PDBsum entry 1uk2

Hydrolase

PDB id: 1uk2

Contents

Protein chains

302 a.a. *

Waters ×80

* Residue conservation analysis

PDB id:

1uk2

Name:

Hydrolase

Title:

Crystal structure of sars coronavirus main proteinase (3clpro) at ph8.0

Structure:

3c-like proteinase. Chain: a, b. Synonym: sars coronavirus main proteinase, 3clpro. Engineered: yes

Source:

Sars coronavirus. Organism_taxid: 227859. Strain: sars. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

2.20Å R-factor: 0.226 R-free: 0.253

Authors:

H.Yang,M.Yang,Y.Liu,M.Bartlam,Y.Ding,Z.Lou,L.Sun,Z.Zhou,S.Ye,K.Anand, H.Pang,G.F.Gao,R.Hilgenfeld,Z.Rao

Key ref:

H.Yang et al. (2003). The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor. Proc Natl Acad Sci U S A, 100, 13190-13195. PubMed id: 14585926 DOI: 10.1073/pnas.1835675100

Date:

14-Aug-03 Release date: 18-Nov-03

Protein chains

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

Seq: 7073 a.a.

Struc: 302 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: 10.1073/pnas.1835675100

Proc Natl Acad Sci U S A 100:13190-13195 (2003)

PubMed id: 14585926

The crystal structures of severe acute respiratory syndrome virus main protease and its complex with an inhibitor.

H.Yang, M.Yang, Y.Ding, Y.Liu, Z.Lou, Z.Zhou, L.Sun, L.Mo, S.Ye, H.Pang, G.F.Gao, K.Anand, M.Bartlam, R.Hilgenfeld, Z.Rao.

ABSTRACT

A newly identified severe acute respiratory syndrome coronavirus (SARS-CoV), is the etiological agent responsible for the outbreak of SARS. The SARS-CoV main protease, which is a 33.8-kDa protease (also called the 3C-like protease), plays a pivotal role in mediating viral replication and transcription functions through extensive proteolytic processing of two replicase polyproteins, pp1a (486 kDa) and pp1ab (790 kDa). Here, we report the crystal structures of the SARS-CoV main protease at different pH values and in complex with a specific inhibitor. The protease structure has a fold that can be described as an augmented serine-protease, but with a Cys-His at the active site. This series of crystal structures, which is the first, to our knowledge, of any protein from the SARS virus, reveal substantial pH-dependent conformational changes, and an unexpected mode of inhibitor binding, providing a structural basis for rational drug design.

Selected figure(s)

Figure 1.
Fig. 1. The SARS-CoV Mpro dimer structure complexed with a substrate-analogue hexapeptidyl CMK inhibitor. (A) The SARS-CoV Mpro dimer structure is presented as ribbons, and inhibitor molecules are shown as ball-and-stick models. Protomer A (the catalytically competent enzyme) is red, protomer B (the inactive enzyme) is blue, and the inhibitor molecules are yellow. The N-finger residues of protomer B are green. The molecular surface of the dimer is superimposed. (B) A cartoon diagram illustrating the important role of the N-finger in both dimerization and maintenance of the active form of the enzyme.

Figure 4.
Fig. 4. Molecular recognition interactions in the substrate-analogue hexapetidyl CMK inhibitor (Cbz-Val-Asn-Ser-Thr-Leu-Gln-CMK) complexed with SARS Mpro. (A) A stereoview of the substrate-binding pocket (green) in protomer A of the CMK inhibitor complex. The inhibitor molecule (red) is shown in the 2.5-Å original F[o] - F[c] difference electron-density map (1.5 ). Hydrogen bonds are shown as dashed lines. The Gln-P1 is bound to the S1 substrate-specificity subsite, but Leu-P2 fails to bind at the S2 subsite (near Asp-A187), which is instead occupied by Thr-P3. The amino acid residues of the protein are labeled in single letters; for example, H163A stands for His-163 of monomer A (i.e., His-A163). (B) A stereoview of the substrate-binding pocket (green) in protomer B of the CMK inhibitor complex. The inhibitor molecule (red) is shown in the original F[o] - F[c] difference electron-density map (1.5 ). The Gln-P1 does not bind to the partly collapsed S1 subsite in this protomer, but Leu-P2 and Ser-P4 are in their canonical binding sites. See text for further details.

Figures were selected by an automated process.