2f8e: Difference between revisions

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-[[Image:2f8e.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2f8e", creates the "Structure Box" on the page.
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-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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-{{STRUCTURE_2f8e|  PDB=2f8e  |  SCENE=  }}
-'''Foot and Mouth Disease Virus RNA-dependent RNA polymerase in complex with uridylylated VPg protein'''
+==Foot and Mouth Disease Virus RNA-dependent RNA polymerase in complex with uridylylated VPg protein==
+<StructureSection load='2f8e' size='340' side='right'caption='[[2f8e]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2f8e]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Foot_and_mouth_disease_virus_C Foot and mouth disease virus C] and [https://en.wikipedia.org/wiki/Foot-and-mouth_disease_virus_Asia_1 Foot-and-mouth disease virus Asia 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F8E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F8E FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9&#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=MN:MANGANESE+(II)+ION'>MN</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=2f8e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f8e OCA], [https://pdbe.org/2f8e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f8e RCSB], [https://www.ebi.ac.uk/pdbsum/2f8e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f8e ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q0QEE0_9PICO Q0QEE0_9PICO]
+== 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/f8/2f8e_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2f8e ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Picornavirus RNA replication is initiated by the covalent attachment of a UMP molecule to the hydroxyl group of a tyrosine in the terminal protein VPg. This reaction is carried out by the viral RNA-dependent RNA polymerase (3D). Here, we report the X-ray structure of two complexes between foot-and-mouth disease virus 3D, VPg1, the substrate UTP and divalent cations, in the absence and in the presence of an oligoadenylate of 10 residues. In both complexes, VPg fits the RNA binding cleft of the polymerase and projects the key residue Tyr3 into the active site of 3D. This is achieved by multiple interactions with residues of motif F and helix alpha8 of the fingers domain and helix alpha13 of the thumb domain of the polymerase. The complex obtained in the presence of the oligoadenylate showed the product of the VPg uridylylation (VPg-UMP). Two metal ions and the catalytic aspartic acids of the polymerase active site, together with the basic residues of motif F, have been identified as participating in the priming reaction.
-==Overview==
+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:16456546<ref>PMID:16456546</ref>
-Picornavirus RNA replication is initiated by the covalent attachment of a UMP molecule to the hydroxyl group of a tyrosine in the terminal protein VPg. This reaction is carried out by the viral RNA-dependent RNA polymerase (3D). Here, we report the X-ray structure of two complexes between foot-and-mouth disease virus 3D, VPg1, the substrate UTP and divalent cations, in the absence and in the presence of an oligoadenylate of 10 residues. In both complexes, VPg fits the RNA binding cleft of the polymerase and projects the key residue Tyr3 into the active site of 3D. This is achieved by multiple interactions with residues of motif F and helix alpha8 of the fingers domain and helix alpha13 of the thumb domain of the polymerase. The complex obtained in the presence of the oligoadenylate showed the product of the VPg uridylylation (VPg-UMP). Two metal ions and the catalytic aspartic acids of the polymerase active site, together with the basic residues of motif F, have been identified as participating in the priming reaction.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-F8E is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Foot-and-mouth_disease_virus_c Foot-and-mouth disease virus c]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F8E OCA].
+</div>
+<div class="pdbe-citations 2f8e" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-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]
+*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
-[[Category: Foot-and-mouth disease virus c]]
+== References ==
-[[Category: RNA-directed RNA polymerase]]
+<references/>
-[[Category: Single protein]]
+__TOC__
-[[Category: Arias, A.]]
+</StructureSection>
-[[Category: Domingo, E.]]
+[[Category: Foot and mouth disease virus C]]
-[[Category: Escarmis, C.]]
+[[Category: Foot-and-mouth disease virus Asia 1]]
-[[Category: Ferrer-Orta, C.]]
+[[Category: Large Structures]]
-[[Category: Perez-Luque, R.]]
+[[Category: Arias A]]
-[[Category: Verdaguer, N.]]
+[[Category: Domingo E]]
-[[Category: Foot and mouth disease virus]]
+[[Category: Escarmis C]]
-[[Category: Protein primer]]
+[[Category: Ferrer-Orta C]]
-[[Category: Rna-dependent rna polymerase ,vpg protein]]
+[[Category: Perez-Luque R]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 03:35:12 2008''
+[[Category: Verdaguer N]]