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Protein

PDZ and LIM domain protein 7

Gene

Pdlim7

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

May function as a scaffold on which the coordinated assembly of proteins can occur. May play a role as an adapter that, via its PDZ domain, localizes LIM-binding proteins to actin filaments of both skeletal muscle and nonmuscle tissues. Involved in both of the two fundamental mechanisms of bone formation, direct bone formation (e.g. embryonic flat bones mandible and cranium), and endochondral bone formation (e.g. embryonic long bone development). Plays a role during fracture repair. Involved in BMP6 signaling pathway (By similarity).By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Developmental protein

Keywords - Biological processi

Differentiation, Osteogenesis

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-MMU-8853659. RET signaling.

Names & Taxonomyi

Protein namesi
Recommended name:
PDZ and LIM domain protein 7
Alternative name(s):
LIM mineralization protein
Short name:
LMP
Protein enigma
Gene namesi
Name:Pdlim7
Synonyms:Enigma
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 13

Organism-specific databases

MGIiMGI:1914649. Pdlim7.

Subcellular locationi

  • Cytoplasm By similarity
  • Cytoplasmcytoskeleton By similarity

  • Note: Colocalizes with RET to the cell periphery and in some cytoskeletal components. Colocalizes with TPM2 near the Z line in muscle. Colocalizes with TBX4 and TBX5 to actin filaments (By similarity).By similarity

GO - Cellular componenti

  • actin cytoskeleton Source: MGI
  • cell-cell junction Source: MGI
  • cytoplasm Source: MGI
  • focal adhesion Source: MGI
  • nucleus Source: MGI
  • ruffle Source: MGI
  • stress fiber Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Cytoskeleton

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000758821 – 457PDZ and LIM domain protein 7Add BLAST457

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei78PhosphoserineBy similarity1
Modified residuei96PhosphothreonineBy similarity1
Modified residuei103Asymmetric dimethylarginineBy similarity1
Modified residuei111PhosphoserineBy similarity1
Modified residuei247PhosphoserineCombined sources1

Keywords - PTMi

Methylation, Phosphoprotein

Proteomic databases

EPDiQ3TJD7.
MaxQBiQ3TJD7.
PaxDbiQ3TJD7.
PeptideAtlasiQ3TJD7.
PRIDEiQ3TJD7.

PTM databases

iPTMnetiQ3TJD7.
PhosphoSitePlusiQ3TJD7.

Expressioni

Developmental stagei

At E13.5 expressed in epaxial, intercostal, and other skeletal muscles at the brachial level, including the latissimus dorsi muscle. Expressed in the intrinsic and extrinsic muscle mass of the tongue. At E15 expressed in mesenchymal tissue surrounding the cartilaginous anlage of immature bones, and in the future joint spaces. As endochondral ossification progresses, and the hypertrophic cartilage zone is replaced by mineralized bone, expression appears in the mineralizing portion of the bone. Expressed in mesoderm derived bones of the skull base and neural crest-derived endochondral bones such as the proximal mandible.2 Publications

Gene expression databases

BgeeiENSMUSG00000021493.
CleanExiMM_PDLIM7.
ExpressionAtlasiQ3TJD7. baseline and differential.
GenevisibleiQ3TJD7. MM.

Interactioni

Subunit structurei

Specifically binds via its LIM zinc-binding 3 domain (LIM 3) domain to endocytic codes of INSR, but not with those of IGF1R, LDLR, TFRC, or EGFR. Interacts with various PKC isoforms through the LIM zinc-binding domains. Binds to RET in a phosphorylation-independent manner via its LIM zinc-binding domain 2 (LIM 2). Probably part of a complex with SHC and the RET dimer. Interacts with TPM2, TBX4 and TBX5 (By similarity).By similarity

Protein-protein interaction databases

BioGridi212162. 3 interactors.
STRINGi10090.ENSMUSP00000047173.

Structurei

3D structure databases

ProteinModelPortaliQ3TJD7.
SMRiQ3TJD7.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini1 – 85PDZPROSITE-ProRule annotationAdd BLAST85
Domaini280 – 338LIM zinc-binding 1PROSITE-ProRule annotationAdd BLAST59
Domaini339 – 398LIM zinc-binding 2PROSITE-ProRule annotationAdd BLAST60
Domaini399 – 457LIM zinc-binding 3PROSITE-ProRule annotationAdd BLAST59

Domaini

The LIM zinc-binding 2 domain (LIM 2) interacts with TBX4.By similarity
The LIM zinc-binding 3 domain (LIM 3) provides the structural basis for recognition of tyrosine-containing tight turn structures. This domain is necessary and sufficient for interaction with TBX5 (By similarity).By similarity
Anchored to cell periphery via its N-terminal PDZ domain.By similarity

Sequence similaritiesi

Contains 3 LIM zinc-binding domains.PROSITE-ProRule annotation
Contains 1 PDZ (DHR) domain.PROSITE-ProRule annotation

Keywords - Domaini

LIM domain, Repeat

Phylogenomic databases

eggNOGiKOG1703. Eukaryota.
ENOG410XRD4. LUCA.
GeneTreeiENSGT00760000118910.
HOGENOMiHOG000220936.
HOVERGENiHBG051478.
InParanoidiQ3TJD7.
OMAiRPLCKSH.
OrthoDBiEOG091G06JR.
PhylomeDBiQ3TJD7.
TreeFamiTF106408.

Family and domain databases

Gene3Di2.10.110.10. 3 hits.
2.30.42.10. 1 hit.
InterProiIPR001478. PDZ.
IPR001781. Znf_LIM.
[Graphical view]
PfamiPF00412. LIM. 3 hits.
PF00595. PDZ. 1 hit.
[Graphical view]
SMARTiSM00132. LIM. 3 hits.
SM00228. PDZ. 1 hit.
[Graphical view]
SUPFAMiSSF50156. SSF50156. 1 hit.
PROSITEiPS00478. LIM_DOMAIN_1. 2 hits.
PS50023. LIM_DOMAIN_2. 3 hits.
PS50106. PDZ. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q3TJD7-1) [UniParc]FASTAAdd to basket
Also known as: LMP-1

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
MDSFKVVLEG PAPWGFRLQG GKDFNVPLSI SRLTPGGKAA QAGVAVGDWV
60 70 80 90 100
LNIDGENAGS LTHIEAQNKI RACGERLSLG LSRAQPVQSK PQKALTPPAD
110 120 130 140 150
PPRYTFAPSA SLNKTARPFG APPPTDSTLR QNGQLLRQPV PDASKQRLME
160 170 180 190 200
DTEDWRPRPG TGQSRSFRIL AHLTGTEFMQ DPDEEFMKKS SQVPRTEAPA
210 220 230 240 250
PASTIPQESW PGPTTPSPTS RPPWAVDPAF AERYAPDKTS TVLTRHSQPA
260 270 280 290 300
TPTPLQNRTS IVQAAAGGGT GGGSNNGKTP VCHQCHKIIR GRYLVALGHA
310 320 330 340 350
YHPEEFVCSQ CGKVLEEGGF FEEKGAIFCP SCYDVRYAPN CAKCKKKITG
360 370 380 390 400
EIMHALKMTW HVHCFTCAAC KTPIRNRAFY MEEGAPYCER DYEKMFGTKC
410 420 430 440 450
RGCDFKIDAG DRFLEALGFS WHDTCFVCAI CQINLEGKTF YSKKDKPLCK

SHAFSHV
Length:457
Mass (Da):50,119
Last modified:October 11, 2005 - v1
Checksum:i8556AEBF1077D7F7
GO
Isoform 2 (identifier: Q3TJD7-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     94-133: ALTPPADPPRYTFAPSASLNKTARPFGAPPPTDSTLRQNG → VQTSDK
     191-222: SQVPRTEAPAPASTIPQESWPGPTTPSPTSRP → REKYVLELQSPRYTRLRDWHHQRSAHVLNVQS
     223-457: Missing.

Show »
Length:188
Mass (Da):21,155
Checksum:i0AF16D8F9CBAADA0
GO
Isoform 3 (identifier: Q3TJD7-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     134-153: QLLRQPVPDASKQRLMEDTE → CRPLTNSCSDSRSPMPASSG
     154-457: Missing.

Show »
Length:153
Mass (Da):16,036
Checksum:i07F1A40AC2B568BE
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti85Q → P in BAB22725 (PubMed:16141072).Curated1
Sequence conflicti151D → G in AAH49565 (PubMed:15489334).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_01651794 – 133ALTPP…LRQNG → VQTSDK in isoform 2. 2 PublicationsAdd BLAST40
Alternative sequenceiVSP_016518134 – 153QLLRQ…MEDTE → CRPLTNSCSDSRSPMPASSG in isoform 3. 1 PublicationAdd BLAST20
Alternative sequenceiVSP_016519154 – 457Missing in isoform 3. 1 PublicationAdd BLAST304
Alternative sequenceiVSP_016520191 – 222SQVPR…PTSRP → REKYVLELQSPRYTRLRDWH HQRSAHVLNVQS in isoform 2. 2 PublicationsAdd BLAST32
Alternative sequenceiVSP_016521223 – 457Missing in isoform 2. 2 PublicationsAdd BLAST235

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK003338 mRNA. Translation: BAB22725.1.
AK010141 mRNA. Translation: BAB26726.1.
AK003019 mRNA. Translation: BAC25017.1.
AK167476 mRNA. Translation: BAE39558.1.
BC045528 mRNA. Translation: AAH45528.1.
BC049565 mRNA. Translation: AAH49565.1.
CCDSiCCDS26547.1. [Q3TJD7-2]
CCDS49275.1. [Q3TJD7-1]
RefSeqiNP_001107560.1. NM_001114088.2. [Q3TJD7-1]
NP_080407.3. NM_026131.4. [Q3TJD7-2]
UniGeneiMm.275648.
Mm.288737.

Genome annotation databases

EnsembliENSMUST00000046246; ENSMUSP00000047173; ENSMUSG00000021493. [Q3TJD7-1]
ENSMUST00000069929; ENSMUSP00000064219; ENSMUSG00000021493. [Q3TJD7-2]
ENSMUST00000155098; ENSMUSP00000120465; ENSMUSG00000021493. [Q3TJD7-1]
GeneIDi67399.
KEGGimmu:67399.
UCSCiuc007qrg.3. mouse. [Q3TJD7-1]
uc007qri.3. mouse. [Q3TJD7-2]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK003338 mRNA. Translation: BAB22725.1.
AK010141 mRNA. Translation: BAB26726.1.
AK003019 mRNA. Translation: BAC25017.1.
AK167476 mRNA. Translation: BAE39558.1.
BC045528 mRNA. Translation: AAH45528.1.
BC049565 mRNA. Translation: AAH49565.1.
CCDSiCCDS26547.1. [Q3TJD7-2]
CCDS49275.1. [Q3TJD7-1]
RefSeqiNP_001107560.1. NM_001114088.2. [Q3TJD7-1]
NP_080407.3. NM_026131.4. [Q3TJD7-2]
UniGeneiMm.275648.
Mm.288737.

3D structure databases

ProteinModelPortaliQ3TJD7.
SMRiQ3TJD7.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi212162. 3 interactors.
STRINGi10090.ENSMUSP00000047173.

PTM databases

iPTMnetiQ3TJD7.
PhosphoSitePlusiQ3TJD7.

Proteomic databases

EPDiQ3TJD7.
MaxQBiQ3TJD7.
PaxDbiQ3TJD7.
PeptideAtlasiQ3TJD7.
PRIDEiQ3TJD7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000046246; ENSMUSP00000047173; ENSMUSG00000021493. [Q3TJD7-1]
ENSMUST00000069929; ENSMUSP00000064219; ENSMUSG00000021493. [Q3TJD7-2]
ENSMUST00000155098; ENSMUSP00000120465; ENSMUSG00000021493. [Q3TJD7-1]
GeneIDi67399.
KEGGimmu:67399.
UCSCiuc007qrg.3. mouse. [Q3TJD7-1]
uc007qri.3. mouse. [Q3TJD7-2]

Organism-specific databases

CTDi9260.
MGIiMGI:1914649. Pdlim7.

Phylogenomic databases

eggNOGiKOG1703. Eukaryota.
ENOG410XRD4. LUCA.
GeneTreeiENSGT00760000118910.
HOGENOMiHOG000220936.
HOVERGENiHBG051478.
InParanoidiQ3TJD7.
OMAiRPLCKSH.
OrthoDBiEOG091G06JR.
PhylomeDBiQ3TJD7.
TreeFamiTF106408.

Enzyme and pathway databases

ReactomeiR-MMU-8853659. RET signaling.

Miscellaneous databases

ChiTaRSiPdlim7. mouse.
PROiQ3TJD7.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000021493.
CleanExiMM_PDLIM7.
ExpressionAtlasiQ3TJD7. baseline and differential.
GenevisibleiQ3TJD7. MM.

Family and domain databases

Gene3Di2.10.110.10. 3 hits.
2.30.42.10. 1 hit.
InterProiIPR001478. PDZ.
IPR001781. Znf_LIM.
[Graphical view]
PfamiPF00412. LIM. 3 hits.
PF00595. PDZ. 1 hit.
[Graphical view]
SMARTiSM00132. LIM. 3 hits.
SM00228. PDZ. 1 hit.
[Graphical view]
SUPFAMiSSF50156. SSF50156. 1 hit.
PROSITEiPS00478. LIM_DOMAIN_1. 2 hits.
PS50023. LIM_DOMAIN_2. 3 hits.
PS50106. PDZ. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPDLI7_MOUSE
AccessioniPrimary (citable) accession number: Q3TJD7
Secondary accession number(s): Q80ZY6
, Q810S3, Q8C1S4, Q9CRA1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 6, 2005
Last sequence update: October 11, 2005
Last modified: November 2, 2016
This is version 104 of the entry and version 1 of the sequence. [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
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.