2ckw

From Proteopedia

(Difference between revisions)

Current revision

The 2.3 A resolution structure of the Sapporo virus RNA dependant RNA polymerase.

Structural highlights

2ckw is a 1 chain structure with sequence from Sapporo virus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.3Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

POLG_SVM93 NTPase presumably plays a role in replication. Despite having similarities with helicases, does not seem to display any helicase activity (By similarity). Viral genome-linked protein is covalently linked to the 5'-end of the positive-strand, negative-strand genomic RNAs and subgenomic RNA. Acts as a genome-linked replication primer. May recruit ribosome to viral RNA thereby promoting viral proteins translation (By similarity). Protease-polymerase processes the polyprotein: Pro-Pol is first released by autocleavage, then all other proteins are cleaved (By similarity). Protease-polymerase is a RNA-directed RNA polymerase which replicates genomic and antigenomic viral RNA by recognizing specific signals. Catalyzes the covalent attachment VPg with viral RNAs (By similarity). Capsid protein self assembles to form an icosahedral capsid with a T=3 symmetry, about 38 nm in diameter, and consisting of 180 capsid proteins. The capsid encapsulate the genomic RNA and VP2 proteins. Attaches virion to target cells, inducing endocytosis of the viral particle. Acidification of the endosome induces conformational change of capsid protein thereby injecting virus genomic RNA into host cytoplasm (By similarity).

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

Sapoviruses are one of the major agents of acute gastroenteritis in childhood. They form a tight genetic cluster (genus) in the Caliciviridae family that regroups both animal and human pathogenic strains. No permissive tissue culture has been developed for human sapovirus, limiting its characterization to surrogate systems. We report here on the first extensive characterization of the key enzyme of replication, the RNA-dependent RNA polymerase (RdRp) associated with the 3D(pol)-like protein. Enzymatically active sapovirus 3D(pol) and its defective mutant were expressed in Escherichia coli and purified. The overall structure of the sapovirus 3D(pol) was determined by X-ray crystallography to 2.32-A resolution. It revealed a right hand fold typical for template-dependent polynucleotide polymerases. The carboxyl terminus is located within the active site cleft, as observed in the RdRp of some (norovirus) but not other (lagovirus) caliciviruses. Sapovirus 3D(pol) prefers Mn(2+) over Mg(2+) but may utilize either as a cofactor in vitro. In a synthetic RNA template-dependent reaction, sapovirus 3D(pol) synthesizes a double-stranded RNA or labels the template 3' terminus by terminal transferase activity. Initiation of RNA synthesis occurs de novo on heteropolymeric templates or in a primer-dependent manner on polyadenylated templates. Strikingly, this mode of initiation of RNA synthesis was also described for norovirus, but not for lagovirus, suggesting structural and functional homologies in the RNA-dependent RNA polymerase of human pathogenic caliciviruses. This first experimental evidence makes sapovirus 3D(pol) an attractive target for developing drugs to control calicivirus infection in humans.

Structural and functional characterization of sapovirus RNA-dependent RNA polymerase.,Fullerton SW, Blaschke M, Coutard B, Gebhardt J, Gorbalenya A, Canard B, Tucker PA, Rohayem J J Virol. 2007 Feb;81(4):1858-71. Epub 2006 Nov 22. PMID:17121797^[1]

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

References

↑ Fullerton SW, Blaschke M, Coutard B, Gebhardt J, Gorbalenya A, Canard B, Tucker PA, Rohayem J. Structural and functional characterization of sapovirus RNA-dependent RNA polymerase. J Virol. 2007 Feb;81(4):1858-71. Epub 2006 Nov 22. PMID:17121797 doi:http://dx.doi.org/10.1128/JVI.01462-06

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/2ckw"

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:2ckw.png|left|200px]]
-<!--
+==The 2.3 A resolution structure of the Sapporo virus RNA dependant RNA polymerase.==
-The line below this paragraph, containing "STRUCTURE_2ckw", creates the "Structure Box" on the page.
+<StructureSection load='2ckw' size='340' side='right'caption='[[2ckw]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2ckw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Sapporo_virus Sapporo virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CKW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2CKW FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</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=2ckw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ckw OCA], [https://pdbe.org/2ckw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ckw RCSB], [https://www.ebi.ac.uk/pdbsum/2ckw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ckw ProSAT]</span></td></tr>
-{{STRUCTURE_2ckw|  PDB=2ckw  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/POLG_SVM93 POLG_SVM93] NTPase presumably plays a role in replication. Despite having similarities with helicases, does not seem to display any helicase activity (By similarity).  Viral genome-linked protein is covalently linked to the 5'-end of the positive-strand, negative-strand genomic RNAs and subgenomic RNA. Acts as a genome-linked replication primer. May recruit ribosome to viral RNA thereby promoting viral proteins translation (By similarity).  Protease-polymerase processes the polyprotein: Pro-Pol is first released by autocleavage, then all other proteins are cleaved (By similarity).  Protease-polymerase is a RNA-directed RNA polymerase which replicates genomic and antigenomic viral RNA by recognizing specific signals. Catalyzes the covalent attachment VPg with viral RNAs (By similarity).  Capsid protein self assembles to form an icosahedral capsid with a T=3 symmetry, about 38 nm in diameter, and consisting of 180 capsid proteins. The capsid encapsulate the genomic RNA and VP2 proteins. Attaches virion to target cells, inducing endocytosis of the viral particle. Acidification of the endosome induces conformational change of capsid protein thereby injecting virus genomic RNA into host cytoplasm (By similarity).
+== 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/ck/2ckw_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=2ckw ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Sapoviruses are one of the major agents of acute gastroenteritis in childhood. They form a tight genetic cluster (genus) in the Caliciviridae family that regroups both animal and human pathogenic strains. No permissive tissue culture has been developed for human sapovirus, limiting its characterization to surrogate systems. We report here on the first extensive characterization of the key enzyme of replication, the RNA-dependent RNA polymerase (RdRp) associated with the 3D(pol)-like protein. Enzymatically active sapovirus 3D(pol) and its defective mutant were expressed in Escherichia coli and purified. The overall structure of the sapovirus 3D(pol) was determined by X-ray crystallography to 2.32-A resolution. It revealed a right hand fold typical for template-dependent polynucleotide polymerases. The carboxyl terminus is located within the active site cleft, as observed in the RdRp of some (norovirus) but not other (lagovirus) caliciviruses. Sapovirus 3D(pol) prefers Mn(2+) over Mg(2+) but may utilize either as a cofactor in vitro. In a synthetic RNA template-dependent reaction, sapovirus 3D(pol) synthesizes a double-stranded RNA or labels the template 3' terminus by terminal transferase activity. Initiation of RNA synthesis occurs de novo on heteropolymeric templates or in a primer-dependent manner on polyadenylated templates. Strikingly, this mode of initiation of RNA synthesis was also described for norovirus, but not for lagovirus, suggesting structural and functional homologies in the RNA-dependent RNA polymerase of human pathogenic caliciviruses. This first experimental evidence makes sapovirus 3D(pol) an attractive target for developing drugs to control calicivirus infection in humans.
-===THE 2.3 A RESOLUTION STRUCTURE OF THE SAPPORO VIRUS RNA DEPENDANT RNA POLYMERASE.===
+Structural and functional characterization of sapovirus RNA-dependent RNA polymerase.,Fullerton SW, Blaschke M, Coutard B, Gebhardt J, Gorbalenya A, Canard B, Tucker PA, Rohayem J J Virol. 2007 Feb;81(4):1858-71. Epub 2006 Nov 22. PMID:17121797<ref>PMID:17121797</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2ckw" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17121797}}, adds the Publication Abstract to the page
+*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17121797 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17121797}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-CKW is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Sapporo_virus Sapporo virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2CKW OCA].
-==Reference==
-<ref group="xtra">PMID:17121797</ref><references group="xtra"/>
-[[Category: RNA-directed RNA polymerase]]
 [[Category: Sapporo virus]]
-[[Category: Canard, B.]]
+[[Category: Canard B]]
-[[Category: Coutard, B.]]
+[[Category: Coutard B]]
-[[Category: Fullerton, S W.B.]]
+[[Category: Fullerton SWB]]
-[[Category: Gebhardt, J.]]
+[[Category: Gebhardt J]]
-[[Category: Gorbalenya, A.]]
+[[Category: Gorbalenya A]]
-[[Category: Rohayem, J.]]
+[[Category: Rohayem J]]
-[[Category: Tucker, P A.]]
+[[Category: Tucker PA]]
-[[Category: Atp-binding]]
-[[Category: Capsid protein]]
-[[Category: Covalent protein-rna linkage]]
-[[Category: Helicase]]
-[[Category: Hydrolase]]
-[[Category: Mutant]]
-[[Category: Nucleotide-binding]]
-[[Category: Nucleotidyltransferase]]
-[[Category: Polymerase]]
-[[Category: Polyprotein]]
-[[Category: Protease]]
-[[Category: Rna elongation]]
-[[Category: Rna replication]]
-[[Category: Rna-directed rna polymerase]]
-[[Category: Structural protein]]
-[[Category: Thiol protease]]
-[[Category: Transferase]]
-[[Category: Transferase activity]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 07:55:32 2009''

2ckw

From Proteopedia

Current revision

The 2.3 A resolution structure of the Sapporo virus RNA dependant RNA polymerase.

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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