Protein Name

NS2-3 protease


Hepatitis C virus(HCV)

Biological Context

HCV is a virus that has been causing global health problems. Infection of HCV is usually chronic and can lead to serious liver disorder such as cirrhosis and liver cancer. Although about 170 million people suffer from HCV, there is no effective therapy for this disease. Therefore, researches on HCV lifecycle are important to develop anti-HCV therapies.

One of the key steps in the lifecycle of HCV is the restricted proteolysis during viral replication. The HCV genome is composed of 9.6 kb positive-strand RNA which encodes a long protein-precursor polypeptide (fig1). After being transcribed, the polypeptide is processed into virus particle structural and nonstructural proteins by multiple proteases. At first, the structural proteins (C, E1, E2 and p7) are released from the polypeptide by host’s signal peptidase. Then, the reminder of the polypeptide containing precursor of nonstructural proteins (NS2, NS3, NS4A, NS4B, NS5A and NS5B) are processed by two autocatalytic proteases, NS2-3 protease and NS3-4A protease. NS2-3 protease consisting of NS2 and N terminal of NS3 cleaves at a single site of NS2/NS3 junction, and subsequently activates NS3-4A protease consisting NS3 and NS4A. The active NS3-4A, on the other hand, cleaves at the multiple downstream sites(between NS3/NS4A, NS4A/ NS4B, NS4B,/NS5A and NS5A/NS5B). NS2B is a RNA polymerase, thus initiates viral replication.


fig1. Protein-precursor polypeptide of HCV. This polypeptide yields ten mature HCV proteins.

Structure Description


Partial structure of NS2-3 protease (94-217 residue of NS2: NS2pro) is shown here. Monomeric NS2pro consists of N- and C terminal domains connected by an extended linker(fig2). The N terminal domain contains two antiparallel α-helices (H1 and H2), whereas the C terminal domain contains four-stranded antiparallel β-sheet. NS2-3 protease had been considered to work as a monomer until Lorenz et al. showed that homodimeric NS2-3 protease is the functional enzyme with two active sites. The N terminal domain of one subunit interacts with the C terminal domain of the other subunit and vice versa. The critical amino acid residues for proteolytic activity are within the interface of two subunits; His143 and Glu163 in the N terminal domain and Cys184 in the C terminal domain (fig3). Superimposition of these residues with known cysteine proteases revealed a similar spatial distribution. Therefore, NS2-3 protease would be a novel dimeric fold containing cysteine protease.


fig2. The structure of NS2pro monomer.


fig3. The structure of NS2pro homodimer. Two subunits are colored green and red respectively. The catalytic residues His143, Glu163 and Cys184 are shown as blue, pink and yellow.

Protein Data Bank (PDB)



Lorenz, I.C. Marcotrigiano, J. Dentzer, T.G. Rice, C.M.; "Structure of the catalytic domain of the hepatitis C virus NS2-3 protease."; Nature; (2006) 442:831-835 PubMed:16862121.


author: Daisuke Ino

Japanese version:PDB:2HD0