2ja9

From Proteopedia

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Revision as of 07:21, 11 July 2018

Structure of the N-terminal deletion of yeast exosome component Rrp40

Structural highlights

2ja9 is a 1 chain structure with sequence from Atcc 18824. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RRP40_YEAST] Non-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. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and in RNA surveillance pathways, preventing translation of aberrant mRNAs. 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. RRP40 as peripheral part of the Exo-9 complex is thought to stabilize the hexameric ring of RNase PH-domain subunits.^[1] ^[2] ^[3]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The exosome is a protein complex that is important in both degradation and 3'-processing of eukaryotic RNAs. We present the crystal structure of the Rrp40 exosome subunit from Saccharomyces cerevisiae at a resolution of 2.2 A. The structure comprises an S1 domain and an unusual KH (K homology) domain. Close packing of the S1 and KH domains is stabilized by a GxNG sequence, which is uniquely conserved in exosome KH domains. Nuclear magnetic resonance data reveal the presence of a manganese-binding site at the interface of the two domains. Isothermal titration calorimetry shows that Rrp40 and archaeal Rrp4 alone have very low intrinsic affinity for RNA. The affinity of an archaeal core exosome for RNA is significantly increased in the presence of the S1-KH subunit Rrp4, indicating that multiple subunits might contribute to cooperative binding of RNA substrates by the exosome.

Structural and biochemical characterization of the yeast exosome component Rrp40.,Oddone A, Lorentzen E, Basquin J, Gasch A, Rybin V, Conti E, Sattler M EMBO Rep. 2007 Jan;8(1):63-9. Epub 2006 Dec 8. PMID:17159918^[4]

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

References

↑ 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
↑ Dziembowski A, Lorentzen E, Conti E, Seraphin B. A single subunit, Dis3, is essentially responsible for yeast exosome core activity. Nat Struct Mol Biol. 2007 Jan;14(1):15-22. Epub 2006 Dec 17. PMID:17173052 doi:http://dx.doi.org/nsmb1184
↑ Schaeffer D, Tsanova B, Barbas A, Reis FP, Dastidar EG, Sanchez-Rotunno M, Arraiano CM, van Hoof A. The exosome contains domains with specific endoribonuclease, exoribonuclease and cytoplasmic mRNA decay activities. Nat Struct Mol Biol. 2009 Jan;16(1):56-62. doi: 10.1038/nsmb.1528. Epub 2008 Dec , 7. PMID:19060898 doi:http://dx.doi.org/10.1038/nsmb.1528
↑ Oddone A, Lorentzen E, Basquin J, Gasch A, Rybin V, Conti E, Sattler M. Structural and biochemical characterization of the yeast exosome component Rrp40. EMBO Rep. 2007 Jan;8(1):63-9. Epub 2006 Dec 8. PMID:17159918

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2ja9"

@@ Line 1: / Line 1: @@
-==STRUCTURE OF THE N-TERMINAL DELETION OF YEAST EXOSOME COMPONENT RRP40==
+==Structure of the N-terminal deletion of yeast exosome component Rrp40==
 <StructureSection load='2ja9' size='340' side='right' caption='[[2ja9]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
 <table><tr><td colspan='2'>[[2ja9]] is a 1 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=2JA9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JA9 FirstGlance]. <br>
-</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=2ja9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ja9 OCA], [http://pdbe.org/2ja9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ja9 RCSB], [http://www.ebi.ac.uk/pdbsum/2ja9 PDBsum]</span></td></tr>
+</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=2ja9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ja9 OCA], [http://pdbe.org/2ja9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ja9 RCSB], [http://www.ebi.ac.uk/pdbsum/2ja9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ja9 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 11: / Line 12: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ja/2ja9_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ja/2ja9_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 28: / Line 29: @@
 ==See Also==
-*[[Exonuclease|Exonuclease]]
 *[[Exosome|Exosome]]
 == References ==
@@ Line 50: / Line 50: @@
 [[Category: Nucleic-acid binding]]
 [[Category: Rna]]
+[[Category: Rna binding protein]]
 [[Category: Rna-binding]]
 [[Category: Rna-binding protein]]
 [[Category: Rrna processing]]
 [[Category: S1 domain]]

2ja9

From Proteopedia

Revision as of 07:21, 11 July 2018

Structure of the N-terminal deletion of yeast exosome component Rrp40

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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