2PNL

Crystal structure of VP4 protease from infectious pancreatic necrosis virus (IPNV) in space group P1

2PNL の概要

• エントリーDOI: 10.2210/pdb2pnl/pdb
• 関連するPDBエントリー: 2GEF 2PNM
• 分子名称: Protease VP4, GUANIDINE (3 entities in total)
• 機能のキーワード: acyl-enzyme, protease, ser/lys dyad, viral protease, substrate complex, product complex, hydrolase
• 由来する生物種: Infectious pancreatic necrosis virus
• 細胞内の位置: Capsid protein VP2: Virion (Potential). Capsid protein VP3: Virion (Potential). Structural peptide 1: Virion (Potential). Structural peptide 2: Virion (Potential). Structural peptide 3: Virion (Potential): Q703G9
• タンパク質・核酸の鎖数: 10
• 化学式量合計: 218566.01

構造登録者

Paetzel, M.,Lee, J.,Feldman, A.R.,Delmas, B. (登録日: 2007-04-24, 公開日: 2007-06-05, 最終更新日: 2024-10-30)

主引用文献

Lee, J.,Feldman, A.R.,Delmas, B.,Paetzel, M.
Crystal structure of the VP4 protease from infectious pancreatic necrosis virus reveals the acyl-enzyme complex for an intermolecular self-cleavage reaction.
J.Biol.Chem., 282:24928-24937, 2007

PubMed Abstract: 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.

PubMed: 17553791
DOI: 10.1074/jbc.M701551200

実験手法

X-RAY DIFFRACTION (2.21 Å)