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Protein

PDZ and LIM domain protein 7

Gene

PDLIM7

Organism
Homo sapiens (Human)
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 similarity2 Publications

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-HSA-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
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 5

Organism-specific databases

HGNCiHGNC:22958. 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: HPA
  • cell-cell junction Source: BHF-UCL
  • cytoplasm Source: UniProtKB-SubCell
  • focal adhesion Source: HPA
  • nucleus Source: HPA
  • ruffle Source: Ensembl
  • stress fiber Source: Ensembl
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Cytoskeleton

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi15 – 16GF → AA: Loss of binding to TPM2. 1 Publication2
Mutagenesisi63H → A: Loss of binding to TPM2. 1 Publication1

Organism-specific databases

DisGeNETi9260.
OpenTargetsiENSG00000196923.
PharmGKBiPA128394546.

Polymorphism and mutation databases

BioMutaiPDLIM7.
DMDMi74752914.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000758811 – 457PDZ and LIM domain protein 7Add BLAST457

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei78PhosphoserineCombined sources1
Modified residuei103Asymmetric dimethylarginineCombined sources1
Modified residuei111PhosphoserineCombined sources1
Modified residuei247PhosphoserineCombined sources1

Keywords - PTMi

Methylation, Phosphoprotein

Proteomic databases

EPDiQ9NR12.
MaxQBiQ9NR12.
PaxDbiQ9NR12.
PeptideAtlasiQ9NR12.
PRIDEiQ9NR12.

PTM databases

iPTMnetiQ9NR12.
PhosphoSitePlusiQ9NR12.
SwissPalmiQ9NR12.

Expressioni

Tissue specificityi

Isoform 1 and isoform 2 are expressed ubiquitously, however, isoform 2 predominates in skeletal muscle, isoform 1 is more abundant in lung, spleen, leukocytes and fetal liver.1 Publication

Gene expression databases

BgeeiENSG00000196923.
CleanExiHS_PDLIM7.
ExpressionAtlasiQ9NR12. baseline and differential.
GenevisibleiQ9NR12. HS.

Organism-specific databases

HPAiHPA018794.
HPA048815.

Interactioni

Subunit structurei

Binds via its LIM zinc-binding 3 domain (LIM 3) 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. Interacts with TBX4 and TBX5 (By similarity).By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
ENKD1Q9H0I23EBI-350517,EBI-744099
GEMP550403EBI-350517,EBI-744104
Hoxa1P090223EBI-350517,EBI-3957603From a different organism.
IQGAP1A4QPB03EBI-350517,EBI-9512851
PHF1O431893EBI-350517,EBI-530034
TSG101Q998165EBI-350517,EBI-346882
UBQLN4Q9NRR52EBI-350517,EBI-711226
WWP2O003084EBI-350517,EBI-743923

Protein-protein interaction databases

BioGridi114682. 135 interactors.
IntActiQ9NR12. 121 interactors.
MINTiMINT-94304.
STRINGi9606.ENSP00000348099.

Structurei

Secondary structure

1457
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi1 – 12Combined sources12
Beta strandi16 – 21Combined sources6
Helixi22 – 24Combined sources3
Beta strandi26 – 33Combined sources8
Helixi38 – 41Combined sources4
Beta strandi49 – 53Combined sources5
Helixi58 – 60Combined sources3
Helixi63 – 71Combined sources9
Beta strandi76 – 84Combined sources9

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2Q3GX-ray1.11A/B1-84[»]
ProteinModelPortaliQ9NR12.
SMRiQ9NR12.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9NR12.

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 (LIM 2) domain 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.

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.
HOVERGENiHBG051478.
InParanoidiQ9NR12.
OMAiRPLCKSH.
OrthoDBiEOG091G06JR.
PhylomeDBiQ9NR12.
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 (6)i

Sequence statusi: Complete.

This entry describes 6 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9NR12-1) [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
LSIDGENAGS LTHIEAQNKI RACGERLSLG LSRAQPVQSK PQKASAPAAD
110 120 130 140 150
PPRYTFAPSV SLNKTARPFG APPPADSAPQ QNGQPLRPLV PDASKQRLME
160 170 180 190 200
NTEDWRPRPG TGQSRSFRIL AHLTGTEFMQ DPDEEHLKKS SQVPRTEAPA
210 220 230 240 250
PASSTPQEPW PGPTAPSPTS RPPWAVDPAF AERYAPDKTS TVLTRHSQPA
260 270 280 290 300
TPTPLQSRTS IVQAAAGGVP GGGSNNGKTP VCHQCHKVIR GRYLVALGHA
310 320 330 340 350
YHPEEFVCSQ CGKVLEEGGF FEEKGAIFCP PCYDVRYAPS CAKCKKKITG
360 370 380 390 400
EIMHALKMTW HVHCFTCAAC KTPIRNRAFY MEEGVPYCER DYEKMFGTKC
410 420 430 440 450
HGCDFKIDAG DRFLEALGFS WHDTCFVCAI CQINLEGKTF YSKKDRPLCK

SHAFSHV
Length:457
Mass (Da):49,845
Last modified:October 1, 2000 - v1
Checksum:iAA37F9E8E987D990
GO
Isoform 2 (identifier: Q9NR12-2) [UniParc]FASTAAdd to basket
Also known as: LMP-2

The sequence of this isoform differs from the canonical sequence as follows:
     94-133: ASAPAADPPRYTFAPSVSLNKTARPFGAPPPADSAPQQNG → VQTPDK

Note: Did not induce bone induction.
Show »
Length:423
Mass (Da):46,510
Checksum:i486E854CABB4D494
GO
Isoform 3 (identifier: Q9NR12-3) [UniParc]FASTAAdd to basket
Also known as: LMP-3

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

Note: Same activity as isoform 1 in bone nodule induction.
Show »
Length:153
Mass (Da):16,034
Checksum:i257AD5C3CD61F6F1
GO
Isoform 4 (identifier: Q9NR12-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     191-287: SQVPRTEAPA...KTPVCHQCHK → RPYRPQPYQP...PRVPPGGVCV
     288-457: Missing.

Note: No experimental confirmation available.
Show »
Length:287
Mass (Da):30,411
Checksum:i7B30CF3E6197899C
GO
Isoform 5 (identifier: Q9NR12-5) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     192-457: Missing.

Note: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay. No experimental confirmation available.
Show »
Length:191
Mass (Da):20,514
Checksum:iB9B6B99E12B23B25
GO
Isoform 6 (identifier: Q9NR12-6) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     191-222: SQVPRTEAPAPASSTPQEPWPGPTAPSPTSRP → REKYVLELQSPRYTRLRDWHHQRSAHVLNVQS
     223-457: Missing.

Note: No experimental confirmation available.
Show »
Length:222
Mass (Da):24,413
Checksum:iADF21719E4928621
GO

Sequence cautioni

The sequence AAC37565 differs from that shown. Reason: Frameshift at positions 103, 128, 161, 183, 195 and 245.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti138P → Q in BC067806 (PubMed:15489334).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_050168326A → T.Corresponds to variant rs2306764dbSNPEnsembl.1
Natural variantiVAR_036193450K → N in a breast cancer sample; somatic mutation. 1 Publication1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_01650994 – 133ASAPA…PQQNG → VQTPDK in isoform 2. 1 PublicationAdd BLAST40
Alternative sequenceiVSP_016510134 – 153QPLRP…MENTE → CRPLTNSRSDRWSQMPASSG in isoform 3. 1 PublicationAdd BLAST20
Alternative sequenceiVSP_016513154 – 457Missing in isoform 3. 1 PublicationAdd BLAST304
Alternative sequenceiVSP_016511191 – 287SQVPR…HQCHK → RPYRPQPYQPPALGCGPCVC RALCPGQNEHSADPAQPAGH AHAAAEPHLHCAGSCRRGAR RGQQQRQDSRVSPVPQGHPG PLPGGAGPRVPPGGVCV in isoform 4. 1 PublicationAdd BLAST97
Alternative sequenceiVSP_016512191 – 222SQVPR…PTSRP → REKYVLELQSPRYTRLRDWH HQRSAHVLNVQS in isoform 6. 1 PublicationAdd BLAST32
Alternative sequenceiVSP_016514192 – 457Missing in isoform 5. 1 PublicationAdd BLAST266
Alternative sequenceiVSP_016515223 – 457Missing in isoform 6. 1 PublicationAdd BLAST235
Alternative sequenceiVSP_016516288 – 457Missing in isoform 4. 1 PublicationAdd BLAST170

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L35240 Genomic DNA. Translation: AAC37565.1. Frameshift.
AF345904 mRNA. Translation: AAK30567.1.
AF345905 mRNA. Translation: AAK30568.1.
AF345906 mRNA. Translation: AAK30569.1.
AF265209 mRNA. Translation: AAF76152.1.
BC001093 mRNA. Translation: AAH01093.1.
BC014521 mRNA. Translation: AAH14521.1.
BC067806 mRNA. No translation available.
BC084575 mRNA. Translation: AAH84575.1.
CCDSiCCDS4422.1. [Q9NR12-1]
CCDS4423.1. [Q9NR12-2]
CCDS4424.1. [Q9NR12-6]
PIRiA55050.
RefSeqiNP_005442.2. NM_005451.4. [Q9NR12-1]
NP_976227.1. NM_203352.2. [Q9NR12-2]
NP_998801.1. NM_213636.2. [Q9NR12-6]
UniGeneiHs.533040.
Hs.736984.

Genome annotation databases

EnsembliENST00000355572; ENSP00000347776; ENSG00000196923. [Q9NR12-6]
ENST00000355841; ENSP00000348099; ENSG00000196923. [Q9NR12-1]
ENST00000359895; ENSP00000352964; ENSG00000196923. [Q9NR12-2]
ENST00000393551; ENSP00000377182; ENSG00000196923. [Q9NR12-4]
ENST00000486828; ENSP00000439157; ENSG00000196923. [Q9NR12-5]
ENST00000493815; ENSP00000431236; ENSG00000196923. [Q9NR12-3]
GeneIDi9260.
KEGGihsa:9260.
UCSCiuc003mhb.3. human. [Q9NR12-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L35240 Genomic DNA. Translation: AAC37565.1. Frameshift.
AF345904 mRNA. Translation: AAK30567.1.
AF345905 mRNA. Translation: AAK30568.1.
AF345906 mRNA. Translation: AAK30569.1.
AF265209 mRNA. Translation: AAF76152.1.
BC001093 mRNA. Translation: AAH01093.1.
BC014521 mRNA. Translation: AAH14521.1.
BC067806 mRNA. No translation available.
BC084575 mRNA. Translation: AAH84575.1.
CCDSiCCDS4422.1. [Q9NR12-1]
CCDS4423.1. [Q9NR12-2]
CCDS4424.1. [Q9NR12-6]
PIRiA55050.
RefSeqiNP_005442.2. NM_005451.4. [Q9NR12-1]
NP_976227.1. NM_203352.2. [Q9NR12-2]
NP_998801.1. NM_213636.2. [Q9NR12-6]
UniGeneiHs.533040.
Hs.736984.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2Q3GX-ray1.11A/B1-84[»]
ProteinModelPortaliQ9NR12.
SMRiQ9NR12.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi114682. 135 interactors.
IntActiQ9NR12. 121 interactors.
MINTiMINT-94304.
STRINGi9606.ENSP00000348099.

PTM databases

iPTMnetiQ9NR12.
PhosphoSitePlusiQ9NR12.
SwissPalmiQ9NR12.

Polymorphism and mutation databases

BioMutaiPDLIM7.
DMDMi74752914.

Proteomic databases

EPDiQ9NR12.
MaxQBiQ9NR12.
PaxDbiQ9NR12.
PeptideAtlasiQ9NR12.
PRIDEiQ9NR12.

Protocols and materials databases

DNASUi9260.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000355572; ENSP00000347776; ENSG00000196923. [Q9NR12-6]
ENST00000355841; ENSP00000348099; ENSG00000196923. [Q9NR12-1]
ENST00000359895; ENSP00000352964; ENSG00000196923. [Q9NR12-2]
ENST00000393551; ENSP00000377182; ENSG00000196923. [Q9NR12-4]
ENST00000486828; ENSP00000439157; ENSG00000196923. [Q9NR12-5]
ENST00000493815; ENSP00000431236; ENSG00000196923. [Q9NR12-3]
GeneIDi9260.
KEGGihsa:9260.
UCSCiuc003mhb.3. human. [Q9NR12-1]

Organism-specific databases

CTDi9260.
DisGeNETi9260.
GeneCardsiPDLIM7.
HGNCiHGNC:22958. PDLIM7.
HPAiHPA018794.
HPA048815.
MIMi605903. gene.
neXtProtiNX_Q9NR12.
OpenTargetsiENSG00000196923.
PharmGKBiPA128394546.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1703. Eukaryota.
ENOG410XRD4. LUCA.
GeneTreeiENSGT00760000118910.
HOVERGENiHBG051478.
InParanoidiQ9NR12.
OMAiRPLCKSH.
OrthoDBiEOG091G06JR.
PhylomeDBiQ9NR12.
TreeFamiTF106408.

Enzyme and pathway databases

ReactomeiR-HSA-8853659. RET signaling.

Miscellaneous databases

ChiTaRSiPDLIM7. human.
EvolutionaryTraceiQ9NR12.
GeneWikiiPDLIM7.
GenomeRNAii9260.
PROiQ9NR12.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000196923.
CleanExiHS_PDLIM7.
ExpressionAtlasiQ9NR12. baseline and differential.
GenevisibleiQ9NR12. HS.

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_HUMAN
AccessioniPrimary (citable) accession number: Q9NR12
Secondary accession number(s): Q14250
, Q5XG82, Q6NVZ5, Q96C91, Q9BXB8, Q9BXB9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 6, 2005
Last sequence update: October 1, 2000
Last modified: November 30, 2016
This is version 144 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 5
    Human chromosome 5: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. 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.