Reviewed, UniProtKB/Swiss-Prot P48059 (LIMS1_HUMAN)

Names and origin

Protein names

Recommended name:
    LIM and senescent cell antigen-like-containing domain protein 1
Alternative name(s):
    Particularly interesting new Cys-His protein 1
      Short name=PINCH-1
    Renal carcinoma antigen NY-REN-48

Gene names

Name:	LIMS1
Synonyms:	PINCH, PINCH1

Organism

Homo sapiens (Human) [Complete proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	325 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	Effector of integrin and growth factor signaling, coupling surface receptors to downstream signaling molecules involved in the regulation of cell survival, cell proliferation and cell differentiation. Focal adhesion protein part of the complex ILK-PINCH. This complex is considered to be one of the convergence points of integrin- and growth factor-signaling pathway.
Subunit structure	Interacts (via LIM zinc-binding 5) with TGFB1I1 By similarity. Interacts (via LIM zinc-binding 1) with ILK. Interacts with SH3/SH2 adapter NCK2. Ref.7 Ref.9
Subcellular location	Cell junction › focal adhesion. Cell membrane; Peripheral membrane protein; Cytoplasmic side Ref.9 Ref.15.
Tissue specificity	In most tissues, except in the brain.
Sequence similarities	Contains 5 LIM zinc-binding domains.

Ontologies

Keywords
Cellular component	Cell junction Cell membrane Membrane
Domain	LIM domain Repeat
Ligand	Metal-binding Zinc
PTM	Acetylation
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	cell aging Ref.1 Traceable author statement. Source: ProtInc
Cellular component	cytosol Inferred from Experiment. Source: Reactome extrinsic to membrane Inferred from electronic annotation. Source: UniProtKB-SubCell focal adhesion Ref.15 Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	protein binding Ref.14 Inferred from physical interaction. Source: UniProtKB zinc ion binding Ref.14 Inferred from direct assay. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.6

Chain

2 – 325

324

LIM and senescent cell antigen-like-containing domain protein 1

PRO_0000075888

Regions

Domain

10 – 62

53

LIM zinc-binding 1

Domain

71 – 121

51

LIM zinc-binding 2

Domain

135 – 184

50

LIM zinc-binding 3

Domain

193 – 243

51

LIM zinc-binding 4

Domain

252 – 303

52

LIM zinc-binding 5

Amino acid modifications

Modified residue

2

1

N-acetylalanine Ref.6

Experimental info

Mutagenesis

42

1

F → A: Loss of interaction with ILK and loss of localization to focal adhesion. Ref.15 Ref.14

Mutagenesis

56

1

R → A: Alters interaction with ILK. Ref.15

Mutagenesis

61

1

H → D: Alters interaction with ILK. Ref.14

Mutagenesis

62

1

D → A: Alters interaction with ILK. Ref.14

Mutagenesis

66

1

L → D: Alters interaction with ILK. Ref.14

Sequence conflict

78

1

I → T in AAH05341. Ref.5

Sequence conflict

262

1

D → G in AAH05341. Ref.5

Secondary structure

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325

Helix Strand Turn

Details...

Beta strand

11 – 13

3

Turn

20 – 22

3

Beta strand

24 – 26

3

Beta strand

29 – 31

3

Turn

33 – 35

3

Turn

39 – 41

3

Helix

46 – 48

3

Beta strand

50 – 53

4

Beta strand

56 – 58

3

Helix

60 – 66

7

Beta strand

72 – 74

3

Beta strand

83 – 85

3

Beta strand

88 – 90

3

Turn

92 – 94

3

Beta strand

98 – 100

3

Beta strand

105 – 107

3

Beta strand

110 – 112

3

Beta strand

115 – 117

3

Turn

136 – 138

3

Beta strand

150 – 152

3

Turn

156 – 158

3

Beta strand

162 – 164

3

Beta strand

173 – 175

3

Beta strand

178 – 180

3

Helix

182 – 186

5

Turn

194 – 197

4

Beta strand

210 – 213

4

Turn

214 – 216

3

Turn

220 – 222

3

Beta strand

227 – 229

3

Beta strand

232 – 234

3

Beta strand

237 – 239

3

Helix

241 – 247

7

Sequences

	Sequence		Length	Mass (Da)
	P48059-1 [UniParc]. Last modified January 23, 2007. Version 4. Checksum: E665FEB11D849CAE	FASTA	325	37,251
	10 20 30 40 50 60 MANALASATC ERCKGGFAPA EKIVNSNGEL YHEQCFVCAQ CFQQFPEGLF YEFEGRKYCE 70 80 90 100 110 120 HDFQMLFAPC CHQCGEFIIG RVIKAMNNSW HPECFRCDLC QEVLADIGFV KNAGRHLCRP 130 140 150 160 170 180 CHNREKARGL GKYICQKCHA IIDEQPLIFK NDPYHPDHFN CANCGKELTA DARELKGELY 190 200 210 220 230 240 CLPCHDKMGV PICGACRRPI EGRVVNAMGK QWHVEHFVCA KCEKPFLGHR HYERKGLAYC 250 260 270 280 290 300 ETHYNQLFGD VCFHCNRVIE GDVVSALNKA WCVNCFACST CNTKLTLKNK FVEFDMKPVC 310 320 KKCYEKFPLE LKKRLKKLAE TLGRK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"A new LIM protein containing an autoepitope homologous to 'senescent cell antigen'." Rearden A. Biochem. Biophys. Res. Commun. 201:1124-1131(1994) [PubMed: 7517666] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA]. Tissue: Fetal liver.
[2]	Rearden A. Submitted (MAR-2001) to the EMBL/GenBank/DDBJ databases Cited for: SEQUENCE REVISION TO C-TERMINUS.
[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: 14702039] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[4]	"Generation and annotation of the DNA sequences of human chromosomes 2 and 4." Hillier L.W., Graves T.A., Fulton R.S., Fulton L.A., Pepin K.H., Minx P., Wagner-McPherson C., Layman D., Wylie K., Sekhon M., Becker M.C., Fewell G.A., Delehaunty K.D., Miner T.L., Nash W.E., Kremitzki C., Oddy L., Du H. , Sun H., Bradshaw-Cordum H., Ali J., Carter J., Cordes M., Harris A., Isak A., van Brunt A., Nguyen C., Du F., Courtney L., Kalicki J., Ozersky P., Abbott S., Armstrong J., Belter E.A., Caruso L., Cedroni M., Cotton M., Davidson T., Desai A., Elliott G., Erb T., Fronick C., Gaige T., Haakenson W., Haglund K., Holmes A., Harkins R., Kim K., Kruchowski S.S., Strong C.M., Grewal N., Goyea E., Hou S., Levy A., Martinka S., Mead K., McLellan M.D., Meyer R., Randall-Maher J., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Shah N., Swearengen-Shahid S., Snider J., Strong J.T., Thompson J., Yoakum M., Leonard S., Pearman C., Trani L., Radionenko M., Waligorski J.E., Wang C., Rock S.M., Tin-Wollam A.-M., Maupin R., Latreille P., Wendl M.C., Yang S.-P., Pohl C., Wallis J.W., Spieth J., Bieri T.A., Berkowicz N., Nelson J.O., Osborne J., Ding L., Meyer R., Sabo A., Shotland Y., Sinha P., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Jones T.A., She X., Ciccarelli F.D., Izaurralde E., Taylor J., Schmutz J., Myers R.M., Cox D.R., Huang X., McPherson J.D., Mardis E.R., Clifton S.W., Warren W.C., Chinwalla A.T., Eddy S.R., Marra M.A., Ovcharenko I., Furey T.S., Miller W., Eichler E.E., Bork P., Suyama M., Torrents D., Waterston R.H., Wilson R.K. Nature 434:724-731(2005) [PubMed: 15815621] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]	"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: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Bone marrow.
[6]	"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: 12665801] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-12, ACETYLATION AT ALA-2. Tissue: Platelet.
[7]	"Nck-2, a novel Src homology2/3-containing adaptor protein that interacts with the LIM-only protein PINCH and components of growth factor receptor kinase-signaling pathways." Tu Y., Li F., Wu C. Mol. Biol. Cell 9:3367-3382(1998) [PubMed: 9843575] [Abstract] Cited for: INTERACTION WITH NCK2.
[8]	"Antigens recognized by autologous antibody in patients with renal-cell carcinoma." Scanlan M.J., Gordan J.D., Williamson B., Stockert E., Bander N.H., Jongeneel C.V., Gure A.O., Jaeger D., Jaeger E., Knuth A., Chen Y.-T., Old L.J. Int. J. Cancer 83:456-464(1999) [PubMed: 10508479] [Abstract] Cited for: IDENTIFICATION AS A RENAL CANCER ANTIGEN. Tissue: Renal cell carcinoma.
[9]	"The LIM-only protein PINCH directly interacts with integrin-linked kinase and is recruited to integrin-rich sites in spreading cells." Tu Y., Li F., Goicoechea S., Wu C. Mol. Cell. Biol. 19:2425-2434(1999) [PubMed: 10022929] [Abstract] Cited for: INTERACTION WITH ILK AND NCK2, SUBCELLULAR LOCATION.
[10]	Colinge J., Superti-Furga G., Bennett K.L. Submitted (OCT-2008) to UniProtKB Cited for: IDENTIFICATION [LARGE SCALE ANALYSIS], MASS SPECTROMETRY.
[11]	"Solution structure of the focal adhesion adaptor PINCH LIM1 domain and characterization of its interaction with the integrin-linked kinase ankyrin repeat domain." Velyvis A., Yang Y., Wu C., Qin J. J. Biol. Chem. 276:4932-4939(2001) [PubMed: 11078733] [Abstract] Cited for: STRUCTURE BY NMR OF 1-70.
[12]	"Structural and functional insights into PINCH LIM4 domain-mediated integrin signaling." Velyvis A., Vaynberg J., Yang Y., Vinogradova O., Zhang Y., Wu C., Qin J. Nat. Struct. Biol. 10:558-564(2003) [PubMed: 12794636] [Abstract] Cited for: STRUCTURE BY NMR OF 188-251.
[13]	"Solution structure of the second and third LIM domain of particularly interesting new Cys-His protein (PINCH)." RIKEN structural genomics initiative (RSGI) Submitted (JUN-2006) to the PDB data bank Cited for: STRUCTURE BY NMR OF 71-190.
[14]	"The structural basis of integrin-linked kinase-PINCH interactions." Chiswell B.P., Zhang R., Murphy J.W., Boggon T.J., Calderwood D.A. Proc. Natl. Acad. Sci. U.S.A. 105:20677-20682(2008) [PubMed: 19074270] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS) OF 6-68 IN COMPLEX WITH ILK, MUTAGENESIS OF PHE-42; HIS-61; ASP-62 AND LEU-66.
[15]	"Structural basis of focal adhesion localization of LIM-only adaptor PINCH by integrin-linked kinase." Yang Y., Wang X., Hawkins C.A., Chen K., Vaynberg J., Mao X., Tu Y., Zuo X., Wang J., Wang Y.-X., Wu C., Tjandra N., Qin J. J. Biol. Chem. 284:5836-5844(2009) [PubMed: 19117955] [Abstract] Cited for: STRUCTURE BY NMR OF 1-70 IN COMPLEX WITH ILK, MUTAGENESIS OF PHE-42 AND ARG-56, SUBCELLULAR LOCATION.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U09284 mRNA. Translation: AAA20086.2.
AC010095 Genomic DNA. Translation: AAY14983.1.
AK314217 mRNA. Translation: BAG36891.1.
BC005341 mRNA. Translation: AAH05341.1.

IPI

IPI00788612.

PIR

JC2324.

RefSeq

NP_004978.2.

UniGene

Hs.597715
Hs.613268

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1G47	NMR	-	A	1-70	[»]
1NYP	NMR	-	A	188-251	[»]
1U5S	NMR	-	B	188-251	[»]
2COR	NMR	-	A	125-190	[»]
2D8X	NMR	-	A	71-126	[»]
2KBX	NMR	-	B	1-70	[»]
3F6Q	X-ray	1.60	B	6-68	[»]

SMR

P48059. Positions 6-100, 70-259, 192-307.

ModBase

Search...

Protein-protein interaction databases

IntAct

P48059. 7 interactions.

STRING

P48059.

2-D gel databases

OGP

P48059.

Proteomic databases

PRIDE

P48059.

Genome annotation databases

Ensembl

ENST00000332345; ENSP00000331775; ENSG00000169756; Homo sapiens. [Genome view]
ENST00000338045; ENSP00000337598; ENSG00000169756; Homo sapiens. [Genome view]
ENST00000393310; ENSP00000376987; ENSG00000169756; Homo sapiens. [Genome view]
ENST00000409441; ENSP00000387264; ENSG00000169756; Homo sapiens. [Genome view]
ENST00000410093; ENSP00000386926; ENSG00000169756; Homo sapiens. [Genome view]

GeneID

3987.

KEGG

hsa:3987.

UCSC

uc002teg.1. human.

Organism-specific databases

CTD

3987.

GeneCards

GC02M110638.
GC02P108609.

H-InvDB

HIX0002356.

HGNC

HGNC:6616. LIMS1.

MIM

602567. gene.

PharmGKB

PA30389.

GenAtlas

Search...

Phylogenomic databases

eggNOG

prNOG08115.

HOVERGEN

P48059.

InParanoid

P48059.

Enzyme and pathway databases

Reactome

REACT_20676. Cell junction organization.

Gene expression databases

ArrayExpress

P48059.

Bgee

P48059.

CleanEx

HS_LIMS1.

Genevestigator

P48059.

GermOnline

ENSG00000169756. Homo sapiens.

Family and domain databases

InterPro

IPR017351. PINCH.
IPR001781. Znf_LIM.
[Graphical view]

Gene3D

G3DSA:2.10.110.10. Znf_LIM. 3 hits.

Pfam

PF00412. LIM. 5 hits.
[Graphical view]

PIRSF

PIRSF038003. PINCH. 1 hit.

SMART

SM00132. LIM. 5 hits.
[Graphical view]

PROSITE

PS00478. LIM_DOMAIN_1. 4 hits.
PS50023. LIM_DOMAIN_2. 5 hits.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

15640.

SOURCE

Search...

Entry information

Entry name

LIMS1_HUMAN

Accession

Primary (citable) accession number: P48059
Secondary accession number(s): B2RAJ4, Q53TE0, Q9BS44

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1996
Last sequence update:	January 23, 2007
Last modified:	February 9, 2010
This is version 105 of the entry and version 4 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)

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.