2GEF image
Deposition Date 2006-03-20
Release Date 2006-05-02
Last Version Date 2024-11-20
Entry Detail
PDB ID:
2GEF
Keywords:
Title:
Crystal structure of a Novel viral protease with a serine/lysine catalytic dyad mechanism
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
2.20 Å
R-Value Free:
0.26
R-Value Work:
0.22
R-Value Observed:
0.25
Space Group:
I 2 3
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Protease VP4
Chain IDs:A, B
Chain Length:217
Number of Molecules:2
Biological Source:Blotched snakehead virus
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
MSE A MET SELENOMETHIONINE
Primary Citation
Crystal structure of a novel viral protease with a serine/lysine catalytic dyad mechanism
J.Mol.Biol. 358 1378 1389 (2006)
PMID: 16584747 DOI: 10.1016/j.jmb.2006.02.045

Abstact

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.

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Primary Citation of related structures