This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2c1w

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

The structure of XendoU: a splicing independent snoRNA processing endoribonuclease

Structural highlights

2c1w is a 3 chain structure with sequence from Xenopus laevis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.2Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ENDUA_XENLA Poly(U)-specific endoribonuclease involved in the biosynthesis of intron-encoded box C/D snoRNAs, such as U16 and U86. Releases products that have 2'-3'-cyclic phosphate termini.^[1] ^[2] ^[3] ^[4]

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

Small nucleolar RNAs (snoRNAs) play a key role in eukaryotic ribosome biogenesis. In most cases, snoRNAs are encoded in introns and are released through the splicing reaction. Some snoRNAs are, instead, produced by an alternative pathway consisting of endonucleolytic processing of pre-mRNA. XendoU, the endoribonuclease responsible for this activity, is a U-specific, metal-dependent enzyme that releases products with 2'-3' cyclic phosphate termini. XendoU is broadly conserved among eukaryotes, and it is a genetic marker of nidoviruses, including the severe acute respiratory syndrome coronavirus, where it is essential for replication and transcription. We have determined by crystallography the structure of XendoU that, by refined search methodologies, appears to display a unique fold. Based on sequence conservation, mutagenesis, and docking simulations, we have identified the active site. The conserved structural determinants of this site may provide a framework for attempting to design antiviral drugs to interfere with the infectious nidovirus life cycle.

The structure of the endoribonuclease XendoU: From small nucleolar RNA processing to severe acute respiratory syndrome coronavirus replication.,Renzi F, Caffarelli E, Laneve P, Bozzoni I, Brunori M, Vallone B Proc Natl Acad Sci U S A. 2006 Aug 15;103(33):12365-70. Epub 2006 Aug 8. PMID:16895992^[5]

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

References

↑ Laneve P, Altieri F, Fiori ME, Scaloni A, Bozzoni I, Caffarelli E. Purification, cloning, and characterization of XendoU, a novel endoribonuclease involved in processing of intron-encoded small nucleolar RNAs in Xenopus laevis. J Biol Chem. 2003 Apr 11;278(15):13026-32. Epub 2003 Feb 5. PMID:12571235 doi:http://dx.doi.org/10.1074/jbc.M211937200
↑ Gioia U, Laneve P, Dlakic M, Arceci M, Bozzoni I, Caffarelli E. Functional characterization of XendoU, the endoribonuclease involved in small nucleolar RNA biosynthesis. J Biol Chem. 2005 May 13;280(19):18996-9002. Epub 2005 Mar 7. PMID:15755742 doi:http://dx.doi.org/M501160200
↑ Caffarelli E, Arese M, Santoro B, Fragapane P, Bozzoni I. In vitro study of processing of the intron-encoded U16 small nucleolar RNA in Xenopus laevis. Mol Cell Biol. 1994 May;14(5):2966-74. PMID:7513048
↑ Caffarelli E, Maggi L, Fatica A, Jiricny J, Bozzoni I. A novel Mn++-dependent ribonuclease that functions in U16 SnoRNA processing in X. laevis. Biochem Biophys Res Commun. 1997 Apr 17;233(2):514-7. PMID:9144568 doi:http://dx.doi.org/S0006-291X(97)96487-1
↑ Renzi F, Caffarelli E, Laneve P, Bozzoni I, Brunori M, Vallone B. The structure of the endoribonuclease XendoU: From small nucleolar RNA processing to severe acute respiratory syndrome coronavirus replication. Proc Natl Acad Sci U S A. 2006 Aug 15;103(33):12365-70. Epub 2006 Aug 8. PMID:16895992

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2c1w"

@@ Line 1: / Line 1: @@
-==THE STRUCTURE OF XENDOU: A SPLICING INDEPENDENT SNORNA PROCESSING ENDORIBONUCLEASE==
-<StructureSection load='2c1w' size='340' side='right' caption='[[2c1w]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+==The structure of XendoU: a splicing independent snoRNA processing endoribonuclease==
+<StructureSection load='2c1w' size='340' side='right'caption='[[2c1w]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2c1w]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C1W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2C1W FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2c1w]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2C1W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2C1W FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.2&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2c09|2c09]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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=2c1w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c1w OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2c1w RCSB], [http://www.ebi.ac.uk/pdbsum/2c1w PDBsum]</span></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=2c1w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2c1w OCA], [https://pdbe.org/2c1w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2c1w RCSB], [https://www.ebi.ac.uk/pdbsum/2c1w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2c1w ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/ENDUA_XENLA ENDUA_XENLA] Poly(U)-specific endoribonuclease involved in the biosynthesis of intron-encoded box C/D snoRNAs, such as U16 and U86. Releases products that have 2'-3'-cyclic phosphate termini.<ref>PMID:12571235</ref> <ref>PMID:15755742</ref> <ref>PMID:7513048</ref> <ref>PMID:9144568</ref>
 == Evolutionary Conservation ==
 [[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/c1/2c1w_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c1/2c1w_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2c1w ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 25: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2c1w" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Xenopus laevis]]
-[[Category: Bozzoni, I]]
+[[Category: Bozzoni I]]
-[[Category: Brunori, M]]
+[[Category: Brunori M]]
-[[Category: Caffarelli, E]]
+[[Category: Caffarelli E]]
-[[Category: Laneve, P]]
+[[Category: Laneve P]]
-[[Category: Renzi, F]]
+[[Category: Renzi F]]
-[[Category: Vallone, B]]
+[[Category: Vallone B]]
-[[Category: Endoribonuclease]]
-[[Category: Nuclease]]
-[[Category: Snorna]]
-[[Category: Splicing independent processing]]

2c1w

From Proteopedia

Current revision

The structure of XendoU: a splicing independent snoRNA processing endoribonuclease

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox