4568 Biochemistry 2004, 43, 4568-4574 3C-like Proteinase from SARS Coronavirus Catalyzes Substrate Hydrolysis by a General Base Mechanism† Changkang Huang,‡ Ping Wei,‡ Keqiang Fan,‡ Ying Liu,‡ and Luhua Lai*,‡,§ State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, and Center for Theoretical Biology, Peking UniVersity, Beijing 100871, China ReceiVed NoVember 11, 2003; ReVised Manuscript ReceiVed January 26, 2004 ABSTRACT: SARS 3C-like proteinase has been proposed to be a key enzyme for drug design against SARS. Lack of a suitable assay has been a major hindrance for enzyme kinetic studies and a large-scale inhibitor screen for SARS 3CL proteinase. Since SARS 3CL proteinase belongs to the cysteine protease family (family C3 in clan CB) with a chymotrypsin fold, it is important to understand the catalytic mechanism of SARS 3CL proteinase to determine whether the proteolysis proceeds through a general base catalysis mechanism like chymotrypsin or an ion pair mechanism like papain. We have established a continuous colorimetric assay for SARS 3CL proteinase and applied it to study the enzyme catalytic mechanism. The proposed catalytic residues His41 and Cys145 were confirmed to be critical for catalysis by mutating to Ala, while the Cys145 to Ser mutation resulted in an active enzyme with a 40-fold lower activity. From the pH dependency of catalytic activity, the pKa’s for His41 and Cys145 in the wild-type enzyme were estimated to be 6.38 and 8.34, while the pKa’s for His41 and Ser145 in the C145S mutant were estimated to be 6.15 and 9.09, respectively. The C145S mutant has a normal isotope effect in D2O for general base catalysis, that is, reacts slower in D2O, while the wild-type enzyme shows an inverse isotope effect which may come from the lower activation enthalpy. The pKa values measured for the active site residues and the activity of the C145S mutant are consistent with a general base catalysis mechanism and cannot be explained by a thiolate-imidazolium ion pair model. A novel form of coronavirus has been attributed as the Homology modeling for the SARS 3CL proteinase has been major cause of severe acute respiratory syndrome (SARS) performed by various groups (5-7), and the conformational that broke out in early 2003 (1, 2). The genome of SARS flexibility of the substrate binding site has been studied (7). coronavirus has been sequenced within a short period of time Virtual screening of small molecule libraries has predicted after isolation of the virus (3, 4). Coronaviruses are members possible inhibitors (6). An 8-mer peptide has been docked of positive-stranded RNA viruses featuring the largest viral on the model of SARS 3CL proteinase to study the RNA genomes known to date. Translation of the SARS interaction of SARS 3CL with its substrates (8). coronavirus replicase gene produces two proteins with Two crystal structures of coronavirus 3CL proteinase from overlapping sequences, polyproteins 1a (∼450 kDa) and 1ab transmissible gastroenteritis virus (TGEV) (9) and human (∼750 kDa), which are conserved both in length and in coronavirus (hCoV) 229E have been reported (5). Recently, amino acid sequence to other coronavirus replicase proteins. the crystal structure of SARS coronavirus 3CL proteinase Polyproteins 1a and 1ab are cleaved by the internally encoded has also been solved by two groups, with the coordinates 3C-like proteinase (3CL) to release functional proteins deposited in the Protein Data Bank (http://www.rcsb.org). necessary for virus replication. SARS 3CL1 proteinase is fully In addition, Z. H. Rao’s group also elucidated the complex conserved among all released SARS coronavirus genome structure of SARS 3CL proteinase with a covalent bonded sequences and is highly homologous with other coronavirus substrate analogue, which provided insights on the substrate 3CL proteinases. Due to its functional importance in the viral binding site (10). All of the reported structures of coronavirus life cycle, SARS 3CL proteinase has been proposed to be a 3CL proteinases are similar. The first two domains form a key target for structure-based drug design against SARS (5). chymotrypsin fold which is responsible for the catalytic reaction, and the third domain is R helical with unclear † This work was supported by the 863 High-Technology Project, the National Basic Research Project (2003CB715900), and NSFC biological function. Coronavirus 3CL proteinase shares the (10345004, 90103029, 20173001, 20228306). chymotrypsin fold with the 3C proteinases from other viruses * Corresponding author. Tel: +86 10 62757486. Fax: +86 10 such as rhinovirus, picornavirus, and hepatitis A virus (11- 62751725. E-mail: [email protected]. 13). The 3C proteinase of rhinovirus has been targeted to ‡ State Key Laboratory for Structural Chemistry of Unstable and - Stable Species, College of Chemistry and Molecular Engineering, develop drugs against the common cold (14 20). Peking University. As 3C proteinases and the catalytic domain in 3CL § Center for Theoretical Biology, Peking University. 1 proteinases are all cysteine proteinases with a chymotrypsin Abbreviations: SARS 3CL, SARS coronavirus 3C-like proteinase; - CD, circular dichroism; BME, 2′-mercaptoethanol; DTT, 1,4-dithio- fold, it is interesting to know whether they follow a thiolate threitol. imidazolium ion pair catalytic mechanism as found with 10.1021/bi036022q CCC: $27.50 © 2004 American Chemical Society Published on Web 03/12/2004 General Base Catalysis by SARS 3CL Proteinase Biochemistry, Vol. 43, No. 15, 2004 4569 Table 1: Primers Used to Generate SARS 3CL Proteinase Mutants mutants sequence H41A sense primer: 5′-CAGTATACTGTCCAAGAGCAGTCATTTGCACAGCAGAAGAC-3′ antisense primer: 5′-GTCTTCTGCTGTGCAAATGACTGCTCTTGGACAGTATACTG-3′ C145A sense primer: 5′-CTTTCCTTAATGGATCAGCAGGTAGTGTTGGTTTTAAC-3′ antisense primer: 5′-GTTAAAACCAACACTACCTGCTGATCCATTAAGGAAAG-3′ C145S sense primer: 5′-CTTTCCTTAATGGATCATCTGGTAGTGTTGGTTTTAAC-3′ antisense primer: 5′-GTTAAAACCAACACTACCAGATGATCCATTAAGGAAAG-3′ papain (21-24). It was recently shown that 3C proteinases eluted with another 180 mL of buffer C. The purity of each from picornain virus, poliovirus, and sortase from Staphyl- mutant was verified by SDS-PAGE. Secondary and tertiary ococcus aureus do not contain a thiolate-imidazolium ion structures of the mutants were determined to be essentially pair in their active site (25-27). Compared to the catalytic the same as the wild-type enzyme (data not shown) as triad in 3C proteinase, only two catalytic residues were found monitored by far- and near-UV CD. in 3CL proteinases of coronaviruses (5, 9, 28). Whether 3CL Construction of Plasmid pET 3CLP-21h, Protein Expres- proteinase of coronavirus follows an ion pair mechanism or sion, and Purification. The non-His-tagged SARS 3C-like a general base catalytic mechanism is important to understand proteinase was amplified by PCR from the plasmid pET the kinetic mechanism and to carry out structural and/or 3CLP-21x using primers 3CLP-Nhe (5′-CACTGCTAGCG- mechanism-based drug design. On the basis of our previous GTTTTAGGAAAATGGCATTCCC-3′) and 3CLP-Hind(5′- study on the cloning, expression, and substrate specificity CCTCAAGCTTATTGGAAGGTAACACCAGAGC-3′). The of SARS 3CL proteinase (29), we have established a colorimetric assay using a synthetic substrate for SARS 3CL PCR product was inserted into the NheI and HindIII sites of proteinase and characterized its enzyme catalysis mechanism. pET21a DNA. The resulting plasmid pET 3CLP-21h was While His41 and Cys145 were confirmed to be crucial for transformed into E. coli BL21(DE3) cells for expression. The catalysis by mutating to Ala, the substitution of Cys145 with recombinant 3CLP-21h was purified by fractional precipita- Ser resulted in an active enzyme. From pH-dependent tion with ammonium sulfate and further purified by using an anion-exchange column, HiTrap Q HP (Amersham catalytic activities, the calculated pKa values for His41 and Cys145 in the wild-type enzyme and for His41 and Ser145 Bioscience), and a gel filtration column, Sephacryl S-200 in the C145S mutant indicated that the enzyme catalysis HR (Amersham Bioscience). follows a general base catalysis mechanism and does not Substrate Specificity of C145S. Three substrate peptides contain a thiolate-imidazolium ion pair in its active site. derived from the natural cleavage sites of the SARS-CoV polyprotein were used in this study and were synthesized as EXPERIMENTAL PROCEDURES previously described (29). Their sequences are listed in Table Site-Directed Mutagenesis of SARS-CoV 3CL Proteinase. 3. The SARS 3CL proteinase C145S mutant was incubated The construction of the plasmid pET 3CLP-21x and the with different substrates in 40 mM Tris-HCl buffer, pH 7.3, expression and purification of the C-terminal His-tagged with a final enzyme concentration of 76.9 µM. The concen- SARS-CoV 3CL proteinase have been reported previously trations of substrate peptides were 0.4 mM for S01 and S06 (29). The H41A, C145A, C145S mutants in SARS-CoV 3CL and 0.2 mM for S09. The reaction mixture was analyzed by proteinase were prepared with the QuikChange site-directed RP-HPLC using a 15 min, 0-50% linear gradient of mutagenesis kit (Stratagene) using pET 3CLP-21x as a acetonitrile with 0.1% trifluoroacetic acid after 25 h. kcat/Km template. The nucleotide sequences of primers used for site- was calculated using the equation: directed mutagenesis are listed in Table 1. The mutations ) - were verified by sequencing. The 3CL proteinase mutants ln PA ln PA0 kcatCEt/Km (1) were expressed in Escherichia coli, purified, and analyzed using a similar procedure for the wild-type protein (29). where PA was the peak area of the substrate peptide in the Briefly, appropriate plasmids were transformed into E. coli reacting mixture after 25 h, PA0 was the origin peak area of BL21(DE3) cells. Cultures were grown at 37 °Cin1Lof the substrate peptide, and CE was the total concentration of LB containing ampicillin (100 µg/mL) until the OD at 600 3C-like proteinase. nm reached 0.8 and induced with 0.5 mM IPTG at 30 °C for 3 h.