3p06: Difference between revisions

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 == Structural highlights ==
 <table><tr><td colspan='2'>[[3p06]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Tellina_virus_1 Tellina virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3P06 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3P06 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=URE:UREA'>URE</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]] 2.1&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BME:BETA-MERCAPTOETHANOL'>BME</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=URE:UREA'>URE</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2pnl|2pnl]], [[2pnm|2pnm]], [[2gef|2gef]]</div></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">viral protein 4 (VP4) ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=321302 Tellina virus 1])</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Infectious_pancreatic_necrosis_birnavirus_Vp4_peptidase Infectious pancreatic necrosis birnavirus Vp4 peptidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.115 3.4.21.115] </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=3p06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3p06 OCA], [https://pdbe.org/3p06 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3p06 RCSB], [https://www.ebi.ac.uk/pdbsum/3p06 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3p06 ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/Q2PBR5_9VIRU Q2PBR5_9VIRU]
-Viruses of the Birnaviridae family are characterized by their bisegmented double-stranded RNA genome that resides within a single-shelled non-enveloped icosahedral particle. They infect birds, aquatic organisms and insects. Tellina virus 1 (TV-1) is an Aquabirnavirus isolated from the mollusk Tellina tenuis. It encodes a polyprotein (NH2-pVP2-X-VP4-VP3-COOH) that is cleaved by the self-encoded protease VP4 to yield capsid precursor protein pVP2, peptide X and ribonucleoprotein VP3. Here we report the crystal structure of an intramolecular (cis) acyl-enzyme complex of TV-1 VP4 at 2.1 A resolution. The structure reveals how the enzyme can recognize its own carboxy-terminus during the VP4/VP3 cleavage event. The methyl sidechains of Ala830(P1) and Ala828(P3) at the VP4/VP3 junction point into complementary shallow and hydrophobic S1 and S3 binding pockets adjacent to the VP4 catalytic residues: nucleophile Ser738 and general base Lys777. The electron density clearly shows that the carbonyl carbon of Ala830 is covalently attached via an ester bond to the Ogamma of Ser738. A highly ordered water molecule in the active site is coordinated in the proper position to act as the deacylating water. A comparative analysis of this intramolecular (cis) acyl-enzyme structure with the previously solved intermolecular (trans) acyl-enzyme structure of infectious pancreatic necrosis virus (IPNV) VP4 explains the narrower specificity observed in the cleavage sites of TV-1 VP4.
-Crystal structure of a viral protease intramolecular acyl-enzyme complex. Insights into cis-cleavage at the VP4/VP3 junction of Tellina birnavirus.,Chung IY, Paetzel M J Biol Chem. 2011 Feb 2. PMID:21288899<ref>PMID:21288899</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3p06" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Infectious pancreatic necrosis birnavirus Vp4 peptidase]]
 [[Category: Large Structures]]
 [[Category: Tellina virus 1]]
-[[Category: Chung, I Y.W]]
+[[Category: Chung IYW]]
-[[Category: Paetzel, M]]
+[[Category: Paetzel M]]
-[[Category: Acyl-enzyme]]
-[[Category: Alpha/beta protein]]
-[[Category: Cis-cleavage]]
-[[Category: Ester-linkage]]
-[[Category: Hydrolase]]
-[[Category: Intramolecular acyl-enzyme]]
-[[Category: Polyprotein processing]]
-[[Category: Protease]]