PDBsum entry 2zu2

Hydrolase/hydrolase inhibitor

PDB id: 2zu2

Contents

Protein chains

300 a.a. *

Ligands

MPD

DTZ ×2

Waters ×469

* Residue conservation analysis

PDB id:

2zu2

Name:

Hydrolase/hydrolase inhibitor

Title:

Complex structure of cov 229e 3cl protease with epdtc

Structure:

3c-like proteinase. Chain: a, b. Synonym: 3cl-pro, 3clp, m-pro, p34, nsp5. Engineered: yes

Source:

Human coronavirus. Hcov-229e. Organism_taxid: 11137. Strain: 229e. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.80Å R-factor: 0.187 R-free: 0.222

Authors:

C.C.Lee,A.H.-J.Wang

Key ref:

C.C.Lee et al. (2009). Structural basis of inhibition specificities of 3C and 3C-like proteases by zinc-coordinating and peptidomimetic compounds. J Biol Chem, 284, 7646-7655. PubMed id: 19144641 DOI: 10.1074/jbc.M807947200

Date:

12-Oct-08 Release date: 13-Jan-09

Protein chains

P0C6U2  (R1A_CVH22) -  Replicase polyprotein 1a from Human coronavirus 229E

Seq: 4085 a.a.

Struc: 300 a.a.

Enzyme reactions

• Enzyme class 2: 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 3: E.C.3.4.22.- - ?????

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.

DOI no: 10.1074/jbc.M807947200

J Biol Chem 284:7646-7655 (2009)

PubMed id: 19144641

Structural basis of inhibition specificities of 3C and 3C-like proteases by zinc-coordinating and peptidomimetic compounds.

C.C.Lee, C.J.Kuo, T.P.Ko, M.F.Hsu, Y.C.Tsui, S.C.Chang, S.Yang, S.J.Chen, H.C.Chen, M.C.Hsu, S.R.Shih, P.H.Liang, A.H.Wang.

ABSTRACT

Human coxsackievirus (CV) belongs to the picornavirus family, which consists of over 200 medically relevant viruses. In picornavirus, a chymotrypsin-like protease (3C(pro)) is required for viral replication by processing the polyproteins, and thus it is regarded as an antiviral drug target. A 3C-like protease (3CL(pro)) also exists in human coronaviruses (CoV) such as 229E and the one causing severe acute respiratory syndrome (SARS). To combat SARS, we previously had developed peptidomimetic and zinc-coordinating inhibitors of 3CL(pro). As shown in the present study, some of these compounds were also found to be active against 3C(pro) of CV strain B3 (CVB3). Several crystal structures of 3C(pro) from CVB3 and 3CL(pro) from CoV-229E and SARS-CoV in complex with the inhibitors were solved. The zinc-coordinating inhibitor is tetrahedrally coordinated to the His(40)-Cys(147) catalytic dyad of CVB3 3C(pro). The presence of specific binding pockets for the residues of peptidomimetic inhibitors explains the binding specificity. Our results provide a structural basis for inhibitor optimization and development of potential drugs for antiviral therapies.

Selected figure(s)

Figure 4.
Peptidomimetic inhibitors bound to the proteases. A, the active site of CVB3 3C^pro with the bound TG-0204998. Protein is rendered as a semitransparent solvent-accessible surface with associated protein backbone and side chain atoms. The oxygen atoms are shown in red, nitrogen in blue, sulfur in yellow, and protein carbon atoms in magenta. The inhibitor atoms are shown as ball-and-stick form and colored in orange for carbon. The sulfur atom of Cys^147 is covalently attached to the inhibitor carbon. The substrate binding subsites are designated as S1′, S1, S2, S3, and S4. B, conserved water molecules, identified by superimposing the two molecules of CVB3 3C^pro C147A mutant on the TG-0204998 complex of CVB3 3C^pro. The water molecules are shown here as spheres colored green/orange (C147A) and magenta (complex). The protein model of the TG-0204998 complex structure is shown as an electrostatic surface and TG-0204998 as sticks. The conserved water molecules of the C147A mutant structure in the active site are marked. The black star indicates the Michael addition site. C and D, the active site of SARS 3CL^pro with bound TG-0204998 (C) and TG-0205486 (D), colored as in A. The substrate-binding subsites are also indicated.

Figure 5.
Omit maps of inhibitors. F[o] – F[c] omit maps (magenta) were calculated for the five inhibitors and contoured at the 2.0 σ level. The inhibitor and inhibitor-binding residues are shown as ball-and-stick models with carbon atoms in green and gray. The sulfur, nitrogen, and oxygen atoms are colored in yellow, blue, and red, respectively. A and B, EPDTC bound to CVB3 3C^pro and CoV-229E 3CL^pro. The zinc ion (cyan sphere) of EPDTC was coordinated to the Cys and His residues. C and D, TG-0204998 in covalent bond with the Cys of CVB3 3C^pro and SARS-CoV 3CL^pro. E, TG-0205486 in covalent bond with the Cys of SARS-CoV 3CL^pro.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2009, 284, 7646-7655) copyright 2009.

Figures were selected by an automated process.