B5DEH0 (LIMD1_RAT) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
LIM domain-containing protein 1

Gene names

Name:

Limd1

Organism

Rattus norvegicus (Rat) [Reference proteome]

Taxonomic identifier

10116 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Rattus

Protein attributes

Sequence length	663 AA.
Sequence status	Complete.
Protein existence	Evidence at transcript level

General annotation (Comments)

Function	Adapter or scaffold protein which participates in the assembly of numerous protein complexes and is involved in several cellular processes such as cell fate determination, cytoskeletal organization, repression of gene transcription, cell-cell adhesion, cell differentiation, proliferation and migration. Positively regulates microRNA (miRNA)-mediated gene silencing and is essential for P-body formation and integrity. Acts as a hypoxic regulator by bridging an association between the prolyl hydroxylases and VHL enabling efficient degradation of HIF1A. Acts as a transcriptional corepressor for SNAI1- and SNAI2/SLUG-dependent repression of E-cadherin transcription. Negatively regulates the Hippo signaling pathway and antagonizes phosphorylation of YAP1. Inhibits E2F-mediated transcription, and suppresses the expression of the majority of genes with E2F1-responsive elements. Regulates osteoblast development, function, differentiation and stress osteoclastogenesis. Enhances the ability of TRAF6 to activate adapter protein complex 1 (AP-1) and negatively regulates the canonical Wnt receptor signaling pathway in osteoblasts. May act as a tumor suppressor by inhibiting cell proliferation By similarity.
Subunit structure	Interacts with SQSTM1 and RB1. Interacts with EIF4E, EIF2C1, EIF2C2, DCP2, DDX6, LATS1, LATS2, EGLN1/PHD2, EGLN2/PHD1 and EGLN3/PHD3. Interacts (via LIM zinc-binding 2) with VHL. Found in a complex composed of LIMD1, VHL, EGLN1/PHD2, TCEB2 AND CUL2. Found in a complex with TRAF6, PRKCZ and SQSTM1. Interacts (via LIM domains) with TRAF6. Interacts (via LIM domains) with SNAI1 (via SNAG domain), SNAI2/SLUG (via SNAG domain) and SCRT1 (via SNAG domain) By similarity.
Subcellular location	Cytoplasm By similarity. Nucleus By similarity. Cytoplasm › P-body By similarity. Cell junction › adherens junction By similarity. Cell junction › focal adhesion By similarity. Note: Shuttles between cytoplasm and nucleus but is localized predominantly to the cytoplasm. Found in the nucleus but not nucleoli. Co-localizes with VCL in the focal adhesions By similarity.
Post-translational modification	Phosphorylated during mitosis By similarity.
Sequence similarities	Belongs to the zyxin/ajuba family. Contains 3 LIM zinc-binding domains.

Ontologies

Keywords
Biological process	RNA-mediated gene silencing Transcription Transcription regulation
Cellular component	Cell junction Cytoplasm Nucleus
Disease	Tumor suppressor
Domain	LIM domain Repeat
Ligand	Metal-binding Zinc
Molecular function	Repressor
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	cell migration Inferred from electronic annotation. Source: Compara cytoplasmic mRNA processing body assembly Inferred from electronic annotation. Source: Compara cytoskeleton organization Inferred from electronic annotation. Source: Compara gene silencing by miRNA Inferred from electronic annotation. Source: Compara negative regulation of canonical Wnt receptor signaling pathway Inferred from sequence or structural similarity. Source: UniProtKB negative regulation of hippo signaling cascade Inferred from sequence or structural similarity. Source: UniProtKB negative regulation of osteoblast differentiation Inferred from sequence or structural similarity. Source: UniProtKB negative regulation of transcription, DNA-dependent Inferred from sequence or structural similarity. Source: UniProtKB osteoblast development Inferred from sequence or structural similarity. Source: UniProtKB phosphorylation Inferred from sequence or structural similarity. Source: UniProtKB positive regulation of gene silencing by miRNA Inferred from sequence or structural similarity. Source: UniProtKB regulation of cell shape Inferred from electronic annotation. Source: Compara response to hypoxia Inferred from sequence or structural similarity. Source: UniProtKB transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	RNA-induced silencing complex Inferred from electronic annotation. Source: Compara cytoplasm Inferred from sequence or structural similarity. Source: UniProtKB cytoplasmic mRNA processing body Inferred from electronic annotation. Source: UniProtKB-SubCell focal adhesion Inferred from sequence or structural similarity. Source: UniProtKB nucleus Inferred from sequence or structural similarity. Source: UniProtKB
Molecular_function	transcription corepressor activity Inferred from sequence or structural similarity. Source: UniProtKB 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
	Chain	1 – 663	663	LIM domain-containing protein 1		PRO_0000416961
Regions
	Domain	457 – 518	62	LIM zinc-binding 1
	Domain	522 – 582	61	LIM zinc-binding 2
	Domain	583 – 651	69	LIM zinc-binding 3
	Region	54 – 128	75	Mediates nuclear export By similarity
	Region	180 – 251	72	Interaction with EGLN1/PHD2 By similarity
	Region	391 – 429	39	Interaction with RB1 By similarity
	Region	459 – 663	205	Necessary for nuclear localization By similarity
	Compositional bias	58 – 64	7	Poly-Gln
Amino acid modifications
	Modified residue	268	1	Phosphoserine By similarity
	Modified residue	291	1	Phosphoserine By similarity
	Modified residue	408	1	Phosphoserine By similarity

Sequences

	Sequence		Length	Mass (Da)
	B5DEH0 [UniParc]. Last modified October 14, 2008. Version 1. Checksum: E28C6B3DB3AE3629	FASTA	663	71,393
	10 20 30 40 50 60 MDKYDDLGLE ASKFIEDLNM YEASKDGLFR VDKGASNNPE FEETRRVFAT KMAKIHLQQQ 70 80 90 100 110 120 QQQQLLQEEA LPRAGRSPIN GGNRQGVSSK LAADGAAKPP LAVPTVAPGL ATTTMAVQSS 130 140 150 160 170 180 YPPQEQRTRP SAHGARPGSQ NCGSREGPVS SQRPALHGLG PCEDPSCLTH GDYYDNFSLA 190 200 210 220 230 240 SPQWGDKPEE SPSMSLSVGS GWPGCPGNDS LSHRSCGDSH PYHPQLSMCS GRSFESGQDS 250 260 270 280 290 300 GIGGHSSEKP TGLWSTASSQ RVNLGFSSTG LENGTPAQPK GTTVSAPMVP SSTSQGACLR 310 320 330 340 350 360 RDSSLGYEAP GRVFKPLVDT QPWLQDGPKS YLSVSAPLSS TTSKDNAQTG MTAGLDPKLG 370 380 390 400 410 420 CVESGTSPKP SPTSNVHPVM SAPSELSCKE SPPSWSTDSS LGPVLPESPT PSRVRLPCQT 430 440 450 460 470 480 LTPGPELGPS TAELKLEALT QRLEREMDAH PKADYFGACV KCSKGVFGAG QACQAMGDLY 490 500 510 520 530 540 HDACFTCAAC SRKLRGKAFY FVNGKVFCEE DFLYSGFQQS ADRCFLCGHL IMDMILQALG 550 560 570 580 590 600 KSYHPGCFRC VICNECLDGV PFTVDSENKI YCVRDYHKVL APKCAACGLP ILPPEGSDET 610 620 630 640 650 660 IRVVSMDRDY HVECYHCEDC GLELNDEDGH RCYPLEDHLF CHSCHVKRLE KGPSPASLHQ HHF

References

[1]	"Genome sequence of the Brown Norway rat yields insights into mammalian evolution." Gibbs R.A., Weinstock G.M., Metzker M.L., Muzny D.M., Sodergren E.J., Scherer S., Scott G., Steffen D., Worley K.C., Burch P.E., Okwuonu G., Hines S., Lewis L., Deramo C., Delgado O., Dugan-Rocha S., Miner G., Morgan M. , Hawes A., Gill R., Holt R.A., Adams M.D., Amanatides P.G., Baden-Tillson H., Barnstead M., Chin S., Evans C.A., Ferriera S., Fosler C., Glodek A., Gu Z., Jennings D., Kraft C.L., Nguyen T., Pfannkoch C.M., Sitter C., Sutton G.G., Venter J.C., Woodage T., Smith D., Lee H.-M., Gustafson E., Cahill P., Kana A., Doucette-Stamm L., Weinstock K., Fechtel K., Weiss R.B., Dunn D.M., Green E.D., Blakesley R.W., Bouffard G.G., De Jong P.J., Osoegawa K., Zhu B., Marra M., Schein J., Bosdet I., Fjell C., Jones S., Krzywinski M., Mathewson C., Siddiqui A., Wye N., McPherson J., Zhao S., Fraser C.M., Shetty J., Shatsman S., Geer K., Chen Y., Abramzon S., Nierman W.C., Havlak P.H., Chen R., Durbin K.J., Egan A., Ren Y., Song X.-Z., Li B., Liu Y., Qin X., Cawley S., Cooney A.J., D'Souza L.M., Martin K., Wu J.Q., Gonzalez-Garay M.L., Jackson A.R., Kalafus K.J., McLeod M.P., Milosavljevic A., Virk D., Volkov A., Wheeler D.A., Zhang Z., Bailey J.A., Eichler E.E., Tuzun E., Birney E., Mongin E., Ureta-Vidal A., Woodwark C., Zdobnov E., Bork P., Suyama M., Torrents D., Alexandersson M., Trask B.J., Young J.M., Huang H., Wang H., Xing H., Daniels S., Gietzen D., Schmidt J., Stevens K., Vitt U., Wingrove J., Camara F., Mar Alba M., Abril J.F., Guigo R., Smit A., Dubchak I., Rubin E.M., Couronne O., Poliakov A., Huebner N., Ganten D., Goesele C., Hummel O., Kreitler T., Lee Y.-A., Monti J., Schulz H., Zimdahl H., Himmelbauer H., Lehrach H., Jacob H.J., Bromberg S., Gullings-Handley J., Jensen-Seaman M.I., Kwitek A.E., Lazar J., Pasko D., Tonellato P.J., Twigger S., Ponting C.P., Duarte J.M., Rice S., Goodstadt L., Beatson S.A., Emes R.D., Winter E.E., Webber C., Brandt P., Nyakatura G., Adetobi M., Chiaromonte F., Elnitski L., Eswara P., Hardison R.C., Hou M., Kolbe D., Makova K., Miller W., Nekrutenko A., Riemer C., Schwartz S., Taylor J., Yang S., Zhang Y., Lindpaintner K., Andrews T.D., Caccamo M., Clamp M., Clarke L., Curwen V., Durbin R.M., Eyras E., Searle S.M., Cooper G.M., Batzoglou S., Brudno M., Sidow A., Stone E.A., Payseur B.A., Bourque G., Lopez-Otin C., Puente X.S., Chakrabarti K., Chatterji S., Dewey C., Pachter L., Bray N., Yap V.B., Caspi A., Tesler G., Pevzner P.A., Haussler D., Roskin K.M., Baertsch R., Clawson H., Furey T.S., Hinrichs A.S., Karolchik D., Kent W.J., Rosenbloom K.R., Trumbower H., Weirauch M., Cooper D.N., Stenson P.D., Ma B., Brent M., Arumugam M., Shteynberg D., Copley R.R., Taylor M.S., Riethman H., Mudunuri U., Peterson J., Guyer M., Felsenfeld A., Old S., Mockrin S., Collins F.S. Nature 428:493-521(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: Brown Norway.
[2]	Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C. Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: Brown Norway.
[3]	"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: Prostate.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AABR03062206 Genomic DNA. No translation available. AABR03062956 Genomic DNA. No translation available. CH473954 Genomic DNA. Translation: EDL76759.1. BC168666 mRNA. Translation: AAI68666.1.
IPI	IPI00371306.
RefSeq	NP_001106208.1. NM_001112737.2.
UniGene	Rn.228776.
3D structure databases
ModBase	Search...
Proteomic databases
PaxDb	B5DEH0.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENSRNOT00000006554; ENSRNOP00000006554; ENSRNOG00000004837.
GeneID	316101.
KEGG	rno:316101.
UCSC	RGD:1309830. rat.
Organism-specific databases
CTD	8994.
RGD	1309830. Limd1.
Phylogenomic databases
eggNOG	NOG331290.
GeneTree	ENSGT00610000085810.
HOGENOM	HOG000072700.
HOVERGEN	HBG052327.
KO	K16682.
OMA	SLASPKW.
OrthoDB	EOG42BX96.
Gene expression databases
Genevestigator	B5DEH0.
Family and domain databases
Gene3D	2.10.110.10. 3 hits.
InterPro	IPR001781. Znf_LIM. [Graphical view]
Pfam	PF00412. LIM. 3 hits. [Graphical view]
SMART	SM00132. LIM. 3 hits. [Graphical view]
PROSITE	PS00478. LIM_DOMAIN_1. 2 hits. PS50023. LIM_DOMAIN_2. 3 hits. [Graphical view]
ProtoNet	Search...
Other
NextBio	670435.

Entry information

Entry name

LIMD1_RAT

Accession

Primary (citable) accession number: B5DEH0

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 18, 2012
Last sequence update:	October 14, 2008
Last modified:	April 3, 2013
This is version 37 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program