O00151 (PDLI1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
PDZ and LIM domain protein 1

Alternative name(s):
C-terminal LIM domain protein 1
Elfin
LIM domain protein CLP-36

Gene names

Name:	PDLIM1
Synonyms:	CLIM1, CLP36

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	329 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Cytoskeletal protein that may act as an adapter that brings other proteins (like kinases) to the cytoskeleton.
Subunit structure	Interacts with alpha-actinins 1, 2 and 4. Ref.9 Ref.10
Subcellular location	Cytoplasm By similarity. Cytoplasm › cytoskeleton By similarity. Note: Associates with the actin stress fibers By similarity.
Tissue specificity	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.
Sequence similarities	Contains 1 LIM zinc-binding domain. Contains 1 PDZ (DHR) domain.

Ontologies

Keywords
Cellular component	Cytoplasm Cytoskeleton
Coding sequence diversity	Polymorphism
Domain	LIM domain
Ligand	Metal-binding Zinc
PTM	Acetylation Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: Compara response to hypoxia Inferred from electronic annotation. Source: Compara response to oxidative stress Traceable author statement PubMed 8522188. Source: ProtInc
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell cytoskeleton Inferred from electronic annotation. Source: UniProtKB-SubCell transcription factor complex Inferred from electronic annotation. Source: Compara
Molecular_function	transcription coactivator activity Inferred from electronic annotation. Source: Compara zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.7 Ref.8

Chain

2 – 329

328

PDZ and LIM domain protein 1

PRO_0000075859

Regions

Domain

3 – 85

83

PDZ

Domain

258 – 317

60

LIM zinc-binding

Sites

Metal binding

260

1

Zinc 1

Metal binding

263

1

Zinc 1

Metal binding

280

1

Zinc 1

Metal binding

283

1

Zinc 1

Metal binding

286

1

Zinc 2

Metal binding

289

1

Zinc 2

Metal binding

307

1

Zinc 2

Metal binding

310

1

Zinc 2

Amino acid modifications

Modified residue

2

1

N-acetylthreonine Ref.8

Modified residue

90

1

Phosphoserine Ref.13 Ref.14 Ref.15 Ref.17 Ref.19

Modified residue

130

1

Phosphoserine Ref.17

Modified residue

144

1

Phosphotyrosine Ref.12

Modified residue

321

1

Phosphotyrosine Ref.11

Natural variations

Natural variant

175

1

N → S. Ref.3 Ref.4
Corresponds to variant rs2296961 [ dbSNP | Ensembl ].

VAR_022271

Experimental info

Sequence conflict

21

1

G → R in AAC05580. Ref.1

Secondary structure

1

.

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329

Helix Strand Turn

Details...

Beta strand

2 – 12

11

Beta strand

15 – 21

7

Helix

22 – 24

3

Beta strand

26 – 33

8

Helix

38 – 41

4

Beta strand

49 – 53

5

Helix

63 – 71

9

Beta strand

74 – 84

11

Beta strand

261 – 263

3

Turn

281 – 284

4

Beta strand

287 – 289

3

Helix

293 – 296

4

Beta strand

299 – 303

5

Helix

308 – 314

7

Sequences

	Sequence		Length	Mass (Da)
	O00151 [UniParc]. Last modified January 23, 2007. Version 4. Checksum: C85881A04D63D314	FASTA	329	36,072
	10 20 30 40 50 60 MTTQQIDLQG PGPWGFRLVG GKDFEQPLAI SRVTPGSKAA LANLCIGDVI TAIDGENTSN 70 80 90 100 110 120 MTHLEAQNRI KGCTDNLTLT VARSEHKVWS PLVTEEGKRH PYKMNLASEP QEVLHIGSAH 130 140 150 160 170 180 NRSAMPFTAS PASSTTARVI TNQYNNPAGL YSSENISNFN NALESKTAAS GVEANSRPLD 190 200 210 220 230 240 HAQPPSSLVI DKESEVYKML QEKQELNEPP KQSTSFLVLQ EILESEEKGD PNKPSGFRSV 250 260 270 280 290 300 KAPVTKVAAS IGNAQKLPMC DKCGTGIVGV FVKLRDRHRH PECYVCTDCG TNLKQKGHFF 310 320 VEDQIYCEKH ARERVTPPEG YEVVTVFPK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Characterization of the human 36-kDa carboxyl terminal LIM domain protein (hCLIM1)." Kotaka M., Ngai S.M., Garcia-Barcelo M., Tsui S.K.W., Fung K.P., Lee C.Y., Waye M.M.Y. J. Cell. Biochem. 72:279-285(1999) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA]. Tissue: Heart.
[2]	"Human CLP-36, a PDZ-domain and LIM-domain protein, binds to alpha-actinin-1 and associates with actin filaments and stress fibers in activated platelets and endothelial cells." Bauer K., Kratzer M., Otte M., Luber de Quintana K., Hagmann J., Arnold G.J., Eckerskorn C., Lottspeich F., Siess W. Blood 96:4236-4245(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[3]	"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], VARIANT SER-175.
[4]	NIEHS SNPs program Submitted (FEB-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], VARIANT SER-175.
[5]	"The DNA sequence and comparative analysis of human chromosome 10." Deloukas P., Earthrowl M.E., Grafham D.V., Rubenfield M., French L., Steward C.A., Sims S.K., Jones M.C., Searle S., Scott C., Howe K., Hunt S.E., Andrews T.D., Gilbert J.G.R., Swarbreck D., Ashurst J.L., Taylor A., Battles J. , Bird C.P., Ainscough R., Almeida J.P., Ashwell R.I.S., Ambrose K.D., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Bates K., Beasley H., Bray-Allen S., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Cahill P., Camire D., Carter N.P., Chapman J.C., Clark S.Y., Clarke G., Clee C.M., Clegg S., Corby N., Coulson A., Dhami P., Dutta I., Dunn M., Faulkner L., Frankish A., Frankland J.A., Garner P., Garnett J., Gribble S., Griffiths C., Grocock R., Gustafson E., Hammond S., Harley J.L., Hart E., Heath P.D., Ho T.P., Hopkins B., Horne J., Howden P.J., Huckle E., Hynds C., Johnson C., Johnson D., Kana A., Kay M., Kimberley A.M., Kershaw J.K., Kokkinaki M., Laird G.K., Lawlor S., Lee H.M., Leongamornlert D.A., Laird G., Lloyd C., Lloyd D.M., Loveland J., Lovell J., McLaren S., McLay K.E., McMurray A., Mashreghi-Mohammadi M., Matthews L., Milne S., Nickerson T., Nguyen M., Overton-Larty E., Palmer S.A., Pearce A.V., Peck A.I., Pelan S., Phillimore B., Porter K., Rice C.M., Rogosin A., Ross M.T., Sarafidou T., Sehra H.K., Shownkeen R., Skuce C.D., Smith M., Standring L., Sycamore N., Tester J., Thorpe A., Torcasso W., Tracey A., Tromans A., Tsolas J., Wall M., Walsh J., Wang H., Weinstock K., West A.P., Willey D.L., Whitehead S.L., Wilming L., Wray P.W., Young L., Chen Y., Lovering R.C., Moschonas N.K., Siebert R., Fechtel K., Bentley D., Durbin R.M., Hubbard T., Doucette-Stamm L., Beck S., Smith D.R., Rogers J. Nature 429:375-381(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[6]	"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]. Tissue: Pancreas and Placenta.
[7]	"Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides." Gevaert K., Goethals M., Martens L., Van Damme J., Staes A., Thomas G.R., Vandekerckhove J. Nat. Biotechnol. 21:566-569(2003) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-17. Tissue: Platelet.
[8]	Bienvenut W.V., Claeys D. Submitted (NOV-2005) to UniProtKB Cited for: PROTEIN SEQUENCE OF 2-17; 23-32; 139-166; 212-238 AND 247-256, CLEAVAGE OF INITIATOR METHIONINE, ACETYLATION AT THR-2, MASS SPECTROMETRY. Tissue: Platelet.
[9]	"Interaction of hCLIM1, an enigma family protein, with alpha-actinin 2." Kotaka M., Kostin S., Ngai S., Chan K., Lau Y., Lee S.M., Li H.Y., Ng E.K., Schaper J., Tsui S.K.W., Fung K.P., Lee C.Y., Waye M.M.Y. J. Cell. Biochem. 78:558-565(2000) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH ALPHA-ACTININ-2.
[10]	"CLP-36 PDZ-LIM protein associates with nonmuscle alpha-actinin-1 and alpha-actinin-4." Vallenius T., Luukko K., Makela T.P. J. Biol. Chem. 275:11100-11105(2000) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH ALPHA-ACTININ-1 AND ALPHA-ACTININ-4.
[11]	"Robust phosphoproteomic profiling of tyrosine phosphorylation sites from human T cells using immobilized metal affinity chromatography and tandem mass spectrometry." Brill L.M., Salomon A.R., Ficarro S.B., Mukherji M., Stettler-Gill M., Peters E.C. Anal. Chem. 76:2763-2772(2004) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-321, MASS SPECTROMETRY. Tissue: Leukemic T-cell.
[12]	"Immunoaffinity profiling of tyrosine phosphorylation in cancer cells." Rush J., Moritz A., Lee K.A., Guo A., Goss V.L., Spek E.J., Zhang H., Zha X.-M., Polakiewicz R.D., Comb M.J. Nat. Biotechnol. 23:94-101(2005) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-144, MASS SPECTROMETRY.
[13]	"Improved titanium dioxide enrichment of phosphopeptides from HeLa cells and high confident phosphopeptide identification by cross-validation of MS/MS and MS/MS/MS spectra." Yu L.-R., Zhu Z., Chan K.C., Issaq H.J., Dimitrov D.S., Veenstra T.D. J. Proteome Res. 6:4150-4162(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-90, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[14]	"Phosphoproteome of resting human platelets." Zahedi R.P., Lewandrowski U., Wiesner J., Wortelkamp S., Moebius J., Schuetz C., Walter U., Gambaryan S., Sickmann A. J. Proteome Res. 7:526-534(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-90, MASS SPECTROMETRY. Tissue: Platelet.
[15]	"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-90, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[16]	"Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions." Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K. Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. Tissue: Leukemic T-cell.
[17]	"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: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-90 AND SER-130, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[18]	"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].
[19]	"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-90, MASS SPECTROMETRY.
[20]	"Solution structure of the LIM domain of carboxyl terminal LIM domain protein 1." RIKEN structural genomics initiative (RSGI) Submitted (NOV-2005) to the PDB data bank Cited for: STRUCTURE BY NMR OF 250-315, ZINC-BINDING SITES.
+	Additional computationally mapped references.

Web resources

NIEHS-SNPs

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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.

IPI

IPI00010414.

RefSeq

NP_066272.1. NM_020992.3.

UniGene

Hs.368525.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1X62	NMR	-	A	250-314	[»]
2PKT	X-ray	1.50	A	1-86	[»]

ProteinModelPortal

O00151.

ModBase

Search...

Protein-protein interaction databases

IntAct

O00151. 8 interactions.

MINT

MINT-5005794.

STRING

9606.ENSP00000360305.

PTM databases

PhosphoSite

O00151.

2D gel databases

OGP

O00151.

UCD-2DPAGE

O00151.

Proteomic databases

PaxDb

O00151.

PeptideAtlas

O00151.

PRIDE

O00151.

Protocols and materials databases

DNASU

9124.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000329399; ENSP00000360305; ENSG00000107438.

GeneID

9124.

KEGG

hsa:9124.

UCSC

uc001kkh.3. human.

Organism-specific databases

CTD

9124.

GeneCards

GC10M096997.

HGNC

HGNC:2067. PDLIM1.

HPA

HPA017010.

MIM

605900. gene.

neXtProt

NX_O00151.

PharmGKB

PA33158.

GenAtlas

Search...

Phylogenomic databases

eggNOG

NOG250485.

HOGENOM

HOG000290704.

HOVERGEN

HBG061371.

InParanoid

O00151.

OMA

QIVLQGP.

OrthoDB

EOG4DV5MH.

PhylomeDB

O00151.

Gene expression databases

Bgee

O00151.

CleanEx

HS_PDLIM1.

Genevestigator

O00151.

GermOnline

ENSG00000107438. Homo sapiens.

Family and domain databases

Gene3D

2.10.110.10. 1 hit.

InterPro

IPR001478. PDZ.
IPR006643. ZASP.
IPR001781. Znf_LIM.
[Graphical view]

Pfam

PF00412. LIM. 1 hit.
PF00595. PDZ. 1 hit.
[Graphical view]

SMART

SM00132. LIM. 1 hit.
SM00228. PDZ. 1 hit.
SM00735. ZM. 1 hit.
[Graphical view]

SUPFAM

SSF50156. PDZ. 1 hit.

PROSITE

PS00478. LIM_DOMAIN_1. 1 hit.
PS50023. LIM_DOMAIN_2. 1 hit.
PS50106. PDZ. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

ChiTaRS

PDLIM1. human.

EvolutionaryTrace

O00151.

GenomeRNAi

9124.

NextBio

34201.

SOURCE

Search...

Entry information

Entry name

PDLI1_HUMAN

Accession

Primary (citable) accession number: O00151
Secondary accession number(s): B2RBS6, Q5VZH5, Q9BPZ9

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 30, 2000
Last sequence update:	January 23, 2007
Last modified:	May 1, 2013
This is version 129 of the entry and version 4 of the sequence. [Complete history]

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.