51
|
Huitema C, Zhang J, Yin J, James MNG, Vederas JC, Eltis LD. Heteroaromatic ester inhibitors of hepatitis A virus 3C proteinase: Evaluation of mode of action. Bioorg Med Chem 2008; 16:5761-77. [PMID: 18407505 PMCID: PMC7125897 DOI: 10.1016/j.bmc.2008.03.059] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2008] [Accepted: 03/24/2008] [Indexed: 11/23/2022]
Abstract
The related 3C and 3C-like proteinase (3C(pro) and 3CL(pro)) of picornaviruses and coronaviruses, respectively, are good drug targets. As part of an effort to generate broad-spectrum inhibitors of these enzymes, we screened a library of inhibitors based on a halopyridinyl ester from a previous study of the severe acute respiratory syndrome (SARS) 3CL proteinase against Hepatitis A virus (HAV) 3C(pro). Three of the compounds, which also had furan rings, inhibited the cleavage activity of HAV 3C(pro) with K(ic)s of 120-240nM. HPLC-based assays revealed that the inhibitors were slowly hydrolyzed by both HAV 3C(pro) and SARS 3CL(pro), confirming the identity of the expected products. Mass spectrometric analyses indicated that this hydrolysis proceeded via an acyl-enzyme intermediate. Modeling studies indicated that the halopyridinyl moiety of the inhibitor fits tightly into the S1-binding pocket, consistent with the lack of tolerance of the inhibitors to modification in this portion of the molecule. These compounds are among the most potent non-peptidic inhibitors reported to date against a 3C(pro).
Collapse
Affiliation(s)
- Carly Huitema
- Department of Microbiology, University of British Columbia, 2350 Health Science Mall, Vancouver, British Columbia, Canada V6T 1Z3
| | | | | | | | | | | |
Collapse
|
52
|
Interaction between polypeptide 3ABC and the 5'-terminal structural elements of the genome of Aichi virus: implication for negative-strand RNA synthesis. J Virol 2008; 82:6161-71. [PMID: 18448525 DOI: 10.1128/jvi.02151-07] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Secondary structural elements at the 5' end of picornavirus genomic RNA function as cis-acting replication elements and are known to interact specifically with viral P3 proteins in several picornaviruses. In poliovirus, ribonucleoprotein complex formation at the 5' end of the genome is required for negative-strand synthesis. We have previously shown that the 5'-end 115 nucleotides of the Aichi virus genome, which are predicted to fold into two stem-loops (SL-A and SL-C) and one pseudoknot (PK-B), act as a cis-acting replication element and that correct folding of these structures is required for negative-strand synthesis. In this study, we investigated the interaction between the 5'-terminal 120 nucleotides of the genome and the P3 proteins, 3AB, 3ABC, 3C, and 3CD, by gel shift assay and Northwestern analysis. The results showed that 3ABC and 3CD bound to the 5'-terminal region specifically. The binding of 3ABC was observed on both assays, while that of 3CD was detected only on Northwestern analysis. No binding of 3AB or 3C was observed. Binding assays using mutant RNAs demonstrated that disruption of the base pairings of the stem of SL-A and one of the two stem segments of PK-B (stem-B1) abolished the 3ABC binding. In addition, the specific nucleotide sequence of stem-B1 was responsible for the efficient 3ABC binding. These results suggest that the interaction of 3ABC with the 5'-terminal region of the genome is involved in negative-strand synthesis. On the other hand, the ability of 3CD to interact with the 5'-terminal region did not correlate with the RNA replication ability.
Collapse
|
53
|
Shen M, Reitman ZJ, Zhao Y, Moustafa I, Wang Q, Arnold JJ, Pathak HB, Cameron CE. Picornavirus genome replication. Identification of the surface of the poliovirus (PV) 3C dimer that interacts with PV 3Dpol during VPg uridylylation and construction of a structural model for the PV 3C2-3Dpol complex. J Biol Chem 2008; 283:875-88. [PMID: 17993457 PMCID: PMC2186065 DOI: 10.1074/jbc.m707907200] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Picornaviruses have a peptide termed VPg covalently linked to the 5'-end of the genome. Attachment of VPg to the genome occurs in at least two steps. First, Tyr-3 of VPg, or some precursor thereof, is used as a primer by the viral RNA-dependent RNA polymerase, 3Dpol, to produce VPg-pUpU. Second, VPg-pUpU is used as a primer to produce full-length genomic RNA. Production of VPg-pUpU is templated by a single adenylate residue located in the loop of an RNA stem-loop structure termed oriI by using a slide-back mechanism. Recruitment of 3Dpol to and its stability on oriI have been suggested to require an interaction between the back of the thumb subdomain of 3Dpol and an undefined region of the 3C domain of viral protein 3CD. We have performed surface acidic-to-alanine-scanning mutagenesis of 3C to identify the surface of 3C with which 3Dpol interacts. This analysis identified numerous viable poliovirus mutants with reduced growth kinetics that correlated to reduced kinetics of RNA synthesis that was attributable to a change in VPg-pUpU production. Importantly, these 3C derivatives were all capable of binding to oriI as well as wild-type 3C. Synthetic lethality was observed for these mutants when placed in the context of a poliovirus mutant containing 3Dpol-R455A, a residue on the back of the thumb required for VPg uridylylation. These data were used to guide molecular docking of the structures for a poliovirus 3C dimer and 3Dpol, leading to a structural model for the 3C(2)-3Dpol complex that extrapolates well to all picornaviruses.
Collapse
Affiliation(s)
- Miaoqing Shen
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | | | | | | | | | | | | | | |
Collapse
|
54
|
Yeang CH, Haussler D. Detecting coevolution in and among protein domains. PLoS Comput Biol 2007; 3:e211. [PMID: 17983264 PMCID: PMC2098842 DOI: 10.1371/journal.pcbi.0030211] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2007] [Accepted: 09/17/2007] [Indexed: 01/17/2023] Open
Abstract
Correlated changes of nucleic or amino acids have provided strong information about the structures and interactions of molecules. Despite the rich literature in coevolutionary sequence analysis, previous methods often have to trade off between generality, simplicity, phylogenetic information, and specific knowledge about interactions. Furthermore, despite the evidence of coevolution in selected protein families, a comprehensive screening of coevolution among all protein domains is still lacking. We propose an augmented continuous-time Markov process model for sequence coevolution. The model can handle different types of interactions, incorporate phylogenetic information and sequence substitution, has only one extra free parameter, and requires no knowledge about interaction rules. We employ this model to large-scale screenings on the entire protein domain database (Pfam). Strikingly, with 0.1 trillion tests executed, the majority of the inferred coevolving protein domains are functionally related, and the coevolving amino acid residues are spatially coupled. Moreover, many of the coevolving positions are located at functionally important sites of proteins/protein complexes, such as the subunit linkers of superoxide dismutase, the tRNA binding sites of ribosomes, the DNA binding region of RNA polymerase, and the active and ligand binding sites of various enzymes. The results suggest sequence coevolution manifests structural and functional constraints of proteins. The intricate relations between sequence coevolution and various selective constraints are worth pursuing at a deeper level. The sequences of different components within and across genes often undergo coordinated changes in order to maintain the structures or functions of the genes. Identifying the coordinated changes—the “coevolution”—of those components in the context of evolution is important in predicting the structures, interactions, and functions of genes. The authors incur a large-scale screening on all the known protein sequences and build a compendium about the coevolving relations of all protein domains—subunits of proteins. The majority of the coevolving protein domains either belongs to the same proteins, appears in the same protein complexes, or shares the same functional annotations. Furthermore, coevolving positions in the same proteins or protein complexes are spatially coupled, as they tend to be closer than random positions in the 3-D structures of the proteins/protein complexes. More strikingly, many coevolving positions are located at functionally important sites of the molecules. The results provide useful insights about the relations between sequence evolution and protein structures and functions.
Collapse
Affiliation(s)
- Chen-Hsiang Yeang
- Simons Center for Systems Biology, Institute for Advanced Study, Princeton, New Jersey, United States of America.
| | | |
Collapse
|
55
|
Xu Z, Lam LSM, Lam LH, Chau SF, Ng TB, Au SWN. Molecular basis of the redox regulation of SUMO proteases: a protective mechanism of intermolecular disulfide linkage against irreversible sulfhydryl oxidation. FASEB J 2007; 22:127-37. [PMID: 17704192 DOI: 10.1096/fj.06-7871com] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Sumoylation has emerged as an indispensable post-translational modification that modulates the functions of a broad spectrum of proteins. Recent studies have demonstrated that reactive oxygen species influence the equilibrium of sumoylation-desumoylation. We show herein that H2O2 induces formation of an intermolecular disulfide linkage of human SUMO protease SENP1 via the active-site Cys 603 and a unique residue Cys 613. Such reversible modification confers a higher recovery of enzyme activity, which is also observed in yeast Ulp1, but not in human SENP2, suggesting its protective role against irreversible sulfhydryl oxidation. In vivo formation of a disulfide-linked dimer of SENP1 is also detected in cultured cells in response to oxidative stress. The modifications are further elucidated by the crystal structures of Ulp1 with the catalytic cysteine oxidized to sulfenic, sulfinic, and sulfonic acids. Our findings suggest that, in addition to SUMO conjugating enzymes, SUMO proteases may act as redox sensors and effectors modulating the desumoylation pathway and specific cellular responses to oxidative stress.
Collapse
Affiliation(s)
- Zheng Xu
- Centre of Protein Science and Crystallography, Department of Biochemistry, Faculty of Science, The Chinese University of Hong Kong, Hong Kong
| | | | | | | | | | | |
Collapse
|
56
|
Curry S, Roqué-Rosell N, Sweeney TR, Zunszain PA, Leatherbarrow RJ. Structural analysis of foot-and-mouth disease virus 3C protease: a viable target for antiviral drugs? Biochem Soc Trans 2007; 35:594-8. [PMID: 17511659 DOI: 10.1042/bst0350594] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Foot-and-mouth disease virus causes a major global agricultural problem that is difficult to control with existing vaccines. Structural analyses of the viral 3C protease not only have provided fresh insights into the catalytic mechanism of an unusual class of chymotrypsin-like cysteine proteases, but also are generating valuable information to drive the quest for effective antiviral therapies.
Collapse
Affiliation(s)
- S Curry
- Biophysics Section, Division of Cell and Molecular Biology, Blackett Laboratory, Imperial College, Exhibition Road, London SW7 2AZ, UK.
| | | | | | | | | |
Collapse
|
57
|
Yang Y, Liang Y, Qu L, Chen Z, Yi M, Li K, Lemon SM. Disruption of innate immunity due to mitochondrial targeting of a picornaviral protease precursor. Proc Natl Acad Sci U S A 2007; 104:7253-8. [PMID: 17438296 PMCID: PMC1855380 DOI: 10.1073/pnas.0611506104] [Citation(s) in RCA: 241] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Mitochondrial antiviral signaling protein (MAVS) is an essential component of virus-activated signaling pathways that induce protective IFN responses. Its localization to the outer mitochondrial membrane suggests an important yet unexplained role for mitochondria in innate immunity. Here, we show that hepatitis A virus (HAV), a hepatotropic picornavirus, ablates type 1 IFN responses by targeting the 3ABC precursor of its 3C(pro) cysteine protease to mitochondria where it colocalizes with and cleaves MAVS, thereby disrupting activation of IRF3 through the MDA5 pathway. The 3ABC cleavage of MAVS requires both the protease activity of 3C(pro) and a transmembrane domain in 3A that directs 3ABC to mitochondria. Lacking this domain, mature 3C(pro) protease is incapable of MAVS proteolysis. HAV thus disrupts host signaling by a mechanism that parallels that of the serine NS3/4A protease of hepatitis C virus, but differs in its use of a stable, catalytically active polyprotein processing intermediate. The unique requirement for mitochondrial localization of 3ABC underscores the importance of mitochondria to host control of virus infections within the liver.
Collapse
Affiliation(s)
- Yan Yang
- Center for Hepatitis Research, Institute for Human Infections and Immunity, Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555-1019
| | - Yuqiong Liang
- Center for Hepatitis Research, Institute for Human Infections and Immunity, Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555-1019
| | - Lin Qu
- Center for Hepatitis Research, Institute for Human Infections and Immunity, Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555-1019
| | - Zeming Chen
- Center for Hepatitis Research, Institute for Human Infections and Immunity, Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555-1019
| | - MinKyung Yi
- Center for Hepatitis Research, Institute for Human Infections and Immunity, Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555-1019
| | - Kui Li
- Center for Hepatitis Research, Institute for Human Infections and Immunity, Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555-1019
| | - Stanley M. Lemon
- Center for Hepatitis Research, Institute for Human Infections and Immunity, Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555-1019
- To whom correspondence should be addressed. E-mail:
| |
Collapse
|
58
|
Sweeney TR, Roqué-Rosell N, Birtley JR, Leatherbarrow RJ, Curry S. Structural and mutagenic analysis of foot-and-mouth disease virus 3C protease reveals the role of the beta-ribbon in proteolysis. J Virol 2007; 81:115-24. [PMID: 17065215 PMCID: PMC1797255 DOI: 10.1128/jvi.01587-06] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2006] [Accepted: 10/11/2006] [Indexed: 11/20/2022] Open
Abstract
The 3C protease (3C(pro)) from foot-and-mouth disease virus (FMDV), the causative agent of a widespread and economically devastating disease of domestic livestock, is a potential target for antiviral drug design. We have determined the structure of a new crystal form of FMDV 3C(pro), a chymotrypsin-like cysteine protease, which reveals features that are important for catalytic activity. In particular, we show that a surface loop which was disordered in previous structures adopts a beta-ribbon structure that is conformationally similar to equivalent regions on other picornaviral 3C proteases and some serine proteases. This beta-ribbon folds over the peptide binding cleft and clearly contributes to substrate recognition. Replacement of Cys142 at the tip of the beta-ribbon with different amino acids has a significant impact on enzyme activity and shows that higher activity is obtained with more hydrophobic side chains. Comparison of the structure of FMDV 3C(pro) with homologous enzyme-peptide complexes suggests that this correlation arises because the side chain of Cys142 contacts the hydrophobic portions of the P2 and P4 residues in the peptide substrate. Collectively, these findings provide compelling evidence for the role of the beta-ribbon in catalytic activity and provide valuable insights for the design of FMDV 3C(pro) inhibitors.
Collapse
Affiliation(s)
- Trevor R Sweeney
- Biophysics Section, Blackett Laboratory, Imperial College, London SW7 2AZ, United Kingdom
| | | | | | | | | |
Collapse
|
59
|
Nayak A, Goodfellow IG, Woolaway KE, Birtley J, Curry S, Belsham GJ. Role of RNA structure and RNA binding activity of foot-and-mouth disease virus 3C protein in VPg uridylylation and virus replication. J Virol 2006; 80:9865-75. [PMID: 16973591 PMCID: PMC1617274 DOI: 10.1128/jvi.00561-06] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The uridylylation of the VPg peptide primer is the first stage in the replication of picornavirus RNA. This process can be achieved in vitro using purified components, including 3B (VPg) with the RNA dependent RNA polymerase (3Dpol), the precursor 3CD, and an RNA template containing the cre/bus. We show that certain RNA sequences within the foot-and-mouth disease virus (FMDV) 5' untranslated region but outside of the cre/bus can enhance VPg uridylylation activity. Furthermore, we have shown that the FMDV 3C protein alone can substitute for 3CD, albeit less efficiently. In addition, the VPg precursors, 3B(3)3C and 3B(123)3C, can function as substrates for uridylylation in the absence of added 3C or 3CD. Residues within the FMDV 3C protein involved in interaction with the cre/bus RNA have been identified and are located on the face of the protein opposite from the catalytic site. These residues within 3C are also essential for VPg uridylylation activity and efficient virus replication.
Collapse
Affiliation(s)
- Arabinda Nayak
- BBSRC Institute for Animal Health, Pirbright, Woking, Surrey GU24 0NF, United Kingdom
| | | | | | | | | | | |
Collapse
|
60
|
Yin J, Cherney MM, Bergmann EM, Zhang J, Huitema C, Pettersson H, Eltis LD, Vederas JC, James MNG. An episulfide cation (thiiranium ring) trapped in the active site of HAV 3C proteinase inactivated by peptide-based ketone inhibitors. J Mol Biol 2006; 361:673-86. [PMID: 16860823 PMCID: PMC7172884 DOI: 10.1016/j.jmb.2006.06.047] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2006] [Revised: 06/19/2006] [Accepted: 06/20/2006] [Indexed: 11/17/2022]
Abstract
We have solved the crystal and molecular structures of hepatitis A viral (HAV) 3C proteinase, a cysteine peptidase having a chymotrypsin-like protein fold, in complex with each of three tetrapeptidyl-based methyl ketone inhibitors to resolutions beyond 1.4 A, the highest resolution to date for a 3C or a 3C-Like (e.g. SARS viral main proteinase) peptidase. The residues of the beta-hairpin motif (residues 138-158), an extension of two beta-strands of the C-terminal beta-barrel of HAV 3C are critical for the interactions between the enzyme and the tetrapeptide portion of these inhibitors that are analogous to the residues at the P4 to P1 positions in the natural substrates of picornaviral 3C proteinases. Unexpectedly, the Sgamma of Cys172 forms two covalent bonds with each inhibitor, yielding an unusual episulfide cation (thiiranium ring) stabilized by a nearby oxyanion. This result suggests a mechanism of inactivation of 3C peptidases by methyl ketone inhibitors that is distinct from that occurring in the structurally related serine proteinases or in the papain-like cysteine peptidases. It also provides insight into the mechanisms underlying both the inactivation of HAV 3C by these inhibitors and on the proteolysis of natural substrates by this viral cysteine peptidase.
Collapse
Key Words
- hav, hepatitis a virus
- fmdv, foot-and-mouth disease virus
- tgev, transmissible gastroenteritis coronavirus
- sars, severe acute respiratory syndrome
- bbl, carboxylbenzyloxyl-l-serine-β-lactone
- cmk, chloromethylketone
- fmk, fluoromethylketone
- ac, acetyl
- qmm, n, n-dimethyl glutamine
- hepatitis a virus
- 3c proteinase
- inhibitor design
- methylketone
- episulfide
Collapse
Affiliation(s)
- Jiang Yin
- Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, AB, Canada T6G 2H7
| | | | | | | | | | | | | | | | | |
Collapse
|
61
|
Curry S, Roqué-Rosell N, Zunszain PA, Leatherbarrow RJ. Foot-and-mouth disease virus 3C protease: recent structural and functional insights into an antiviral target. Int J Biochem Cell Biol 2006; 39:1-6. [PMID: 16979372 PMCID: PMC7185863 DOI: 10.1016/j.biocel.2006.07.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2006] [Revised: 07/25/2006] [Accepted: 07/26/2006] [Indexed: 02/05/2023]
Abstract
The 3C protease from foot-and-mouth disease virus (FMDV 3C(pro)) is critical for viral pathogenesis, having vital roles in both the processing of the polyprotein precursor and RNA replication. Although recent structural and functional studies have revealed new insights into the mechanism and function of the enzyme, key questions remain that must be addressed before the potential of FMDV 3C(pro) as an antiviral drug target can be realised.
Collapse
Affiliation(s)
- Stephen Curry
- Biophysics Section, Division of Cell and Molecular Biology, Blackett Laboratory, Imperial College, Exhibition Road, London SW7 2AZ, UK.
| | | | | | | |
Collapse
|
62
|
Zeitler CE, Estes MK, Venkataram Prasad BV. X-ray crystallographic structure of the Norwalk virus protease at 1.5-A resolution. J Virol 2006; 80:5050-8. [PMID: 16641296 PMCID: PMC1472067 DOI: 10.1128/jvi.80.10.5050-5058.2006] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Norwalk virus (NV), a member of the Caliciviridae family, is the major cause of acute, epidemic, viral gastroenteritis. The NV genome is a positive sense, single-stranded RNA that encodes three open reading frames (ORFs). The first ORF produces a polyprotein that is processed by the viral cysteine protease into six nonstructural proteins. We have determined the structure of the NV protease to 1.5 and 2.2 A from crystals grown in the absence or presence, respectively, of the protease inhibitor AEBSF [4-(2-aminoethyl)-benzenesulfonyl fluoride]. The protease, which crystallizes as a stable dimer, exhibits a two-domain structure similar to those of other viral cysteine proteases with a catalytic triad composed of His 30, Glu 54, and Cys 139. The native structure of the protease reveals strong hydrogen bond interactions between His 30 and Glu 54, in the favorable syn configuration, indicating a role of Glu 54 during proteolysis. Mutation of this residue to Ala abolished the protease activity, in a fluorogenic peptide substrate assay, further substantiating the role of Glu 54 during proteolysis. These observations contrast with the suggestion, from a previous study of another norovirus protease, that this residue may not have a prominent role in proteolysis (K. Nakamura, Y. Someya, T. Kumasaka, G. Ueno, M. Yamamoto, T. Sato, N. Takeda, T. Miyamura, and N. Tanaka, J. Virol. 79:13685-13693, 2005). In the structure from crystals grown in the presence of AEBSF, Glu 54 undergoes a conformational change leading to disruption of the hydrogen bond interactions with His 30. Since AEBSF was not apparent in the electron density map, it is possible that these conformational changes are due to subtle changes in pH caused by its addition during crystallization.
Collapse
Affiliation(s)
- Corinne E Zeitler
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | |
Collapse
|
63
|
Pang YP. Three-dimensional model of a substrate-bound SARS chymotrypsin-like cysteine proteinase predicted by multiple molecular dynamics simulations: catalytic efficiency regulated by substrate binding. Proteins 2006; 57:747-57. [PMID: 15690493 PMCID: PMC7167676 DOI: 10.1002/prot.20249] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Severe acute respiratory syndrome (SARS) is a contagious and deadly disease caused by a new coronavirus. The protein sequence of the chymotrypsin-like cysteine proteinase (CCP) responsible for SARS viral replication has been identified as a target for developing anti-SARS drugs. Here, I report the ATVRLQ(p1)A(p1')-bound CCP 3D model predicted by 420 different molecular dynamics simulations (2.0 ns for each simulation with a 1.0-fs time step). This theoretical model was released at the Protein Data Bank (PDB; code: 1P76) before the release of the first X-ray structure of CCP (PDB code: 1Q2W). In contrast to the catalytic dyad observed in X-ray structures of CCP and other coronavirus cysteine proteinases, a catalytic triad comprising Asp187, His41, and Cys145 is found in the theoretical model of the substrate-bound CCP. The simulations of the CCP complex suggest that substrate binding leads to the displacement of a water molecule entrapped by Asp187 and His41, thus converting the dyad to a more efficient catalytic triad. The CCP complex structure has an expanded active-site pocket that is useful for anti-SARS drug design. In addition, this work demonstrates that multiple molecular dynamics simulations are effective in correcting errors that result from low-sequence-identity homology modeling.
Collapse
Affiliation(s)
- Yuan-Ping Pang
- Computer-Aided Molecular Design Laboratory, Mayo Clinic College of Medicine, Rochester, Minnesota 55905, USA.
| |
Collapse
|
64
|
Smits SL, Snijder EJ, de Groot RJ. Characterization of a torovirus main proteinase. J Virol 2006; 80:4157-67. [PMID: 16571831 PMCID: PMC1440467 DOI: 10.1128/jvi.80.8.4157-4167.2006] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2005] [Accepted: 02/02/2006] [Indexed: 11/20/2022] Open
Abstract
Viruses of the order Nidovirales encode huge replicase polyproteins. These are processed primarily by the chymotrypsin-like main proteinases (M(pro)s). So far, M(pro)s have been studied only for corona-, arteri-, and roniviruses. Here, we report the characterization of the M(pro) of toroviruses, the fourth main Nidovirus branch. Comparative sequence analysis of polyprotein 1a of equine torovirus (EToV) strain Berne, identified a serine proteinase domain, flanked by hydrophobic regions. Heterologous expression of this domain resulted in autoprocessing at flanking cleavage sites. N-terminal sequence analysis of cleavage products tentatively identified FxxQ downward arrow(S, A) as the substrate consensus sequence. EToV M(pro) combines several traits of its closest relatives. It has a predicted three-domain structure, with two catalytic beta-barrel domains and an additional C-terminal domain of unknown function. With respect to substrate specificity, the EToV M(pro) resembles its coronavirus homologue in its preference for P1-Gln, but its substrate-binding subsite, S1, more closely resembles that of arteri- and ronivirus M(pro)s, which prefer P1-Glu. Surprisingly, in contrast to the M(pro)s of corona- and roniviruses, but like that of arterivirus, the torovirus M(pro) uses serine instead of cysteine as its principal nucleophile. Under the premise that the M(pro)s of corona- and toroviruses are more closely related to each other than to those of arteri- and roniviruses, the transition from serine- to cysteine-based proteolytic catalysis (or vice versa) must have happened more than once in the course of nidovirus evolution. In this respect, it is of interest that a mutant EToV M(pro) with a Ser165-->Cys substitution retained partial enzymatic activity.
Collapse
Affiliation(s)
- Saskia L Smits
- Virology Division, Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, 3584 CL Utrecht, The Netherlands
| | | | | |
Collapse
|
65
|
Hardy ME. Norovirus protein structure and function. FEMS Microbiol Lett 2006; 253:1-8. [PMID: 16168575 DOI: 10.1016/j.femsle.2005.08.031] [Citation(s) in RCA: 150] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2005] [Revised: 07/26/2005] [Accepted: 08/20/2005] [Indexed: 10/25/2022] Open
Abstract
Noroviruses are positive strand RNA viruses that have received increased attention in recent years because their role as etiologic agents in acute gastroenteritis outbreaks is now clearly established. Much has been learned about the epidemiology of these viruses and the extent of genetic diversity among circulating strains. In contrast, progress on understanding the basic mechanisms of virus replication has been far slower due to the inability to cultivate virus in the laboratory. Despite this limitation, significant progress has been made in defining some basic functions of the norovirus proteins, and the structures of two have been solved to near atomic resolution. This minireview summarizes these recent advances in understanding the structure and function of the norovirus proteins and provides speculation about what roles they may play in the virus replication cycle.
Collapse
Affiliation(s)
- Michele E Hardy
- Veterinary Molecular Biology, P.O. Box 173610, Montana State University, Bozeman, MT 59717, USA.
| |
Collapse
|
66
|
Abstract
Fungi and viruses encode a variety of peptidases having a plethora of functions. Many fungal peptidases are extracellular and are likely used to degrade proteins in their environment. Viral peptidases are processing enzymes, intimately involved in the virus infectious cycle. The viral RNA genome is translated by the host-cell machinery into a large polyprotein that is cleaved by the viral peptidases into mature capsid proteins, non-structural proteins and enzymes. I review the structure and catalytic mechanism of scytalidoglutamic peptidase isolated from the wood-destroying fungus Scytalidium lignicolum. This enzyme has a unique beta-sandwich fold and a novel catalytic mechanism based on a glutamate, a glutamine and a nucleophilic water molecule. Hepatitis A virus (HAV) 3C peptidase was the first structure identified for a viral 3C enzyme that exhibited the three-dimensional fold of the chymotrypsin family of serine peptidases but had a cysteine sulfur atom instead of the serine oxygen as the nucleophile. The structure of HAV 3C was unusual in that the Asp residue expected as the third member of the catalytic triad did not interact with the general base His. The present structure is of a beta-lactone-inhibited version of HAV 3C that has a restored catalytic triad.
Collapse
Affiliation(s)
- Michael N G James
- CIHR Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alberta T6G 2H7, Canada.
| |
Collapse
|
67
|
Yin J, Bergmann EM, Cherney MM, Lall MS, Jain RP, Vederas JC, James MN. Dual modes of modification of hepatitis A virus 3C protease by a serine-derived beta-lactone: selective crystallization and formation of a functional catalytic triad in the active site. J Mol Biol 2005; 354:854-71. [PMID: 16288920 PMCID: PMC7118759 DOI: 10.1016/j.jmb.2005.09.074] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2005] [Revised: 09/22/2005] [Accepted: 09/23/2005] [Indexed: 12/30/2022]
Abstract
Hepatitis A virus (HAV) 3C proteinase is a member of the picornain cysteine proteases responsible for the processing of the viral polyprotein, a function essential for viral maturation and infectivity. This and its structural similarity to other 3C and 3C-like proteases make it an attractive target for the development of antiviral drugs. Previous solution NMR studies have shown that a Cys24Ser (C24S) variant of HAV 3C protein, which displays catalytic properties indistinguishable from the native enzyme, is irreversibly inactivated by N-benzyloxycarbonyl-l-serine-beta-lactone (1a) through alkylation of the sulfur atom at the active site Cys172. However, crystallization of an enzyme-inhibitor adduct from the reaction mixture followed by X-ray structural analysis shows only covalent modification of the epsilon2-nitrogen of the surface His102 by the beta-lactone with no reaction at Cys172. Re-examination of the heteronuclear multiple quantum coherence (HMQC) NMR spectra of the enzyme-inhibitor mixture indicates that dual modes of single covalent modification occur with a >/=3:1 ratio of S-alkylation of Cys172 to N-alkylation of His102. The latter product crystallizes readily, probably due to the interaction between the phenyl ring of the N-benzyloxycarbonyl (N-Cbz) moiety and a hydrophobic pocket of a neighboring protein molecule in the crystal. Furthermore, significant structural changes are observed in the active site of the 3C protease, which lead to the formation of a functional catalytic triad with Asp84 accepting one hydrogen bond from His44. Although the 3C protease modified at Cys172 is catalytically inactive, the singly modified His102 N(epsilon2)-alkylated protein displays a significant level of enzymatic activity, which can be further modified/inhibited by N-iodoacetyl-valine-phenylalanine-amide (IVF) (in solution and in crystal) or excessive amount of the same beta-lactone inhibitor (in solution). The success of soaking IVF into HAV 3C-1a crystals demonstrates the usefulness of this new crystal form in the study of enzyme-inhibitor interactions in the proteolytic active site.
Collapse
Affiliation(s)
- Jiang Yin
- CIHR Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alta., Canada T6G 2H7
| | - Ernst M. Bergmann
- CIHR Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alta., Canada T6G 2H7
- Alberta Synchrotron Institute, University of Alberta, Edmonton, Alta., Canada T6G 2E1
| | - Maia M. Cherney
- CIHR Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alta., Canada T6G 2H7
| | - Manjinder S. Lall
- Department of Chemistry, University of Alberta, Edmonton, Alta., Canada T6G 2G2
| | - Rajendra P. Jain
- Department of Chemistry, University of Alberta, Edmonton, Alta., Canada T6G 2G2
| | - John C. Vederas
- Department of Chemistry, University of Alberta, Edmonton, Alta., Canada T6G 2G2
| | - Michael N.G. James
- CIHR Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, Alta., Canada T6G 2H7
- Alberta Synchrotron Institute, University of Alberta, Edmonton, Alta., Canada T6G 2E1
| |
Collapse
|
68
|
Nakamura K, Someya Y, Kumasaka T, Ueno G, Yamamoto M, Sato T, Takeda N, Miyamura T, Tanaka N. A norovirus protease structure provides insights into active and substrate binding site integrity. J Virol 2005; 79:13685-93. [PMID: 16227288 PMCID: PMC1262588 DOI: 10.1128/jvi.79.21.13685-13693.2005] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2005] [Accepted: 08/09/2005] [Indexed: 11/20/2022] Open
Abstract
Norovirus 3C-like proteases are crucial to proteolytic processing of norovirus polyproteins. We determined the crystal structure of the 3C-like protease from Chiba virus, a norovirus, at 2.8-A resolution. An active site including Cys139 and His30 is present, as is a hydrogen bond network that stabilizes the active site conformation. In the oxyanion hole backbone, a structural difference was observed probably upon substrate binding. A peptide substrate/enzyme model shows that several interactions between the two components are critical for substrate binding and that the S1 and S2 sites appropriately accommodate the substrate P1 and P2 residues, respectively. Knowledge of the structure and a previous mutagenesis study allow us to correlate proteolysis and structure.
Collapse
Affiliation(s)
- Kentaro Nakamura
- Department of Life Science, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
69
|
Abstract
Structural studies of foot-and-mouth disease virus (FMDV) have largely focused on the mature viral particle, providing atomic resolution images of the spherical protein capsid for a number of sero- and sub-types, structures of the highly immunogenic surface loop, Fab and GAG receptor complexes. Additionally, structures are available for a few non-structural proteins. The chapter reviews our current structural knowledge and its impact on our understanding of the virus life cycle proceeding from the mature virus through immune evasion/inactivation, cell-receptor binding and replication and alludes to future structural targets.
Collapse
Affiliation(s)
- E E Fry
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7BN, UK
| | | | | |
Collapse
|
70
|
Zell R, Seitz S, Henke A, Munder T, Wutzler P. Linkage map of protein-protein interactions of Porcine teschovirus. J Gen Virol 2005; 86:2763-2768. [PMID: 16186230 DOI: 10.1099/vir.0.81144-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A yeast two-hybrid study was conducted to catalogue the protein-protein interactions of the Porcine teschovirus non-structural proteins. Five homodimer, three reciprocal heterodimer and four unidirectional heterodimer interactions were observed. While several interactions are similar to those described in previous studies using enteroviruses, such as homo- and heterodimeric interactions of the 2B, 3CD and 3D proteins, several were not found previously. Among these is the binding of the leader protein L to the proteinases 3C and 3CD. Unlike the poliovirus 3C, the teschovirus 3C proteinase dimerizes and interacts with 2BC, 3CD and 3D. The strongest interactions were observed for L-3C, L-3CD and 3C-3CD.
Collapse
Affiliation(s)
- Roland Zell
- Institute for Virology and Antiviral Therapy, Hans-Knöll-Str. 2, D-07745 Jena, Germany
| | - Simone Seitz
- Institute for Virology and Antiviral Therapy, Hans-Knöll-Str. 2, D-07745 Jena, Germany
| | - Andreas Henke
- Institute for Virology and Antiviral Therapy, Hans-Knöll-Str. 2, D-07745 Jena, Germany
| | - Thomas Munder
- Leibniz Institute for Natural Products Research and Infection Biology, Hans Knöll Institute, Beutenbergstr. 11a, D-07745 Jena, Germany
| | - Peter Wutzler
- Institute for Virology and Antiviral Therapy, Hans-Knöll-Str. 2, D-07745 Jena, Germany
| |
Collapse
|
71
|
Nunn CM, Jeeves M, Cliff MJ, Urquhart GT, George RR, Chao LH, Tscuchia Y, Djordjevic S. Crystal structure of tobacco etch virus protease shows the protein C terminus bound within the active site. J Mol Biol 2005; 350:145-55. [PMID: 15919091 DOI: 10.1016/j.jmb.2005.04.013] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2005] [Revised: 04/06/2005] [Accepted: 04/07/2005] [Indexed: 11/29/2022]
Abstract
Tobacco etch virus (TEV) protease is a cysteine protease exhibiting stringent sequence specificity. The enzyme is widely used in biotechnology for the removal of the affinity tags from recombinant fusion proteins. Crystal structures of two TEV protease mutants as complexes with a substrate and a product peptide provided the first insight into the mechanism of substrate specificity of this enzyme. We now report a 2.7A crystal structure of a full-length inactive C151A mutant protein crystallised in the absence of peptide. The structure reveals the C terminus of the protease bound to the active site. In addition, we determined dissociation constants of TEV protease substrate and product peptides using isothermal titration calorimetry for various forms of this enzyme. Data suggest that TEV protease could be inhibited by the peptide product of autolysis. Separate modes of recognition for native substrates and the site of TEV protease self-cleavage are proposed.
Collapse
Affiliation(s)
- Christine M Nunn
- Department of Biochemistry and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | | | | | | | | | | | | | | |
Collapse
|
72
|
Kuang WF, Chow LP, Wu MH, Hwang LH. Mutational and inhibitive analysis of SARS coronavirus 3C-like protease by fluorescence resonance energy transfer-based assays. Biochem Biophys Res Commun 2005; 331:1554-9. [PMID: 15883050 PMCID: PMC7092943 DOI: 10.1016/j.bbrc.2005.04.072] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2005] [Indexed: 12/15/2022]
Abstract
The 3C-like protease (3CLpro) of severe acute respiratory syndrome coronavirus (SARS-CoV) plays key roles in viral replication and is an attractive target for anti-SARS drug discovery. In this report, a fluorescence resonance energy transfer (FRET)-based method was developed to assess the proteolytic activity of SARS-CoV 3CLpro. Two internally quenched fluorogenic peptides, 1NC and 2NC, corresponding to the N-terminal and the C-terminal autocleavage sites of SARS-CoV 3CLpro, respectively, were used as substrates. SARS-CoV 3CLpro seemed to work more efficiently on 1NC than on 2NC in trans-cleavage assay. Mutational analysis demonstrated that the His41 residue, the N-terminal 7 amino acids, and the domain III of SARS-CoV 3CLpro were important for the enzymatic activity. Antibodies recognizing domain III could significantly inhibit the enzymatic activity of SARS-CoV 3CLpro. The effects of class-specific protease inhibitors on the trans-cleavage activity revealed that this enzyme worked more like a serine protease rather than the papain protease.
Collapse
Affiliation(s)
- Wan-Fen Kuang
- Hepatitis Research Center, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan, ROC
| | - Lu-Ping Chow
- Graduate Institute of Biochemistry and Molecular Biology, National Taiwan University College of Medicine, Taipei, Taiwan, ROC
| | - Mei-Hua Wu
- Hepatitis Research Center, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan, ROC
| | - Lih-Hwa Hwang
- Hepatitis Research Center, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan, ROC
- Corresponding author. Fax: +886 2 23825962
| |
Collapse
|
73
|
Peters H, Kusov Y, Meyer S, Benie A, Bäuml E, Wolff M, Rademacher C, Peters T, Gauss-Müller V. Hepatitis A virus proteinase 3C binding to viral RNA: correlation with substrate binding and enzyme dimerization. Biochem J 2005; 385:363-70. [PMID: 15361063 PMCID: PMC1134706 DOI: 10.1042/bj20041153] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Proteinase 3C of hepatitis A virus (HAV) plays a key role in the viral life cycle by generating mature viral proteins from the precursor polyprotein. In addition to its proteolytic activity, 3C binds to viral RNA, and thus influences viral genome replication. In order to investigate the interplay between proteolytic activity and RNA binding at the molecular level, we subjected HAV 3C and three variants carrying mutations of the cysteine residues [C24S (Cys-24-->Ser), C172A and C24S/C172A] to proteolysis assays with peptide substrates, and to surface plasmon resonance binding studies with peptides and viral RNA. We report that the enzyme readily forms dimers via disulphide bridges involving Cys-24. Dissociation constants (K(D)) for peptides were in the millimolar range. The binding kinetics for the peptides were characterized by k(on) and k(off) values of the order of 10(2) M(-1) x s(-1) and 10(-2) to 10(-1) s(-1) respectively. In contrast, 3C binding to immobilized viral RNA, representing the structure of the 5'-terminal domain, followed fast binding kinetics with k(on) and k(off) values beyond the limits of the kinetic resolution of the technique. The affinity of viral RNA depended strongly on the dimerization status of 3C. Whereas monomeric 3C bound to the viral RNA with a K(D) in the millimolar range, dimeric 3C had a significantly increased binding affinity with K(D) values in the micromolar range. A model of the 3C dimer suggests that spatial proximity of the presumed RNA-binding motifs KFRDI is possible. 3C binding to RNA was also promoted in the presence of substrate peptides, indicating co-operativity between RNA binding and protease activity. The data imply that the dual functions of 3C are mutually dependent, and regulate protein and RNA synthesis during the viral life cycle.
Collapse
Affiliation(s)
- Hannelore Peters
- *Institute of Chemistry, University of Lübeck, Ratzeburger Allee 160, D-23538 Lübeck, Germany
| | - Yuri Y. Kusov
- †Institute of Medical Molecular Biology, University of Lübeck, Ratzeburger Allee 160, D-23538 Lübeck, Germany
| | - Sonja Meyer
- *Institute of Chemistry, University of Lübeck, Ratzeburger Allee 160, D-23538 Lübeck, Germany
| | - Andrew J. Benie
- *Institute of Chemistry, University of Lübeck, Ratzeburger Allee 160, D-23538 Lübeck, Germany
| | - Englbert Bäuml
- *Institute of Chemistry, University of Lübeck, Ratzeburger Allee 160, D-23538 Lübeck, Germany
| | - Maike Wolff
- *Institute of Chemistry, University of Lübeck, Ratzeburger Allee 160, D-23538 Lübeck, Germany
| | - Christoph Rademacher
- *Institute of Chemistry, University of Lübeck, Ratzeburger Allee 160, D-23538 Lübeck, Germany
| | - Thomas Peters
- *Institute of Chemistry, University of Lübeck, Ratzeburger Allee 160, D-23538 Lübeck, Germany
- To whom correspondence should be addressed (email )
| | - Verena Gauss-Müller
- †Institute of Medical Molecular Biology, University of Lübeck, Ratzeburger Allee 160, D-23538 Lübeck, Germany
| |
Collapse
|
74
|
Someya Y, Takeda N, Miyamura T. Characterization of the norovirus 3C-like protease. Virus Res 2005; 110:91-7. [PMID: 15845259 PMCID: PMC7114197 DOI: 10.1016/j.virusres.2005.02.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2004] [Revised: 02/08/2005] [Accepted: 02/08/2005] [Indexed: 11/17/2022]
Abstract
The recombinant 3C-like protease of Chiba virus, a Norovirus, expressed in Escherichia coli cells was purified and characterized as to effects of pH, temperature, salt contents, and SH reagents on its proteolytic activity. The optimal pH and temperature of the 3C-like protease for the proteolytic activity were 8.6 and 37 degrees C, respectively. Increased concentration (approximately 100 mM) of monovalent cations such as Na+ and K+ was inhibitory to the activity. Hg2+ and Zn2+ remarkably inhibited the protease activity, while Mg2+ and Ca2+ had no virtual effect. Several sulfhydryl reagents such as p-chloromercuribenzoic acid, methyl methanethiosulfonate, N-ethylmaleimide and N-phenylmaleimide also blocked the activity, confirming the previous result that cysteine residue(s) were responsible for the proteolysis.
Collapse
Affiliation(s)
| | | | - Tatsuo Miyamura
- Department of Virology II, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo 162-8640, Japan
| |
Collapse
|
75
|
Birtley JR, Knox SR, Jaulent AM, Brick P, Leatherbarrow RJ, Curry S. Crystal structure of foot-and-mouth disease virus 3C protease. New insights into catalytic mechanism and cleavage specificity. J Biol Chem 2005; 280:11520-7. [PMID: 15654079 DOI: 10.1074/jbc.m413254200] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Foot-and-mouth disease virus (FMDV) causes a widespread and economically devastating disease of domestic livestock. Although FMDV vaccines are available, political and technical problems associated with their use are driving a renewed search for alternative methods of disease control. The viral RNA genome is translated as a single polypeptide precursor that must be cleaved into functional proteins by virally encoded proteases. 10 of the 13 cleavages are performed by the highly conserved 3C protease (3C(pro)), making the enzyme an attractive target for antiviral drugs. We have developed a soluble, recombinant form of FMDV 3C(pro), determined the crystal structure to 1.9-angstroms resolution, and analyzed the cleavage specificity of the enzyme. The structure indicates that FMDV 3C(pro) adopts a chymotrypsin-like fold and possesses a Cys-His-Asp catalytic triad in a similar conformation to the Ser-His-Asp triad conserved in almost all serine proteases. This observation suggests that the dyad-based mechanisms proposed for this class of cysteine proteases need to be reassessed. Peptide cleavage assays revealed that the recognition sequence spans at least four residues either side of the scissile bond (P4-P4') and that FMDV 3C(pro) discriminates only weakly in favor of P1-Gln over P1-Glu, in contrast to other 3C(pro) enzymes that strongly favor P1-Gln. The relaxed specificity may be due to the unexpected absence in FMDV 3C(pro) of an extended beta-ribbon that folds over the substrate binding cleft in other picornavirus 3C(pro) structures. Collectively, these results establish a valuable framework for the development of FMDV 3C(pro) inhibitors.
Collapse
Affiliation(s)
- James R Birtley
- Biophysics Section, Division of Cell and Molecular Biology, Blackett Laboratory, Imperial College, South Kensington Campus, London, United Kingdom
| | | | | | | | | | | |
Collapse
|
76
|
Abstract
Coronavirus genome replication and transcription take place at cytoplasmic membranes and involve coordinated processes of both continuous and discontinuous RNA synthesis that are mediated by the viral replicase, a huge protein complex encoded by the 20-kb replicase gene. The replicase complex is believed to be comprised of up to 16 viral subunits and a number of cellular proteins. Besides RNA-dependent RNA polymerase, RNA helicase, and protease activities, which are common to RNA viruses, the coronavirus replicase was recently predicted to employ a variety of RNA processing enzymes that are not (or extremely rarely) found in other RNA viruses and include putative sequence-specific endoribonuclease, 3′-to-5′ exoribonuclease, 2′-O-ribose methyltransferase, ADP ribose 1′-phosphatase and, in a subset of group 2 coronaviruses, cyclic phosphodiesterase activities. This chapter reviews (1) the organization of the coronavirus replicase gene, (2) the proteolytic processing of the replicase by viral proteases, (3) the available functional and structural information on individual subunits of the replicase, such as proteases, RNA helicase, and the RNA-dependent RNA polymerase, and (4) the subcellular localization of coronavirus proteins involved in RNA synthesis. Although many molecular details of the coronavirus life cycle remain to be investigated, the available information suggests that these viruses and their distant nidovirus relatives employ a unique collection of enzymatic activities and other protein functions to synthesize a set of 5′-leader-containing subgenomic mRNAs and to replicate the largest RNA virus genomes currently known.
Collapse
Affiliation(s)
- J Ziebuhr
- Institute of Virology and Immunology, University of Würzburg, Versbacher Str 7, 97078 Würzburg, Germany.
| |
Collapse
|
77
|
Liu HL, Lin JC, Ho Y, Hsieh WC, Chen CW, Su YC. Molecular dynamics simulations of various coronavirus main proteinases. J Biomol Struct Dyn 2005; 22:65-77. [PMID: 15214807 DOI: 10.1080/07391102.2004.10506982] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
In this study, two homology models (denoted as MproST and MproSH) of main proteinase (Mpro) from the novel coronavirus associated with severe acute respiratory syndrome (SARS-CoV) were constructed based on the crystal structures of Mpro from transmissible gastroenteritis coronavirus (TGEV) (MproT) and human coronavirus HcoV-229E (MproH), respectively. Both MproST and MproSH exhibit similar folds as their respective template proteins. These homology models reveal three distinct functional domains as well as an intervening loop connecting domains II and III as found in both template proteins. A catalytic cleft containing the substrate binding sites S1 and S2 between domains I and II are also observed. S2 undergoes more significant structural fluctuation than S1 during the 400 ps molecular dynamics simulations because it is located at the open mouth of the catalytic cleft, while S1 is situated in the very bottom of this cleft. The thermal unfolding of these proteins begins at domain III, where the structure is least conserved among these proteins. Mpro may still maintain its proteolytic activity while it is partially unfolded. The electrostatic interaction between Arg40 and Asp186 plays an important role in maintaining the structural integrity of both S1 and S2.
Collapse
Affiliation(s)
- H-L Liu
- Department of Chemical Engineering and Graduate Institute of Biotechnology, National Taipei University of Technology, 1 Section 3 Chung-Hsiao East Road, Taipei, Taiwan 10608.
| | | | | | | | | | | |
Collapse
|
78
|
Coronavirus main proteinase: target for antiviral drug therapy. CORONAVIRUSES WITH SPECIAL EMPHASIS ON FIRST INSIGHTS CONCERNING SARS 2005. [PMCID: PMC7123552 DOI: 10.1007/3-7643-7339-3_9] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
79
|
Fuentes-Prior P, Salvesen G. The protein structures that shape caspase activity, specificity, activation and inhibition. Biochem J 2004; 384:201-32. [PMID: 15450003 PMCID: PMC1134104 DOI: 10.1042/bj20041142] [Citation(s) in RCA: 609] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2004] [Revised: 08/31/2004] [Accepted: 09/27/2004] [Indexed: 02/07/2023]
Abstract
The death morphology commonly known as apoptosis results from a post-translational pathway driven largely by specific limited proteolysis. In the last decade the structural basis for apoptosis regulation has moved from nothing to 'quite good', and we now know the fundamental structures of examples from the initiator phase, the pre-mitochondrial regulator phase, the executioner phase, inhibitors and their antagonists, and even the structures of some substrates. The field is as well advanced as the best known of proteolytic pathways, the coagulation cascade. Fundamentally new mechanisms in protease regulation have been disclosed. Structural evidence suggests that caspases have an unusual catalytic mechanism, and that they are activated by apparently unrelated events, depending on which position in the apoptotic pathway they occupy. Some naturally occurring caspase inhibitors have adopted classic inhibition strategies, but other have revealed completely novel mechanisms. All of the structural and mechanistic information can, and is, being applied to drive therapeutic strategies to combat overactivation of apoptosis in degenerative disease, and underactivation in neoplasia. We present a comprehensive review of the caspases, their regulators and inhibitors from a structural and mechanistic point of view, and with an aim to consolidate the many threads that define the rapid growth of this field.
Collapse
Key Words
- apoptosis
- caspase
- inhibitor
- inhibitor of apoptosis protein (iap)
- protease
- zymogen
- alps, autoimmune lymphoproliferative syndrome
- apaf-1, apoptotic protease activating factor-1
- asc/pycard, apoptosis-associated speck-like protein containing a card/pyd- and card-containing molecule
- bir, baculoviral iap repeat
- cad, caspase-activated dnase
- card, caspase-recruitment domain
- carp, caspase-associated ring protein
- ced, cell death-defective
- clarp, caspase-like apoptosis-regulatory protein
- cradd/raidd, caspase-2 and ripk1 domain-containing adaptor with death domain/rip-associated protein with a death domain
- crma, cytokine response modifier a
- dd, death domain
- ded, death effector domain
- dff, dna fragmentation factor
- diablo, direct iap-binding protein with low pi
- diap1, drosophila inhibitor of apoptosis 1
- disc, death-inducing signalling complex
- dronc, drosophila nedd2-like caspase
- fadd, fas (tnfrsf6)-associated via death domain
- flice, fadd-like ice
- flip, flice inhibitory protein
- iap, inhibitor of apoptosis protein
- ibm, iap binding motif
- icad, inhibitor of cad
- ice, interleukin-1β-converting enzyme
- ipaf/clan, ice-protease-activating factor/card, lrr and nacht-containing protein
- lrr, leucine-rich repeat
- nacht, ntpase-domain named after naip, ciita, het-e and tp1
- nalp1, nacht, lrr and pyrin domain containing 1
- nbd, nucleotide-binding domain
- nf-κb, nuclear factor-κb
- nod, nucleotide-binding and oligomerization domain-containing protein
- parp, poly(adp-ribose) polymerase
- pidd, p53-induced protein with a death domain
- rick/cardiak, rip-like interacting clarp kinase/card-containing ice-associated kinase
- ring, really interesting new gene
- rip, receptor-interacting protein
- serpin, serine protease inhibitor
- smac, second mitochondrial activator of caspases
- tfpi, tissue factor pathway inhibitor
- tlr, toll-like receptor
- tnf, tumour necrosis factor
- tradd, tnfrsf1a-associated via death domain
- traf, tnf receptor-associated factor
- trail, tnf-related apoptosis-inducing ligand
- xiap/birc4, x-linked iap/baculoviral iap repeat-containing 4
- p1, p2, …pn and p1′, p2′, …pm′ designate the side chains in substrates and inhibitors in the n- and c-terminal direction respectively from the p1–p1′ scissile peptide bond
- s1, s2, …sn and s1′, s2′, …sm′ refer to the cognate pockets on the protease that accept these side chains [1]
Collapse
Affiliation(s)
- Pablo Fuentes-Prior
- *Abteilung Strukturforschung, Max-Planck-Institut für Biochemie, Am Klopferspitz 18a, D82152, Planegg-Martinsried, Germany and Cardiovascular Research Center, Sant Antoni Ma. Claret 167, 08025 Barcelona, Spain
| | - Guy S. Salvesen
- †The Program in Apoptosis and Cell Death Research, Burnham Institute, 10901 North Torrey Pines Road, La Jolla, CA 92037, U.S.A
| |
Collapse
|
80
|
Homology models of main proteinase from coronavirus associated with SARS. Chem Phys Lett 2004; 401:24-29. [PMID: 32226085 PMCID: PMC7094242 DOI: 10.1016/j.cplett.2004.11.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2004] [Revised: 11/03/2004] [Indexed: 11/23/2022]
Abstract
In this study, two homology models of the main proteinase (Mpro) from the novel coronavirus associated with severe acute respiratory syndrome (SARS-CoV) were constructed. These models reveal three distinct functional domains, in which an intervening loop connecting domains II and III as well as a catalytic cleft containing the substrate binding subsites S1 and S2 between domains I and II are observed. S2 exhibits structural variations more significantly than S1 during the 200 ps molecular dynamics simulations because it is located at the open mouth of the catalytic cleft and the amino acid residues lining up this subsite are least conserved. In addition, the higher structural variation of S2 makes it flexible enough to accommodate a bulky hydrophobic residue from the substrate.
Collapse
|
81
|
Huang C, Wei P, Fan K, Liu Y, Lai L. 3C-like proteinase from SARS coronavirus catalyzes substrate hydrolysis by a general base mechanism. Biochemistry 2004; 43:4568-74. [PMID: 15078103 DOI: 10.1021/bi036022q] [Citation(s) in RCA: 157] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
SARS 3C-like proteinase has been proposed to be a key enzyme for drug design against SARS. Lack of a suitable assay has been a major hindrance for enzyme kinetic studies and a large-scale inhibitor screen for SARS 3CL proteinase. Since SARS 3CL proteinase belongs to the cysteine protease family (family C3 in clan CB) with a chymotrypsin fold, it is important to understand the catalytic mechanism of SARS 3CL proteinase to determine whether the proteolysis proceeds through a general base catalysis mechanism like chymotrypsin or an ion pair mechanism like papain. We have established a continuous colorimetric assay for SARS 3CL proteinase and applied it to study the enzyme catalytic mechanism. The proposed catalytic residues His41 and Cys145 were confirmed to be critical for catalysis by mutating to Ala, while the Cys145 to Ser mutation resulted in an active enzyme with a 40-fold lower activity. From the pH dependency of catalytic activity, the pK(a)'s for His41 and Cys145 in the wild-type enzyme were estimated to be 6.38 and 8.34, while the pK(a)'s for His41 and Ser145 in the C145S mutant were estimated to be 6.15 and 9.09, respectively. The C145S mutant has a normal isotope effect in D(2)O for general base catalysis, that is, reacts slower in D(2)O, while the wild-type enzyme shows an inverse isotope effect which may come from the lower activation enthalpy. The pK(a) values measured for the active site residues and the activity of the C145S mutant are consistent with a general base catalysis mechanism and cannot be explained by a thiolate-imidazolium ion pair model.
Collapse
Affiliation(s)
- Changkang Huang
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | | | | | | | | |
Collapse
|
82
|
Kuyumcu-Martinez M, Belliot G, Sosnovtsev SV, Chang KO, Green KY, Lloyd RE. Calicivirus 3C-like proteinase inhibits cellular translation by cleavage of poly(A)-binding protein. J Virol 2004; 78:8172-82. [PMID: 15254188 PMCID: PMC446144 DOI: 10.1128/jvi.78.15.8172-8182.2004] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2003] [Accepted: 03/23/2004] [Indexed: 11/20/2022] Open
Abstract
Caliciviruses are single-stranded RNA viruses that cause a wide range of diseases in both humans and animals, but little is known about the regulation of cellular translation during infection. We used two distinct calicivirus strains, MD145-12 (genus Norovirus) and feline calicivirus (FCV) (genus Vesivirus), to investigate potential strategies used by the caliciviruses to inhibit cellular translation. Recombinant 3C-like proteinases (r3CL(pro)) from norovirus and FCV were found to cleave poly(A)-binding protein (PABP) in the absence of other viral proteins. The norovirus r3CL(pro) PABP cleavage products were indistinguishable from those generated by poliovirus (PV) 3C(pro) cleavage, while the FCV r3CL(pro) products differed due to cleavage at an alternate cleavage site 24 amino acids downstream of one of the PV 3C(pro) cleavage sites. All cleavages by calicivirus or PV proteases separated the C-terminal domain of PABP that binds translation factors eIF4B and eRF3 from the N-terminal RNA-binding domain of PABP. The effect of PABP cleavage by the norovirus r3CL(pro) was analyzed in HeLa cell translation extracts, and the presence of r3CL(pro) inhibited translation of both endogenous and exogenous mRNAs. Translation inhibition was poly(A) dependent, and replenishment of the extracts with PABP restored translation. Analysis of FCV-infected feline kidney cells showed that the levels of de novo cellular protein synthesis decreased over time as virus-specific proteins accumulated, and cleavage of PABP occurred in virus-infected cells. Our data indicate that the calicivirus 3CL(pro), like PV 3C(pro), mediates the cleavage of PABP as part of its strategy to inhibit cellular translation. PABP cleavage may be a common mechanism among certain virus families to manipulate cellular translation.
Collapse
Affiliation(s)
- Muge Kuyumcu-Martinez
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | | | | | | | |
Collapse
|
83
|
Meijers R, Blagova EV, Levdikov VM, Rudenskaya GN, Chestukhina GG, Akimkina TV, Kostrov SV, Lamzin VS, Kuranova IP. The Crystal Structure of Glutamyl Endopeptidase from Bacillus intermedius Reveals a Structural Link between Zymogen Activation and Charge Compensation. Biochemistry 2004; 43:2784-91. [PMID: 15005613 DOI: 10.1021/bi035354s] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Extracellular glutamyl endopeptidase from Bacillus intermedius (BIEP) is a chymotrypsin-like serine protease which cleaves the peptide bond on the carboxyl side of glutamic acid. Its three-dimensional structure was determined for C222(1) and C2 crystal forms of BIEP to 1.5 and 1.75 A resolution, respectively. The topology of BIEP diverges from the most common chymotrypsin architecture, because one of the domains consists of a beta-sandwich consisting of two antiparallel beta-sheets and two helices. In the C2 crystals, a 2-methyl-2,4-pentanediol (MPD) molecule was found in the substrate binding site, mimicking a glutamic acid. This enabled the identification of the residues involved in the substrate recognition. The presence of the MPD molecule causes a change in the active site; the interaction between two catalytic residues (His47 and Ser171) is disrupted. The N-terminal end of the enzyme is involved in the formation of the substrate binding pocket. This indicates a direct relation between zymogen activation and substrate charge compensation.
Collapse
Affiliation(s)
- Rob Meijers
- European Molecular Biology Laboratory, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
84
|
Schwarzenbacher R, Deacon AM, Jaroszewski L, Brinen LS, Canaves JM, Dai X, Elsliger MA, Floyd R, Godzik A, Grittini C, Grzechnik SK, Klock HE, Koesema E, Kovarik JS, Kreusch A, Kuhn P, Lesley SA, McMullan D, McPhillips TM, Miller MD, Morse A, Moy K, Nelson MS, Ouyang J, Page R, Robb A, Quijano K, Spraggon G, Stevens RC, van den Bedem H, Velasquez J, Vincent J, von Delft F, Wang X, West B, Wolf G, Hodgson KO, Wooley J, Wilson IA. Crystal structure of a putative glutamine amido transferase (TM1158) from Thermotoga maritima
at 1.7 Å resolution. Proteins 2004; 54:801-5. [PMID: 14997577 DOI: 10.1002/prot.10614] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
85
|
Graff J, Emerson SU. Importance of amino acid 216 in nonstructural protein 2B for replication of hepatitis A virus in cell culture and in vivo. J Med Virol 2003; 71:7-17. [PMID: 12858403 DOI: 10.1002/jmv.10457] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Clinical isolates of hepatitis A virus (HAV) replicate inefficiently in cell culture unless mutations are acquired throughout the genome. An Ala-to-Val substitution in the nonstructural protein 2B (2B-216) was known to have a major impact on replication in cell culture. Analysis of chimeric viruses confirmed that the 2B-A[216]V change was critical for efficient replication and that Leu or Ile could substitute for Val. Viruses containing Val, Ile, or Leu at 2B-216 all replicated with similar kinetics in cell culture, whereas the virus containing Ala at this position grew 10- to 20-fold less efficiently. In contrast, in vivo, virus with either Ala or Val at 2B-216 replicated equally efficiently when tested in a chimpanzee and in tamarins, and each amino acid was stably maintained. Attempts to complement wild-type 2B in trans with adapted 2B provided by co-infection with a second viable HAV mutant failed to enhance replication of the virus containing the wild-type 2B sequence.
Collapse
Affiliation(s)
- Judith Graff
- Molecular Hepatitis Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infections Diseases, National Institutes of Health, Bethesda, Maryland 20892-8009, USA.
| | | |
Collapse
|
86
|
Losick VP, Schlax PE, Emmons RA, Lawson TG. Signals in hepatitis A virus P3 region proteins recognized by the ubiquitin-mediated proteolytic system. Virology 2003; 309:306-19. [PMID: 12758177 DOI: 10.1016/s0042-6822(03)00071-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The hepatitis A virus 3C protease and 3D RNA polymerase are present in low concentrations in infected cells. The 3C protease was previously shown to be rapidly degraded by the ubiquitin/26S proteasome system and we present evidence here that the 3D polymerase is also subject to ubiquitination-mediated proteolysis. Our results show that the sequence (32)LGVKDDWLLV(41) in the 3C protease serves as a protein destruction signal recognized by the ubiquitin-protein ligase E3alpha and that the destruction signal for the RNA polymerase does not require the carboxyl-terminal 137 amino acids. Both the viral 3ABCD polyprotein and the 3CD diprotein were also found to be substrates for ubiquitin-mediated proteolysis. Attempts to determine if the 3C protease or the 3D polymerase destruction signals trigger the ubiquitination and degradation of these precursors yielded evidence suggesting, but not unequivocally proving, that the recognition of the 3D polymerase by the ubiquitin system is responsible.
Collapse
Affiliation(s)
- Vicki P Losick
- Department of Chemistry, Bates College, Lewiston, ME 04240, USA
| | | | | | | |
Collapse
|
87
|
Abstract
The number of synonymous mutations per synonymous site (K(s)), the number of nonsynonymous mutations per nonsynonymous site (K(a)), and the codon usage statistic (N(c)) were calculated for several hepatitis A virus (HAV) isolates. While K(s) was similar to those of poliovirus (PV) and foot-and-mouth disease virus (FMDV), K(a) was 1 order of magnitude lower. The N(c) parameter provides information on codon usage bias and decreases when bias increases. The N(c) value in HAV was about 38, while in PV and FMDV, it was about 53. The emergence of 22 rare codons in front of 8 in PV and 7 in FMDV was detected. Most of the conserved rare codons of the P1 region were strategically located at the carboxy borders of beta barrels and alpha helices, their potential function being the assurance of proper folding of the capsid proteins through a decrease in the translation speed. This strategic location was not observed for amino acids encoded by the conserved rare codons of the 3D region. The percentage of bases with low pairing number values was higher in the latter region, suggesting a role of the conserved rare codons in the maintenance of RNA structure. Many of the rare codons in HAV are among the most frequent in humans, unlike in PV or in FMDV. This fact may be explained by the lack of cellular shutoff in HAV. One hypothesis is that HAV has evolved in order to avoid competition with its host for cellular tRNAs.
Collapse
Affiliation(s)
- Glòria Sánchez
- Grup Virus Entèrics, Department of Microbiology, University of Barcelona, Spain
| | | | | |
Collapse
|
88
|
Ziebuhr J, Bayer S, Cowley JA, Gorbalenya AE. The 3C-like proteinase of an invertebrate nidovirus links coronavirus and potyvirus homologs. J Virol 2003; 77:1415-26. [PMID: 12502857 PMCID: PMC140795 DOI: 10.1128/jvi.77.2.1415-1426.2003] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2002] [Accepted: 10/15/2002] [Indexed: 11/20/2022] Open
Abstract
Gill-associated virus (GAV), a positive-stranded RNA virus of prawns, is the prototype of newly recognized taxa (genus Okavirus, family Roniviridae) within the order NIDOVIRALES: In this study, a putative GAV cysteine proteinase (3C-like proteinase [3CL(pro)]), which is predicted to be the key enzyme involved in processing of the GAV replicase polyprotein precursors, pp1a and pp1ab, was characterized. Comparative sequence analysis indicated that, like its coronavirus homologs, 3CL(pro) has a three-domain organization and is flanked by hydrophobic domains. The putative 3CL(pro) domain including flanking regions (pp1a residues 2793 to 3143) was fused to the Escherichia coli maltose-binding protein (MBP) and, when expressed in E. coli, was found to possess N-terminal autoprocessing activity that was not dependent on the presence of the 3CL(pro) C-terminal domain. N-terminal sequence analysis of the processed protein revealed that cleavage occurred at the location (2827)LVTHE downward arrow VRTGN(2836). The trans-processing activity of the purified recombinant 3CL(pro) (pp1a residues 2832 to 3126) was used to identify another cleavage site, (6441)KVNHE downward arrow LYHVA(6450), in the C-terminal pp1ab region. Taken together, the data tentatively identify VxHE downward arrow (L,V) as the substrate consensus sequence for the GAV 3CL(pro). The study revealed that the GAV and potyvirus 3CL(pro)s possess similar substrate specificities which correlate with structural similarities in their respective substrate-binding sites, identified in sequence comparisons. Analysis of the proteolytic activities of MBP-3CL(pro) fusion proteins carrying replacements of putative active-site residues provided evidence that, in contrast to most other 3C/3CL(pro)s but in common with coronavirus 3CL(pro)s, the GAV 3CL(pro) employs a Cys(2968)-His(2879) catalytic dyad. The properties of the GAV 3CL(pro) define a novel RNA virus proteinase variant that bridges the gap between the distantly related chymotrypsin-like cysteine proteinases of coronaviruses and potyviruses.
Collapse
Affiliation(s)
- John Ziebuhr
- Institute of Virology and Immunology, University of Würzburg, Germany.
| | | | | | | |
Collapse
|
89
|
Affiliation(s)
- Michael S Chapman
- Department of Chemistry and Biochemistry, Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306, USA
| | | |
Collapse
|
90
|
Phan J, Zdanov A, Evdokimov AG, Tropea JE, Peters HK, Kapust RB, Li M, Wlodawer A, Waugh DS. Structural basis for the substrate specificity of tobacco etch virus protease. J Biol Chem 2002; 277:50564-72. [PMID: 12377789 DOI: 10.1074/jbc.m207224200] [Citation(s) in RCA: 181] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Because of its stringent sequence specificity, the 3C-type protease from tobacco etch virus (TEV) is frequently used to remove affinity tags from recombinant proteins. It is unclear, however, exactly how TEV protease recognizes its substrates with such high selectivity. The crystal structures of two TEV protease mutants, inactive C151A and autolysis-resistant S219D, have now been solved at 2.2- and 1.8-A resolution as complexes with a substrate and product peptide, respectively. The enzyme does not appear to have been perturbed by the mutations in either structure, and the modes of binding of the product and substrate are virtually identical. Analysis of the protein-ligand interactions helps to delineate the structural determinants of substrate specificity and provides guidance for reengineering the enzyme to further improve its utility for biotechnological applications.
Collapse
Affiliation(s)
- Jason Phan
- Macromolecular Crystallography Laboratory, Center for Cancer Research, NCI-Frederick, National Institutes of Health, Frederick, Maryland 21702-1201, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
91
|
Affiliation(s)
- Liang Tong
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA.
| |
Collapse
|
92
|
Abstract
The Norwalk Virus (NV) is the prototype strain of human caliciviruses that cause epidemic outbreaks of foodborne and waterborne gastroenteritis. These viruses do not grow in cell culture and the mechanisms of virus replication are obscure. The NV genome is a 7.7 kb ssRNA molecule that encodes three open reading frames (ORFs). The first ORF is a 1789 amino acid polyprotein that is processed into nonstructural proteins by a viral protease similar to the picornavirus 3C protease. Primary cleavage sites in the ORF1 polyprotein of two Norwalk-like viruses have been identified as QG dipeptides. We studied primary cleavage sites in the NV polyprotein and residues surrounding the scissile bond that are important in substrate recognition. A series of mutations were made at amino acids occupying positions implicated as important in cleavage site recognition for chymotrypsin-like viral proteases. We determined that effective processing at amino acid 398 to release the N-terminal p48 protein is necessary for proteolytic release of the p41 protein, that the P4 position N-terminal to the scissile bond is important for efficient processing, and that substitution of large hydrophobic residues were tolerated at this position. Finally, we defined the acidic residue of the 3CL(pro) catalytic site.
Collapse
Affiliation(s)
- Michele E Hardy
- Veterinary Molecular Biology, P.O. Box 173610 Montana State University, Bozeman, MT 59717, USA.
| | | | | | | |
Collapse
|
93
|
Anand K, Palm GJ, Mesters JR, Siddell SG, Ziebuhr J, Hilgenfeld R. Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra alpha-helical domain. EMBO J 2002; 21:3213-24. [PMID: 12093723 PMCID: PMC126080 DOI: 10.1093/emboj/cdf327] [Citation(s) in RCA: 472] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The key enzyme in coronavirus polyprotein processing is the viral main proteinase, M(pro), a protein with extremely low sequence similarity to other viral and cellular proteinases. Here, the crystal structure of the 33.1 kDa transmissible gastroenteritis (corona)virus M(pro) is reported. The structure was refined to 1.96 A resolution and revealed three dimers in the asymmetric unit. The mutual arrangement of the protomers in each of the dimers suggests that M(pro) self-processing occurs in trans. The active site, comprised of Cys144 and His41, is part of a chymotrypsin-like fold that is connected by a 16 residue loop to an extra domain featuring a novel alpha-helical fold. Molecular modelling and mutagenesis data implicate the loop in substrate binding and elucidate S1 and S2 subsites suitable to accommodate the side chains of the P1 glutamine and P2 leucine residues of M(pro) substrates. Interactions involving the N-terminus and the alpha-helical domain stabilize the loop in the orientation required for trans-cleavage activity. The study illustrates that RNA viruses have evolved unprecedented variations of the classical chymotrypsin fold.
Collapse
Affiliation(s)
| | | | | | - Stuart G. Siddell
- Department of Structural Biology and Crystallography, Institute of Molecular Biotechnology, D-07745 Jena and
Institute of Virology and Immunology, University of Würzburg, D-97078 Würzburg, Germany Corresponding authors e-mail: or
| | - John Ziebuhr
- Department of Structural Biology and Crystallography, Institute of Molecular Biotechnology, D-07745 Jena and
Institute of Virology and Immunology, University of Würzburg, D-97078 Würzburg, Germany Corresponding authors e-mail: or
| | - Rolf Hilgenfeld
- Department of Structural Biology and Crystallography, Institute of Molecular Biotechnology, D-07745 Jena and
Institute of Virology and Immunology, University of Würzburg, D-97078 Würzburg, Germany Corresponding authors e-mail: or
| |
Collapse
|
94
|
Someya Y, Takeda N, Miyamura T. Identification of active-site amino acid residues in the Chiba virus 3C-like protease. J Virol 2002; 76:5949-58. [PMID: 12021327 PMCID: PMC136217 DOI: 10.1128/jvi.76.12.5949-5958.2002] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2001] [Accepted: 03/20/2002] [Indexed: 11/20/2022] Open
Abstract
The 3C-like protease of the Chiba virus, a Norwalk-like virus, is one of the chymotrypsin-like proteases. To identify active-site amino acid residues in this protease, 37 charged amino acid residues and a putative nucleophile, Cys139, within the GDCG sequence were individually replaced with Ala in the 3BC precursor, followed by expression in Escherichia coli, where the active 3C-like protease would cleave 3BC into 3B (VPg) and 3C (protease). Among 38 Ala mutants, 7 mutants (R8A, H30A, K88A, R89A, D138A, C139A, and H157A) completely or nearly completely lost the proteolytic activity. Cys139 was replaceable only with Ser, suggesting that an SH or OH group in the less bulky side chain was required for the side chain of the residue at position 139. His30, Arg89, and Asp138 could not be replaced with any other amino acids. Although Arg8 was also not replaceable for the 3B/3C cleavage and the 3C/3D cleavage, the N-terminal truncated mutant devoid of Arg8 significantly cleaved 3CD into 3C and 3D (polymerase), indicating that Arg8 itself was not directly involved in the proteolytic cleavage. As for position 88, a positively charged residue was required because the Arg mutant showed significant activity. As deduced by the X-ray structure of the hepatitis A virus 3C protease, Arg8, Lys88, and Arg89 are far away from the active site, and the side chain of Asp138 is directed away from the active site. Therefore, these are not catalytic residues. On the other hand, all of the mutants of His157 in the S1 specificity pocket tended to retain very slight activity, suggesting a decreased level of substrate recognition. These results, together with a sequence alignment with the picornavirus 3C proteases, indicate that His30 and Cys139 are active-site residues, forming a catalytic dyad without a carboxylate directly participating in the proteolysis.
Collapse
Affiliation(s)
- Yuichi Someya
- Department of Virology II, National Institute of Infectious Diseases, Shinjuku, Tokyo 162-8640, Japan.
| | | | | |
Collapse
|
95
|
Ramtohul YK, James MNG, Vederas JC. Synthesis and evaluation of keto-glutamine analogues as inhibitors of hepatitis A virus 3C proteinase. J Org Chem 2002; 67:3169-78. [PMID: 12003522 DOI: 10.1021/jo0157831] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hepatitis A virus (HAV) 3C enzyme is a picornaviral cysteine proteinase involved in the processing of the initially synthesized viral polyprotein and is therefore important for viral maturation and infectivity. Although it is a cysteine proteinase, this enzyme has a topology similar to those of the chymotrypsin-like serine proteinases. Since the enzyme recognizes peptide substrates with a glutamine residue at the P(1) site, a number of ketone-containing glutamine compounds analogous to nanomolar inhibitors of cathepsin K were synthesized and tested for inhibition against HAV 3C proteinase. In addition, a 3-azetidinone scaffold was incorporated into the glutamine fragment but gave only modest inhibition. However, introduction of a phthalhydrazido group alpha to the ketone moiety gave significantly better inhibitors with IC(50) values ranging from 13 to 164 microM, presumably due to the effect of intramolecular hydrogen bonding to the ketone. In addition, the tetrapeptide phthalhydrazide 24 was found to be a competitive reversible inhibitor (K(i) = 9 x 10(-6) M) and also showed no loss of inhibitory potency in the presence of dithiothreitol.
Collapse
Affiliation(s)
- Yeeman K Ramtohul
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | | | | |
Collapse
|
96
|
van Rensburg H, Haydon D, Joubert F, Bastos A, Heath L, Nel L. Genetic heterogeneity in the foot-and-mouth disease virus Leader and 3C proteinases. Gene 2002; 289:19-29. [PMID: 12036580 DOI: 10.1016/s0378-1119(02)00471-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Leader and 3C proteinases of foot-and-mouth disease virus (FMDV) are responsible for almost all the proteolytic processing events of the viral polyprotein precursor. Investigation into the genetic heterogeneity of the regions encoding these proteins from isolates of six FMDV serotypes revealed the 3C proteinase to be more conserved than the Leader proteinase. Maximum likelihood analysis indicated similar phylogenetic groupings for the non-structural protein coding regions of both the Leader and 3C. These groupings were different from the structural VP1 protein coding region which, as shown previously, grouped according to serotype. Two distinct clades were apparent for both the Leader and 3C coding regions: one comprising of serotypes A, O and C together with SAT (South African Territories) isolates from eastern Africa. The other clade consisted of SAT isolates originating from southern Africa. Only one virus isolate, obtained from a buffalo in Uganda, did not conform to this phylogenetic pattern. This SAT 1 virus grouped with types A, O and C in the Leader analysis, but with the southern African SAT types in the 3C analysis, implicating intertypic recombination. The leader proteinases of southern African SAT type isolates differed from those present in European type isolates, particularly in the self-processing region. A three-dimensional structure was modeled for the Leader proteinase of one of the SAT type viruses, ZIM/7/83/2, and compared with the previously elucidated crystal structure of O(1)Kaufbeuren Leader proteinase. The active sites of the two leaders were found to superimpose closely, despite the observed sequence variation between the two molecules. Comparison of the 3C proteinase P1 cleavage sites suggested that the FMDV 3C proteinase may possess a broader substrate specificity, as observed in hepatitis A virus 3C proteinase.
Collapse
Affiliation(s)
- Hester van Rensburg
- Exotic Diseases Division, Onderstepoort Veterinary Institute, Private Bag X05, Onderstepoort 0110, South Africa.
| | | | | | | | | | | |
Collapse
|
97
|
Mari J, Poulos BT, Lightner DV, Bonami JR. Shrimp Taura syndrome virus: genomic characterization and similarity with members of the genus Cricket paralysis-like viruses. J Gen Virol 2002; 83:915-926. [PMID: 11907342 DOI: 10.1099/0022-1317-83-4-915] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The single-stranded genomic RNA of Taura syndrome virus (TSV) is 10205 nucleotides in length, excluding the 3' poly(A) tail, and contains two large open reading frames (ORFs) that are separated by an intergenic region of 207 nucleotides. The ORFs are flanked by a 377 nucleotide 5' untranslated region (UTR) and a 226 nucleotide 3' UTR followed by a poly(A) tail. The predicted amino acid sequence of ORF1 revealed sequence motifs characteristic of a helicase, a protease and an RNA-dependent RNA polymerase, similar to the non-structural proteins of several plant and animal RNA viruses. In addition, a short amino acid sequence located in the N-terminal region of ORF1 presented a significant similarity with a baculovirus IAP repeat (BIR) domain of inhibitor of apoptosis proteins from double-stranded DNA viruses and from animals. The presence of this BIR-like sequence is the first reported in a single-stranded RNA virus, but its function is unknown. The N-terminal amino acid sequence of three TSV capsid proteins (55, 40 and 24 kDa) were mapped in ORF2, which is not in the same reading frame as ORF1 and possesses an AUG codon upstream of the structural genes. However, the intergenic region shows nucleotide sequence similarity with those of the genus Cricket paralysis-like viruses, suggesting a similar non-AUG-mediated translation mechanism. The structure of the TSV genome [5' UTR-non-structural proteins-intergenic UTR-structural proteins-3' UTR-poly(A) tail] is similar to those of small insect-infecting RNA viruses, which were recently regrouped into a new virus genus, Cricket paralysis-like viruses.
Collapse
Affiliation(s)
- Jocelyne Mari
- UMR 5098, CNRS/IFREMER/UM2, cc080, Place East Bataillon, 34095 Montpellier Cedex 5, France2
- Aquaculture Pathology Group, Department of Veterinary Science and Microbiology, The University of Arizona, 1117 East Lowell Street, Tucson, Arizona 85721, USA1
| | - Bonnie T Poulos
- Aquaculture Pathology Group, Department of Veterinary Science and Microbiology, The University of Arizona, 1117 East Lowell Street, Tucson, Arizona 85721, USA1
| | - Donald V Lightner
- Aquaculture Pathology Group, Department of Veterinary Science and Microbiology, The University of Arizona, 1117 East Lowell Street, Tucson, Arizona 85721, USA1
| | - Jean-Robert Bonami
- UMR 5098, CNRS/IFREMER/UM2, cc080, Place East Bataillon, 34095 Montpellier Cedex 5, France2
| |
Collapse
|
98
|
Lall MS, Ramtohul YK, James MNG, Vederas JC. Serine and threonine beta-lactones: a new class of hepatitis A virus 3C cysteine proteinase inhibitors. J Org Chem 2002; 67:1536-47. [PMID: 11871884 DOI: 10.1021/jo0109016] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hepatitis A virus (HAV) 3C enzyme is a cysteine proteinase essential for viral replication and infectivity and represents a target for the development of antiviral drugs. A number of serine and threonine beta-lactones were synthesized and tested against HAV 3C proteinase. The D-N-Cbz-serine beta-lactone 5a displays competitive reversible inhibition with a K(i) value of 1.50 x 10(-6) M. Its enantiomer, L-N-Cbz-serine beta-lactone 5b is an irreversible inactivator with k(inact) = 0.70 min(-1), K(Iota) = 1.84 x 10(-4) M and k(inact)/K(Iota) = 3800 M(-1) min(-1). Mass spectrometry and HMQC NMR studies using (13)C-labeled 5b show that inactivation of the enzyme occurs by nucleophilic attack of the cysteine thiol (Cys-172) at the beta-position of the oxetanone ring. Although the N-Cbz-serine beta-lactones 5a and 5b display potent inhibition, other related analogues with an N-Cbz side chain, such as the five-membered ring homoserine gamma-lactones 14a and 14b, the four-membered ring beta-lactam 33, 2-methylene oxetane 34, cyclobutanone 36, and 3-azetidinone 39, fail to give significant inhibition of HAV 3C proteinase, thus demonstrating the importance of the beta-lactone ring for binding.
Collapse
Affiliation(s)
- Manjinder S Lall
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2G2
| | | | | | | |
Collapse
|
99
|
Hegyi A, Friebe A, Gorbalenya AE, Ziebuhr J. Mutational analysis of the active centre of coronavirus 3C-like proteases. J Gen Virol 2002; 83:581-593. [PMID: 11842253 DOI: 10.1099/0022-1317-83-3-581] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Formation of the coronavirus replication-transcription complex involves the synthesis of large polyprotein precursors that are extensively processed by virus-encoded cysteine proteases. In this study, the coding sequence of the feline infectious peritonitis virus (FIPV) main protease, 3CL(pro), was determined. Comparative sequence analyses revealed that FIPV 3CL(pro) and other coronavirus main proteases are related most closely to the 3C-like proteases of potyviruses. The predicted active centre of the coronavirus enzymes has accepted unique replacements that were probed by extensive mutational analysis. The wild-type FIPV 3CL(pro) domain and 25 mutants were expressed in Escherichia coli and tested for proteolytic activity in a peptide-based assay. The data strongly suggest that, first, the FIPV 3CL(pro) catalytic system employs His(41) and Cys(144) as the principal catalytic residues. Second, the amino acids Tyr(160) and His(162), which are part of the conserved sequence signature Tyr(160)-Met(161)-His(162) and are believed to be involved in substrate recognition, were found to be indispensable for proteolytic activity. Third, replacements of Gly(83) and Asn(64), which were candidates to occupy the position spatially equivalent to that of the catalytic Asp residue of chymotrypsin-like proteases, resulted in proteolytically active proteins. Surprisingly, some of the Asn(64) mutants even exhibited strongly increased activities. Similar results were obtained for human coronavirus (HCoV) 3CL(pro) mutants in which the equivalent Asn residue (HCoV 3CL(pro) Asn(64)) was substituted. These data lead us to conclude that both the catalytic systems and substrate-binding pockets of coronavirus main proteases differ from those of other RNA virus 3C and 3C-like proteases.
Collapse
Affiliation(s)
- Annette Hegyi
- Institute of Virology and Immunology, University of Würzburg, Versbacher Straße 7, 97078 Würzburg, Germany1
| | - Agnes Friebe
- Institute of Virology and Immunology, University of Würzburg, Versbacher Straße 7, 97078 Würzburg, Germany1
| | - Alexander E Gorbalenya
- Advanced Biomedical Computing Center, 430 Miller Dr. Rm 228, SAIC/NCI-Frederick, Frederick, MD 21702-1201, USA2
| | - John Ziebuhr
- Institute of Virology and Immunology, University of Würzburg, Versbacher Straße 7, 97078 Würzburg, Germany1
| |
Collapse
|
100
|
Yi M, Lemon SM. Replication of subgenomic hepatitis A virus RNAs expressing firefly luciferase is enhanced by mutations associated with adaptation of virus to growth in cultured cells. J Virol 2002; 76:1171-80. [PMID: 11773393 PMCID: PMC135777 DOI: 10.1128/jvi.76.3.1171-1180.2002] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Replication of hepatitis A virus (HAV) in cultured cells is inefficient and difficult to study due to its protracted and generally noncytopathic cycle. To gain a better understanding of the mechanisms involved, we constructed a subgenomic HAV replicon by replacing most of the P1 capsid-coding sequence from an infectious cDNA copy of the cell culture-adapted HM175/18f virus genome with sequence encoding firefly luciferase. Replication of this RNA in transfected Huh-7 cells (derived from a human hepatocellular carcinoma) led to increased expression of luciferase relative to that in cells transfected with similar RNA transcripts containing a lethal premature termination mutation in 3D(pol) (RNA polymerase). However, replication could not be confirmed in either FrhK4 cells or BSC-1 cells, cells that are typically used for propagation of HAV. Replication was substantially slower than that observed with replicons derived from other picornaviruses, as the basal luciferase activity produced by translation of input RNA did not begin to increase until 24 to 48 h after transfection. Replication of the RNA was reversibly inhibited by guanidine. The inclusion of VP4 sequence downstream of the viral internal ribosomal entry site had no effect on the basal level of luciferase or subsequent increases in luciferase related to its amplification. Thus, in this system this sequence does not contribute to viral translation or replication, as suggested previously. Amplification of the replicon RNA was profoundly enhanced by the inclusion of P2 (but not 5' noncoding sequence or P3) segment mutations associated with adaptation of wild-type virus to growth in cell culture. These results provide a simple reporter system for monitoring the translation and replication of HAV RNA and show that critical mutations that enhance the growth of virus in cultured cells do so by promoting replication of viral RNA in the absence of encapsidation, packaging, and cellular export of the viral genome.
Collapse
Affiliation(s)
- MinKyung Yi
- Department of Microbiology and Immunology, The University of Texas Medical Branch at Galveston, Galveston, Texas 77555-1019, USA
| | | |
Collapse
|