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UniProtKB - Q9NR12 (PDLI7_HUMAN)

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Protein

PDZ and LIM domain protein 7

Gene

PDLIM7

Organism
Homo sapiens (Human)
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 similarity2 Publications

GO - Molecular functioni

View the complete GO annotation on QuickGO ...

GO - Biological processi

View the complete GO annotation on QuickGO ...

Keywordsi

Molecular functionDevelopmental protein
Biological processDifferentiation, Osteogenesis
LigandMetal-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 lineageiEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo
Proteomesi
  • UP000005640 Componenti: Chromosome 5

Organism-specific databases

EuPathDBiHostDB:ENSG00000196923.13
HGNCiHGNC:22958 PDLIM7
MIMi605903 gene
neXtProtiNX_Q9NR12

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

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
ProteomicsDBi82244
82245 [Q9NR12-2]
82246 [Q9NR12-3]
82247 [Q9NR12-4]
82248 [Q9NR12-5]
82249 [Q9NR12-6]

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

Show more details

Protein-protein interaction databases

BioGridi114682, 156 interactors
IntActiQ9NR12, 149 interactors
MINTiQ9NR12
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

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.

Keywords - Domaini

LIM domain, Repeat

Phylogenomic databases

eggNOGiKOG1703 Eukaryota
ENOG410XRD4 LUCA
GeneTreeiENSGT00760000118910
HOVERGENiHBG051478
InParanoidiQ9NR12
OMAiRPLCKSH
OrthoDBiEOG091G06JR
PhylomeDBiQ9NR12
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 (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 dbSNP:rs2306764Ensembl.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

Similar proteinsi

Entry informationi

Entry nameiPDLI7_HUMAN
AccessioniPrimary (citable) accession number: Q9NR12
Secondary accession number(s): Q14250
, Q5XG82, Q6NVZ5, Q96C91, Q9BXB8, Q9BXB9
Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 6, 2005
Last sequence update: October 1, 2000
Last modified: July 18, 2018
This is version 158 of the entry and version 1 of the sequence. See 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

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