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Protein

PDZ and LIM domain protein 7

Gene

Pdlim7

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: -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

Keywordsi

Molecular functionDevelopmental protein
Biological processDifferentiation, Osteogenesis
LigandMetal-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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 13

Organism-specific databases

MGIiMGI:1914649 Pdlim7

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

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 Expressed in 232 organ(s), highest expression level in ear vesicle
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, 4 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

Keywords - Domaini

LIM domain, Repeat

Phylogenomic databases

eggNOGiKOG1703 Eukaryota
ENOG410XRD4 LUCA
GeneTreeiENSGT00760000118910
HOGENOMiHOG000220936
HOVERGENiHBG051478
InParanoidiQ3TJD7
OMAiCHDNRYA
OrthoDBiEOG091G06JR
PhylomeDBiQ3TJD7
TreeFamiTF106408

Family and domain databases

InterProiView protein in InterPro
IPR001478 PDZ
IPR036034 PDZ_sf
IPR001781 Znf_LIM
PfamiView protein in Pfam
PF00412 LIM, 3 hits
PF00595 PDZ, 1 hit
SMARTiView protein in SMART
SM00132 LIM, 3 hits
SM00228 PDZ, 1 hit
SUPFAMiSSF50156 SSF50156, 1 hit
PROSITEiView protein in PROSITE
PS00478 LIM_DOMAIN_1, 2 hits
PS50023 LIM_DOMAIN_2, 3 hits
PS50106 PDZ, 1 hit

Sequences (3+)i

Sequence statusi: Complete.

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

This entry has 3 described isoforms and 4 potential isoforms that are computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There are 4 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
B8JJB2B8JJB2_MOUSE
PDZ and LIM domain protein 7
Pdlim7
124Annotation score:
Q8BVJ7Q8BVJ7_MOUSE
PDZ and LIM domain 7, isoform CRA_f
Pdlim7 mCG_3180
222Annotation score:
B8JJB1B8JJB1_MOUSE
PDZ and LIM domain protein 7
Pdlim7
58Annotation score:
B8JJB3B8JJB3_MOUSE
PDZ and LIM domain 7, isoform CRA_g
Pdlim7 mCG_3180
219Annotation score:

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

Similar proteinsi

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, 4 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
OMAiCHDNRYA
OrthoDBiEOG091G06JR
PhylomeDBiQ3TJD7
TreeFamiTF106408

Enzyme and pathway databases

ReactomeiR-MMU-8853659 RET signaling

Miscellaneous databases

ChiTaRSiPdlim7 mouse
PROiPR:Q3TJD7
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000021493 Expressed in 232 organ(s), highest expression level in ear vesicle
CleanExiMM_PDLIM7
ExpressionAtlasiQ3TJD7 baseline and differential
GenevisibleiQ3TJD7 MM

Family and domain databases

InterProiView protein in InterPro
IPR001478 PDZ
IPR036034 PDZ_sf
IPR001781 Znf_LIM
PfamiView protein in Pfam
PF00412 LIM, 3 hits
PF00595 PDZ, 1 hit
SMARTiView protein in SMART
SM00132 LIM, 3 hits
SM00228 PDZ, 1 hit
SUPFAMiSSF50156 SSF50156, 1 hit
PROSITEiView protein in PROSITE
PS00478 LIM_DOMAIN_1, 2 hits
PS50023 LIM_DOMAIN_2, 3 hits
PS50106 PDZ, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiPDLI7_MOUSE
AccessioniPrimary (citable) accession number: Q3TJD7
Secondary accession number(s): Q80ZY6
, Q810S3, Q8C1S4, Q9CRA1
Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 6, 2005
Last sequence update: October 11, 2005
Last modified: November 7, 2018
This is version 114 of the entry and version 1 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
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Main funding by: National Institutes of Health

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