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Protein

PDZ and LIM domain protein 1

Gene

PDLIM1

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

Functioni

Cytoskeletal protein that may act as an adapter that brings other proteins (like kinases) to the cytoskeleton.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi260Zinc 11
Metal bindingi263Zinc 11
Metal bindingi280Zinc 11
Metal bindingi283Zinc 11
Metal bindingi286Zinc 21
Metal bindingi289Zinc 21
Metal bindingi307Zinc 21
Metal bindingi310Zinc 21

GO - Molecular functioni

GO - Biological processi

  • regulation of transcription, DNA-templated Source: Ensembl
  • response to hypoxia Source: Ensembl
  • response to oxidative stress Source: ProtInc
Complete GO annotation...

Keywords - Ligandi

Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
PDZ and LIM domain protein 1
Alternative name(s):
C-terminal LIM domain protein 1
Elfin
LIM domain protein CLP-36
Gene namesi
Name:PDLIM1
Synonyms:CLIM1, CLP36
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 10

Organism-specific databases

HGNCiHGNC:2067. PDLIM1.

Subcellular locationi

GO - Cellular componenti

  • cell-cell adherens junction Source: BHF-UCL
  • cytoplasm Source: UniProtKB-SubCell
  • cytoskeleton Source: UniProtKB-SubCell
  • focal adhesion Source: UniProtKB
  • transcription factor complex Source: Ensembl
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Cytoskeleton

Pathology & Biotechi

Organism-specific databases

DisGeNETi9124.
OpenTargetsiENSG00000107438.
PharmGKBiPA33158.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources2 Publications
ChainiPRO_00000758592 – 329PDZ and LIM domain protein 1Add BLAST328

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylthreonineCombined sources1 Publication1
Modified residuei90PhosphoserineCombined sources1
Modified residuei130PhosphoserineCombined sources1
Modified residuei144PhosphotyrosineCombined sources1
Modified residuei316PhosphothreonineCombined sources1
Modified residuei321PhosphotyrosineCombined sources1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiO00151.
PaxDbiO00151.
PeptideAtlasiO00151.
PRIDEiO00151.

2D gel databases

OGPiO00151.
UCD-2DPAGEO00151.

PTM databases

iPTMnetiO00151.
PhosphoSitePlusiO00151.
SwissPalmiO00151.

Expressioni

Tissue specificityi

Strongly expressed in the heart and skeletal muscle, moderately expressed in the spleen, small intestine, colon, placenta, and lung. A lower level expression is seen in liver, thymus, kidney, prostate and pancreas and is not found in the brain, testis, ovary, and peripheral blood leukocytes.

Gene expression databases

BgeeiENSG00000107438.
CleanExiHS_PDLIM1.
ExpressionAtlasiO00151. baseline and differential.
GenevisibleiO00151. HS.

Organism-specific databases

HPAiCAB072838.
CAB072840.
HPA017010.

Interactioni

Subunit structurei

Interacts with alpha-actinins 1, 2 and 4.2 Publications

GO - Molecular functioni

  • cadherin binding involved in cell-cell adhesion Source: BHF-UCL

Protein-protein interaction databases

BioGridi114572. 30 interactors.
IntActiO00151. 14 interactors.
MINTiMINT-5005794.
STRINGi9606.ENSP00000360305.

Structurei

Secondary structure

1329
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 12Combined sources11
Beta strandi15 – 21Combined sources7
Helixi22 – 24Combined sources3
Beta strandi26 – 33Combined sources8
Helixi38 – 41Combined sources4
Beta strandi49 – 53Combined sources5
Helixi63 – 71Combined sources9
Beta strandi74 – 84Combined sources11
Beta strandi261 – 263Combined sources3
Turni281 – 284Combined sources4
Beta strandi287 – 289Combined sources3
Helixi293 – 296Combined sources4
Beta strandi299 – 303Combined sources5
Helixi308 – 315Combined sources8

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1X62NMR-A250-315[»]
2PKTX-ray1.50A1-86[»]
ProteinModelPortaliO00151.
SMRiO00151.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO00151.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini3 – 85PDZPROSITE-ProRule annotationAdd BLAST83
Domaini258 – 317LIM zinc-bindingPROSITE-ProRule annotationAdd BLAST60

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.
InParanoidiO00151.
OMAiATANLCI.
OrthoDBiEOG091G0A6C.
PhylomeDBiO00151.
TreeFamiTF106408.

Family and domain databases

Gene3Di2.10.110.10. 1 hit.
2.30.42.10. 1 hit.
InterProiIPR031847. DUF4749.
IPR028537. PDLIM1.
IPR001478. PDZ.
IPR006643. Zasp-like_motif.
IPR001781. Znf_LIM.
[Graphical view]
PANTHERiPTHR24214:SF5. PTHR24214:SF5. 1 hit.
PfamiPF15936. DUF4749. 1 hit.
PF00412. LIM. 1 hit.
PF00595. PDZ. 1 hit.
[Graphical view]
SMARTiSM00132. LIM. 1 hit.
SM00228. PDZ. 1 hit.
SM00735. ZM. 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]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

O00151-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTTQQIDLQG PGPWGFRLVG GKDFEQPLAI SRVTPGSKAA LANLCIGDVI
60 70 80 90 100
TAIDGENTSN MTHLEAQNRI KGCTDNLTLT VARSEHKVWS PLVTEEGKRH
110 120 130 140 150
PYKMNLASEP QEVLHIGSAH NRSAMPFTAS PASSTTARVI TNQYNNPAGL
160 170 180 190 200
YSSENISNFN NALESKTAAS GVEANSRPLD HAQPPSSLVI DKESEVYKML
210 220 230 240 250
QEKQELNEPP KQSTSFLVLQ EILESEEKGD PNKPSGFRSV KAPVTKVAAS
260 270 280 290 300
IGNAQKLPMC DKCGTGIVGV FVKLRDRHRH PECYVCTDCG TNLKQKGHFF
310 320
VEDQIYCEKH ARERVTPPEG YEVVTVFPK
Length:329
Mass (Da):36,072
Last modified:January 23, 2007 - v4
Checksum:iC85881A04D63D314
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti21G → R in AAC05580 (PubMed:10022510).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_022271175N → S.2 PublicationsCorresponds to variant rs2296961dbSNPEnsembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U90878 mRNA. Translation: AAC05580.1.
AJ310549 mRNA. Translation: CAC32846.1.
AK314792 mRNA. Translation: BAG37323.1.
AY923052 Genomic DNA. Translation: AAW82438.1.
AL160288, AL157834 Genomic DNA. Translation: CAH70720.1.
AL157834, AL160288 Genomic DNA. Translation: CAH72341.1.
BC000915 mRNA. Translation: AAH00915.1.
BC018755 mRNA. Translation: AAH18755.1.
CCDSiCCDS7441.1.
RefSeqiNP_066272.1. NM_020992.3.
UniGeneiHs.368525.

Genome annotation databases

EnsembliENST00000329399; ENSP00000360305; ENSG00000107438.
GeneIDi9124.
KEGGihsa:9124.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Web resourcesi

NIEHS-SNPs

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U90878 mRNA. Translation: AAC05580.1.
AJ310549 mRNA. Translation: CAC32846.1.
AK314792 mRNA. Translation: BAG37323.1.
AY923052 Genomic DNA. Translation: AAW82438.1.
AL160288, AL157834 Genomic DNA. Translation: CAH70720.1.
AL157834, AL160288 Genomic DNA. Translation: CAH72341.1.
BC000915 mRNA. Translation: AAH00915.1.
BC018755 mRNA. Translation: AAH18755.1.
CCDSiCCDS7441.1.
RefSeqiNP_066272.1. NM_020992.3.
UniGeneiHs.368525.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1X62NMR-A250-315[»]
2PKTX-ray1.50A1-86[»]
ProteinModelPortaliO00151.
SMRiO00151.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi114572. 30 interactors.
IntActiO00151. 14 interactors.
MINTiMINT-5005794.
STRINGi9606.ENSP00000360305.

PTM databases

iPTMnetiO00151.
PhosphoSitePlusiO00151.
SwissPalmiO00151.

2D gel databases

OGPiO00151.
UCD-2DPAGEO00151.

Proteomic databases

EPDiO00151.
PaxDbiO00151.
PeptideAtlasiO00151.
PRIDEiO00151.

Protocols and materials databases

DNASUi9124.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000329399; ENSP00000360305; ENSG00000107438.
GeneIDi9124.
KEGGihsa:9124.

Organism-specific databases

CTDi9124.
DisGeNETi9124.
GeneCardsiPDLIM1.
HGNCiHGNC:2067. PDLIM1.
HPAiCAB072838.
CAB072840.
HPA017010.
MIMi605900. gene.
neXtProtiNX_O00151.
OpenTargetsiENSG00000107438.
PharmGKBiPA33158.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1703. Eukaryota.
ENOG410XRD4. LUCA.
GeneTreeiENSGT00590000082980.
HOGENOMiHOG000290704.
HOVERGENiHBG061371.
InParanoidiO00151.
OMAiATANLCI.
OrthoDBiEOG091G0A6C.
PhylomeDBiO00151.
TreeFamiTF106408.

Miscellaneous databases

ChiTaRSiPDLIM1. human.
EvolutionaryTraceiO00151.
GeneWikiiPDLIM1.
GenomeRNAii9124.
PROiO00151.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000107438.
CleanExiHS_PDLIM1.
ExpressionAtlasiO00151. baseline and differential.
GenevisibleiO00151. HS.

Family and domain databases

Gene3Di2.10.110.10. 1 hit.
2.30.42.10. 1 hit.
InterProiIPR031847. DUF4749.
IPR028537. PDLIM1.
IPR001478. PDZ.
IPR006643. Zasp-like_motif.
IPR001781. Znf_LIM.
[Graphical view]
PANTHERiPTHR24214:SF5. PTHR24214:SF5. 1 hit.
PfamiPF15936. DUF4749. 1 hit.
PF00412. LIM. 1 hit.
PF00595. PDZ. 1 hit.
[Graphical view]
SMARTiSM00132. LIM. 1 hit.
SM00228. PDZ. 1 hit.
SM00735. ZM. 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...

Entry informationi

Entry nameiPDLI1_HUMAN
AccessioniPrimary (citable) accession number: O00151
Secondary accession number(s): B2RBS6, Q5VZH5, Q9BPZ9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: January 23, 2007
Last modified: November 2, 2016
This is version 162 of the entry and version 4 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, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 10
    Human chromosome 10: 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.