View source for 2gef


==Crystal structure of a Novel viral protease with a serine/lysine catalytic dyad mechanism==
<StructureSection load='2gef' size='340' side='right' caption='[[2gef]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2gef]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bsnv Bsnv]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GEF FirstGlance]. <br>
</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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">birnaviridae ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=311176 BSNV])</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2gef FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gef OCA], [http://pdbe.org/2gef PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2gef RCSB], [http://www.ebi.ac.uk/pdbsum/2gef PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2gef ProSAT]</span></td></tr>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/POLS_BSNV POLS_BSNV]] Capsid protein VP2 self assembles to form an icosahedral capsid with a T=13 symmetry, about 70 nm in diameter, and consisting of 260 VP2 trimers. The capsid encapsulates the genomic dsRNA. VP2 is also involved in attachment and entry into the host cell (By similarity).  The precursor of VP2 plays an important role in capsid assembly. First, pre-VP2 and VP2 oligomers assemble to form a procapsid. Then, the pre-VP2 intermediates may be processed into VP2 proteins by proteolytic cleavage mediated by VP4 to obtain the mature virion. The final capsid is composed of pentamers and hexamers but VP2 has a natural tendency to assemble into all-pentameric structures. Therefore pre-VP2 may be required to allow formation of the hexameric structures (By similarity).  Protease VP4 is a serine protease that cleaves the polyprotein into its final products. Pre-VP2 is first partially cleaved, and may be completely processed by VP4 upon capsid maturation (By similarity).  Capsid protein VP3 plays a key role in virion assembly by providing a scaffold for the capsid made of VP2. May self-assemble to form a T=4-like icosahedral inner-capsid composed of at least 180 trimers. Plays a role in genomic RNA packaging by recruiting VP1 into the capsid and interacting with the dsRNA genome segments to form a ribonucleoprotein complex. Additionally, the interaction of the VP3 C-terminal tail with VP1 removes the inherent structural blockade of the polymerase active site. Thus, VP3 can also function as a transcriptional activator (By similarity).  Structural peptide 1 is a small peptide derived from pre-VP2 C-terminus. It destabilizes and perforates cell membranes, suggesting a role during entry (By similarity).  Structural peptide 2 is a small peptide derived from pre-VP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing (By similarity).  Structural peptide 3 is a small peptide derived from pre-VP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing (By similarity).  Structural peptide 4 is a small peptide derived from pre-VP2 C-terminus. It is essential for the virus viability (By similarity). 
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== 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.,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>
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== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Bsnv]]
[[Category: Delmas, B]]
[[Category: Feldman, A R]]
[[Category: Lee, J]]
[[Category: Paetzel, M]]
[[Category: Birnavirus]]
[[Category: Hydrolase]]
[[Category: Lysine general base]]
[[Category: Serine/lysine dyad mechamism]]