UniProtKB - Q9NR12 (PDLI7_HUMAN)
PDZ and LIM domain protein 7
PDLIM7
Functioni
GO - Molecular functioni
- actin binding Source: GO_Central
- metal ion binding Source: UniProtKB-KW
- muscle alpha-actinin binding Source: GO_Central
GO - Biological processi
- actin cytoskeleton organization Source: GO_Central
- axon guidance Source: Reactome
- heart development Source: GO_Central
- muscle structure development Source: GO_Central
- ossification Source: UniProtKB-KW
- positive regulation of osteoblast differentiation Source: Ensembl
- receptor-mediated endocytosis Source: ProtInc
Keywordsi
Molecular function | Developmental protein |
Biological process | Differentiation, Osteogenesis |
Ligand | Metal-binding, Zinc |
Enzyme and pathway databases
PathwayCommonsi | Q9NR12 |
Reactomei | R-HSA-8853659, RET signaling |
Names & Taxonomyi
Protein namesi | Recommended name: PDZ and LIM domain protein 7Alternative name(s): LIM mineralization protein Short name: LMP Protein enigma |
Gene namesi | Name:PDLIM7 Synonyms:ENIGMA |
Organismi | Homo sapiens (Human) |
Taxonomic identifieri | 9606 [NCBI] |
Taxonomic lineagei | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo |
Proteomesi |
|
Organism-specific databases
EuPathDBi | HostDB:ENSG00000196923.13 |
HGNCi | HGNC:22958, PDLIM7 |
MIMi | 605903, gene |
neXtProti | NX_Q9NR12 |
Subcellular locationi
Cytoskeleton
- cytoskeleton By similarity
Other locations
- Cytoplasm 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
Cytoskeleton
- actin cytoskeleton Source: HPA
- filamentous actin Source: GO_Central
- stress fiber Source: GO_Central
Cytosol
- cytosol Source: Reactome
Nucleus
- nucleoplasm Source: HPA
Other locations
- adherens junction Source: BHF-UCL
- focal adhesion Source: HPA
- ruffle Source: Ensembl
- Z disc Source: GO_Central
Keywords - Cellular componenti
Cytoplasm, CytoskeletonPathology & Biotechi
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 15 – 16 | GF → AA: Loss of binding to TPM2. 1 Publication | 2 | |
Mutagenesisi | 63 | H → A: Loss of binding to TPM2. 1 Publication | 1 |
Organism-specific databases
DisGeNETi | 9260 |
OpenTargetsi | ENSG00000196923 |
PharmGKBi | PA128394546 |
Miscellaneous databases
Pharosi | Q9NR12, Tbio |
Polymorphism and mutation databases
BioMutai | PDLIM7 |
DMDMi | 74752914 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000075881 | 1 – 457 | PDZ and LIM domain protein 7Add BLAST | 457 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Modified residuei | 78 | PhosphoserineCombined sources | 1 | |
Modified residuei | 103 | Asymmetric dimethylarginineCombined sources | 1 | |
Modified residuei | 111 | PhosphoserineCombined sources | 1 | |
Modified residuei | 247 | PhosphoserineCombined sources | 1 |
Keywords - PTMi
Methylation, PhosphoproteinProteomic databases
CPTACi | CPTAC-107 CPTAC-108 |
EPDi | Q9NR12 |
jPOSTi | Q9NR12 |
MassIVEi | Q9NR12 |
MaxQBi | Q9NR12 |
PaxDbi | Q9NR12 |
PeptideAtlasi | Q9NR12 |
PRIDEi | Q9NR12 |
ProteomicsDBi | 82244 [Q9NR12-1] 82245 [Q9NR12-2] 82246 [Q9NR12-3] 82247 [Q9NR12-4] 82248 [Q9NR12-5] 82249 [Q9NR12-6] |
PTM databases
GlyConnecti | 2908, 1 O-Linked glycan (1 site) [Q9NR12-4] |
GlyGeni | Q9NR12, 1 site, 1 O-linked glycan (1 site) |
iPTMneti | Q9NR12 |
MetOSitei | Q9NR12 |
PhosphoSitePlusi | Q9NR12 |
SwissPalmi | Q9NR12 |
Expressioni
Tissue specificityi
Gene expression databases
Bgeei | ENSG00000196923, Expressed in thoracic aorta and 202 other tissues |
ExpressionAtlasi | Q9NR12, baseline and differential |
Genevisiblei | Q9NR12, HS |
Organism-specific databases
HPAi | ENSG00000196923, Tissue enhanced (skeletal) |
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 similarityBinary interactionsi
Hide detailsQ9NR12
GO - Molecular functioni
- actin binding Source: GO_Central
- muscle alpha-actinin binding Source: GO_Central
Protein-protein interaction databases
BioGRIDi | 114682, 192 interactors |
IntActi | Q9NR12, 191 interactors |
MINTi | Q9NR12 |
STRINGi | 9606.ENSP00000348099 |
Miscellaneous databases
RNActi | Q9NR12, protein |
Structurei
Secondary structure
3D structure databases
SMRi | Q9NR12 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | Q9NR12 |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 1 – 85 | PDZPROSITE-ProRule annotationAdd BLAST | 85 | |
Domaini | 280 – 338 | LIM zinc-binding 1PROSITE-ProRule annotationAdd BLAST | 59 | |
Domaini | 339 – 398 | LIM zinc-binding 2PROSITE-ProRule annotationAdd BLAST | 60 | |
Domaini | 399 – 457 | LIM zinc-binding 3PROSITE-ProRule annotationAdd BLAST | 59 |
Domaini
Keywords - Domaini
LIM domain, RepeatPhylogenomic databases
eggNOGi | KOG1703, Eukaryota |
GeneTreei | ENSGT00940000159626 |
HOGENOMi | CLU_001357_8_1_1 |
InParanoidi | Q9NR12 |
OMAi | HQCHKII |
OrthoDBi | 1013114at2759 |
PhylomeDBi | Q9NR12 |
TreeFami | TF106408 |
Family and domain databases
Gene3Di | 2.30.42.10, 1 hit |
InterProi | View protein in InterPro IPR001478, PDZ IPR036034, PDZ_sf IPR001781, Znf_LIM |
Pfami | View protein in Pfam PF00412, LIM, 3 hits PF00595, PDZ, 1 hit |
SMARTi | View protein in SMART SM00132, LIM, 3 hits SM00228, PDZ, 1 hit |
SUPFAMi | SSF50156, SSF50156, 1 hit |
PROSITEi | View protein in PROSITE PS00478, LIM_DOMAIN_1, 2 hits PS50023, LIM_DOMAIN_2, 3 hits PS50106, PDZ, 1 hit |
s (6+)i Sequence
Sequence statusi: Complete.
This entry describes 6 produced by isoformsialternative splicing. AlignAdd to basketThis entry has 6 described isoforms and 5 potential isoforms that are computationally mapped.Show allAlign All
This isoform has been chosen as the sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry. canonicali
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
Computationally mapped potential isoform sequencesi
There are 5 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basketH7BYK4 | H7BYK4_HUMAN | PDZ and LIM domain protein 7 | PDLIM7 | 195 | Annotation score: | ||
D6RH06 | D6RH06_HUMAN | PDZ and LIM domain protein 7 | PDLIM7 | 287 | Annotation score: | ||
D6RF83 | D6RF83_HUMAN | PDZ and LIM domain protein 7 | PDLIM7 | 173 | Annotation score: | ||
H0Y8W6 | H0Y8W6_HUMAN | PDZ and LIM domain protein 7 | PDLIM7 | 120 | Annotation score: | ||
D6RAN1 | D6RAN1_HUMAN | PDZ and LIM domain protein 7 | PDLIM7 | 90 | Annotation score: |
Sequence cautioni
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 138 | P → Q in BC067806 (PubMed:15489334).Curated | 1 |
Natural variant
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Natural variantiVAR_050168 | 326 | A → T. Corresponds to variant dbSNP:rs2306764Ensembl. | 1 | |
Natural variantiVAR_036193 | 450 | K → N in a breast cancer sample; somatic mutation. 1 Publication | 1 |
Alternative sequence
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Alternative sequenceiVSP_016509 | 94 – 133 | ASAPA…PQQNG → VQTPDK in isoform 2. 1 PublicationAdd BLAST | 40 | |
Alternative sequenceiVSP_016510 | 134 – 153 | QPLRP…MENTE → CRPLTNSRSDRWSQMPASSG in isoform 3. 1 PublicationAdd BLAST | 20 | |
Alternative sequenceiVSP_016513 | 154 – 457 | Missing in isoform 3. 1 PublicationAdd BLAST | 304 | |
Alternative sequenceiVSP_016511 | 191 – 287 | SQVPR…HQCHK → RPYRPQPYQPPALGCGPCVC RALCPGQNEHSADPAQPAGH AHAAAEPHLHCAGSCRRGAR RGQQQRQDSRVSPVPQGHPG PLPGGAGPRVPPGGVCV in isoform 4. 1 PublicationAdd BLAST | 97 | |
Alternative sequenceiVSP_016512 | 191 – 222 | SQVPR…PTSRP → REKYVLELQSPRYTRLRDWH HQRSAHVLNVQS in isoform 6. 1 PublicationAdd BLAST | 32 | |
Alternative sequenceiVSP_016514 | 192 – 457 | Missing in isoform 5. 1 PublicationAdd BLAST | 266 | |
Alternative sequenceiVSP_016515 | 223 – 457 | Missing in isoform 6. 1 PublicationAdd BLAST | 235 | |
Alternative sequenceiVSP_016516 | 288 – 457 | Missing in isoform 4. 1 PublicationAdd BLAST | 170 |
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 |
CCDSi | CCDS4422.1 [Q9NR12-1] CCDS4423.1 [Q9NR12-2] CCDS4424.1 [Q9NR12-6] |
PIRi | A55050 |
RefSeqi | NP_005442.2, NM_005451.4 [Q9NR12-1] NP_976227.1, NM_203352.2 [Q9NR12-2] NP_998801.1, NM_213636.2 [Q9NR12-6] |
Genome annotation databases
Ensembli | ENST00000355572; 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] |
GeneIDi | 9260 |
KEGGi | hsa:9260 |
UCSCi | uc003mhb.3, human [Q9NR12-1] |
Keywords - Coding sequence diversityi
Alternative splicing, PolymorphismSimilar proteinsi
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 |
CCDSi | CCDS4422.1 [Q9NR12-1] CCDS4423.1 [Q9NR12-2] CCDS4424.1 [Q9NR12-6] |
PIRi | A55050 |
RefSeqi | NP_005442.2, NM_005451.4 [Q9NR12-1] NP_976227.1, NM_203352.2 [Q9NR12-2] NP_998801.1, NM_213636.2 [Q9NR12-6] |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
2Q3G | X-ray | 1.11 | A/B | 1-84 | [»] | |
SMRi | Q9NR12 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 114682, 192 interactors |
IntActi | Q9NR12, 191 interactors |
MINTi | Q9NR12 |
STRINGi | 9606.ENSP00000348099 |
PTM databases
GlyConnecti | 2908, 1 O-Linked glycan (1 site) [Q9NR12-4] |
GlyGeni | Q9NR12, 1 site, 1 O-linked glycan (1 site) |
iPTMneti | Q9NR12 |
MetOSitei | Q9NR12 |
PhosphoSitePlusi | Q9NR12 |
SwissPalmi | Q9NR12 |
Polymorphism and mutation databases
BioMutai | PDLIM7 |
DMDMi | 74752914 |
Proteomic databases
CPTACi | CPTAC-107 CPTAC-108 |
EPDi | Q9NR12 |
jPOSTi | Q9NR12 |
MassIVEi | Q9NR12 |
MaxQBi | Q9NR12 |
PaxDbi | Q9NR12 |
PeptideAtlasi | Q9NR12 |
PRIDEi | Q9NR12 |
ProteomicsDBi | 82244 [Q9NR12-1] 82245 [Q9NR12-2] 82246 [Q9NR12-3] 82247 [Q9NR12-4] 82248 [Q9NR12-5] 82249 [Q9NR12-6] |
Protocols and materials databases
Antibodypediai | 17442, 134 antibodies |
DNASUi | 9260 |
Genome annotation databases
Ensembli | ENST00000355572; 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] |
GeneIDi | 9260 |
KEGGi | hsa:9260 |
UCSCi | uc003mhb.3, human [Q9NR12-1] |
Organism-specific databases
CTDi | 9260 |
DisGeNETi | 9260 |
EuPathDBi | HostDB:ENSG00000196923.13 |
GeneCardsi | PDLIM7 |
HGNCi | HGNC:22958, PDLIM7 |
HPAi | ENSG00000196923, Tissue enhanced (skeletal) |
MIMi | 605903, gene |
neXtProti | NX_Q9NR12 |
OpenTargetsi | ENSG00000196923 |
PharmGKBi | PA128394546 |
GenAtlasi | Search... |
Phylogenomic databases
eggNOGi | KOG1703, Eukaryota |
GeneTreei | ENSGT00940000159626 |
HOGENOMi | CLU_001357_8_1_1 |
InParanoidi | Q9NR12 |
OMAi | HQCHKII |
OrthoDBi | 1013114at2759 |
PhylomeDBi | Q9NR12 |
TreeFami | TF106408 |
Enzyme and pathway databases
PathwayCommonsi | Q9NR12 |
Reactomei | R-HSA-8853659, RET signaling |
Miscellaneous databases
BioGRID-ORCSi | 9260, 16 hits in 844 CRISPR screens |
ChiTaRSi | PDLIM7, human |
EvolutionaryTracei | Q9NR12 |
GeneWikii | PDLIM7 |
GenomeRNAii | 9260 |
Pharosi | Q9NR12, Tbio |
PROi | PR:Q9NR12 |
RNActi | Q9NR12, protein |
SOURCEi | Search... |
Gene expression databases
Bgeei | ENSG00000196923, Expressed in thoracic aorta and 202 other tissues |
ExpressionAtlasi | Q9NR12, baseline and differential |
Genevisiblei | Q9NR12, HS |
Family and domain databases
Gene3Di | 2.30.42.10, 1 hit |
InterProi | View protein in InterPro IPR001478, PDZ IPR036034, PDZ_sf IPR001781, Znf_LIM |
Pfami | View protein in Pfam PF00412, LIM, 3 hits PF00595, PDZ, 1 hit |
SMARTi | View protein in SMART SM00132, LIM, 3 hits SM00228, PDZ, 1 hit |
SUPFAMi | SSF50156, SSF50156, 1 hit |
PROSITEi | View protein in PROSITE PS00478, LIM_DOMAIN_1, 2 hits PS50023, LIM_DOMAIN_2, 3 hits PS50106, PDZ, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | PDLI7_HUMAN | |
Accessioni | Q9NR12Primary (citable) accession number: Q9NR12 Secondary accession number(s): Q14250 Q9BXB9 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | December 6, 2005 |
Last sequence update: | October 1, 2000 | |
Last modified: | December 2, 2020 | |
This is version 178 of the entry and version 1 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Chordata Protein Annotation Program | |
Disclaimer | Any 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, Direct protein sequencing, Reference proteomeDocuments
- Human chromosome 5
Human chromosome 5: entries, gene names and cross-references to MIM - Human polymorphisms and disease mutations
Index of human polymorphisms and disease mutations - MIM cross-references
Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot - PDB cross-references
Index of Protein Data Bank (PDB) cross-references - Human entries with polymorphisms or disease mutations
List of human entries with polymorphisms or disease mutations