2c37: Difference between revisions

Latest revision as of 14:04, 13 December 2023

RNASE 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:	CL, NA, RP5, U5P
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

↑ 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
↑ 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
↑ 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

Proteopedia Page Contributors and Editors (what is this?)

OCA

[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

[1]

[2]

[3]

@@ Line 3: / Line 3: @@
 <StructureSection load='2c37' size='340' side='right'caption='[[2c37]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2c37]] is a 24 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_35091 Atcc 35091]. 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>
+<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>
-</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=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>
+</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>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2br2|2br2]], [[2c38|2c38]], [[2c39|2c39]]</div></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=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>
 == Function ==
-[[https://www.uniprot.org/uniprot/ECX2_SULSO ECX2_SULSO]] Probably involved in the 3'->5' degradation of a variety of RNA species (Potential). [[https://www.uniprot.org/uniprot/ECX1_SULSO ECX1_SULSO]] Probably involved in the 3'->5' degradation of a variety of RNA species (Potential).
+[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 ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 33: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Atcc 35091]]
 [[Category: Exosomes]]
 [[Category: Large Structures]]
 [[Category: RCSB PDB Molecule of the Month]]
-[[Category: Conti, E]]
+[[Category: Saccharolobus solfataricus]]
-[[Category: Lorentzen, E]]
+[[Category: Conti E]]
-[[Category: Archaeal]]
+[[Category: Lorentzen E]]
-[[Category: Exoribonuclease]]
-[[Category: Exosome]]
-[[Category: Hydrolase]]
-[[Category: Rna degradation]]
-[[Category: Rrp41]]
-[[Category: Rrp42]]

2c37: Difference between revisions

Latest revision as of 14:04, 13 December 2023

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

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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