107 S -> F (in Ref. 1; CAA69648).
{ECO:0000305}.
SEQUENCE 330 AA; 35556 MW; BB3421541BFC086E CRC64;
MTHSVTLRGP SPWGFRLVGG RDFSAPLTIS RVHAGSKAAL AALCPGDLIQ AINGESTELM
THLEAQNRIK GCHDHLTLSV SRPENKNWPS APDDKAQAHR IHIDPESQDC SPATSRRSSV
SGISLEDNRS GLGSPYGQPP RLPVPHNGSS NEATLPAQMS ALHVSPPTSA DTARVLPRNR
DCRVDLGSEV YRMLREPAEP TASEPKQSGS FRYLQGMLEA GEGGDRPGSG GPRNLKPAAS
KLGAPLSGLQ GLPECTRCGH GIVGTIVKAR DKLYHPECFM CSDCGLNLKQ RGYFFLDERL
YCENHAKARV KPPEGYDVVA VYPNAKVELV


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