5c0y

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of the Rrp6 catalytic domain bound to poly(U) RNA

Structural highlights

5c0y is a 4 chain structure with sequence from Saccharomyces cerevisiae S288C and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.1Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RRP6_YEAST Nuclear-specific catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the nucleus, the RNA exosome complex is involved in proper maturation of stable RNA species such as rRNA, snRNA and snoRNA, in the elimination of RNA processing by-products and non-coding 'pervasive' transcripts, such as antisense RNA species and cryptic unstable transcripts (CUTs), and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. The catalytic inactive RNA exosome core complex of 9 subunits (Exo-9) is proposed to play a pivotal role in the binding and presentation of RNA for ribonucleolysis, and to serve as a scaffold for the association with catalytic subunits and accessory proteins or complexes. RRP6 has 3'-5' exonuclease activity which is not modulated upon association with Exo-9 suggesting that the complex inner RNA-binding path is not used to access its active site.^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

The eukaryotic exosome is a conserved RNA-degrading complex that functions in RNA surveillance, turnover and processing. How the same machinery can either completely degrade or precisely trim RNA substrates has long remained unexplained. Here we report the crystal structures of a yeast nuclear exosome containing the 9-subunit core, the 3'-5' RNases Rrp44 and Rrp6, and the obligate Rrp6-binding partner Rrp47 in complex with different RNAs. The combined structural and biochemical data of this 12-subunit complex reveal how a single-stranded RNA can reach the Rrp44 or Rrp6 active sites directly or can bind Rrp6 and be threaded via the central channel towards the distal RNase Rrp44. When a bulky RNA is stalled at the entrance of the channel, Rrp6-Rrp47 swings open. The results suggest how the same molecular machine can coordinate processive degradation and partial trimming in an RNA-dependent manner by a concerted swinging mechanism of the two RNase subunits.

RNA degradation paths in a 12-subunit nuclear exosome complex.,Makino DL, Schuch B, Stegmann E, Baumgartner M, Basquin C, Conti E Nature. 2015 Jul 29. doi: 10.1038/nature14865. PMID:26222026^[5]

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

References

↑ Briggs MW, Burkard KT, Butler JS. Rrp6p, the yeast homologue of the human PM-Scl 100-kDa autoantigen, is essential for efficient 5.8 S rRNA 3' end formation. J Biol Chem. 1998 May 22;273(21):13255-63. PMID:9582370
↑ Allmang C, Petfalski E, Podtelejnikov A, Mann M, Tollervey D, Mitchell P. The yeast exosome and human PM-Scl are related complexes of 3' --> 5' exonucleases. Genes Dev. 1999 Aug 15;13(16):2148-58. PMID:10465791
↑ Burkard KT, Butler JS. A nuclear 3'-5' exonuclease involved in mRNA degradation interacts with Poly(A) polymerase and the hnRNA protein Npl3p. Mol Cell Biol. 2000 Jan;20(2):604-16. PMID:10611239
↑ Hieronymus H, Yu MC, Silver PA. Genome-wide mRNA surveillance is coupled to mRNA export. Genes Dev. 2004 Nov 1;18(21):2652-62. Epub 2004 Oct 15. PMID:15489286 doi:http://dx.doi.org/gad.1241204
↑ Makino DL, Schuch B, Stegmann E, Baumgartner M, Basquin C, Conti E. RNA degradation paths in a 12-subunit nuclear exosome complex. Nature. 2015 Jul 29. doi: 10.1038/nature14865. PMID:26222026 doi:http://dx.doi.org/10.1038/nature14865

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5c0y"

Categories: Large Structures | Saccharomyces cerevisiae S288C | Synthetic construct | Conti E | Schuch B

@@ Line 4: / Line 4: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[5c0y]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C0Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5C0Y FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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]] 2.1&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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'>[https://proteopedia.org/fgij/fg.htm?mol=5c0y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c0y OCA], [https://pdbe.org/5c0y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5c0y RCSB], [https://www.ebi.ac.uk/pdbsum/5c0y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5c0y ProSAT]</span></td></tr>
 </table>

5c0y

From Proteopedia

Current revision

Crystal structure of the Rrp6 catalytic domain bound to poly(U) RNA

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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