4izj: Difference between revisions

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-{{STRUCTURE_4izj|  PDB=4izj  |  SCENE=  }}
-===Crystal structure of yellowtail ascites virus VP4 protease with a wild-type active site reveals acyl-enzyme complexes and product complexes.===
-{{ABSTRACT_PUBMED_23511637}}
-==About this Structure==
+==Crystal structure of yellowtail ascites virus VP4 protease with a wild-type active site reveals acyl-enzyme complexes and product complexes.==
-[[4izj]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Yellowtail_ascites_virus_-_y-6 Yellowtail ascites virus - y-6]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3r0b 3r0b]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IZJ OCA].
+<StructureSection load='4izj' size='340' side='right'caption='[[4izj]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
-[[Category: Infectious pancreatic necrosis birnavirus Vp4 peptidase]]
+== Structural highlights ==
-[[Category: Yellowtail ascites virus - y-6]]
+<table><tr><td colspan='2'>[[4izj]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Yellowtail_ascites_virus_-_Y-6 Yellowtail ascites virus - Y-6]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3r0b 3r0b]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IZJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IZJ FirstGlance]. <br>
-[[Category: Chung, I Y.W.]]
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
-[[Category: Paetzel, M.]]
+<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=CSO:S-HYDROXYCYSTEINE'>CSO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-[[Category: Acyl-enzyme]]
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4izj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4izj OCA], [https://pdbe.org/4izj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4izj RCSB], [https://www.ebi.ac.uk/pdbsum/4izj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4izj ProSAT]</span></td></tr>
-[[Category: Alpha-beta protein fold]]
+</table>
-[[Category: Birnavirus]]
+== Function ==
-[[Category: Hydrolase]]
+[https://www.uniprot.org/uniprot/P89521_9VIRU P89521_9VIRU]
-[[Category: Lysine general base]]
+<div style="background-color:#fffaf0;">
-[[Category: Product complex]]
+== Publication Abstract from PubMed ==
-[[Category: Serine-lysine dyad mechanism]]
+Yellowtail ascites virus (YAV) is an Aquabirnavirus that causes ascites in yellowtail, a fish often used in sushi. Segment A of the YAV genome codes for a polyprotein (pVP2-VP4-VP3) where processing by its own VP4 protease yields the capsid protein precursor pVP2, the ribonucleoprotein-forming VP3 and free VP4. VP4 protease utilizes the rarely observed serine-lysine catalytic dyad mechanism. Here we have confirmed the existence of an internal cleavage site, preceding the VP4/VP3 cleavage site. The resulting C-terminally truncated enzyme (ending at Ala716) is active as shown by a trans full-length VP4 cleavage assay and a fluorometric peptide cleavage assay. We present a crystal structure of a native active site YAV VP4 with the internal cleavage site trapped as trans product complexes and trans acyl-enzyme complexes. The acyl-enzyme complexes confirm directly the role of Ser633 as the nucleophile. A crystal structure of the lysine general base mutant (K674A) reveals the acyl-enzyme and empty binding site states of VP4, which allows for the observation of structural changes upon substrate or product binding. These snapshots of three different stages in the VP4 protease reaction mechanism will aid in the design of anti-birnavirus compounds, provide insight into previous site-directed mutagenesis results and contribute to the understanding of the serine-lysine dyad protease mechanism. In addition, we have discovered that this protease contains a channel that leads from the enzyme surface (adjacent to the substrate binding groove) to the active site and the deacylating water.
-[[Category: Viral protease]]
+Crystal structures of Yellowtail ascites virus VP4 protease: trapping an internal cleavage site trans acyl-enzyme complex in a native Ser/Lys dyad active site.,Chung IY, Paetzel M J Biol Chem. 2013 Mar 19. PMID:23511637<ref>PMID:23511637</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 4izj" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Virus protease 3D structures|Virus protease 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Yellowtail ascites virus - Y-6]]
+[[Category: Chung IYW]]
+[[Category: Paetzel M]]