2gef: Difference between revisions

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-{{Seed}}
-[[Image:2gef.png|left|200px]]
-<!--
+==Crystal structure of a Novel viral protease with a serine/lysine catalytic dyad mechanism==
-The line below this paragraph, containing "STRUCTURE_2gef", creates the "Structure Box" on the page.
+<StructureSection load='2gef' size='340' side='right'caption='[[2gef]], [[Resolution|resolution]] 2.20&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'>[[2gef]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Blotched_snakehead_virus Blotched snakehead virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GEF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GEF 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]] 2.2&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-{{STRUCTURE_2gef|  PDB=2gef  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2gef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gef OCA], [https://pdbe.org/2gef PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gef RCSB], [https://www.ebi.ac.uk/pdbsum/2gef PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gef ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The blotched snakehead virus (BSNV), an aquatic birnavirus, encodes a polyprotein (NH2-pVP2-X-VP4-VP3-COOH) that is processed through the proteolytic activity of its own protease (VP4) to liberate itself and the viral proteins pVP2, X and VP3. The protein pVP2 is further processed by VP4 to give rise to the capsid protein VP2 and four structural peptides. We report here the crystal structure of a VP4 protease from BSNV, which displays a catalytic serine/lysine dyad in its active site. This is the first crystal structure of a birnavirus protease and the first crystal structure of a viral protease that utilizes a lysine general base in its catalytic mechanism. The topology of the VP4 substrate binding site is consistent with the enzymes substrate specificity and a nucleophilic attack from the si-face of the substrates scissile bond. Despite low levels of sequence identity, VP4 shows similarities in its active site to other characterized Ser/Lys proteases such as signal peptidase, LexA protease and Lon protease. Together, the structure of VP4 provides insights into the mechanism of a recently characterized clan of serine proteases that utilize a lysine general base and reveals the structure of potential targets for antiviral therapy, especially for other related and economically important viruses, such as infectious bursal disease virus in poultry and infectious pancreatic necrosis virus in aquaculture.
-===Crystal structure of a Novel viral protease with a serine/lysine catalytic dyad mechanism===
+Crystal structure of a novel viral protease with a serine/lysine catalytic dyad mechanism.,Feldman AR, Lee J, Delmas B, Paetzel M J Mol Biol. 2006 May 19;358(5):1378-89. Epub 2006 Mar 6. PMID:16584747<ref>PMID:16584747</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_16584747}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2gef" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 16584747 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16584747}}
+__TOC__
+</StructureSection>
-==About this Structure==
-GEF is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Blotched_snakehead_virus Blotched snakehead virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GEF OCA].
-==Reference==
-Crystal structure of a novel viral protease with a serine/lysine catalytic dyad mechanism., Feldman AR, Lee J, Delmas B, Paetzel M, J Mol Biol. 2006 May 19;358(5):1378-89. Epub 2006 Mar 6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16584747 16584747]
 [[Category: Blotched snakehead virus]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Delmas, B.]]
+[[Category: Delmas B]]
-[[Category: Feldman, A R.]]
+[[Category: Feldman AR]]
-[[Category: Lee, J.]]
+[[Category: Lee J]]
-[[Category: Paetzel, M.]]
+[[Category: Paetzel M]]
-[[Category: Birnavirus]]
-[[Category: Lysine general base]]
-[[Category: Serine/lysine dyad mechamism]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 01:37:33 2008''