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Protein

PDZ and LIM domain protein 4

Gene

Pdlim4

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

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).By similarity

GO - Molecular functioni

GO - Biological processi

Keywordsi

LigandMetal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
PDZ and LIM domain protein 4
Alternative name(s):
LIM protein RIL
Reversion-induced LIM protein
Gene namesi
Name:Pdlim4
Synonyms:Ril
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 11

Organism-specific databases

MGIiMGI:1353470 Pdlim4

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 projection, Cytoplasm, Cytoskeleton, Endosome, Membrane, Nucleus, Synapse, Synaptosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi261G → A: No loss of interaction with PTPN13 (via PDZ domains); when associated with A-263. 1 Publication1
Mutagenesisi263V → A: No loss of interaction with PTPN13 (via PDZ domains); when associated with A-261. 1 Publication1
Mutagenesisi264G → A: No loss of interaction with PTPN13 (via PDZ domains); when associated with A-266. 1 Publication1
Mutagenesisi265T → A: No loss of interaction with PTPN13 (via PDZ domains); when associated with A-267. 1 Publication1
Mutagenesisi266I → A: No loss of interaction with PTPN13 (via PDZ domains); when associated with A-264. 1 Publication1
Mutagenesisi267V → A: No loss of interaction with PTPN13 (via PDZ domains); when associated with A-265. 1 Publication1
Mutagenesisi272K → A: No loss of interaction with PTPN13 (via PDZ domains); when associated with A-274. 1 Publication1
Mutagenesisi274Y → A: No loss of interaction with PTPN13 (via PDZ domains); when associated with A-272. 1 Publication1
Mutagenesisi276P → A: No loss of interaction with PTPN13 (via PDZ domains); when associated with A-277. 1 Publication1
Mutagenesisi277E → A: No loss of interaction with PTPN13 (via PDZ domains); when associated with A-276. 1 Publication1
Mutagenesisi280M → A: No loss of interaction with PTPN13 (via PDZ domains). 1 Publication1
Mutagenesisi286L → A: No loss of interaction with PTPN13 (via PDZ domains); when associated with A-288. 1 Publication1
Mutagenesisi287N → A: No loss of interaction with PTPN13 (via PDZ domains). 1 Publication1
Mutagenesisi288L → A: No loss of interaction with PTPN13 (via PDZ domains); when associated with A-286. 1 Publication1
Mutagenesisi291R → A: No loss of interaction with PTPN13 (via PDZ domains); when associated with A-292. 1 Publication1
Mutagenesisi292G → A: No loss of interaction with PTPN13 (via PDZ domains); when associated with A-291. 1 Publication1
Mutagenesisi294F → A: No loss of interaction with PTPN13 (via PDZ domains); when associated with A-295. 1 Publication1
Mutagenesisi295F → A: No loss of interaction with PTPN13 (via PDZ domains); when associated with A-294. 1 Publication1
Mutagenesisi299R → A: No loss of interaction with PTPN13 (via PDZ domains); when associated with A-301. 1 Publication1
Mutagenesisi301Y → A: No loss of interaction with PTPN13 (via PDZ domains); when associated with A-299. 1 Publication1
Mutagenesisi326 – 330Missing : Interaction with TRIP6. 1 Publication5

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000758741 – 330PDZ and LIM domain protein 4Add BLAST330

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei107PhosphoserineCombined sources1
Modified residuei111PhosphoserineCombined sources1
Modified residuei115PhosphoserineCombined sources1
Modified residuei118PhosphoserineCombined sources1
Modified residuei119PhosphoserineCombined sources1
Modified residuei124PhosphoserineCombined sources1
Modified residuei134PhosphoserineBy similarity1

Post-translational modificationi

Phosphorylated on tyrosine residue(s). Can be dephosphorylated by PTPN13.1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP70271
PaxDbiP70271
PeptideAtlasiP70271
PRIDEiP70271

PTM databases

iPTMnetiP70271
PhosphoSitePlusiP70271

Expressioni

Tissue specificityi

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.1 Publication

Gene expression databases

BgeeiENSMUSG00000020388 Expressed in 254 organ(s), highest expression level in urinary bladder
CleanExiMM_PDLIM4
ExpressionAtlasiP70271 baseline and differential
GenevisibleiP70271 MM

Interactioni

Subunit structurei

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).By similarity3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
Trip6Q9Z1Y42EBI-7288319,EBI-643879

GO - Molecular functioni

Protein-protein interaction databases

BioGridi205965, 4 interactors
IntActiP70271, 3 interactors
MINTiP70271
STRINGi10090.ENSMUSP00000018755

Structurei

3D structure databases

ProteinModelPortaliP70271
SMRiP70271
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini1 – 84PDZPROSITE-ProRule annotationAdd BLAST84
Domaini255 – 305LIM zinc-bindingPROSITE-ProRule annotationAdd BLAST51

Keywords - Domaini

LIM domain

Phylogenomic databases

eggNOGiKOG1703 Eukaryota
ENOG410XRD4 LUCA
GeneTreeiENSGT00590000082980
HOGENOMiHOG000290704
HOVERGENiHBG061371
InParanoidiP70271
OMAiQAYRINI
OrthoDBiEOG091G0A6C
TreeFamiTF106408

Family and domain databases

InterProiView protein in InterPro
IPR031847 DUF4749
IPR001478 PDZ
IPR036034 PDZ_sf
IPR001781 Znf_LIM
PfamiView protein in Pfam
PF15936 DUF4749, 1 hit
PF00412 LIM, 1 hit
PF00595 PDZ, 1 hit
SMARTiView protein in SMART
SM00132 LIM, 1 hit
SM00228 PDZ, 1 hit
SUPFAMiSSF50156 SSF50156, 1 hit
PROSITEiView protein in PROSITE
PS00478 LIM_DOMAIN_1, 1 hit
PS50023 LIM_DOMAIN_2, 1 hit
PS50106 PDZ, 1 hit

Sequence (1+)i

Sequence statusi: Complete.

This entry has 1 described isoform and 2 potential isoforms that are computationally mapped.Show allAlign All

P70271-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MTHSVTLRGP SPWGFRLVGG RDFSAPLTIS RVHAGSKAAL AALCPGDLIQ
60 70 80 90 100
AINGESTELM THLEAQNRIK GCHDHLTLSV SRPENKNWPS APDDKAQAHR
110 120 130 140 150
IHIDPESQDC SPATSRRSSV SGISLEDNRS GLGSPYGQPP RLPVPHNGSS
160 170 180 190 200
NEATLPAQMS ALHVSPPTSA DTARVLPRNR DCRVDLGSEV YRMLREPAEP
210 220 230 240 250
TASEPKQSGS FRYLQGMLEA GEGGDRPGSG GPRNLKPAAS KLGAPLSGLQ
260 270 280 290 300
GLPECTRCGH GIVGTIVKAR DKLYHPECFM CSDCGLNLKQ RGYFFLDERL
310 320 330
YCENHAKARV KPPEGYDVVA VYPNAKVELV
Length:330
Mass (Da):35,556
Last modified:July 27, 2011 - v3
Checksum:iBB3421541BFC086E
GO

Computationally mapped potential isoform sequencesi

There are 2 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
Q5SWV3Q5SWV3_MOUSE
PDZ and LIM domain protein 4
Pdlim4
246Annotation score:
A8Y5C3A8Y5C3_MOUSE
PDZ and LIM domain protein 4
Pdlim4
121Annotation score:

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti25A → L in CAA69648 (PubMed:9487134).Curated1
Sequence conflicti91A → S in CAA69648 (PubMed:9487134).Curated1
Sequence conflicti107S → F in CAA69648 (PubMed:9487134).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y08361 mRNA Translation: CAA69648.1
AL596444 Genomic DNA Translation: CAI25321.1
CH466575 Genomic DNA Translation: EDL33550.1
BC030068 mRNA Translation: AAH30068.1
CCDSiCCDS24690.1
RefSeqiNP_062290.2, NM_019417.3
UniGeneiMm.21830

Genome annotation databases

EnsembliENSMUST00000018755; ENSMUSP00000018755; ENSMUSG00000020388
GeneIDi30794
KEGGimmu:30794
UCSCiuc007ixf.2 mouse

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y08361 mRNA Translation: CAA69648.1
AL596444 Genomic DNA Translation: CAI25321.1
CH466575 Genomic DNA Translation: EDL33550.1
BC030068 mRNA Translation: AAH30068.1
CCDSiCCDS24690.1
RefSeqiNP_062290.2, NM_019417.3
UniGeneiMm.21830

3D structure databases

ProteinModelPortaliP70271
SMRiP70271
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi205965, 4 interactors
IntActiP70271, 3 interactors
MINTiP70271
STRINGi10090.ENSMUSP00000018755

PTM databases

iPTMnetiP70271
PhosphoSitePlusiP70271

Proteomic databases

MaxQBiP70271
PaxDbiP70271
PeptideAtlasiP70271
PRIDEiP70271

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000018755; ENSMUSP00000018755; ENSMUSG00000020388
GeneIDi30794
KEGGimmu:30794
UCSCiuc007ixf.2 mouse

Organism-specific databases

CTDi8572
MGIiMGI:1353470 Pdlim4

Phylogenomic databases

eggNOGiKOG1703 Eukaryota
ENOG410XRD4 LUCA
GeneTreeiENSGT00590000082980
HOGENOMiHOG000290704
HOVERGENiHBG061371
InParanoidiP70271
OMAiQAYRINI
OrthoDBiEOG091G0A6C
TreeFamiTF106408

Miscellaneous databases

PROiPR:P70271
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000020388 Expressed in 254 organ(s), highest expression level in urinary bladder
CleanExiMM_PDLIM4
ExpressionAtlasiP70271 baseline and differential
GenevisibleiP70271 MM

Family and domain databases

InterProiView protein in InterPro
IPR031847 DUF4749
IPR001478 PDZ
IPR036034 PDZ_sf
IPR001781 Znf_LIM
PfamiView protein in Pfam
PF15936 DUF4749, 1 hit
PF00412 LIM, 1 hit
PF00595 PDZ, 1 hit
SMARTiView protein in SMART
SM00132 LIM, 1 hit
SM00228 PDZ, 1 hit
SUPFAMiSSF50156 SSF50156, 1 hit
PROSITEiView protein in PROSITE
PS00478 LIM_DOMAIN_1, 1 hit
PS50023 LIM_DOMAIN_2, 1 hit
PS50106 PDZ, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiPDLI4_MOUSE
AccessioniPrimary (citable) accession number: P70271
Secondary accession number(s): Q5SWV2, Q8K0W4
Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 15, 2004
Last sequence update: July 27, 2011
Last modified: November 7, 2018
This is version 138 of the entry and version 3 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

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