5lmf

From Proteopedia

(Difference between revisions)

Current revision

Structure of C-terminal domain from S. cerevisiae Pat1 decapping activator bound to Dcp2 HLM3 peptide (region 484-500)

Structural highlights

5lmf is a 4 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.15Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9] ^[10] ^[11] ^[12] ^[13] ^[14] ^[15] ^[16] ^[17] ^[18]

Publication Abstract from PubMed

The Pat1 protein is a central player of eukaryotic mRNA decay that has also been implicated in translational control. It is commonly considered a central platform responsible for the recruitment of several RNA decay factors. We demonstrate here that a yeast-specific C-terminal region from Pat1 interacts with several short motifs, named helical leucine-rich motifs (HLMs), spread in the long C-terminal region of yeast Dcp2 decapping enzyme. Structures of Pat1-HLM complexes reveal the basis for HLM recognition by Pat1. We also identify a HLM present in yeast Xrn1, the main 5'-3' exonuclease involved in mRNA decay. We show further that the ability of yeast Pat1 to bind HLMs is required for efficient growth and normal mRNA decay. Overall, our analyses indicate that yeast Pat1 uses a single binding surface to successively recruit several mRNA decay factors and show that interaction between those factors is highly polymorphic between species.

A unique surface on Pat1 C-terminal domain directly interacts with Dcp2 decapping enzyme and Xrn1 5'-3' mRNA exonuclease in yeast.,Charenton C, Gaudon-Plesse C, Fourati Z, Taverniti V, Back R, Kolesnikova O, Seraphin B, Graille M Proc Natl Acad Sci U S A. 2017 Oct 24. pii: 201711680. doi:, 10.1073/pnas.1711680114. PMID:29078363^[19]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ 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
↑ Charenton C, Gaudon-Plesse C, Fourati Z, Taverniti V, Back R, Kolesnikova O, Seraphin B, Graille M. A unique surface on Pat1 C-terminal domain directly interacts with Dcp2 decapping enzyme and Xrn1 5'-3' mRNA exonuclease in yeast. Proc Natl Acad Sci U S A. 2017 Oct 24. pii: 201711680. doi:, 10.1073/pnas.1711680114. PMID:29078363 doi:http://dx.doi.org/10.1073/pnas.1711680114

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5lmf"

@@ Line 1: / Line 1: @@
 ==Structure of C-terminal domain from S. cerevisiae Pat1 decapping activator bound to Dcp2 HLM3 peptide (region 484-500)==
-<StructureSection load='5lmf' size='340' side='right' caption='[[5lmf]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
+<StructureSection load='5lmf' size='340' side='right'caption='[[5lmf]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5lmf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LMF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LMF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5lmf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LMF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LMF FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.15&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PAT1, MRT1, YCR077C, YCR77C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5lmf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lmf OCA], [http://pdbe.org/5lmf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5lmf RCSB], [http://www.ebi.ac.uk/pdbsum/5lmf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5lmf ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5lmf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5lmf OCA], [https://pdbe.org/5lmf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5lmf RCSB], [https://www.ebi.ac.uk/pdbsum/5lmf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5lmf ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PAT1_YEAST 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.<ref>PMID:8816497</ref> <ref>PMID:8972867</ref> <ref>PMID:10523645</ref> <ref>PMID:10394921</ref> <ref>PMID:10747033</ref> <ref>PMID:10779343</ref> <ref>PMID:10913177</ref> <ref>PMID:11027264</ref> <ref>PMID:10761922</ref> <ref>PMID:11514438</ref> <ref>PMID:12773554</ref> <ref>PMID:16179257</ref> <ref>PMID:17875743</ref> <ref>PMID:17429074</ref> <ref>PMID:17513695</ref> <ref>PMID:18086885</ref> <ref>PMID:19901074</ref> <ref>PMID:20832728</ref>
+[https://www.uniprot.org/uniprot/PAT1_YEAST 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.<ref>PMID:8816497</ref> <ref>PMID:8972867</ref> <ref>PMID:10523645</ref> <ref>PMID:10394921</ref> <ref>PMID:10747033</ref> <ref>PMID:10779343</ref> <ref>PMID:10913177</ref> <ref>PMID:11027264</ref> <ref>PMID:10761922</ref> <ref>PMID:11514438</ref> <ref>PMID:12773554</ref> <ref>PMID:16179257</ref> <ref>PMID:17875743</ref> <ref>PMID:17429074</ref> <ref>PMID:17513695</ref> <ref>PMID:18086885</ref> <ref>PMID:19901074</ref> <ref>PMID:20832728</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 18824]]
+[[Category: Large Structures]]
-[[Category: Back, R]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Charenton, C]]
+[[Category: Back R]]
-[[Category: Fourati, Z]]
+[[Category: Charenton C]]
-[[Category: Gaudon-Plesse, C]]
+[[Category: Fourati Z]]
-[[Category: Graille, M]]
+[[Category: Gaudon-Plesse C]]
-[[Category: Kolesnikova, O]]
+[[Category: Graille M]]
-[[Category: Seraphin, B]]
+[[Category: Kolesnikova O]]
-[[Category: Taverniti, V]]
+[[Category: Seraphin B]]
-[[Category: Isomerase]]
+[[Category: Taverniti V]]
-[[Category: Protein peptide complex]]
-[[Category: Rna binding protein]]

5lmf

From Proteopedia

Current revision

Structure of C-terminal domain from S. cerevisiae Pat1 decapping activator bound to Dcp2 HLM3 peptide (region 484-500)

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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