4ogp

From Proteopedia

(Difference between revisions)

Revision as of 07:24, 25 January 2023

X-ray structure of the C-terminal domain of Pat1 (decapping activator)

Structural highlights

4ogp is a 2 chain structure with sequence from Saccharomyces cerevisiae S288C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
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

Eukaryotic mRNA decay is a highly regulated process allowing cells to rapidly modulate protein production in response to internal and environmental cues. Mature translatable eukaryotic mRNAs are protected from fast and uncontrolled degradation in the cytoplasm by two cis-acting stability determinants: a methylguanosine (m(7)G) cap and a poly(A) tail at their 5' and 3' extremities, respectively. The hydrolysis of the m(7)G cap structure, known as decapping, is performed by the complex composed of the Dcp2 catalytic subunit and its partner Dcp1. The Dcp1-Dcp2 decapping complex has a low intrinsic activity and requires accessory factors to be fully active. Among these factors, Pat1 is considered to be a central scaffolding protein involved in Dcp2 activation but also in inhibition of translation initiation. Here, we present the structural and functional study of the C-terminal domain from S. cerevisiae Pat1 protein. We have identified two conserved and functionally important regions located at both extremities of the domain. The first region is involved in binding to Lsm1-7 complex. The second patch is specific for fungal proteins and is responsible for Pat1 interaction with Edc3. These observations support the plasticity of the protein interaction network involved in mRNA decay and show that evolution has extended the C-terminal alpha-helical domain from fungal Pat1 proteins to generate a new binding platform for protein partners.

The C-terminal domain from S. cerevisiae Pat1 displays two conserved regions involved in decapping factor recruitment.,Fourati Z, Kolesnikova O, Back R, Keller J, Charenton C, Taverniti V, Plesse CG, Lazar N, Durand D, van Tilbeurgh H, Seraphin B, Graille M PLoS One. 2014 May 15;9(5):e96828. doi: 10.1371/journal.pone.0096828. eCollection, 2014. PMID:24830408^[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
↑ Fourati Z, Kolesnikova O, Back R, Keller J, Charenton C, Taverniti V, Plesse CG, Lazar N, Durand D, van Tilbeurgh H, Seraphin B, Graille M. The C-terminal domain from S. cerevisiae Pat1 displays two conserved regions involved in decapping factor recruitment. PLoS One. 2014 May 15;9(5):e96828. doi: 10.1371/journal.pone.0096828. eCollection, 2014. PMID:24830408 doi:http://dx.doi.org/10.1371/journal.pone.0096828

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/4ogp"

@@ Line 3: / Line 3: @@
 <StructureSection load='4ogp' size='340' side='right'caption='[[4ogp]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4ogp]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OGP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4OGP FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4ogp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4OGP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4OGP FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ojj|4ojj]]</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=4ogp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ogp OCA], [https://pdbe.org/4ogp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ogp RCSB], [https://www.ebi.ac.uk/pdbsum/4ogp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ogp ProSAT]</span></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=559292 Baker's yeast])</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=4ogp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ogp OCA], [http://pdbe.org/4ogp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ogp RCSB], [http://www.ebi.ac.uk/pdbsum/4ogp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ogp 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 24: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Baker's yeast]]
 [[Category: Large Structures]]
-[[Category: Back, R]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Fourati-Kammoun, Z]]
+[[Category: Back R]]
-[[Category: Gaudon-Plesse, C]]
+[[Category: Fourati-Kammoun Z]]
-[[Category: Graille, M]]
+[[Category: Gaudon-Plesse C]]
-[[Category: Keller, J]]
+[[Category: Graille M]]
-[[Category: Kolesnikova, O]]
+[[Category: Keller J]]
-[[Category: Lazar, N]]
+[[Category: Kolesnikova O]]
-[[Category: Seraphin, B]]
+[[Category: Lazar N]]
-[[Category: Arm-repeat fold]]
+[[Category: Seraphin B]]
-[[Category: Dcp2]]
-[[Category: Lsm1-7]]
-[[Category: Rna binding protein]]

4ogp

From Proteopedia

Revision as of 07:24, 25 January 2023

X-ray structure of the C-terminal domain of Pat1 (decapping activator)

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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