Picornain 3C
The human rhinovirus 3C is a cysteine protease that is essential for the processing of the viral precursor polyprotein and release of RNA replication proteins. In UniProtKB P04936, the protease 3C portion of the chain is responsible for the cleavage of the sites:
- 330 - 331
- 992 - 993
- 1409 - 1410
- 1486 - 1487
- 1507 - 1508
- 1690 - 1691
Reference Protein and Structure
- Sequence
-
P04936
(2.7.7.48, 3.4.22.28, 3.4.22.29, 3.6.1.15)
(Sequence Homologues)
(PDB Homologues)
- Biological species
-
Human rhinovirus A2 (Virus)
- PDB
-
1cqq
- TYPE 2 RHINOVIRUS 3C PROTEASE WITH AG7088 INHIBITOR
(1.85 Å)
- Catalytic CATH Domains
-
2.40.10.10
(see all for 1cqq)
Enzyme Reaction (EC:3.4.22.28)
+
→
+
Alternative enzyme names: 3C protease, 3C proteinase, Coxsackievirus 3C proteinase, Cysteine proteinase 3C, Foot-and-mouth protease 3C, Foot-and-mouth-disease virus proteinase 3C, Hepatitis A virus 3C proteinase, Picornavirus endopeptidase 3C, Poliovirus protease 3C, Poliovirus proteinase 3C, Protease 3C, Rhinovirus protease 3C, Rhinovirus proteinase 3C, Tomato ringspot nepovirus 3C-related protease,
Enzyme Mechanism
Introduction
In rhinovirus 3C, the catalytically important residues Cys147, His50 and Glu71 form a triad related to that of the serine proteases. The highly conserved sequence Gly-X-Cys-Gly-Gly in viral C3 proteases serves to orientate the Cys147 for nucleophilic attack at the substrate carbonyl. Residue backbone amide groups are positioned to stabilise the anionic tetrahedral intermediate as part of an oxyanion hole. This resembles the mechanism of the serine protease family, suggesting more closely related mechanism to this class of enzymes, rather than that of the cysteine proteases.
Catalytic Residues Roles
| UniProt | PDB* (1cqq) | ||
| Cys1654 (main-N) | Cys147A (main-N) | Implicated in forming part of the oxyanion hole, stabilising the anionic intermediate. | electrostatic stabiliser |
| His1547 | His40A | Hydrogen bonded to the nucleophilic Cys147. It acts as a proton acceptor in the anionic transition state, and then relays the proton to the departing N terminus of the cleaved peptide after the collapse of the tetrahedral intermediate. It also activates the hydrolytic water for attack at the acyl-enzyme intermediate. Hydrogen bonding interactions with Glu71 enhance the residue's acid/base function. | proton shuttle (general acid/base), electrostatic stabiliser |
| Glu1578 | Glu71A | The residue hydrogen bonds to the N(E) atom of His 40, modifying the pKa of the N(delta) atom of the imidazole ring, which is in turn implicated in proton transfer between the nucleophilic Cys147 and substrate. | modifies pKa, electrostatic stabiliser |
| Cys1654 | Cys147A | The residue acts as a nucleophile towards the polypeptide substrate. Hydrogen bonding interactions with His40 allow the proton to be transferred from Cys147 to the N terminus of the cleaved polypeptide with collapse of the anionic intermediate. The resulting acyl-enzyme intermediate is then hydrolysed by water, regenerating the free Cys147 and therefore the active site. | covalent catalysis, proton shuttle (general acid/base), electrostatic stabiliser |
| Gly1652 (main-N) | Gly145A (main-N) | The residue's backbone forms part of the oxyanion hole which stabilises the anionic tetrahedral intermediate. | electrostatic stabiliser |
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file;
y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain;
C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.
Chemical Components
References
- Matthews DA et al. (1994), Cell, 77, 761-771. Structure of human rhinovirus 3C protease reveals a trypsin-like polypeptide fold, RNA-binding site, and means for cleaving precursor polyprotein. DOI:10.1016/0092-8674(94)90059-0. PMID:7515772.
- Hussey RJ et al. (2011), Biochemistry, 50, 240-249. A Structural Study of Norovirus 3C Protease Specificity: Binding of a Designed Active Site-Directed Peptide Inhibitor. DOI:10.1021/bi1008497. PMID:21128685.
- Im I et al. (2009), Bioorg Med Chem Lett, 19, 3632-3636. Structure–activity relationships of heteroaromatic esters as human rhinovirus 3C protease inhibitors. DOI:10.1016/j.bmcl.2009.04.114. PMID:19464175.
- Bjorndahl TC et al. (2007), Biochemistry, 46, 12945-12958. NMR Solution Structures of the Apo and Peptide-Inhibited Human Rhinovirus 3C Protease (Serotype 14): Structural and Dynamic Comparison†. DOI:10.1021/bi7010866. PMID:17944485.
- May Wang Q et al. (2007), Curr Protein Pept Sci, 8, 19-27. Human Rhinovirus 3C Protease as a Potential Target for the Development of Antiviral Agents. DOI:10.2174/138920307779941523.
- Dragovich PS et al. (2002), Bioorg Med Chem Lett, 12, 733-738. Structure-Based Design, Synthesis, and Biological Evaluation of Irreversible Human Rhinovirus 3C Protease Inhibitors. Part 7: Structure–Activity Studies of Bicyclic 2-Pyridone-Containing Peptidomimetics. DOI:10.1016/s0960-894x(02)00008-2.
- Bolognesi M et al. (2001), Biochem Mol Biol Educ, 29, 169-172. Human rhinovirus 3C protease: a cysteine protease showing the trypsin(ogen)-like fold. DOI:10.1111/j.1539-3429.2001.tb00111.x.
- Matthews DA et al. (1999), Proc Natl Acad Sci U S A, 96, 11000-11007. Structure-assisted design of mechanism-based irreversible inhibitors of human rhinovirus 3C protease with potent antiviral activity against multiple rhinovirus serotypes. DOI:10.1073/pnas.96.20.11000. PMID:10500114.
- Gosert R et al. (1997), J Virol, 71, 3062-3068. Identification of active-site residues in protease 3C of hepatitis A virus by site-directed mutagenesis. PMID:9060667.
- Cheah KC et al. (1990), J Biol Chem, 265, 7180-7187. Site-directed mutagenesis suggests close functional relationship between a human rhinovirus 3C cysteine protease and cellular trypsin-like serine proteases. PMID:2158990.
Catalytic Residues Roles
| Residue | Roles |
|---|---|
| Cys147A | proton shuttle (general acid/base), electrostatic stabiliser |
| His40A | electrostatic stabiliser, proton shuttle (general acid/base) |
| Glu71A | electrostatic stabiliser |
| Gly145A (main-N) | electrostatic stabiliser |
| Cys147A (main-N) | electrostatic stabiliser |
| Cys147A | covalent catalysis |
| Glu71A | modifies pKa |