2pnl: Difference between revisions

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-[[Image:2pnl.png|left|200px]]
+==Crystal structure of VP4 protease from infectious pancreatic necrosis virus (IPNV) in space group P1==
+<StructureSection load='2pnl' size='340' side='right' caption='[[2pnl]], [[Resolution|resolution]] 2.21&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2pnl]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Infectious_pancreatic_necrosis_virus Infectious pancreatic necrosis virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PNL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PNL FirstGlance]. <br>
+</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GAI:GUANIDINE'>GAI</scene><br>
+<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
+<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2gef|2gef]], [[2pnm|2pnm]]</td></tr>
+<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2pnl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pnl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pnl RCSB], [http://www.ebi.ac.uk/pdbsum/2pnl PDBsum]</span></td></tr>
+<table>
+== 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/pn/2pnl_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].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Infectious pancreatic necrosis virus (IPNV), an aquatic birnavirus that infects salmonid fish, encodes a large polyprotein (NH(2)-pVP2-VP4-VP3-COOH) that is processed through the proteolytic activity of its own protease, VP4, to release the proteins pVP2 and VP3. pVP2 is further processed to give rise to the capsid protein VP2 and three peptides that are incorporated into the virion. Reported here are two crystal structures of the IPNV VP4 protease solved from two different crystal symmetries. The electron density at the active site in the triclinic crystal form, refined to 2.2-A resolution, reveals the acyl-enzyme complex formed with an internal VP4 cleavage site. The complex was generated using a truncated enzyme in which the general base lysine was substituted. Inside the complex, the nucleophilic Ser(633)Ogamma forms an ester bond with the main-chain carbonyl of the C-terminal residue, Ala(716), of a neighboring VP4. The structure of this substrate-VP4 complex allows us to identify the S1, S3, S5, and S6 substrate binding pockets as well as other substrate-VP4 interactions and therefore provides structural insights into the substrate specificity of this enzyme. The structure from the hexagonal crystal form, refined to 2.3-A resolution, reveals the free-binding site of the protease. Three-dimensional alignment with the VP4 of blotched snakehead virus, another birnavirus, shows that the overall structure of VP4 is conserved despite a low level of sequence identity ( approximately 19%). The structure determinations of IPNV VP4, the first of an acyl-enzyme complex for a Ser/Lys dyad protease, provide insights into the catalytic mechanism and substrate recognition of this type of protease.
-{{STRUCTURE_2pnl|  PDB=2pnl  |  SCENE=  }}
+Crystal structure of the VP4 protease from infectious pancreatic necrosis virus reveals the acyl-enzyme complex for an intermolecular self-cleavage reaction.,Lee J, Feldman AR, Delmas B, Paetzel M J Biol Chem. 2007 Aug 24;282(34):24928-37. Epub 2007 Jun 6. PMID:17553791<ref>PMID:17553791</ref>
-===Crystal structure of VP4 protease from infectious pancreatic necrosis virus (IPNV) in space group P1===
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-{{ABSTRACT_PUBMED_17553791}}
+== References ==
+<references/>
-==About this Structure==
+__TOC__
-[[2pnl]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Infectious_pancreatic_necrosis_virus Infectious pancreatic necrosis virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PNL OCA].
+</StructureSection>
-==Reference==
-<ref group="xtra">PMID:017553791</ref><ref group="xtra">PMID:017142905</ref><references group="xtra"/>
 [[Category: Infectious pancreatic necrosis virus]]
 [[Category: Delmas, B.]]