Q9NR12 (PDLI7_HUMAN) Reviewed, UniProtKB/Swiss-Prot
Last modified
May 29, 2013.
Version 108.
History...
Names·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order
Names·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize orderNames and origin
| Protein names | Recommended name: PDZ and LIM domain protein 7 Alternative name(s): LIM mineralization protein Short name=LMP Protein enigma | ||||
| Gene names |
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| Organism | Homo sapiens (Human) [Reference proteome] | ||||
| Taxonomic identifier | 9606 [NCBI] | ||||
| Taxonomic lineage | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo![]() |
Protein attributes
| Sequence length | 457 AA. |
| Sequence status | Complete. |
| Protein existence | Evidence at protein level |
General annotation (Comments)
| Function | 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. Ref.1 Ref.2 |
| Subunit structure | 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. Ref.1 Ref.6 Ref.7 Ref.8 |
| Subcellular location | Cytoplasm By similarity. Cytoplasm › cytoskeleton By similarity. Note: Colocalizes with RET to the cell periphery and in some cytoskeletal components. Colocalizes with TPM2 near the Z line in muscle. Co-localizes with TBX4 and TBX5 to actin filaments By similarity. Ref.7 |
| Tissue specificity | 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. Ref.2 |
| Domain | 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. Anchored to cell periphery via its N-terminal PDZ domain. |
| Sequence similarities | Contains 3 LIM zinc-binding domains. Contains 1 PDZ (DHR) domain. |
| Sequence caution | The sequence AAC37565.1 differs from that shown. Reason: Frameshift at positions 103, 128, 161, 183, 195 and 245. |
Ontologies
Binary interactions
With | Entry | #Exp. | IntAct | Notes |
|---|---|---|---|---|
| Hoxa1 | P09022 | 3 | EBI-350517,EBI-3957603 | From a different organism. |
| UBQLN4 | Q9NRR5 | 2 | EBI-350517,EBI-711226 |
Alternative products
| This entry describes 6 isoforms produced by alternative splicing. [Align] [Select] | ||||||
| Isoform 1 (identifier: Q9NR12-1) 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. | ||||||
| Isoform 2 (identifier: Q9NR12-2) 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. | ||||||
| Isoform 3 (identifier: Q9NR12-3) 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. | ||||||
| Isoform 4 (identifier: Q9NR12-4) 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. | ||||||
| Isoform 5 (identifier: Q9NR12-5) 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. | ||||||
| Isoform 6 (identifier: Q9NR12-6) The sequence of this isoform differs from the canonical sequence as follows: 191-222: SQVPRTEAPAPASSTPQEPWPGPTAPSPTSRP → REKYVLELQSPRYTRLRDWHHQRSAHVLNVQS 223-457: Missing. | ||||||
| Note: No experimental confirmation available. |
Sequence annotation (Features)
| Feature key | Position(s) | Length | Description | Graphical view | Feature identifier | ||||||||||||||||||||
Molecule processing | |||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Chain | 1 – 457 | 457 | PDZ and LIM domain protein 7 | PRO_0000075881 | |||||||||||||||||||||
Regions | |||||||||||||||||||||||||
| Domain | 1 – 85 | 85 | PDZ | ||||||||||||||||||||||
| Domain | 280 – 338 | 59 | LIM zinc-binding 1 | ||||||||||||||||||||||
| Domain | 339 – 398 | 60 | LIM zinc-binding 2 | ||||||||||||||||||||||
| Domain | 399 – 457 | 59 | LIM zinc-binding 3 | ||||||||||||||||||||||
Amino acid modifications | |||||||||||||||||||||||||
| Modified residue | 247 | 1 | Phosphoserine Ref.9 | ||||||||||||||||||||||
Natural variations | |||||||||||||||||||||||||
| Alternative sequence | 94 – 133 | 40 | ASAPA…PQQNG → VQTPDK in isoform 2. | VSP_016509 | |||||||||||||||||||||
| Alternative sequence | 134 – 153 | 20 | QPLRP…MENTE → CRPLTNSRSDRWSQMPASSG in isoform 3. | VSP_016510 | |||||||||||||||||||||
| Alternative sequence | 154 – 457 | 304 | Missing in isoform 3. | VSP_016513 | |||||||||||||||||||||
| Alternative sequence | 191 – 287 | 97 | SQVPR…HQCHK → RPYRPQPYQPPALGCGPCVC RALCPGQNEHSADPAQPAGH AHAAAEPHLHCAGSCRRGAR RGQQQRQDSRVSPVPQGHPG PLPGGAGPRVPPGGVCV in isoform 4. | VSP_016511 | |||||||||||||||||||||
| Alternative sequence | 191 – 222 | 32 | SQVPR…PTSRP → REKYVLELQSPRYTRLRDWH HQRSAHVLNVQS in isoform 6. | VSP_016512 | |||||||||||||||||||||
| Alternative sequence | 192 – 457 | 266 | Missing in isoform 5. | VSP_016514 | |||||||||||||||||||||
| Alternative sequence | 223 – 457 | 235 | Missing in isoform 6. | VSP_016515 | |||||||||||||||||||||
| Alternative sequence | 288 – 457 | 170 | Missing in isoform 4. | VSP_016516 | |||||||||||||||||||||
| Natural variant | 326 | 1 | A → T. Corresponds to variant rs2306764 [ dbSNP | Ensembl ]. | VAR_050168 | |||||||||||||||||||||
| Natural variant | 450 | 1 | K → N in a breast cancer sample; somatic mutation. Ref.13 | VAR_036193 | |||||||||||||||||||||
Experimental info | |||||||||||||||||||||||||
| Mutagenesis | 15 – 16 | 2 | GF → AA: Loss of binding to TPM2. | ||||||||||||||||||||||
| Mutagenesis | 63 | 1 | H → A: Loss of binding to TPM2. Ref.8 | ||||||||||||||||||||||
| Sequence conflict | 138 | 1 | P → Q in BC067806. Ref.4 | ||||||||||||||||||||||
Secondary structure | |||||||||||||||||||||||||
Helix Strand Turn | |||||||||||||||||||||||||
| Beta strand | 1 – 12 | 12 | |||||||||||||||||||||||
| Beta strand | 16 – 21 | 6 | |||||||||||||||||||||||
| Helix | 22 – 24 | 3 | |||||||||||||||||||||||
| Beta strand | 26 – 33 | 8 | |||||||||||||||||||||||
| Helix | 38 – 41 | 4 | |||||||||||||||||||||||
| Beta strand | 49 – 53 | 5 | |||||||||||||||||||||||
| Helix | 58 – 60 | 3 | |||||||||||||||||||||||
| Helix | 63 – 71 | 9 | |||||||||||||||||||||||
| Beta strand | 76 – 84 | 9 | |||||||||||||||||||||||
Sequences
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References
| « Hide 'large scale' references | |
| [1] | "LIM domain recognition of a tyrosine-containing tight turn." Wu R.-Y., Gill G.N. J. Biol. Chem. 269:25085-25090(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, INTERACTION WITH INSR. |
| [2] | "Overexpressed LIM mineralization proteins do not require LIM domains to induce bone." Liu Y., Hair G.A., Boden S.D., Viggeswarapu M., Titus L. J. Bone Miner. Res. 17:406-414(2002) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1; 2 AND 3), FUNCTION, TISSUE SPECIFICITY, ALTERNATIVE SPLICING. Tissue: Heart. |
| [3] | "Enigma sequence and interaction with Ret." Borrello M.G., Billaud M., Mercalli E., Ghizzoni S., Bidaud C. Submitted (MAY-2000) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1). Tissue: Neuroepithelium. |
| [4] | "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] (ISOFORMS 1; 4; 5 AND 6). Tissue: Brain, Kidney, Mammary gland and Uterus. |
| [5] | Bienvenut W.V., Claeys D. Submitted (NOV-2005) to UniProtKB Cited for: PROTEIN SEQUENCE OF 6-17; 94-103 AND 246-258, MASS SPECTROMETRY. Tissue: Platelet. |
| [6] | "Protein-protein interaction of zinc finger LIM domains with protein kinase C." Kuroda S., Tokunaga C., Kiyohara Y., Higuchi O., Konishi H., Mizuno K., Gill G.N., Kikkawa U. J. Biol. Chem. 271:31029-31032(1996) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH PKC. |
| [7] | "Shc and Enigma are both required for mitogenic signaling by Ret/ptc2." Durick K., Gill G.N., Taylor S.S. Mol. Cell. Biol. 18:2298-2308(1998) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION, INTERACTION WITH RET AND SHC1. |
| [8] | "The PDZ domain of the LIM protein enigma binds to beta-tropomyosin." Guy P.M., Kenny D.A., Gill G.N. Mol. Biol. Cell 10:1973-1984(1999) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH TPM2, MUTAGENESIS OF 15-GLY-PHE-16 AND HIS-63. |
| [9] | "A quantitative atlas of mitotic phosphorylation." Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-247, MASS SPECTROMETRY. Tissue: Cervix carcinoma. |
| [10] | "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis." Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M. Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. Tissue: Cervix carcinoma. |
| [11] | "Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. |
| [12] | "Structure of the PDZ domain of human PDLIM7 bound to a C-terminal extension from human beta-tropomyosin." Structural genomics consortium (SGC) Submitted (FEB-2009) to the PDB data bank Cited for: X-RAY CRYSTALLOGRAPHY (1.11 ANGSTROMS) OF 1-84. |
| [13] | "The consensus coding sequences of human breast and colorectal cancers." Sjoeblom T., Jones S., Wood L.D., Parsons D.W., Lin J., Barber T.D., Mandelker D., Leary R.J., Ptak J., Silliman N., Szabo S., Buckhaults P., Farrell C., Meeh P., Markowitz S.D., Willis J., Dawson D., Willson J.K.V. Velculescu V.E.Science 314:268-274(2006) [PubMed] [Europe PMC] [Abstract] Cited for: VARIANT [LARGE SCALE ANALYSIS] ASN-450. |
| + | Additional computationally mapped references. |
Cross-references
Sequence databases | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| EMBL GenBank DDBJ | 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. | ||||||||||||
| IPI | IPI00023122. IPI00023560. IPI00030835. IPI00060308. IPI00478185. IPI00655883. | ||||||||||||
| PIR | A55050. | ||||||||||||
| RefSeq | NP_005442.2. NM_005451.3. NP_976227.1. NM_203352.1. NP_998801.1. NM_213636.1. | ||||||||||||
| UniGene | Hs.533040. Hs.736984. | ||||||||||||
3D structure databases | |||||||||||||
| PDBe RCSB PDB PDBj |
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| ProteinModelPortal | Q9NR12. | ||||||||||||
| ModBase | Search... | ||||||||||||
Protein-protein interaction databases | |||||||||||||
| IntAct | Q9NR12. 22 interactions. | ||||||||||||
| MINT | MINT-94304. | ||||||||||||
| STRING | 9606.ENSP00000348099. | ||||||||||||
PTM databases | |||||||||||||
| PhosphoSite | Q9NR12. | ||||||||||||
Polymorphism databases | |||||||||||||
| DMDM | 74752914. | ||||||||||||
Proteomic databases | |||||||||||||
| PaxDb | Q9NR12. | ||||||||||||
| PRIDE | Q9NR12. | ||||||||||||
Protocols and materials databases | |||||||||||||
| DNASU | 9260. | ||||||||||||
| StructuralBiologyKnowledgebase | Search... | ||||||||||||
Genome annotation databases | |||||||||||||
| Ensembl | ENST00000355572; ENSP00000347776; ENSG00000196923. ENST00000355841; ENSP00000348099; ENSG00000196923. ENST00000356618; ENSP00000349030; ENSG00000196923. ENST00000359895; ENSP00000352964; ENSG00000196923. ENST00000393551; ENSP00000377182; ENSG00000196923. ENST00000486828; ENSP00000439157; ENSG00000196923. ENST00000493815; ENSP00000431236; ENSG00000196923. | ||||||||||||
| GeneID | 9260. | ||||||||||||
| KEGG | hsa:9260. | ||||||||||||
| UCSC | uc003mha.1. human. uc003mhb.1. human. uc003mhf.3. human. uc003mhg.1. human. | ||||||||||||
Organism-specific databases | |||||||||||||
| CTD | 9260. | ||||||||||||
| GeneCards | GC05M176912. | ||||||||||||
| HGNC | HGNC:22958. PDLIM7. | ||||||||||||
| HPA | HPA018794. | ||||||||||||
| MIM | 605903. gene. | ||||||||||||
| neXtProt | NX_Q9NR12. | ||||||||||||
| PharmGKB | PA128394546. | ||||||||||||
| GenAtlas | Search... | ||||||||||||
Phylogenomic databases | |||||||||||||
| eggNOG | NOG286537. | ||||||||||||
| HOVERGEN | HBG051478. | ||||||||||||
| InParanoid | Q9NR12. | ||||||||||||
| OMA | ATPTPMQ. | ||||||||||||
| PhylomeDB | Q9NR12. | ||||||||||||
Enzyme and pathway databases | |||||||||||||
| Pathway_Interaction_DB | ret_pathway. Signaling events regulated by Ret tyrosine kinase. | ||||||||||||
Gene expression databases | |||||||||||||
| ArrayExpress | Q9NR12. | ||||||||||||
| Bgee | Q9NR12. | ||||||||||||
| CleanEx | HS_PDLIM7. | ||||||||||||
| Genevestigator | Q9NR12. | ||||||||||||
| GermOnline | ENSG00000196923. Homo sapiens. | ||||||||||||
Family and domain databases | |||||||||||||
| Gene3D | 2.10.110.10. 3 hits. | ||||||||||||
| InterPro | IPR001478. PDZ. IPR001781. Znf_LIM. [Graphical view] | ||||||||||||
| Pfam | PF00412. LIM. 3 hits. PF00595. PDZ. 1 hit. [Graphical view] | ||||||||||||
| SMART | SM00132. LIM. 3 hits. SM00228. PDZ. 1 hit. [Graphical view] | ||||||||||||
| SUPFAM | SSF50156. PDZ. 1 hit. | ||||||||||||
| PROSITE | PS00478. LIM_DOMAIN_1. 2 hits. PS50023. LIM_DOMAIN_2. 3 hits. PS50106. PDZ. 1 hit. [Graphical view] | ||||||||||||
| ProtoNet | Search... | ||||||||||||
Other | |||||||||||||
| ChiTaRS | PDLIM7. human. | ||||||||||||
| EvolutionaryTrace | Q9NR12. | ||||||||||||
| GenomeRNAi | 9260. | ||||||||||||
| NextBio | 34707. | ||||||||||||
| SOURCE | Search... | ||||||||||||
Entry information
| Entry name | PDLI7_HUMAN | ||||||||
| Accession | Primary (citable) accession number: Q9NR12 Secondary accession number(s): Q14250 Q9BXB9 | ||||||||
| Entry history |
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| Entry status | 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. | ||||||||
Relevant documents
| Human chromosome 5 Human chromosome 5: entries, gene names and cross-references to MIM |
| Human entries with polymorphisms or disease mutations List of human entries with polymorphisms or disease mutations |
| 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 |
| SIMILARITY comments Index of protein domains and families |

Clusters with
