| Structural highlights
4n0a is a 10 chain structure with sequence from Baker's yeast. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Gene: | LSM3, SMX4, USS2, YLR438C-A (Baker's yeast), LSM2, SMX5, SNP3, YBL026W, YBL0425 (Baker's yeast), MRT1, PAT1, YCR077C, YCR77C (Baker's yeast) |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
[LSM3_YEAST] Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner. Component of the cytoplasmic LSM1-LSM7 complex which is thought to be involved in mRNA degradation by activating the decapping step. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 snRNP, U4/U6.U5 snRNP, and free U6 snRNP). It binds directly to the U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. It probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping. LSM3 binds specifically to the 3'-terminal U-tract of U6 snRNA. LSM2-LSM8 probably is involved in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. LSM3, probably in a complex that contains LSM2-LSM7 but not LSM1 or LSM8, associates with the precursor of the RNA component of RNase P (pre-P RNA) and may be involved in maturing pre-P RNA. LSM3 is required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.[1] [2] [3] [4] [5] [6] [PAT1_YEAST] Activator of decapping that functions as a general and active mechanism of translational repression and required for P-body formation. First decay factor recruited to mRNA, at a time when the mRNA is still associated with translation factors. Subsequently, PAT1 recruits the hepta-heterodimer LSM1-LSM7 complex to P-bodies. In association with the LSM1-LSM7 complex, stabilizes the 3' terminus of mRNAs. This association is also required for mosaic virus genomic RNA translation. Modulates the rates of mRNA-decapping that occur following deadenylation. Might be required for promoting the formation or the stabilization of the preinitiation translation complexes. Required for 40S ribosomal subunit joining to capped and/or polyadenylated mRNA. With other P-body components, enhances the formation of retrotransposition-competent Ty1 virus-like particles. Necessary for accurate chromosome transmission during cell division.[7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [LSM2_YEAST] Component of LSm protein complexes, which are involved in RNA processing and may function in a chaperone-like manner. Component of the cytoplasmic LSM1-LSM7 complex which is thought to be involved in mRNA degradation by activating the decapping step. Component of the nuclear LSM2-LSM8 complex, which is involved in splicing of nuclear mRNAs. LSM2-LSM8 associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 snRNP, U4/U6.U5 snRNP, and free U6 snRNP). It binds directly to the U6 snRNA and plays a role in the biogenesis and stability of the U6 snRNP and U4/U6 snRNP complexes. It probably also is involved degradation of nuclear pre-mRNA by targeting them for decapping. LSM2 binds specifically to the 3'-terminal U-tract of U6 snRNA. LSM2-LSM8 probably is involved in processing of pre-tRNAs, pre-rRNAs and U3 snoRNA. LSM2, probably in a complex that contains LSM2-LSM7 but not LSM1 or LSM8, associates with the precursor of the RNA component of RNase P (pre-P RNA) and may be involved in maturing pre-P RNA. LSM2 is required for processing of pre-tRNAs, pre-rRNAs and U3 snoRNA.[25] [26] [27] [28] [29]
Publication Abstract from PubMed
The evolutionarily conserved Lsm1-7-Pat1 complex is the most critical activator of mRNA decapping in eukaryotic cells and plays many roles in normal decay, AU-rich element-mediated decay, and miRNA silencing, yet how Pat1 interacts with the Lsm1-7 complex is unknown. Here, we show that Lsm2 and Lsm3 bridge the interaction between the C-terminus of Pat1 (Pat1C) and the Lsm1-7 complex. The Lsm2-3-Pat1C complex and the Lsm1-7-Pat1C complex stimulate decapping in vitro to a similar extent and exhibit similar RNA-binding preference. The crystal structure of the Lsm2-3-Pat1C complex shows that Pat1C binds to Lsm2-3 to form an asymmetric complex with three Pat1C molecules surrounding a heptameric ring formed by Lsm2-3. Structure-based mutagenesis revealed the importance of Lsm2-3-Pat1C interactions in decapping activation in vivo. Based on the structure of Lsm2-3-Pat1C, a model of Lsm1-7-Pat1 complex is constructed and how RNA binds to this complex is discussed.Cell Research advance online publication 19 November 2013; doi:10.1038/cr.2013.152.
Lsm2 and Lsm3 bridge the interaction of the Lsm1-7 complex with Pat1 for decapping activation.,Wu D, Muhlrad D, Bowler MW, Liu Z, Parker R, Song H Cell Res. 2013 Nov 19. doi: 10.1038/cr.2013.152. PMID:24247251[30]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Seraphin B. Sm and Sm-like proteins belong to a large family: identification of proteins of the U6 as well as the U1, U2, U4 and U5 snRNPs. EMBO J. 1995 May 1;14(9):2089-98. PMID:7744014
- ↑ Bouveret E, Rigaut G, Shevchenko A, Wilm M, Seraphin B. A Sm-like protein complex that participates in mRNA degradation. EMBO J. 2000 Apr 3;19(7):1661-71. PMID:10747033 doi:10.1093/emboj/19.7.1661
- ↑ Tharun S, He W, Mayes AE, Lennertz P, Beggs JD, Parker R. Yeast Sm-like proteins function in mRNA decapping and decay. Nature. 2000 Mar 30;404(6777):515-8. PMID:10761922 doi:10.1038/35006676
- ↑ Kufel J, Allmang C, Verdone L, Beggs JD, Tollervey D. Lsm proteins are required for normal processing of pre-tRNAs and their efficient association with La-homologous protein Lhp1p. Mol Cell Biol. 2002 Jul;22(14):5248-56. PMID:12077351
- ↑ Kufel J, Allmang C, Petfalski E, Beggs J, Tollervey D. Lsm Proteins are required for normal processing and stability of ribosomal RNAs. J Biol Chem. 2003 Jan 24;278(4):2147-56. Epub 2002 Nov 15. PMID:12438310 doi:http://dx.doi.org/10.1074/jbc.M208856200
- ↑ Kufel J, Bousquet-Antonelli C, Beggs JD, Tollervey D. Nuclear pre-mRNA decapping and 5' degradation in yeast require the Lsm2-8p complex. Mol Cell Biol. 2004 Nov;24(21):9646-57. PMID:15485930 doi:http://dx.doi.org/10.1128/MCB.24.21.9646-9657.2004
- ↑ Hatfield L, Beelman CA, Stevens A, Parker R. Mutations in trans-acting factors affecting mRNA decapping in Saccharomyces cerevisiae. Mol Cell Biol. 1996 Oct;16(10):5830-8. PMID:8816497
- ↑ Wang X, Watt PM, Louis EJ, Borts RH, Hickson ID. Pat1: a topoisomerase II-associated protein required for faithful chromosome transmission in Saccharomyces cerevisiae. Nucleic Acids Res. 1996 Dec 1;24(23):4791-7. PMID:8972867
- ↑ Zhang S, Williams CJ, Hagan K, Peltz SW. Mutations in VPS16 and MRT1 stabilize mRNAs by activating an inhibitor of the decapping enzyme. Mol Cell Biol. 1999 Nov;19(11):7568-76. PMID:10523645
- ↑ Wang X, Watt PM, Borts RH, Louis EJ, Hickson ID. The topoisomerase II-associated protein, Pat1p, is required for maintenance of rDNA locus stability in Saccharomyces cerevisiae. Mol Gen Genet. 1999 Jun;261(4-5):831-40. PMID:10394921
- ↑ Bouveret E, Rigaut G, Shevchenko A, Wilm M, Seraphin B. A Sm-like protein complex that participates in mRNA degradation. EMBO J. 2000 Apr 3;19(7):1661-71. PMID:10747033 doi:10.1093/emboj/19.7.1661
- ↑ Wyers F, Minet M, Dufour ME, Vo LT, Lacroute F. Deletion of the PAT1 gene affects translation initiation and suppresses a PAB1 gene deletion in yeast. Mol Cell Biol. 2000 May;20(10):3538-49. PMID:10779343
- ↑ Bonnerot C, Boeck R, Lapeyre B. The two proteins Pat1p (Mrt1p) and Spb8p interact in vivo, are required for mRNA decay, and are functionally linked to Pab1p. Mol Cell Biol. 2000 Aug;20(16):5939-46. PMID:10913177
- ↑ Schwartz DC, Parker R. mRNA decapping in yeast requires dissociation of the cap binding protein, eukaryotic translation initiation factor 4E. Mol Cell Biol. 2000 Nov;20(21):7933-42. PMID:11027264
- ↑ Tharun S, He W, Mayes AE, Lennertz P, Beggs JD, Parker R. Yeast Sm-like proteins function in mRNA decapping and decay. Nature. 2000 Mar 30;404(6777):515-8. PMID:10761922 doi:10.1038/35006676
- ↑ He W, Parker R. The yeast cytoplasmic LsmI/Pat1p complex protects mRNA 3' termini from partial degradation. Genetics. 2001 Aug;158(4):1445-55. PMID:11514438
- ↑ Noueiry AO, Diez J, Falk SP, Chen J, Ahlquist P. Yeast Lsm1p-7p/Pat1p deadenylation-dependent mRNA-decapping factors are required for brome mosaic virus genomic RNA translation. Mol Cell Biol. 2003 Jun;23(12):4094-106. PMID:12773554
- ↑ Coller J, Parker R. General translational repression by activators of mRNA decapping. Cell. 2005 Sep 23;122(6):875-86. PMID:16179257 doi:10.1016/j.cell.2005.07.012
- ↑ Lotan R, Goler-Baron V, Duek L, Haimovich G, Choder M. The Rpb7p subunit of yeast RNA polymerase II plays roles in the two major cytoplasmic mRNA decay mechanisms. J Cell Biol. 2007 Sep 24;178(7):1133-43. Epub 2007 Sep 17. PMID:17875743 doi:10.1083/jcb.200701165
- ↑ Teixeira D, Parker R. Analysis of P-body assembly in Saccharomyces cerevisiae. Mol Biol Cell. 2007 Jun;18(6):2274-87. Epub 2007 Apr 11. PMID:17429074 doi:10.1091/mbc.E07-03-0199
- ↑ Chowdhury A, Mukhopadhyay J, Tharun S. The decapping activator Lsm1p-7p-Pat1p complex has the intrinsic ability to distinguish between oligoadenylated and polyadenylated RNAs. RNA. 2007 Jul;13(7):998-1016. Epub 2007 May 18. PMID:17513695 doi:rna.502507
- ↑ Pilkington GR, Parker R. Pat1 contains distinct functional domains that promote P-body assembly and activation of decapping. Mol Cell Biol. 2008 Feb;28(4):1298-312. Epub 2007 Dec 17. PMID:18086885 doi:10.1128/MCB.00936-07
- ↑ Checkley MA, Nagashima K, Lockett SJ, Nyswaner KM, Garfinkel DJ. P-body components are required for Ty1 retrotransposition during assembly of retrotransposition-competent virus-like particles. Mol Cell Biol. 2010 Jan;30(2):382-98. doi: 10.1128/MCB.00251-09. Epub 2009 Nov 9. PMID:19901074 doi:10.1128/MCB.00251-09
- ↑ Nissan T, Rajyaguru P, She M, Song H, Parker R. Decapping activators in Saccharomyces cerevisiae act by multiple mechanisms. Mol Cell. 2010 Sep 10;39(5):773-83. doi: 10.1016/j.molcel.2010.08.025. PMID:20832728 doi:10.1016/j.molcel.2010.08.025
- ↑ Bouveret E, Rigaut G, Shevchenko A, Wilm M, Seraphin B. A Sm-like protein complex that participates in mRNA degradation. EMBO J. 2000 Apr 3;19(7):1661-71. PMID:10747033 doi:10.1093/emboj/19.7.1661
- ↑ Kufel J, Allmang C, Verdone L, Beggs JD, Tollervey D. Lsm proteins are required for normal processing of pre-tRNAs and their efficient association with La-homologous protein Lhp1p. Mol Cell Biol. 2002 Jul;22(14):5248-56. PMID:12077351
- ↑ Kufel J, Allmang C, Petfalski E, Beggs J, Tollervey D. Lsm Proteins are required for normal processing and stability of ribosomal RNAs. J Biol Chem. 2003 Jan 24;278(4):2147-56. Epub 2002 Nov 15. PMID:12438310 doi:http://dx.doi.org/10.1074/jbc.M208856200
- ↑ Kufel J, Allmang C, Verdone L, Beggs J, Tollervey D. A complex pathway for 3' processing of the yeast U3 snoRNA. Nucleic Acids Res. 2003 Dec 1;31(23):6788-97. PMID:14627812
- ↑ Kufel J, Bousquet-Antonelli C, Beggs JD, Tollervey D. Nuclear pre-mRNA decapping and 5' degradation in yeast require the Lsm2-8p complex. Mol Cell Biol. 2004 Nov;24(21):9646-57. PMID:15485930 doi:http://dx.doi.org/10.1128/MCB.24.21.9646-9657.2004
- ↑ Wu D, Muhlrad D, Bowler MW, Liu Z, Parker R, Song H. Lsm2 and Lsm3 bridge the interaction of the Lsm1-7 complex with Pat1 for decapping activation. Cell Res. 2013 Nov 19. doi: 10.1038/cr.2013.152. PMID:24247251 doi:http://dx.doi.org/10.1038/cr.2013.152
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