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Protein

PDZ and LIM domain protein 4

Gene

PDLIM4

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

GO - Molecular functioni

Complete GO annotation...

Keywords - Ligandi

Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
PDZ and LIM domain protein 4
Alternative name(s):
LIM protein RIL
Reversion-induced LIM protein
Gene namesi
Name:PDLIM4
Synonyms:RIL
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 5

Organism-specific databases

HGNCiHGNC:16501. PDLIM4.

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA134869796.

Polymorphism and mutation databases

BioMutaiPDLIM4.
DMDMi20141642.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 330330PDZ and LIM domain protein 4PRO_0000075873Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei112 – 1121PhosphoserineCombined sources
Modified residuei116 – 1161PhosphoserineBy similarity
Modified residuei120 – 1201PhosphoserineBy similarity
Modified residuei135 – 1351PhosphoserineBy similarity

Post-translational modificationi

Phosphorylated on tyrosine residue(s). Can be dephosphorylated by PTPN13 (By similarity).By similarity

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiP50479.
MaxQBiP50479.
PaxDbiP50479.
PeptideAtlasiP50479.
PRIDEiP50479.

PTM databases

iPTMnetiP50479.
PhosphoSiteiP50479.

Expressioni

Tissue specificityi

Isoform 2 is found in brain.

Gene expression databases

BgeeiP50479.
CleanExiHS_PDLIM4.
ExpressionAtlasiP50479. baseline and differential.
GenevisibleiP50479. HS.

Organism-specific databases

HPAiHPA011912.

Interactioni

Subunit structurei

Interacts with the LIM domain with the second and fourth PDZ domains of PTPN13.By similarity

Protein-protein interaction databases

BioGridi114140. 4 interactions.
IntActiP50479. 7 interactions.
MINTiMINT-1437771.
STRINGi9606.ENSP00000253754.

Structurei

Secondary structure

1
330
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 119Combined sources
Beta strandi15 – 206Combined sources
Helixi21 – 233Combined sources
Beta strandi25 – 328Combined sources
Beta strandi34 – 363Combined sources
Helixi37 – 404Combined sources
Beta strandi48 – 525Combined sources
Turni57 – 593Combined sources
Helixi62 – 709Combined sources
Beta strandi74 – 818Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2EEGNMR-A1-81[»]
2V1WX-ray1.90A/B1-85[»]
4Q2OX-ray2.10A/B/C/D/E/F1-84[»]
ProteinModelPortaliP50479.
SMRiP50479. Positions 1-84, 250-313.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP50479.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 8484PDZPROSITE-ProRule annotationAdd
BLAST
Domaini253 – 31260LIM zinc-bindingPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Contains 1 LIM zinc-binding domain.PROSITE-ProRule annotation
Contains 1 PDZ (DHR) domain.PROSITE-ProRule annotation

Keywords - Domaini

LIM domain

Phylogenomic databases

eggNOGiKOG1703. Eukaryota.
ENOG410XRD4. LUCA.
GeneTreeiENSGT00590000082980.
HOGENOMiHOG000290704.
HOVERGENiHBG061371.
InParanoidiP50479.
OMAiHIDPEAQ.
OrthoDBiEOG77DJ69.
PhylomeDBiP50479.
TreeFamiTF106408.

Family and domain databases

Gene3Di2.10.110.10. 1 hit.
2.30.42.10. 1 hit.
InterProiIPR031847. DUF4749.
IPR001478. PDZ.
IPR001781. Znf_LIM.
[Graphical view]
PfamiPF15936. DUF4749. 1 hit.
PF00412. LIM. 1 hit.
PF00595. PDZ. 1 hit.
[Graphical view]
SMARTiSM00132. LIM. 1 hit.
SM00228. PDZ. 1 hit.
[Graphical view]
SUPFAMiSSF50156. SSF50156. 1 hit.
PROSITEiPS00478. LIM_DOMAIN_1. 1 hit.
PS50023. LIM_DOMAIN_2. 1 hit.
PS50106. PDZ. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: P50479-1) [UniParc]FASTAAdd to basket

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
MPHSVTLRGP SPWGFRLVGG RDFSAPLTIS RVHAGSKAAL AALCPGDLIQ
60 70 80 90 100
AINGESTELM THLEAQNRIK GCHDHLTLSV SRPEGRSWPS APDDSKAQAH
110 120 130 140 150
RIHIDPEIQD GSPTTSRRPS GTGTGPEDGR PSLGSPYGQP PRFPVPHNGS
160 170 180 190 200
SEATLPAQMS TLHVSPPPSA DPARGLPRSR DCRVDLGSEV YRMLREPAEP
210 220 230 240 250
VAAEPKQSGS FRYLQGMLEA GEGGDWPGPG GPRNLKPTAS KLGAPLSGLQ
260 270 280 290 300
GLPECTRCGH GIVGTIVKAR DKLYHPECFM CSDCGLNLKQ RGYFFLDERL
310 320 330
YCESHAKARV KPPEGYDVVA VYPNAKVELV
Length:330
Mass (Da):35,398
Last modified:January 23, 2002 - v2
Checksum:i68FCA8FD93700E7B
GO
Isoform 2 (identifier: P50479-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     225-330: DWPGPGGPRN...VYPNAKVELV → APSSRHGTSSTIPSASCAVTAA

Show »
Length:246
Mass (Da):25,854
Checksum:i202F54C12328320E
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti20 – 201Missing in CAA63767 (Ref. 1) Curated
Sequence conflicti39 – 391A → S in CAA63767 (Ref. 1) Curated
Sequence conflicti139 – 1391Q → K in CAA63767 (Ref. 1) Curated
Sequence conflicti174 – 1829RGLPRSRDC → EASRGAGS in CAA63767 (Ref. 1) Curated
Sequence conflicti269 – 2691A → E in CAA63767 (Ref. 1) Curated

Polymorphismi

Genetic variations in PDLIM4 may be correlated with bone mineral density (BMD). Low BMD is a risk factor for osteoporotic fracture. Osteoporosis is characterized by reduced bone mineral density, disrutption of bone microarchitecture, and the alteration of the amount and variety of non-collagenous proteins in bone. Osteoporotic bones are more at risk of fracture.

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti118 – 1181R → G.1 Publication
Corresponds to variant rs17851430 [ dbSNP | Ensembl ].
VAR_035205
Natural varianti142 – 1421R → C.1 Publication
Corresponds to variant rs1050805 [ dbSNP | Ensembl ].
VAR_050167
Natural varianti184 – 1841V → I.
Corresponds to variant rs175218 [ dbSNP | Ensembl ].
VAR_035206
Natural varianti259 – 2591G → C.1 Publication
Corresponds to variant rs4877 [ dbSNP | Ensembl ].
VAR_035207

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei225 – 330106DWPGP…KVELV → APSSRHGTSSTIPSASCAVT AA in isoform 2. 2 PublicationsVSP_003124Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X93510 mRNA. Translation: CAA63767.1.
AF153882 mRNA. Translation: AAD38070.1.
AF154335 mRNA. Translation: AAD34646.1.
U82997 Genomic DNA. Translation: AAC52072.1.
AK313508 mRNA. Translation: BAG36288.1.
BT007019 mRNA. Translation: AAP35665.1.
CH471062 Genomic DNA. Translation: EAW62349.1.
CH471062 Genomic DNA. Translation: EAW62351.1.
BC003096 mRNA. Translation: AAH03096.1.
BC016765 mRNA. Translation: AAH16765.1.
CCDSiCCDS4152.1. [P50479-1]
CCDS47261.1. [P50479-2]
RefSeqiNP_001124499.1. NM_001131027.1. [P50479-2]
NP_003678.2. NM_003687.3. [P50479-1]
UniGeneiHs.424312.

Genome annotation databases

EnsembliENST00000253754; ENSP00000253754; ENSG00000131435. [P50479-1]
ENST00000379018; ENSP00000368303; ENSG00000131435. [P50479-2]
GeneIDi8572.
KEGGihsa:8572.
UCSCiuc003kwn.4. human. [P50479-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X93510 mRNA. Translation: CAA63767.1.
AF153882 mRNA. Translation: AAD38070.1.
AF154335 mRNA. Translation: AAD34646.1.
U82997 Genomic DNA. Translation: AAC52072.1.
AK313508 mRNA. Translation: BAG36288.1.
BT007019 mRNA. Translation: AAP35665.1.
CH471062 Genomic DNA. Translation: EAW62349.1.
CH471062 Genomic DNA. Translation: EAW62351.1.
BC003096 mRNA. Translation: AAH03096.1.
BC016765 mRNA. Translation: AAH16765.1.
CCDSiCCDS4152.1. [P50479-1]
CCDS47261.1. [P50479-2]
RefSeqiNP_001124499.1. NM_001131027.1. [P50479-2]
NP_003678.2. NM_003687.3. [P50479-1]
UniGeneiHs.424312.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2EEGNMR-A1-81[»]
2V1WX-ray1.90A/B1-85[»]
4Q2OX-ray2.10A/B/C/D/E/F1-84[»]
ProteinModelPortaliP50479.
SMRiP50479. Positions 1-84, 250-313.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi114140. 4 interactions.
IntActiP50479. 7 interactions.
MINTiMINT-1437771.
STRINGi9606.ENSP00000253754.

PTM databases

iPTMnetiP50479.
PhosphoSiteiP50479.

Polymorphism and mutation databases

BioMutaiPDLIM4.
DMDMi20141642.

Proteomic databases

EPDiP50479.
MaxQBiP50479.
PaxDbiP50479.
PeptideAtlasiP50479.
PRIDEiP50479.

Protocols and materials databases

DNASUi8572.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000253754; ENSP00000253754; ENSG00000131435. [P50479-1]
ENST00000379018; ENSP00000368303; ENSG00000131435. [P50479-2]
GeneIDi8572.
KEGGihsa:8572.
UCSCiuc003kwn.4. human. [P50479-1]

Organism-specific databases

CTDi8572.
GeneCardsiPDLIM4.
HGNCiHGNC:16501. PDLIM4.
HPAiHPA011912.
MIMi603422. gene.
neXtProtiNX_P50479.
PharmGKBiPA134869796.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1703. Eukaryota.
ENOG410XRD4. LUCA.
GeneTreeiENSGT00590000082980.
HOGENOMiHOG000290704.
HOVERGENiHBG061371.
InParanoidiP50479.
OMAiHIDPEAQ.
OrthoDBiEOG77DJ69.
PhylomeDBiP50479.
TreeFamiTF106408.

Miscellaneous databases

EvolutionaryTraceiP50479.
GeneWikiiPDLIM4.
GenomeRNAii8572.
PROiP50479.
SOURCEiSearch...

Gene expression databases

BgeeiP50479.
CleanExiHS_PDLIM4.
ExpressionAtlasiP50479. baseline and differential.
GenevisibleiP50479. HS.

Family and domain databases

Gene3Di2.10.110.10. 1 hit.
2.30.42.10. 1 hit.
InterProiIPR031847. DUF4749.
IPR001478. PDZ.
IPR001781. Znf_LIM.
[Graphical view]
PfamiPF15936. DUF4749. 1 hit.
PF00412. LIM. 1 hit.
PF00595. PDZ. 1 hit.
[Graphical view]
SMARTiSM00132. LIM. 1 hit.
SM00228. PDZ. 1 hit.
[Graphical view]
SUPFAMiSSF50156. SSF50156. 1 hit.
PROSITEiPS00478. LIM_DOMAIN_1. 1 hit.
PS50023. LIM_DOMAIN_2. 1 hit.
PS50106. PDZ. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. Scharm B., Schaefer R.
    Submitted (OCT-1995) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE (ISOFORM 1), VARIANTS CYS-142 AND CYS-259.
    Tissue: Lung.
  2. "The human RIL gene: mapping to human chromosome 5q31.1, genomic organization and alternative transcripts."
    Bashirova A.A., Markelov M.L., Shlykova T.V., Levshenkova E.V., Alibaeva R.A., Frolova E.I.
    Gene 210:239-245(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORMS 1 AND 2).
  3. Bashirova A.A., Markelov M.L., Levshenkova E.V., Shelkunova M.A., Frolova E.I.
    Submitted (MAY-1999) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE (ISOFORM 1).
  4. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
  5. "Cloning of human full-length CDSs in BD Creator(TM) system donor vector."
    Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S., Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y., Phelan M., Farmer A.
    Submitted (MAY-2003) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
  6. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  7. "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 AND 2), VARIANT GLY-118.
    Tissue: Bone marrow and Brain.
  8. "Association of genetic variation of the RIL gene, encoding a PDZ-LIM domain protein and localized in 5q31.1, with low bone mineral density in adult Japanese women."
    Omasu F., Ezura Y., Kajita M., Ishida R., Kodaira M., Yoshida H., Suzuki T., Hosoi T., Inoue S., Shiraki M., Orimo H., Emi M.
    J. Hum. Genet. 48:342-345(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: INVOLVEMENT IN BMD.
  9. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  10. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  11. "System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
    Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
    Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-112, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  12. "Toward a comprehensive characterization of a human cancer cell phosphoproteome."
    Zhou H., Di Palma S., Preisinger C., Peng M., Polat A.N., Heck A.J., Mohammed S.
    J. Proteome Res. 12:260-271(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-112, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Erythroleukemia.
  13. "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome."
    Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D., Wang L., Ye M., Zou H.
    J. Proteomics 96:253-262(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-112, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Liver.
  14. "Solution structure of PDZ domain of PDZ and LIM domain protein."
    RIKEN structural genomics initiative (RSGI)
    Submitted (AUG-2007) to the PDB data bank
    Cited for: STRUCTURE BY NMR OF 1-81.

Entry informationi

Entry nameiPDLI4_HUMAN
AccessioniPrimary (citable) accession number: P50479
Secondary accession number(s): B2R8U1
, Q53Y39, Q96AT8, Q9BTW8, Q9Y292
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: January 23, 2002
Last modified: July 6, 2016
This is version 144 of the entry and version 2 of the sequence. [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, 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
  6. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.