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Showing Protein LIM domain-containing protein 1 (HMDBP14106)

IdentificationBiological propertiesGene propertiesProtein propertiesExternal linksReferencesXMLShow 1 metabolite
Identification
HMDB Protein ID HMDBP14106
Secondary Accession Numbers None
Name LIM domain-containing protein 1
Synonyms Not Available
Gene Name LIMD1
Protein Type Unknown
Biological Properties
General Function Not Available
Specific 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.
Pathways
  • Hippo signaling pathway
  • Hippo signaling pathway - multiple species
Reactions Not Available
GO Classification
Biological Process
regulation of cell shape
cell migration
osteoblast development
cytoskeleton organization
negative regulation of transcription, DNA-dependent
cytoplasmic mRNA processing body assembly
positive regulation of gene silencing by miRNA
negative regulation of canonical Wnt receptor signaling pathway
gene silencing by miRNA
negative regulation of hippo signaling
negative regulation of osteoblast differentiation
regulation of transcription from RNA polymerase II promoter in response to hypoxia
regulation of transcription, DNA-dependent
response to hypoxia
phosphorylation
Cellular Component
cytosol
cytoplasmic mRNA processing body
RNA-induced silencing complex
focal adhesion
cytoplasm
plasma membrane
nucleus
nucleoplasm
adherens junction
transcription factor complex
Molecular Function
metal ion binding
transcription corepressor activity
Cellular Location Not Available
Gene Properties
Chromosome Location Not Available
Locus Not Available
SNPs Not Available
Gene Sequence Not Available
Protein Properties
Number of Residues 676
Molecular Weight 72189.575
Theoretical pI 6.653
Pfam Domain Function
Signals Not Available
Transmembrane Regions Not Available
Protein Sequence Not Available
GenBank ID Protein Not Available
UniProtKB/Swiss-Prot ID Q9UGP4
UniProtKB/Swiss-Prot Entry Name LIMD1_HUMAN
PDB IDs Not Available
GenBank Gene ID Not Available
GeneCard ID Not Available
GenAtlas ID Not Available
HGNC ID Not Available
References
General References
  1. Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G, Klein SL, Old S, Rasooly R, Good P, Guyer M, Peck AM, Derge JG, Lipman D, Collins FS, Jang W, Sherry S, Feolo M, Misquitta L, Lee E, Rotmistrovsky K, Greenhut SF, Schaefer CF, Buetow K, Bonner TI, Haussler D, Kent J, Kiekhaus M, Furey T, Brent M, Prange C, Schreiber K, Shapiro N, Bhat NK, Hopkins RF, Hsie F, Driscoll T, Soares MB, Casavant TL, Scheetz TE, Brown-stein MJ, Usdin TB, Toshiyuki S, Carninci P, Piao Y, Dudekula DB, Ko MS, Kawakami K, Suzuki Y, Sugano S, Gruber CE, Smith MR, Simmons B, Moore T, Waterman R, Johnson SL, Ruan Y, Wei CL, Mathavan S, Gunaratne PH, Wu J, Garcia AM, Hulyk SW, Fuh E, Yuan Y, Sneed A, Kowis C, Hodgson A, Muzny DM, McPherson J, Gibbs RA, Fahey J, Helton E, Ketteman M, Madan A, Rodrigues S, Sanchez A, Whiting M, Madari A, Young AC, Wetherby KD, Granite SJ, Kwong PN, Brinkley CP, Pearson RL, Bouffard GG, Blakesly RW, Green ED, Dickson MC, Rodriguez AC, Grimwood J, Schmutz J, Myers RM, Butterfield YS, Griffith M, Griffith OL, Krzywinski MI, Liao N, Morin R, Palmquist D, Petrescu AS, Skalska U, Smailus DE, Stott JM, Schnerch A, Schein JE, Jones SJ, Holt RA, Baross A, Marra MA, Clifton S, Makowski KA, Bosak S, Malek J: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res. 2004 Oct;14(10B):2121-7. [PubMed:15489334 ]
  2. Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP: A quantitative atlas of mitotic phosphorylation. Proc Natl Acad Sci U S A. 2008 Aug 5;105(31):10762-7. doi: 10.1073/pnas.0805139105. Epub 2008 Jul 31. [PubMed:18669648 ]
  3. Mayya V, Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK: Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions. Sci Signal. 2009 Aug 18;2(84):ra46. doi: 10.1126/scisignal.2000007. [PubMed:19690332 ]
  4. Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S: Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach. Anal Chem. 2009 Jun 1;81(11):4493-501. doi: 10.1021/ac9004309. [PubMed:19413330 ]
  5. Brill LM, Salomon AR, Ficarro SB, Mukherji M, Stettler-Gill M, Peters EC: Robust phosphoproteomic profiling of tyrosine phosphorylation sites from human T cells using immobilized metal affinity chromatography and tandem mass spectrometry. Anal Chem. 2004 May 15;76(10):2763-72. [PubMed:15144186 ]
  6. Kiss H, Kedra D, Kiss C, Kost-Alimova M, Yang Y, Klein G, Imreh S, Dumanski JP: The LZTFL1 gene is a part of a transcriptional map covering 250 kb within the common eliminated region 1 (C3CER1) in 3p21.3. Genomics. 2001 Apr 1;73(1):10-9. [PubMed:11352561 ]
  7. Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M: Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Sci Signal. 2010 Jan 12;3(104):ra3. doi: 10.1126/scisignal.2000475. [PubMed:20068231 ]
  8. Zhou H, Di Palma S, Preisinger C, Peng M, Polat AN, Heck AJ, Mohammed S: Toward a comprehensive characterization of a human cancer cell phosphoproteome. J Proteome Res. 2013 Jan 4;12(1):260-71. doi: 10.1021/pr300630k. Epub 2012 Dec 18. [PubMed:23186163 ]
  9. Burkard TR, Planyavsky M, Kaupe I, Breitwieser FP, Burckstummer T, Bennett KL, Superti-Furga G, Colinge J: Initial characterization of the human central proteome. BMC Syst Biol. 2011 Jan 26;5:17. doi: 10.1186/1752-0509-5-17. [PubMed:21269460 ]
  10. Bai SW, Herrera-Abreu MT, Rohn JL, Racine V, Tajadura V, Suryavanshi N, Bechtel S, Wiemann S, Baum B, Ridley AJ: Identification and characterization of a set of conserved and new regulators of cytoskeletal organization, cell morphology and migration. BMC Biol. 2011 Aug 11;9:54. doi: 10.1186/1741-7007-9-54. [PubMed:21834987 ]
  11. Bian Y, Song C, Cheng K, Dong M, Wang F, Huang J, Sun D, Wang L, Ye M, Zou H: An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome. J Proteomics. 2014 Jan 16;96:253-62. doi: 10.1016/j.jprot.2013.11.014. Epub 2013 Nov 22. [PubMed:24275569 ]
  12. Rigbolt KT, Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova I, Kassem M, Mann M, Olsen JV, Blagoev B: System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation. Sci Signal. 2011 Mar 15;4(164):rs3. doi: 10.1126/scisignal.2001570. [PubMed:21406692 ]
  13. Langer EM, Feng Y, Zhaoyuan H, Rauscher FJ 3rd, Kroll KL, Longmore GD: Ajuba LIM proteins are snail/slug corepressors required for neural crest development in Xenopus. Dev Cell. 2008 Mar;14(3):424-36. doi: 10.1016/j.devcel.2008.01.005. [PubMed:18331720 ]
  14. Das Thakur M, Feng Y, Jagannathan R, Seppa MJ, Skeath JB, Longmore GD: Ajuba LIM proteins are negative regulators of the Hippo signaling pathway. Curr Biol. 2010 Apr 13;20(7):657-62. doi: 10.1016/j.cub.2010.02.035. Epub 2010 Mar 18. [PubMed:20303269 ]
  15. James V, Zhang Y, Foxler DE, de Moor CH, Kong YW, Webb TM, Self TJ, Feng Y, Lagos D, Chu CY, Rana TM, Morley SJ, Longmore GD, Bushell M, Sharp TV: LIM-domain proteins, LIMD1, Ajuba, and WTIP are required for microRNA-mediated gene silencing. Proc Natl Acad Sci U S A. 2010 Jul 13;107(28):12499-504. doi: 10.1073/pnas.0914987107. Epub 2010 Jun 28. [PubMed:20616046 ]
  16. Foxler DE, Bridge KS, James V, Webb TM, Mee M, Wong SC, Feng Y, Constantin-Teodosiu D, Petursdottir TE, Bjornsson J, Ingvarsson S, Ratcliffe PJ, Longmore GD, Sharp TV: The LIMD1 protein bridges an association between the prolyl hydroxylases and VHL to repress HIF-1 activity. Nat Cell Biol. 2012 Jan 29;14(2):201-8. doi: 10.1038/ncb2424. [PubMed:22286099 ]
  17. Feng Y, Longmore GD: The LIM protein Ajuba influences interleukin-1-induced NF-kappaB activation by affecting the assembly and activity of the protein kinase Czeta/p62/TRAF6 signaling complex. Mol Cell Biol. 2005 May;25(10):4010-22. doi: 10.1128/MCB.25.10.4010-4022.2005. [PubMed:15870274 ]
  18. Kiss H, Kedra D, Yang Y, Kost-Alimova M, Kiss C, O'Brien KP, Fransson I, Klein G, Imreh S, Dumanski JP: A novel gene containing LIM domains (LIMD1) is located within the common eliminated region 1 (C3CER1) in 3p21.3. Hum Genet. 1999 Dec;105(6):552-9. doi: 10.1007/s004399900188. [PubMed:10647888 ]
  19. Sharp TV, Munoz F, Bourboulia D, Presneau N, Darai E, Wang HW, Cannon M, Butcher DN, Nicholson AG, Klein G, Imreh S, Boshoff C: LIM domains-containing protein 1 (LIMD1), a tumor suppressor encoded at chromosome 3p21.3, binds pRB and represses E2F-driven transcription. Proc Natl Acad Sci U S A. 2004 Nov 23;101(47):16531-6. doi: 10.1073/pnas.0407123101. Epub 2004 Nov 12. [PubMed:15542589 ]
  20. Huggins CJ, Andrulis IL: Cell cycle regulated phosphorylation of LIMD1 in cell lines and expression in human breast cancers. Cancer Lett. 2008 Aug 18;267(1):55-66. doi: 10.1016/j.canlet.2008.03.015. Epub 2008 Apr 24. [PubMed:18439753 ]
  21. Spendlove I, Al-Attar A, Watherstone O, Webb TM, Ellis IO, Longmore GD, Sharp TV: Differential subcellular localisation of the tumour suppressor protein LIMD1 in breast cancer correlates with patient survival. Int J Cancer. 2008 Nov 15;123(10):2247-53. doi: 10.1002/ijc.23851. [PubMed:18712738 ]