2e9r: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:2e9r.png|left|200px]]
-<!--
+==Foot-and-mouth disease virus RNA-dependent RNA polymerase in complex with a template-primer RNA and with ribavirin==
-The line below this paragraph, containing "STRUCTURE_2e9r", creates the "Structure Box" on the page.
+<StructureSection load='2e9r' size='340' side='right'caption='[[2e9r]], [[Resolution|resolution]] 2.81&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'>[[2e9r]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Foot-and-mouth_disease_virus_C-S8c1 Foot-and-mouth disease virus C-S8c1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E9R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E9R 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]] 2.81&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=RTP:RIBAVIRIN+TRIPHOSPHATE'>RTP</scene></td></tr>
-{{STRUCTURE_2e9r|  PDB=2e9r  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2e9r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e9r OCA], [https://pdbe.org/2e9r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e9r RCSB], [https://www.ebi.ac.uk/pdbsum/2e9r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e9r ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9QCE4_9PICO Q9QCE4_9PICO] Protein 3C is a cysteine protease that generates mature viral proteins from the precursor polyprotein. In addition to its proteolytic activity, it binds to viral RNA, and thus influences viral genome replication. RNA and substrate bind co-operatively to the protease (By similarity).[SAAS:SAAS000199_004_042266]  RNA-directed RNA polymerase 3D-POL replicates genomic and antigenomic RNA by recognizing replications specific signals (By similarity).[SAAS:SAAS000199_004_010047]
+== 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/e9/2e9r_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=2e9r ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+RNA virus replication is an error-prone event caused by the low fidelity of viral RNA-dependent RNA polymerases. Replication fidelity can be decreased further by the use of mutagenic ribonucleoside analogs to a point where viral genetic information can no longer be maintained. For foot-and-mouth disease virus, the antiviral analogs ribavirin and 5-fluorouracil have been shown to be mutagenic, contributing to virus extinction through lethal mutagenesis. Here, we report the x-ray structure of four elongation complexes of foot-and-mouth disease virus polymerase 3D obtained in presence of natural substrates, ATP and UTP, or mutagenic nucleotides, ribavirin triphosphate and 5-fluorouridine triphosphate with different RNAs as template-primer molecules. The ability of these complexes to synthesize RNA in crystals allowed us to capture different successive replication events and to define the critical amino acids involved in (i) the recognition and positioning of the incoming nucleotide or analog; (ii) the positioning of the acceptor base of the template strand; and (iii) the positioning of the 3'-OH group of the primer nucleotide during RNA replication. The structures identify key interactions involved in viral RNA replication and provide insights into the molecular basis of the low fidelity of viral RNA polymerases.
-===Foot-and-mouth disease virus RNA-dependent RNA polymerase in complex with a template-primer RNA and with ribavirin===
+Sequential structures provide insights into the fidelity of RNA replication.,Ferrer-Orta C, Arias A, Perez-Luque R, Escarmis C, Domingo E, Verdaguer N Proc Natl Acad Sci U S A. 2007 May 29;104(22):9463-8. Epub 2007 May 21. PMID:17517631<ref>PMID:17517631</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2e9r" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17517631}}, 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 17517631 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17517631}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Foot-and-mouth disease virus C-S8c1]]
-E9R is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Foot-and-mouth_disease_virus Foot-and-mouth disease virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E9R OCA].
+[[Category: Large Structures]]
+[[Category: Arias A]]
-==Reference==
+[[Category: Domingo E]]
-Sequential structures provide insights into the fidelity of RNA replication., Ferrer-Orta C, Arias A, Perez-Luque R, Escarmis C, Domingo E, Verdaguer N, Proc Natl Acad Sci U S A. 2007 May 29;104(22):9463-8. Epub 2007 May 21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17517631 17517631]
+[[Category: Escarmis C]]
+[[Category: Ferrer-Orta C]]
-The structure of a protein primer-polymerase complex in the initiation of genome replication., Ferrer-Orta C, Arias A, Agudo R, Perez-Luque R, Escarmis C, Domingo E, Verdaguer N, EMBO J. 2006 Feb 22;25(4):880-8. Epub 2006 Feb 2. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16456546 16456546]
+[[Category: Perez-Luque R]]
+[[Category: Verdaguer N]]
-A comparison of viral RNA-dependent RNA polymerases., Ferrer-Orta C, Arias A, Escarmis C, Verdaguer N, Curr Opin Struct Biol. 2006 Feb;16(1):27-34. Epub 2005 Dec 20. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16364629 16364629]
-Structure of foot-and-mouth disease virus RNA-dependent RNA polymerase and its complex with a template-primer RNA., Ferrer-Orta C, Arias A, Perez-Luque R, Escarmis C, Domingo E, Verdaguer N, J Biol Chem. 2004 Nov 5;279(45):47212-21. Epub 2004 Aug 3. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15294895 15294895]
-Mutant viral polymerase in the transition of virus to error catastrophe identifies a critical site for RNA binding., Arias A, Agudo R, Ferrer-Orta C, Perez-Luque R, Airaksinen A, Brocchi E, Domingo E, Verdaguer N, Escarmis C, J Mol Biol. 2005 Nov 11;353(5):1021-32. Epub 2005 Sep 26. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16216271 16216271]
-[[Category: Foot-and-mouth disease virus]]
-[[Category: RNA-directed RNA polymerase]]
-[[Category: Single protein]]
-[[Category: Arias, A.]]
-[[Category: Domingo, E.]]
-[[Category: Escarmis, C.]]
-[[Category: Ferrer-Orta, C.]]
-[[Category: Perez-Luque, R.]]
-[[Category: Verdaguer, N.]]
-[[Category: 3d polymerase]]
-[[Category: Foot-and-mouth disease virus]]
-[[Category: Polymerase]]
-[[Category: Rna-dependent rna polymerase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 14:17:50 2008''