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Protein

PDZ and LIM domain protein 7

Gene

Pdlim7

Organism
Rattus norvegicus (Rat)
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.1 Publication

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Developmental protein

Keywords - Biological processi

Differentiation, Osteogenesis

Keywords - Ligandi

Metal-binding, Zinc

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, Lim1
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 17

Organism-specific databases

RGDi628769. Pdlim7.

Subcellular locationi

  • Cytoplasm 1 Publication
  • 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

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Cytoskeleton

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 457457PDZ and LIM domain protein 7PRO_0000075883Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei96 – 961PhosphothreonineCombined sources
Modified residuei247 – 2471PhosphoserineBy similarity

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiQ9Z1Z9.
PRIDEiQ9Z1Z9.

PTM databases

PhosphoSiteiQ9Z1Z9.

Expressioni

Tissue specificityi

Expressed in kidney, heart, brain, lung, and skeletal muscle. Overexpression results in the synthesis of an unidentified soluble factor which acts on cells in the osteoblast lineage causing them to differentiate and secrete BMP-2.1 Publication

Developmental stagei

At E14 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.1 Publication

Inductioni

Induced by glucocorticoid or BMP6.

Gene expression databases

GenevisibleiQ9Z1Z9. RN.

Interactioni

Subunit structurei

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 2 domain (LIM 2). Probably part of a complex with SHC and the RET dimer. Interacts with TPM2, TBX4 and TBX5 (By similarity). Interacts (via LIM domains) with SIPA1L1.By similarity1 Publication

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000018899.

Structurei

3D structure databases

ProteinModelPortaliQ9Z1Z9.
SMRiQ9Z1Z9. Positions 1-84.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 8585PDZPROSITE-ProRule annotationAdd
BLAST
Domaini280 – 33859LIM zinc-binding 1PROSITE-ProRule annotationAdd
BLAST
Domaini339 – 39860LIM zinc-binding 2PROSITE-ProRule annotationAdd
BLAST
Domaini399 – 45759LIM zinc-binding 3PROSITE-ProRule annotationAdd
BLAST

Domaini

The LIM zinc-binding 2 (LIM 2) interacts with TBX4.By similarity
The LIM zinc-binding 3 (LIM 3) domain 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.
InParanoidiQ9Z1Z9.
OMAiRPLCKSH.
OrthoDBiEOG7HXCQB.
PhylomeDBiQ9Z1Z9.
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]

Sequencei

Sequence statusi: Complete.

Q9Z1Z9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDSFKVVLEG PAPWGFRLQG GKDFNVPLSI SRLTPGGKAA QAGVAVGDWV
60 70 80 90 100
LSIDGENAGS LTHIEAQNKI RACGERLSLG LSRAQPAQSK PQKALTPPAD
110 120 130 140 150
PPRYTFAPSA SLNKTARPFG APPPTDSALS QNGQLLRQLV PDASKQRLME
160 170 180 190 200
NTEDWRPRPG 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 SCYDVRYAPS CAKCKKKITG
360 370 380 390 400
EIMHALKMTW HVPCFTCAAC KTPIRNRAFY MEEGAPYCER DYEKMFGTKC
410 420 430 440 450
RGCDFKIDAG DRFLEALGFS WHDTCFVCAI CQINLEGKTF YSKKDKPLCK

SHAFSHV
Length:457
Mass (Da):49,913
Last modified:May 1, 1999 - v1
Checksum:iB4EE3142D5A90D72
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF095585 mRNA. Translation: AAD13197.1.
BC078693 mRNA. Translation: AAH78693.1.
RefSeqiNP_775148.1. NM_173125.1.
UniGeneiRn.7274.

Genome annotation databases

EnsembliENSRNOT00000018899; ENSRNOP00000018899; ENSRNOG00000013653.
GeneIDi286908.
KEGGirno:286908.
UCSCiRGD:628769. rat.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF095585 mRNA. Translation: AAD13197.1.
BC078693 mRNA. Translation: AAH78693.1.
RefSeqiNP_775148.1. NM_173125.1.
UniGeneiRn.7274.

3D structure databases

ProteinModelPortaliQ9Z1Z9.
SMRiQ9Z1Z9. Positions 1-84.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10116.ENSRNOP00000018899.

PTM databases

PhosphoSiteiQ9Z1Z9.

Proteomic databases

PaxDbiQ9Z1Z9.
PRIDEiQ9Z1Z9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSRNOT00000018899; ENSRNOP00000018899; ENSRNOG00000013653.
GeneIDi286908.
KEGGirno:286908.
UCSCiRGD:628769. rat.

Organism-specific databases

CTDi9260.
RGDi628769. Pdlim7.

Phylogenomic databases

eggNOGiKOG1703. Eukaryota.
ENOG410XRD4. LUCA.
GeneTreeiENSGT00760000118910.
HOGENOMiHOG000220936.
HOVERGENiHBG051478.
InParanoidiQ9Z1Z9.
OMAiRPLCKSH.
OrthoDBiEOG7HXCQB.
PhylomeDBiQ9Z1Z9.
TreeFamiTF106408.

Miscellaneous databases

NextBioi625011.
PROiQ9Z1Z9.

Gene expression databases

GenevisibleiQ9Z1Z9. RN.

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...

Publicationsi

« Hide 'large scale' publications
  1. "LMP-1, a LIM-domain protein, mediates BMP-6 effects on bone formation."
    Boden S.D., Liu Y., Hair G.A., Helms J.A., Hu D., Racine M., Nanes M.S., Titus L.
    Endocrinology 139:5125-5134(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION IN BONE FORMATION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.
    Tissue: Bone.
  2. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Lung.
  3. "Postsynaptic PDLIM5/Enigma homolog binds SPAR and causes dendritic spine shrinkage."
    Herrick S., Evers D.M., Lee J.Y., Udagawa N., Pak D.T.
    Mol. Cell. Neurosci. 43:188-200(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH SIPA1L1, SUBCELLULAR LOCATION.
  4. "Quantitative maps of protein phosphorylation sites across 14 different rat organs and tissues."
    Lundby A., Secher A., Lage K., Nordsborg N.B., Dmytriyev A., Lundby C., Olsen J.V.
    Nat. Commun. 3:876-876(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-96, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiPDLI7_RAT
AccessioniPrimary (citable) accession number: Q9Z1Z9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 6, 2005
Last sequence update: May 1, 1999
Last modified: May 11, 2016
This is version 111 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. 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.