PDBsum entry 2gtb

Hydrolase

PDB id: 2gtb

Contents

Protein chain

299 a.a. *

Ligands

AZP

ACY

Waters ×127

* Residue conservation analysis

PDB id:

2gtb

Name:

Hydrolase

Title:

Crystal structure of sars coronavirus main peptidase (with an additional ala at the n-terminus of each protomer) inhibited by an aza-peptide epoxide in the space group p43212

Structure:

3c-like proteinase. Chain: a. Synonym: 3cl-pro, 3clp, nsp2. Engineered: yes. Mutation: yes

Source:

Sars coronavirus. Organism_taxid: 227859. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.00Å R-factor: 0.200 R-free: 0.270

Authors:

T.-W.Lee,M.M.Cherney,C.Huitema,J.Liu,K.E.James,J.C.Powers

Key ref:

T.W.Lee et al. (2007). Crystal structures reveal an induced-fit binding of a substrate-like Aza-peptide epoxide to SARS coronavirus main peptidase. J Mol Biol, 366, 916-932. PubMed id: 17196984 DOI: 10.1016/j.jmb.2006.11.078

Date:

27-Apr-06 Release date: 26-Dec-06

Protein chain

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

Seq: 7073 a.a.

Struc: 299 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.2006.11.078

J Mol Biol 366:916-932 (2007)

PubMed id: 17196984

Crystal structures reveal an induced-fit binding of a substrate-like Aza-peptide epoxide to SARS coronavirus main peptidase.

T.W.Lee, M.M.Cherney, J.Liu, K.E.James, J.C.Powers, L.D.Eltis, M.N.James.

ABSTRACT

The SARS coronavirus main peptidase (SARS-CoV M(pro)) plays an essential role in the life-cycle of the virus and is a primary target for the development of anti-SARS agents. Here, we report the crystal structure of M(pro) at a resolution of 1.82 Angstroms, in space group P2(1) at pH 6.0. In contrast to the previously reported structure of M(pro) in the same space group at the same pH, the active sites and the S1 specificity pockets of both protomers in the structure of M(pro) reported here are in the catalytically competent conformation, suggesting their conformational flexibility. We report two crystal structures of M(pro) having an additional Ala at the N terminus of each protomer (M(+A(-1))(pro)), both at a resolution of 2.00 Angstroms, in space group P4(3)2(1)2: one unbound and one bound by a substrate-like aza-peptide epoxide (APE). In the unbound form, the active sites and the S1 specificity pockets of both protomers of M(+A(-1))(pro) are observed in a collapsed (catalytically incompetent) conformation; whereas they are in an open (catalytically competent) conformation in the APE-bound form. The observed conformational flexibility of the active sites and the S1 specificity pockets suggests that these parts of M(pro) exist in dynamic equilibrium. The structural data further suggest that the binding of APE to M(pro) follows an induced-fit model. The substrate likely also binds in an induced-fit manner in a process that may help drive the catalytic cycle.

Selected figure(s)

Figure 1.
Figure 1. Inhibition of SARS-CoV M^pro by the aza-peptide epoxides (APEs) synthesized for our study, Cbz-Leu-Phe-AGln-EP-CooEt. The epoxide carbon atoms are numbered and their stereochemistry is omitted for simplicity. The proposed mechanism for the irreversible inhibition of clan CD cysteine peptidases by APEs is indicated by arrows. In the inhibition of M^pro, route I was adopted. Cbz, the benzyloxycarbonyl group; AGln, aza-glutamine; EP, epoxide; COOEt, ethyl ester.

Figure 8.
Figure 8. Aromatic interactions observed between Phe140 and His163 in the crystal structures of SARS-CoV M^pro (wild type and variants). The broken lines indicate the alignment of the partial positive charges (δ+) of the hydrogen atoms on the phenyl ring of Phe140 with the partial negative charges (δ−) in the central part of the imidazole ring of His163.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 366, 916-932) copyright 2007.

Figures were selected by an automated process.