PDBsum entry 1z1i

Hydrolase

PDB id: 1z1i

Contents

Protein chain

301 a.a. *

Waters ×140

* Residue conservation analysis

PDB id:

1z1i

Name:

Hydrolase

Title:

Crystal structure of native sars clpro

Structure:

3c-like proteinase. Chain: a. Fragment: residues 1-306. Synonym: 3cl-pro, 3clp, replicase polyprotein 1ab. Engineered: yes

Source:

Sars coronavirus. Organism_taxid: 227859

Biol. unit:

Dimer (from PQS)

Resolution:

2.80Å R-factor: 0.241 R-free: 0.288

Authors:

P.H.Liang,A.H.Wang

Key ref:

M.F.Hsu et al. (2005). Mechanism of the maturation process of SARS-CoV 3CL protease. J Biol Chem, 280, 31257-31266. PubMed id: 15788388 DOI: 10.1074/jbc.M502577200

Date:

04-Mar-05 Release date: 22-Nov-05

Protein chain

P0C6X7  (R1AB_CVHSA) -  Replicase polyprotein 1ab from Severe acute respiratory syndrome coronavirus

Seq: 7073 a.a.

Struc: 301 a.a.

Enzyme reactions

• Enzyme class 2: E.C.2.1.1.- - ?????
• Enzyme class 3: E.C.2.1.1.56 - mRNA (guanine-N(7))-methyltransferase.
• Reaction: a 5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L- methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-homocysteine
• Enzyme class 4: E.C.2.1.1.57 - methyltransferase cap1.
• Reaction: a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside in mRNA + S-adenosyl-L-methionine = a 5'-end (N(7)-methyl 5'-triphosphoguanosine)- (2'-O-methyl-ribonucleoside) in mRNA + S-adenosyl-L-homocysteine + H⁺
• Enzyme class 5: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• Enzyme class 6: E.C.2.7.7.50 - mRNA guanylyltransferase.
• Reaction: a 5'-end diphospho-ribonucleoside in mRNA + GTP + H⁺ = a 5'-end (5'-triphosphoguanosine)-ribonucleoside in mRNA + diphosphate
• Enzyme class 7: E.C.3.1.13.- - ?????
• Enzyme class 8: E.C.3.4.19.12 - ubiquitinyl hydrolase 1.
• Reaction: Thiol-dependent hydrolysis of ester, thiolester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
• Enzyme class 9: E.C.3.4.22.- - ?????
• Enzyme class 10: E.C.3.4.22.69 - Sars coronavirus main proteinase.
• Enzyme class 11: E.C.3.6.4.12 - Dna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺
• Enzyme class 12: E.C.3.6.4.13 - Rna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺
• Enzyme class 13: E.C.4.6.1.- - ?????

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1074/jbc.M502577200

J Biol Chem 280:31257-31266 (2005)

PubMed id: 15788388

Mechanism of the maturation process of SARS-CoV 3CL protease.

M.F.Hsu, C.J.Kuo, K.T.Chang, H.C.Chang, C.C.Chou, T.P.Ko, H.L.Shr, G.G.Chang, A.H.Wang, P.H.Liang.

ABSTRACT

Severe acute respiratory syndrome (SARS) is an emerging infectious disease caused by a novel human coronavirus. Viral maturation requires a main protease (3CL(pro)) to cleave the virus-encoded polyproteins. We report here that the 3CL(pro) containing additional N- and/or C-terminal segments of the polyprotein sequences undergoes autoprocessing and yields the mature protease in vitro. The dimeric three-dimensional structure of the C145A mutant protease shows that the active site of one protomer binds with the C-terminal six amino acids of the protomer from another asymmetric unit, mimicking the product-bound form and suggesting a possible mechanism for maturation. The P1 pocket of the active site binds the Gln side chain specifically, and the P2 and P4 sites are clustered together to accommodate large hydrophobic side chains. The tagged C145A mutant protein served as a substrate for the wild-type protease, and the N terminus was first digested (55-fold faster) at the Gln(-1)-Ser1 site followed by the C-terminal cleavage at the Gln306-Gly307 site. Analytical ultracentrifuge of the quaternary structures of the tagged and mature proteases reveals the remarkably tighter dimer formation for the mature enzyme (K(d) = 0.35 nm) than for the mutant (C145A) containing 10 extra N-terminal (K(d) = 17.2 nM) or C-terminal amino acids (K(d) = 5.6 nM). The data indicate that immature 3CL(pro) can form dimer enabling it to undergo autoprocessing to yield the mature enzyme, which further serves as a seed for facilitated maturation. Taken together, this study provides insights into the maturation process of the SARS 3CL(pro) from the polyprotein and design of new structure-based inhibitors.

Selected figure(s)

Figure 5.
FIG. 5. Molecular interactions of the active site residues of protomer B with the C-terminal residues of protomer B'. A, stereo view of the electron density map of the C-terminal region (red stick) of protomer B' bound in the S pockets (cyan stick) of protomer B. B, details of the molecular interactions between the active site S1-S6 pockets of protomer B and the C-terminal residues of protomer B'. H-bonds are shown as green broken lines.

Figure 6.
FIG. 6. Superposition of 3CLpro active sites and inhibitors. A, superimposition of the active site of five 3CLpro protease structures: cyan and blue, protomer A and B of C145A; light green and gold, protomer A and B of the wild type, respectively; crimson, HCoV 229E 3CLpro (1P9S); and pink, TGEV 3CLpro (1P9U). B, superimposition of the six C-terminal residues of SARS 3CLpro (SGVTFQ) (cyan), the inhibitor of TGEV 3CLpro (1P9U, pink), the inhibitor of TGEV 3CLpro (VNSTLQ) at the active site of SARS 3CLpro (1UK4, gold), and the inhibitor of Rhinovirus 3CLpro, AG7088 at the active site (1CQQ, green).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 31257-31266) copyright 2005.

Figures were selected by an automated process.