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Q9NR12 (PDLI7_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 117. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
PDZ and LIM domain protein 7
Alternative name(s):
LIM mineralization protein
Short name=LMP
Protein enigma
Gene names
Name:PDLIM7
Synonyms:ENIGMA
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length457 AA.
Sequence statusComplete.
Protein existenceEvidence 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. 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. 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.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Hoxa1P090223EBI-350517,EBI-3957603From a different organism.
UBQLN4Q9NRR52EBI-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 keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 457457PDZ and LIM domain protein 7
PRO_0000075881

Regions

Domain1 – 8585PDZ
Domain280 – 33859LIM zinc-binding 1
Domain339 – 39860LIM zinc-binding 2
Domain399 – 45759LIM zinc-binding 3

Amino acid modifications

Modified residue2471Phosphoserine Ref.9

Natural variations

Alternative sequence94 – 13340ASAPA…PQQNG → VQTPDK in isoform 2.
VSP_016509
Alternative sequence134 – 15320QPLRP…MENTE → CRPLTNSRSDRWSQMPASSG in isoform 3.
VSP_016510
Alternative sequence154 – 457304Missing in isoform 3.
VSP_016513
Alternative sequence191 – 28797SQVPR…HQCHK → RPYRPQPYQPPALGCGPCVC RALCPGQNEHSADPAQPAGH AHAAAEPHLHCAGSCRRGAR RGQQQRQDSRVSPVPQGHPG PLPGGAGPRVPPGGVCV in isoform 4.
VSP_016511
Alternative sequence191 – 22232SQVPR…PTSRP → REKYVLELQSPRYTRLRDWH HQRSAHVLNVQS in isoform 6.
VSP_016512
Alternative sequence192 – 457266Missing in isoform 5.
VSP_016514
Alternative sequence223 – 457235Missing in isoform 6.
VSP_016515
Alternative sequence288 – 457170Missing in isoform 4.
VSP_016516
Natural variant3261A → T.
Corresponds to variant rs2306764 [ dbSNP | Ensembl ].
VAR_050168
Natural variant4501K → N in a breast cancer sample; somatic mutation. Ref.14
VAR_036193

Experimental info

Mutagenesis15 – 162GF → AA: Loss of binding to TPM2.
Mutagenesis631H → A: Loss of binding to TPM2. Ref.8
Sequence conflict1381P → Q in BC067806. Ref.4

Secondary structure

................. 457
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 (LMP-1) [UniParc].

Last modified October 1, 2000. Version 1.
Checksum: AA37F9E8E987D990

FASTA45749,845
        10         20         30         40         50         60 
MDSFKVVLEG PAPWGFRLQG GKDFNVPLSI SRLTPGGKAA QAGVAVGDWV LSIDGENAGS 

        70         80         90        100        110        120 
LTHIEAQNKI RACGERLSLG LSRAQPVQSK PQKASAPAAD PPRYTFAPSV SLNKTARPFG 

       130        140        150        160        170        180 
APPPADSAPQ QNGQPLRPLV PDASKQRLME NTEDWRPRPG TGQSRSFRIL AHLTGTEFMQ 

       190        200        210        220        230        240 
DPDEEHLKKS SQVPRTEAPA PASSTPQEPW PGPTAPSPTS RPPWAVDPAF AERYAPDKTS 

       250        260        270        280        290        300 
TVLTRHSQPA TPTPLQSRTS IVQAAAGGVP GGGSNNGKTP VCHQCHKVIR GRYLVALGHA 

       310        320        330        340        350        360 
YHPEEFVCSQ CGKVLEEGGF FEEKGAIFCP PCYDVRYAPS CAKCKKKITG EIMHALKMTW 

       370        380        390        400        410        420 
HVHCFTCAAC KTPIRNRAFY MEEGVPYCER DYEKMFGTKC HGCDFKIDAG DRFLEALGFS 

       430        440        450 
WHDTCFVCAI CQINLEGKTF YSKKDRPLCK SHAFSHV 

« Hide

Isoform 2 (LMP-2) [UniParc].

Checksum: 486E854CABB4D494
Show »

FASTA42346,510
Isoform 3 (LMP-3) [UniParc].

Checksum: 257AD5C3CD61F6F1
Show »

FASTA15316,034
Isoform 4 [UniParc].

Checksum: 7B30CF3E6197899C
Show »

FASTA28730,411
Isoform 5 [UniParc].

Checksum: B9B6B99E12B23B25
Show »

FASTA19120,514
Isoform 6 [UniParc].

Checksum: ADF21719E4928621
Show »

FASTA22224,413

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, IDENTIFICATION BY 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, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
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]"N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB."
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A., Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[13]"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.
[14]"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. expand/collapse author list , Gazdar A.F., Hartigan J., Wu L., Liu C., Parmigiani G., Park B.H., Bachman K.E., Papadopoulos N., Vogelstein B., Kinzler K.W., 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.
PIRA55050.
RefSeqNP_005442.2. NM_005451.4.
NP_976227.1. NM_203352.2.
NP_998801.1. NM_213636.2.
UniGeneHs.533040.
Hs.736984.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2Q3GX-ray1.11A/B1-84[»]
ProteinModelPortalQ9NR12.
SMRQ9NR12. Positions 1-84, 278-451.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid114682. 42 interactions.
IntActQ9NR12. 26 interactions.
MINTMINT-94304.
STRING9606.ENSP00000348099.

PTM databases

PhosphoSiteQ9NR12.

Polymorphism databases

DMDM74752914.

Proteomic databases

PaxDbQ9NR12.
PRIDEQ9NR12.

Protocols and materials databases

DNASU9260.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000355572; ENSP00000347776; ENSG00000196923. [Q9NR12-6]
ENST00000355841; ENSP00000348099; ENSG00000196923. [Q9NR12-1]
ENST00000356618; ENSP00000349030; ENSG00000196923. [Q9NR12-4]
ENST00000359895; ENSP00000352964; ENSG00000196923. [Q9NR12-2]
ENST00000393551; ENSP00000377182; ENSG00000196923. [Q9NR12-4]
ENST00000486828; ENSP00000439157; ENSG00000196923. [Q9NR12-5]
ENST00000493815; ENSP00000431236; ENSG00000196923. [Q9NR12-3]
GeneID9260.
KEGGhsa:9260.
UCSCuc003mha.1. human. [Q9NR12-1]
uc003mhb.1. human. [Q9NR12-2]
uc003mhf.3. human. [Q9NR12-4]
uc003mhg.1. human. [Q9NR12-6]

Organism-specific databases

CTD9260.
GeneCardsGC05M176912.
HGNCHGNC:22958. PDLIM7.
HPAHPA018794.
HPA048815.
MIM605903. gene.
neXtProtNX_Q9NR12.
PharmGKBPA128394546.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG286537.
HOVERGENHBG051478.
InParanoidQ9NR12.
OMAYYHPEEF.
OrthoDBEOG7HXCQB.
PhylomeDBQ9NR12.
TreeFamTF106408.

Gene expression databases

ArrayExpressQ9NR12.
BgeeQ9NR12.
CleanExHS_PDLIM7.
GenevestigatorQ9NR12.

Family and domain databases

Gene3D2.10.110.10. 3 hits.
2.30.42.10. 1 hit.
InterProIPR001478. PDZ.
IPR001781. Znf_LIM.
[Graphical view]
PfamPF00412. LIM. 3 hits.
PF00595. PDZ. 1 hit.
[Graphical view]
SMARTSM00132. LIM. 3 hits.
SM00228. PDZ. 1 hit.
[Graphical view]
SUPFAMSSF50156. SSF50156. 1 hit.
PROSITEPS00478. LIM_DOMAIN_1. 2 hits.
PS50023. LIM_DOMAIN_2. 3 hits.
PS50106. PDZ. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSPDLIM7. human.
EvolutionaryTraceQ9NR12.
GeneWikiPDLIM7.
GenomeRNAi9260.
NextBio34707.
PROQ9NR12.
SOURCESearch...

Entry information

Entry namePDLI7_HUMAN
AccessionPrimary (citable) accession number: Q9NR12
Secondary accession number(s): Q14250 expand/collapse secondary AC list , Q5XG82, Q6NVZ5, Q96C91, Q9BXB8, Q9BXB9
Entry history
Integrated into UniProtKB/Swiss-Prot: December 6, 2005
Last sequence update: October 1, 2000
Last modified: April 16, 2014
This is version 117 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 5

Human chromosome 5: entries, gene names and cross-references to MIM