ID PDLI7_HUMAN Reviewed; 457 AA.
AC Q9NR12; Q14250; Q5XG82; Q6NVZ5; Q96C91; Q9BXB8; Q9BXB9;
DT 06-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 01-MAY-2013, entry version 107.
DE RecName: Full=PDZ and LIM domain protein 7;
DE AltName: Full=LIM mineralization protein;
DE Short=LMP;
DE AltName: Full=Protein enigma;
GN Name=PDLIM7; Synonyms=ENIGMA;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC Catarrhini; Hominidae; Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, AND INTERACTION WITH
RP INSR.
RX PubMed=7929196;
RA Wu R.-Y., Gill G.N.;
RT "LIM domain recognition of a tyrosine-containing tight turn.";
RL J. Biol. Chem. 269:25085-25090(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1; 2 AND 3), FUNCTION, TISSUE
RP SPECIFICITY, AND ALTERNATIVE SPLICING.
RC TISSUE=Heart;
RX PubMed=11874232; DOI=10.1359/jbmr.2002.17.3.406;
RA Liu Y., Hair G.A., Boden S.D., Viggeswarapu M., Titus L.;
RT "Overexpressed LIM mineralization proteins do not require LIM domains
RT to induce bone.";
RL J. Bone Miner. Res. 17:406-414(2002).
RN [3]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
RC TISSUE=Neuroepithelium;
RA Borrello M.G., Billaud M., Mercalli E., Ghizzoni S., Bidaud C.;
RT "Enigma sequence and interaction with Ret.";
RL Submitted (MAY-2000) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1; 4; 5 AND 6).
RC TISSUE=Brain, Kidney, Mammary gland, and Uterus;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA
RT project: the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [5]
RP PROTEIN SEQUENCE OF 6-17; 94-103 AND 246-258, AND MASS SPECTROMETRY.
RC TISSUE=Platelet;
RA Bienvenut W.V., Claeys D.;
RL Submitted (NOV-2005) to UniProtKB.
RN [6]
RP INTERACTION WITH PKC.
RX PubMed=8940095; DOI=10.1074/jbc.271.49.31029;
RA Kuroda S., Tokunaga C., Kiyohara Y., Higuchi O., Konishi H.,
RA Mizuno K., Gill G.N., Kikkawa U.;
RT "Protein-protein interaction of zinc finger LIM domains with protein
RT kinase C.";
RL J. Biol. Chem. 271:31029-31032(1996).
RN [7]
RP SUBCELLULAR LOCATION, AND INTERACTION WITH RET AND SHC1.
RX PubMed=9528800;
RA Durick K., Gill G.N., Taylor S.S.;
RT "Shc and Enigma are both required for mitogenic signaling by
RT Ret/ptc2.";
RL Mol. Cell. Biol. 18:2298-2308(1998).
RN [8]
RP INTERACTION WITH TPM2, AND MUTAGENESIS OF 15-GLY-PHE-16 AND HIS-63.
RX PubMed=10359609;
RA Guy P.M., Kenny D.A., Gill G.N.;
RT "The PDZ domain of the LIM protein enigma binds to beta-tropomyosin.";
RL Mol. Biol. Cell 10:1973-1984(1999).
RN [9]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-247, AND MASS
RP SPECTROMETRY.
RC TISSUE=Cervix carcinoma;
RX PubMed=18669648; DOI=10.1073/pnas.0805139105;
RA Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E.,
RA Elledge S.J., Gygi S.P.;
RT "A quantitative atlas of mitotic phosphorylation.";
RL Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008).
RN [10]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Cervix carcinoma;
RX PubMed=20068231; DOI=10.1126/scisignal.2000475;
RA Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L.,
RA Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S.,
RA Mann M.;
RT "Quantitative phosphoproteomics reveals widespread full
RT phosphorylation site occupancy during mitosis.";
RL Sci. Signal. 3:RA3-RA3(2010).
RN [11]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21269460; DOI=10.1186/1752-0509-5-17;
RA Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P.,
RA Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.;
RT "Initial characterization of the human central proteome.";
RL BMC Syst. Biol. 5:17-17(2011).
RN [12]
RP X-RAY CRYSTALLOGRAPHY (1.11 ANGSTROMS) OF 1-84.
RG Structural genomics consortium (SGC);
RT "Structure of the PDZ domain of human PDLIM7 bound to a C-terminal
RT extension from human beta-tropomyosin.";
RL Submitted (FEB-2009) to the PDB data bank.
RN [13]
RP VARIANT [LARGE SCALE ANALYSIS] ASN-450.
RX PubMed=16959974; DOI=10.1126/science.1133427;
RA Sjoeblom T., Jones S., Wood L.D., Parsons D.W., Lin J., Barber T.D.,
RA Mandelker D., Leary R.J., Ptak J., Silliman N., Szabo S.,
RA Buckhaults P., Farrell C., Meeh P., Markowitz S.D., Willis J.,
RA Dawson D., Willson J.K.V., Gazdar A.F., Hartigan J., Wu L., Liu C.,
RA Parmigiani G., Park B.H., Bachman K.E., Papadopoulos N.,
RA Vogelstein B., Kinzler K.W., Velculescu V.E.;
RT "The consensus coding sequences of human breast and colorectal
RT cancers.";
RL Science 314:268-274(2006).
CC -!- FUNCTION: May function as a scaffold on which the coordinated
CC assembly of proteins can occur. May play a role as an adapter
CC that, via its PDZ domain, localizes LIM-binding proteins to actin
CC filaments of both skeletal muscle and nonmuscle tissues. Involved
CC in both of the two fundamental mechanisms of bone formation,
CC direct bone formation (e.g. embryonic flat bones mandible and
CC cranium), and endochondral bone formation (e.g. embryonic long
CC bone development). Plays a role during fracture repair. Involved
CC in BMP6 signaling pathway (By similarity).
CC -!- SUBUNIT: Binds via its LIM zinc-binding 3 domain (LIM 3) to
CC endocytic codes of INSR, but not with those of IGF1R, LDLR, TFRC,
CC or EGFR. Interacts with various PKC isoforms through the LIM zinc-
CC binding domains. Binds to RET in a phosphorylation-independent
CC manner via its LIM zinc-binding domain 2 (LIM 2). Probably part of
CC a complex with SHC and the RET dimer. Interacts with TPM2.
CC Interacts with TBX4 and TBX5 (By similarity).
CC -!- INTERACTION:
CC P09022:Hoxa1 (xeno); NbExp=3; IntAct=EBI-350517, EBI-3957603;
CC Q9NRR5:UBQLN4; NbExp=2; IntAct=EBI-350517, EBI-711226;
CC -!- SUBCELLULAR LOCATION: Cytoplasm (By similarity). Cytoplasm,
CC cytoskeleton (By similarity). Note=Colocalizes with RET to the
CC cell periphery and in some cytoskeletal components. Colocalizes
CC with TPM2 near the Z line in muscle. Co-localizes with TBX4 and
CC TBX5 to actin filaments (By similarity).
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=6;
CC Name=1; Synonyms=LMP-1;
CC IsoId=Q9NR12-1; Sequence=Displayed;
CC Name=2; Synonyms=LMP-2;
CC IsoId=Q9NR12-2; Sequence=VSP_016509;
CC Note=Did not induce bone induction;
CC Name=3; Synonyms=LMP-3;
CC IsoId=Q9NR12-3; Sequence=VSP_016510, VSP_016513;
CC Note=Same activity as isoform 1 in bone nodule induction;
CC Name=4;
CC IsoId=Q9NR12-4; Sequence=VSP_016511, VSP_016516;
CC Note=No experimental confirmation available;
CC Name=5;
CC IsoId=Q9NR12-5; Sequence=VSP_016514;
CC Note=May be produced at very low levels due to a premature stop
CC codon in the mRNA, leading to nonsense-mediated mRNA decay. No
CC experimental confirmation available;
CC Name=6;
CC IsoId=Q9NR12-6; Sequence=VSP_016512, VSP_016515;
CC Note=No experimental confirmation available;
CC -!- TISSUE SPECIFICITY: Isoform 1 and isoform 2 are expressed
CC ubiquitously, however, isoform 2 predominates in skeletal muscle,
CC isoform 1 is more abundant in lung, spleen, leukocytes and fetal
CC liver.
CC -!- DOMAIN: The LIM zinc-binding 2 (LIM 2) domain interacts with TBX4
CC (By similarity).
CC -!- DOMAIN: The LIM zinc-binding 3 (LIM 3) domain provides the
CC structural basis for recognition of tyrosine-containing tight turn
CC structures. This domain is necessary and sufficient for
CC interaction with TBX5 (By similarity).
CC -!- DOMAIN: Anchored to cell periphery via its N-terminal PDZ domain.
CC -!- SIMILARITY: Contains 3 LIM zinc-binding domains.
CC -!- SIMILARITY: Contains 1 PDZ (DHR) domain.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAC37565.1; Type=Frameshift; Positions=103, 128, 161, 183, 195, 245;
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DR EMBL; L35240; AAC37565.1; ALT_FRAME; Genomic_DNA.
DR EMBL; AF345904; AAK30567.1; -; mRNA.
DR EMBL; AF345905; AAK30568.1; -; mRNA.
DR EMBL; AF345906; AAK30569.1; -; mRNA.
DR EMBL; AF265209; AAF76152.1; -; mRNA.
DR EMBL; BC001093; AAH01093.1; -; mRNA.
DR EMBL; BC014521; AAH14521.1; -; mRNA.
DR EMBL; BC067806; -; NOT_ANNOTATED_CDS; mRNA.
DR EMBL; BC084575; AAH84575.1; -; mRNA.
DR IPI; IPI00023122; -.
DR IPI; IPI00023560; -.
DR IPI; IPI00030835; -.
DR IPI; IPI00060308; -.
DR IPI; IPI00478185; -.
DR IPI; IPI00655883; -.
DR PIR; A55050; A55050.
DR RefSeq; NP_005442.2; NM_005451.3.
DR RefSeq; NP_976227.1; NM_203352.1.
DR RefSeq; NP_998801.1; NM_213636.1.
DR UniGene; Hs.533040; -.
DR PDB; 2Q3G; X-ray; 1.11 A; A/B=1-84.
DR PDBsum; 2Q3G; -.
DR ProteinModelPortal; Q9NR12; -.
DR IntAct; Q9NR12; 22.
DR MINT; MINT-94304; -.
DR STRING; 9606.ENSP00000348099; -.
DR PhosphoSite; Q9NR12; -.
DR DMDM; 74752914; -.
DR PaxDb; Q9NR12; -.
DR PRIDE; Q9NR12; -.
DR DNASU; 9260; -.
DR Ensembl; ENST00000355572; ENSP00000347776; ENSG00000196923.
DR Ensembl; ENST00000355841; ENSP00000348099; ENSG00000196923.
DR Ensembl; ENST00000356618; ENSP00000349030; ENSG00000196923.
DR Ensembl; ENST00000359895; ENSP00000352964; ENSG00000196923.
DR Ensembl; ENST00000393551; ENSP00000377182; ENSG00000196923.
DR Ensembl; ENST00000486828; ENSP00000439157; ENSG00000196923.
DR Ensembl; ENST00000493815; ENSP00000431236; ENSG00000196923.
DR GeneID; 9260; -.
DR KEGG; hsa:9260; -.
DR UCSC; uc003mha.1; human.
DR UCSC; uc003mhb.1; human.
DR UCSC; uc003mhf.3; human.
DR UCSC; uc003mhg.1; human.
DR CTD; 9260; -.
DR GeneCards; GC05M176912; -.
DR HGNC; HGNC:22958; PDLIM7.
DR HPA; HPA018794; -.
DR MIM; 605903; gene.
DR neXtProt; NX_Q9NR12; -.
DR PharmGKB; PA128394546; -.
DR eggNOG; NOG286537; -.
DR HOVERGEN; HBG051478; -.
DR InParanoid; Q9NR12; -.
DR OMA; ATPTPMQ; -.
DR PhylomeDB; Q9NR12; -.
DR Pathway_Interaction_DB; ret_pathway; Signaling events regulated by Ret tyrosine kinase.
DR ChiTaRS; PDLIM7; human.
DR EvolutionaryTrace; Q9NR12; -.
DR GenomeRNAi; 9260; -.
DR NextBio; 34707; -.
DR ArrayExpress; Q9NR12; -.
DR Bgee; Q9NR12; -.
DR CleanEx; HS_PDLIM7; -.
DR Genevestigator; Q9NR12; -.
DR GermOnline; ENSG00000196923; Homo sapiens.
DR GO; GO:0015629; C:actin cytoskeleton; IDA:HPA.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005925; C:focal adhesion; IDA:HPA.
DR GO; GO:0001726; C:ruffle; IEA:Compara.
DR GO; GO:0001725; C:stress fiber; IEA:Compara.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0030036; P:actin cytoskeleton organization; IEA:Compara.
DR GO; GO:0030154; P:cell differentiation; IEA:UniProtKB-KW.
DR GO; GO:0007275; P:multicellular organismal development; IEA:UniProtKB-KW.
DR GO; GO:0001503; P:ossification; IEA:UniProtKB-KW.
DR GO; GO:0045669; P:positive regulation of osteoblast differentiation; IEA:Compara.
DR GO; GO:0006898; P:receptor-mediated endocytosis; TAS:ProtInc.
DR Gene3D; 2.10.110.10; -; 3.
DR InterPro; IPR001478; PDZ.
DR InterPro; IPR001781; Znf_LIM.
DR Pfam; PF00412; LIM; 3.
DR Pfam; PF00595; PDZ; 1.
DR SMART; SM00132; LIM; 3.
DR SMART; SM00228; PDZ; 1.
DR SUPFAM; SSF50156; PDZ; 1.
DR PROSITE; PS00478; LIM_DOMAIN_1; 2.
DR PROSITE; PS50023; LIM_DOMAIN_2; 3.
DR PROSITE; PS50106; PDZ; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Alternative splicing; Complete proteome; Cytoplasm;
KW Cytoskeleton; Developmental protein; Differentiation;
KW Direct protein sequencing; LIM domain; Metal-binding; Osteogenesis;
KW Phosphoprotein; Polymorphism; Reference proteome; Repeat; Zinc.
FT CHAIN 1 457 PDZ and LIM domain protein 7.
FT /FTId=PRO_0000075881.
FT DOMAIN 1 85 PDZ.
FT DOMAIN 280 338 LIM zinc-binding 1.
FT DOMAIN 339 398 LIM zinc-binding 2.
FT DOMAIN 399 457 LIM zinc-binding 3.
FT MOD_RES 247 247 Phosphoserine.
FT VAR_SEQ 94 133 ASAPAADPPRYTFAPSVSLNKTARPFGAPPPADSAPQQNG
FT -> VQTPDK (in isoform 2).
FT /FTId=VSP_016509.
FT VAR_SEQ 134 153 QPLRPLVPDASKQRLMENTE -> CRPLTNSRSDRWSQMPA
FT SSG (in isoform 3).
FT /FTId=VSP_016510.
FT VAR_SEQ 154 457 Missing (in isoform 3).
FT /FTId=VSP_016513.
FT VAR_SEQ 191 287 SQVPRTEAPAPASSTPQEPWPGPTAPSPTSRPPWAVDPAFA
FT ERYAPDKTSTVLTRHSQPATPTPLQSRTSIVQAAAGGVPGG
FT GSNNGKTPVCHQCHK -> RPYRPQPYQPPALGCGPCVCRA
FT LCPGQNEHSADPAQPAGHAHAAAEPHLHCAGSCRRGARRGQ
FT QQRQDSRVSPVPQGHPGPLPGGAGPRVPPGGVCV (in
FT isoform 4).
FT /FTId=VSP_016511.
FT VAR_SEQ 191 222 SQVPRTEAPAPASSTPQEPWPGPTAPSPTSRP -> REKYV
FT LELQSPRYTRLRDWHHQRSAHVLNVQS (in isoform
FT 6).
FT /FTId=VSP_016512.
FT VAR_SEQ 192 457 Missing (in isoform 5).
FT /FTId=VSP_016514.
FT VAR_SEQ 223 457 Missing (in isoform 6).
FT /FTId=VSP_016515.
FT VAR_SEQ 288 457 Missing (in isoform 4).
FT /FTId=VSP_016516.
FT VARIANT 326 326 A -> T (in dbSNP:rs2306764).
FT /FTId=VAR_050168.
FT VARIANT 450 450 K -> N (in a breast cancer sample;
FT somatic mutation).
FT /FTId=VAR_036193.
FT MUTAGEN 15 16 GF->AA: Loss of binding to TPM2.
FT MUTAGEN 63 63 H->A: Loss of binding to TPM2.
FT CONFLICT 138 138 P -> Q (in Ref. 4; BC067806).
FT STRAND 1 12
FT STRAND 16 21
FT HELIX 22 24
FT STRAND 26 33
FT HELIX 38 41
FT STRAND 49 53
FT HELIX 58 60
FT HELIX 63 71
FT STRAND 76 84
SQ SEQUENCE 457 AA; 49845 MW; AA37F9E8E987D990 CRC64;
MDSFKVVLEG PAPWGFRLQG GKDFNVPLSI SRLTPGGKAA QAGVAVGDWV LSIDGENAGS
LTHIEAQNKI RACGERLSLG LSRAQPVQSK PQKASAPAAD PPRYTFAPSV SLNKTARPFG
APPPADSAPQ QNGQPLRPLV PDASKQRLME NTEDWRPRPG TGQSRSFRIL AHLTGTEFMQ
DPDEEHLKKS SQVPRTEAPA PASSTPQEPW PGPTAPSPTS RPPWAVDPAF AERYAPDKTS
TVLTRHSQPA TPTPLQSRTS IVQAAAGGVP GGGSNNGKTP VCHQCHKVIR GRYLVALGHA
YHPEEFVCSQ CGKVLEEGGF FEEKGAIFCP PCYDVRYAPS CAKCKKKITG EIMHALKMTW
HVHCFTCAAC KTPIRNRAFY MEEGVPYCER DYEKMFGTKC HGCDFKIDAG DRFLEALGFS
WHDTCFVCAI CQINLEGKTF YSKKDRPLCK SHAFSHV
//
