2GEF

Crystal structure of a Novel viral protease with a serine/lysine catalytic dyad mechanism

Summary for 2GEF

• Entry DOI: 10.2210/pdb2gef/pdb
• Descriptor: Protease VP4 (2 entities in total)
• Functional Keywords: birnavirus, serine/lysine dyad mechamism, lysine general base, hydrolase
• Biological source: Blotched snakehead virus
• Cellular location: 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). Structural peptide 4: Virion (Potential): Q8AZM0
• Total number of polymer chains: 2
• Total formula weight: 47312.05

Authors

Paetzel, M.,Feldman, A.R.,Lee, J.,Delmas, B. (deposition date: 2006-03-20, release date: 2006-05-02, Last modification date: 2024-11-20)

Primary citation

Feldman, A.R.,Lee, J.,Delmas, B.,Paetzel, M.
Crystal structure of a novel viral protease with a serine/lysine catalytic dyad mechanism
J.Mol.Biol., 358:1378-1389, 2006

PubMed Abstract: 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.

PubMed: 16584747
DOI: 10.1016/j.jmb.2006.02.045

Experimental method

X-RAY DIFFRACTION (2.2 Å)