PDBsum entry 2bx4

Hydrolase

PDB id: 2bx4

Contents

Protein chain

298 a.a. *

Waters ×46

* Residue conservation analysis

PDB id:

2bx4

Name:

Hydrolase

Title:

Crystal structure of sars coronavirus main proteinase (p21212)

Structure:

3c-like proteinase nsp5. Chain: a. Fragment: residues 3241-3546. Synonym: 3cl-pro,3clp,main protease,mpro,non-structural protein 5, nsp5,sars coronavirus main proteinase. Engineered: yes

Source:

Sars coronavirus sin2774. Organism_taxid: 235410. Gene: 1a. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PDB file)

Resolution:

2.79Å R-factor: 0.221 R-free: 0.302

Authors:

K.H.G.Verschueren,J.R.Mesters,J.Bigalke,R.Hilgenfeld

Key ref:

J.Tan et al. (2005). pH-dependent conformational flexibility of the SARS-CoV main proteinase (M(pro)) dimer: molecular dynamics simulations and multiple X-ray structure analyses. J Mol Biol, 354, 25-40. PubMed id: 16242152 DOI: 10.1016/j.jmb.2005.09.012

Date:

22-Jul-05 Release date: 26-Sep-05

Protein chain

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

Seq: 7073 a.a.

Struc: 298 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: 10.1016/j.jmb.2005.09.012

J Mol Biol 354:25-40 (2005)

PubMed id: 16242152

pH-dependent conformational flexibility of the SARS-CoV main proteinase (M(pro)) dimer: molecular dynamics simulations and multiple X-ray structure analyses.

J.Tan, K.H.Verschueren, K.Anand, J.Shen, M.Yang, Y.Xu, Z.Rao, J.Bigalke, B.Heisen, J.R.Mesters, K.Chen, X.Shen, H.Jiang, R.Hilgenfeld.

ABSTRACT

The SARS coronavirus main proteinase (M(pro)) is a key enzyme in the processing of the viral polyproteins and thus an attractive target for the discovery of drugs directed against SARS. The enzyme has been shown by X-ray crystallography to undergo significant pH-dependent conformational changes. Here, we assess the conformational flexibility of the M(pro) by analysis of multiple crystal structures (including two new crystal forms) and by molecular dynamics (MD) calculations. The MD simulations take into account the different protonation states of two histidine residues in the substrate-binding site and explain the pH-activity profile of the enzyme. The low enzymatic activity of the M(pro) monomer and the need for dimerization are also discussed.

Selected figure(s)

Figure 1.
Figure 1. Structure of the (a) monomer and (b) dimer of SARS-CoV Mpro. (a) Domains I (light blue) and II (green) each contain a six-stranded b-barrel and domain III (orange) is composed mainly of a-helices. The amino and the carboxy terminus are marked by a blue and an orange sphere, respectively. The flexible loops L1, L2, and L3 (red) comprise residues 138-145 (the oxyanion-binding loop), 165-172, and 185-200, respectively. (b) a-Helices are red and b-strands are light blue. The amino and the carboxy termini are marked by blue and orange spheres, respectively. Dimerization is mainly due to interactions between the helical domains III of each monomer (top). (c) Superimposition (in stereo) of the C^a backbone as determined in three different crystal forms. Blue, monoclinic form; red, tetragonal form; green, orthorhombic form. (a) and (b) were prepared by MOLSCRIPT,40 (c) was prepared by PyMOL.41

Figure 8.
Figure 8. Some characteristic distances in the MD simulations of the SARS-CoV Mpro dimer at (a) pH 6.0, (b) pH 7.6, (c) pH 8.0, and (d) pH 5.0. For each simulation, the distance between Glu166 and His163, Glu166 and His172, Glu166 and Ser1(N) of the other monomer in the dimer, and Phe140 (center of mass of phenyl ring) and His163 (center of mass of imidazole ring) are shown. The shorter of the two distances to the carboxylate oxygen atoms of Glu166, Oe1 and Oe2, is displayed. Green, monomer A; blue, monomer B.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 354, 25-40) copyright 2005.

Figures were selected by an automated process.