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[[Image:2c37.gif|left|200px]]


{{Structure
==RNASE PH CORE OF THE ARCHAEAL EXOSOME IN COMPLEX WITH U8 RNA==
|PDB= 2c37 |SIZE=350|CAPTION= <scene name='initialview01'>2c37</scene>, resolution 2.80&Aring;
<StructureSection load='2c37' size='340' side='right'caption='[[2c37]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
|SITE= <scene name='pdbsite=AC1:U5p+Binding+Site+For+Chain+X'>AC1</scene>
== Structural highlights ==
|LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=U5P:URIDINE-5'-MONOPHOSPHATE'>U5P</scene>, <scene name='pdbligand=U5P:URIDINE-5'-MONOPHOSPHATE'>U5P</scene> and <scene name='pdbligand=RP5:RIBOSE-5-PHOSPHATE, PYRANOSE FORM'>RP5</scene>
<table><tr><td colspan='2'>[[2c37]] is a 24 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus Saccharolobus solfataricus]. The February 2007 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Exosomes''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2007_2 10.2210/rcsb_pdb/mom_2007_2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C37 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C37 FirstGlance]. <br>
|ACTIVITY=  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
|GENE=  
<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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=RP5:5-O-PHOSPHONO-BETA-D-RIBOFURANOSE'>RP5</scene>, <scene name='pdbligand=U5P:URIDINE-5-MONOPHOSPHATE'>U5P</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=2c37 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c37 OCA], [https://pdbe.org/2c37 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c37 RCSB], [https://www.ebi.ac.uk/pdbsum/2c37 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c37 ProSAT]</span></td></tr>
 
</table>
'''RNASE PH CORE OF THE ARCHAEAL EXOSOME IN COMPLEX WITH U8 RNA'''
== Function ==
 
[https://www.uniprot.org/uniprot/RRP42_SACS2 RRP42_SACS2] Non-catalytic component of the exosome, which is a complex involved in RNA degradation. Contributes to the structuring of the Rrp41 active site.[HAMAP-Rule:MF_00622]<ref>PMID:15951817</ref> <ref>PMID:20488184</ref>  
 
== Evolutionary Conservation ==
==Overview==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c3/2c37_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2c37 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The exosome is a macromolecular complex that plays fundamental roles in the biogenesis and turnover of a large number of RNA species. Here we report the crystal structures of the Rrp41-Rrp42 core complex of the S. solfataricus exosome bound to short single-stranded RNAs and to ADP. The RNA binding cleft recognizes four nucleotides in a sequence-unspecific manner, mainly by electrostatic interactions with the phosphate groups. Interactions at the 2' hydroxyls of the sugars provide specificity for RNA over DNA. The structures show both the bound substrate and the cleaved product of the reaction, suggesting a catalytic mechanism for the 3'-5' phosphorolytic activity of the exosome.
The exosome is a macromolecular complex that plays fundamental roles in the biogenesis and turnover of a large number of RNA species. Here we report the crystal structures of the Rrp41-Rrp42 core complex of the S. solfataricus exosome bound to short single-stranded RNAs and to ADP. The RNA binding cleft recognizes four nucleotides in a sequence-unspecific manner, mainly by electrostatic interactions with the phosphate groups. Interactions at the 2' hydroxyls of the sugars provide specificity for RNA over DNA. The structures show both the bound substrate and the cleaved product of the reaction, suggesting a catalytic mechanism for the 3'-5' phosphorolytic activity of the exosome.


==About this Structure==
Structural basis of 3' end RNA recognition and exoribonucleolytic cleavage by an exosome RNase PH core.,Lorentzen E, Conti E Mol Cell. 2005 Nov 11;20(3):473-81. PMID:16285928<ref>PMID:16285928</ref>
2C37 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]. The following page contains interesting information on the relation of 2C37 with [[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb86_1.html Exosomes]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C37 OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Structural basis of 3' end RNA recognition and exoribonucleolytic cleavage by an exosome RNase PH core., Lorentzen E, Conti E, Mol Cell. 2005 Nov 11;20(3):473-81. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16285928 16285928]
</div>
<div class="pdbe-citations 2c37" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Exosomes]]
[[Category: Exosomes]]
[[Category: Protein complex]]
[[Category: Large Structures]]
[[Category: Sulfolobus solfataricus]]
[[Category: RCSB PDB Molecule of the Month]]
[[Category: Conti, E.]]
[[Category: Saccharolobus solfataricus]]
[[Category: Lorentzen, E.]]
[[Category: Conti E]]
[[Category: CL]]
[[Category: Lorentzen E]]
[[Category: NA]]
[[Category: RP5]]
[[Category: U5P]]
[[Category: archaeal]]
[[Category: exoribonuclease]]
[[Category: exosome]]
[[Category: hydrolase]]
[[Category: phosphorolytic]]
[[Category: rna degradation]]
[[Category: rnase ph]]
[[Category: rrp41]]
[[Category: rrp42]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:10:11 2008''

Latest revision as of 17:04, 13 December 2023

RNASE PH CORE OF THE ARCHAEAL EXOSOME IN COMPLEX WITH U8 RNARNASE PH CORE OF THE ARCHAEAL EXOSOME IN COMPLEX WITH U8 RNA

Structural highlights

2c37 is a 24 chain structure with sequence from Saccharolobus solfataricus. The February 2007 RCSB PDB Molecule of the Month feature on Exosomes by David S. Goodsell is 10.2210/rcsb_pdb/mom_2007_2. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.8Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RRP42_SACS2 Non-catalytic component of the exosome, which is a complex involved in RNA degradation. Contributes to the structuring of the Rrp41 active site.[HAMAP-Rule:MF_00622][1] [2]

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 macromolecular complex that plays fundamental roles in the biogenesis and turnover of a large number of RNA species. Here we report the crystal structures of the Rrp41-Rrp42 core complex of the S. solfataricus exosome bound to short single-stranded RNAs and to ADP. The RNA binding cleft recognizes four nucleotides in a sequence-unspecific manner, mainly by electrostatic interactions with the phosphate groups. Interactions at the 2' hydroxyls of the sugars provide specificity for RNA over DNA. The structures show both the bound substrate and the cleaved product of the reaction, suggesting a catalytic mechanism for the 3'-5' phosphorolytic activity of the exosome.

Structural basis of 3' end RNA recognition and exoribonucleolytic cleavage by an exosome RNase PH core.,Lorentzen E, Conti E Mol Cell. 2005 Nov 11;20(3):473-81. PMID:16285928[3]

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

References

  1. ↑ Lorentzen E, Walter P, Fribourg S, Evguenieva-Hackenberg E, Klug G, Conti E. The archaeal exosome core is a hexameric ring structure with three catalytic subunits. Nat Struct Mol Biol. 2005 Jul;12(7):575-81. Epub 2005 Jun 12. PMID:15951817 doi:10.1038/nsmb952
  2. ↑ Roppelt V, Klug G, Evguenieva-Hackenberg E. The evolutionarily conserved subunits Rrp4 and Csl4 confer different substrate specificities to the archaeal exosome. FEBS Lett. 2010 Jul 2;584(13):2931-6. PMID:20488184 doi:10.1016/j.febslet.2010.05.014
  3. ↑ Lorentzen E, Conti E. Structural basis of 3' end RNA recognition and exoribonucleolytic cleavage by an exosome RNase PH core. Mol Cell. 2005 Nov 11;20(3):473-81. PMID:16285928 doi:10.1016/j.molcel.2005.10.020

2c37, resolution 2.80Å

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