Conservation of substrate specificities among coronavirus main proteases
Journal of General VirologyPublished 1 March 2002
Annette Hegyi, John Ziebuhr
Citations351
SJR quartileQ2
SJR score1.07
SNIP1.25
Generate an AI Snapshot to get a quick, structured summary of this paper.
Study Snapshot
ObjectiveStudy objective
MethodsResearch methodology
PopulationPopulation studied
Sample sizeSample sizes
OutcomesStudy outcomes here
ResultsStudy results comes here
LimitationsResearch study limitations comes here
A concise AI-generated summary of the paper will appear here once you click Generate AI Snapshot.
TL;DR
The data show that the differential cleavage kinetics of sites within pp1a/pp1ab are a conserved feature of coronavirus main proteases and lead to predict similar processing kinetics for the replicase polyproteins of all coronaviruses.
Abstract
The key enzyme in coronavirus replicase polyprotein processing is the coronavirus main protease, 3CL(pro). The substrate specificities of five coronavirus main proteases, including the prototypic enzymes from the coronavirus groups I, II and III, were characterized. Recombinant main proteases of human coronavirus (HCoV), transmissible gastroenteritis virus (TGEV), feline infectious peritonitis virus, avian infectious bronchitis virus and mouse hepatitis virus (MHV) were tested in peptide-based trans-cleavage assays. The determination of relative rate constants for a set of corresponding HCoV, TGEV and MHV 3CL(pro) cleavage sites revealed a conserved ranking of these sites. Furthermore, a synthetic peptide representing the N-terminal HCoV 3CL(pro) cleavage site was shown to be effectively hydrolysed by noncognate main proteases. The data show that the differential cleavage kinetics of sites within pp1a/pp1ab are a conserved feature of coronavirus main proteases and lead us to predict similar processing kinetics for the replicase polyproteins of all coronaviruses.
Keywords
Agricultural and Biological SciencesMedicine
Biochemical and Biophysical Research CommunicationsOn the size of the active site in proteases. I. Papain
5,220 Citations1967Israël Schechter, Arieh Berger
Journal of General VirologyVirus-encoded proteinases and proteolytic processing in the Nidovirales
1,050 Citations2000John Ziebuhr, Alexander E. Gorbalenya +1 more
This paper presents a meta-anatomy of the EMMARM, a probabilistic model of the immune response to EMT, which states that EMTs are more likely to attack the nervous system than the immune systems of mice.
FEBS LettersCysteine proteases of positive strand RNA viruses and chymotrypsin‐like serine proteases
446 Citations1989Alexander E. Gorbalenya, Alexei P. Donchenko +2 more
The His residue previously implicated in catalysis, together with two partially conserved Gly residues, is predicted to constitute part of the substrate‐binding pocket of 3C proteases, providing the first example of relatedness between proteases belonging, by definition, to different classes.
Journal of General VirologyCompletion of the Sequence of the Genome of the Coronavirus Avian Infectious Bronchitis Virus
434 Citations1987M. E. G. Boursnell, T. D. K. Brown +4 more
The nucleotide sequence determination of the genome of the Beaudette strain of the coronavirus avian infectious bronchitis virus has been completed and the remainder of the sequence, equivalent to the 'unique' region of mRNA F, is thought to code for a polymerase or polymerases which are involved in the replication of the genomes and the production of the subgenomic messenger RNAs.
Proceedings of the National Academy of SciencesViral cysteine proteases are homologous to the trypsin-like family of serine proteases: structural and functional implications.
424 Citations1988J. Fernando Bazán, R.J. Fletterick
This classification allows the molecular mapping of residues from viral sequences onto related tertiary structures and precisely identifies amino acids that are strong determinants of specificity for both small and large viral cysteine proteases.
Journal of VirologyEquine arteritis virus is not a togavirus but belongs to the coronaviruslike superfamily
395 Citations1991Johan A. den Boon, Eric J. Snijder +4 more
The data indicate that EAV, presently considered a togavirus, is evolutionarily related to viruses from the coronaviruslike superfamily.
Proceedings of the National Academy of SciencesEngineering the largest RNA virus genome as an infectious bacterial artificial chromosome
393 Citations2000Fernando Almazán, José M. González +5 more
It is shown that the application of two strategies, cloning of the cDNAs into a bacterial artificial chromosome and nuclear expression of RNAs that are typically produced within the cytoplasm, is useful for the engineering of large RNA molecules.
VirologyThe complete sequence (22 kilobases) of murine coronavirus gene 1 encoding the putative proteases and RNA polymerase
371 Citations1991Han‐Jung Lee, Chien-Kou Shieh +6 more
This study completes the sequence of the MHV genome, which is 31 kb long, and constitutes the largest viral RNA known.
The EMBO JournalAn efficient ribosomal frame‐shifting signal in the polymerase‐encoding region of the coronavirus IBV.
322 Citations1987Ian Brierley, M. E. G. Boursnell +5 more
A cDNA fragment containing the F1/F2 overlap region was cloned within a marker gene and placed under the control of the bacteriophage SP6 promoter in a recombinant plasmid to examine the possibility of ribosomal frame‐shifting in higher eukaryotes.
Nucleic Acids ResearchCoronavirus genome: prediction of putative functional domains in the non-structural polyprotein by comparative amino acid sequence analysis
311 Citations1989Alexander E. Gorbalenya, Eugene V. Koonin +2 more
A partial tentative scheme for the functional organization and expression strategy of the non-structural polyproteins of IBV implies that, despite the general similarity to other positive strand RNA viruses, and particularly to potyviruses, coronaviruses possess a number of unique structural and functional features.
Journal of General VirologyInfectious RNA transcribed in vitro from a cDNA copy of the human coronavirus genome cloned in vaccinia virus
308 Citations2001Volker Thiel, Jens Herold +2 more
A reverse-genetic system is described for the generation of recombinant coronaviruses based upon the in vitro transcription of infectious RNA from a cDNA copy of the human coronavirus 229E genome that has been cloned and propagated in vaccinia virus.
Journal of VirologyReverse Genetics System for the Avian Coronavirus Infectious Bronchitis Virus
272 Citations2001Rosa Casais, Volker Thiel +3 more
The assembly of a full-length cDNA from the positive-sense genomic RNA of the avian coronavirus, infectious bronchitis virus (IBV) is described and a paradigm for generating genetically defined vaccines for IBV is established.
The EMBO JournalCoronavirus mRNA synthesis involves fusion of non‐contiguous sequences.
250 Citations1983Willy J. M. Spaan, Hajo Delius +6 more
Positive‐stranded genomic RNA of coronavirus MHV and its six subgenomic mRNAs are synthesized in the cytoplasm of the host cell by a mechanism which appears to involve an unusual and specific ‘polymerase jumping’ event.
Proceedings of the National Academy of SciencesArterivirus discontinuous mRNA transcription is guided by base pairing between sense and antisense transcription-regulating sequences
219 Citations1999Guido van Marle, Jessika C. Dobbe +4 more
Site-directed mutagenesis of the infectious cDNA clone of the arterivirus equine arteritis virus is used to show that sg mRNA synthesis requires a base-pairing interaction between the leader TRS and the complement of a body TRS in the viral negative strand.
Advances in experimental medicine and biologyA New Model for Coronavirus Transcription
207 Citations1998Stanley G. Sawicki, Dorothea L. Sawicki
A new model for coronavirus transcription is proposed, called 3' discontinuous extension of negative strands, which predicts that subgenome-length negative strands would be derived directly by transcription using the genome RNA as a template, which would make negative strand synthesis discontinuous and subgenomic mRNA synthesis continuous.
Journal of VirologyViral Replicase Gene Products Suffice for Coronavirus Discontinuous Transcription
153 Citations2001Volker Thiel, Jens Herold +2 more
Journal of Biological ChemistryThe Autocatalytic Release of a Putative RNA Virus Transcription Factor from Its Polyprotein Precursor Involves Two Paralogous Papain-like Proteases That Cleave the Same Peptide Bond
150 Citations2001John Ziebuhr, Volker Thiel +1 more
Comparison sequence analysis shows that the respective proteins of all sequenced coronaviruses are flanked by two conserved PLpro cleavage sites and share a complex (multi)domain organization with PL1pro being inactivated in IBV.
VirologyNucleotide Sequence of the Human Coronavirus 229E RNA Polymerase Locus
128 Citations1993Jens Herold, Thomas Raabe +2 more
This analysis completes the nucleotide sequence of the HCV 229E genome and shows that expression of ORF1b can be mediated by ribosomal frame-shifting.
Journal of VirologyCharacterization of a human coronavirus (strain 229E) 3C-like proteinase activity
120 Citations1995John Ziebuhr, Jens Herold +1 more
The putative HCV 229E 3C-like proteinase domain is expressed as part of a beta-galactosidase fusion protein in Escherichia coli and it is shown that the expressed protein has proteolytic activity and the substitution of one amino acid within the predictedproteinase domain abolishes, or at least significantly reduces, this activity.
VirologyComplete Sequence (20 Kilobases) of the Polyprotein-Encoding Gene 1 of Transmissible Gastroenteritis Virus
111 Citations1995Jean‐François Eléouët, Denis Rasschaert +4 more
Analysis of the predicted ORF1a and OrF1b translation products revealed that the putative functional domains identified in infectious bronchitis virus (IBV), mouse hepatitis virus (MHV) and human coronavirus 229E (HCV 229E) are all present in TGEV.
Journal of VirologyProcessing of the Human Coronavirus 229E Replicase Polyproteins by the Virus-Encoded 3C-Like Proteinase: Identification of Proteolytic Products and Cleavage Sites Common to pp1a and pp1ab
106 Citations1999John Ziebuhr, Stuart G. Siddell
It is shown that a chymotrypsin-like enzyme, the virus-encoded 3C-like proteinase (3CLpro), cleaves within a common region of pp1a and pp1ab at four sites, indicating that coronavirus cleavage sites differ significantly with regard to their susceptibilities to proteolysis by 3CLpro.
Journal of VirologyIdentification and characterization of a serine-like proteinase of the murine coronavirus MHV-A59
104 Citations1995Yi Lü, Xiaotao Lu +1 more
This study provides experimental confirmation that the coronaviruses express an active proteinase within the 3C-like proteinase domain of gene 1 ORF 1a and that this proteinase utilizes at least one canonical QS dipeptide as a cleavage site in vitro.
Journal of VirologyThe Putative Helicase of the Coronavirus Mouse Hepatitis Virus Is Processed from the Replicase Gene Polyprotein and Localizes in Complexes That Are Active in Viral RNA Synthesis
102 Citations1999Mark R. Denison, Willy J. M. Spaan +5 more
This study demonstrates that the putative RNA helicase is closely associated with MHV RNA synthesis and suggests that complexes containing helicase, N, and new viral RNA are the viral replication complexes.
Journal of VirologyIdentification of a Novel Cleavage Activity of the First Papain-Like Proteinase Domain Encoded by Open Reading Frame 1a of the Coronavirus <i>Avian Infectious Bronchitis Virus</i> and Characterization of the Cleavage Products
101 Citations2000K. P. Lim, Lisa F. P. Ng +1 more
A novel cleavage activity of PLPD-1 is demonstrated and it is revealed that the proteinase is active on this scissile bond when expressed in vitro in rabbit reticulocyte lysates and can act on the same substrate intrans when expression in intact cells.
Journal of Biological ChemistryCleavage of synthetic peptides by purified poliovirus 3C proteinase
100 Citations1989Peter V. Pallai, F Burkhardt +9 more
The peptide most resistant to cleavage corresponded to the 3C/3D junction, a site known to be cleaved very slowly by 3C in vivo, which supports the hypothesis that the residue in P4 position, in addition to the Gln-Gly in P1 and P1', respectively, contributes to substrate recognition.
Journal of VirologyIdentification of a domain required for autoproteolytic cleavage of murine coronavirus gene A polyprotein
99 Citations1989Susan C. Baker, Chien-Kou Shieh +4 more
A protein domain essential for autoproteolytic cleavage of the gene A polyprotein is identified, which suggests that the sequence in the region between 3.9 and 5.3 kilobases from the 5' end of the genomic RNA is essential for proteolytic Cleavage and contains autoproteolic activity.
Journal of VirologyBiosynthesis, purification, and characterization of the human coronavirus 229E 3C-like proteinase
99 Citations1997John Ziebuhr, Gerhard Heusipp +1 more
The biosynthesis of the human coronavirus 229E 3C-like proteinase in Escherichia coli and the enzymatic properties, inhibitor profile, and substrate specificity of the purified protein are described.
Journal of General VirologyThe RNA structures engaged in replication and transcription of the A59 strain of mouse hepatitis virus
91 Citations2001Dorothea L. Sawicki, Tao Wang +1 more
Kinetics of incorporation of [(3)H]uridine showed that both the RI and TIs were transcriptionally active and the labelling of RI/TIs was not the dead-end product of aberrant negative-strand synthesis, probably due to overdigestion with RNase A.
Journal of VirologyIdentification of Mouse Hepatitis Virus Papain-Like Proteinase 2 Activity
73 Citations2000Amornrat Kanjanahaluethai, Susan C. Baker
This study is the first to report enzymatic activity of the PLP2 domain and to demonstrate that three distinct viral proteinase activities process the MHV replicase polyprotein.
Journal of General VirologyMutational analysis of the active centre of coronavirus 3C-like proteases
71 Citations2002Annette Hegyi, Agnes Friebe +2 more
It is concluded 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.
VirologyCharacterisation and Mutational Analysis of an ORF 1a-Encoding Proteinase Domain Responsible for Proteolytic Processing of the Infectious Bronchitis Virus 1a/1b Polyprotein
68 Citations1995Ding Xiang Liu, T. D. K. Brown
Site-directed mutagenesis studies have confirmed the involvement of the 3C-like proteinase domain in processing of the 1a/1b polyprotein, the predicted catalytic centre of the proteinase, and its cleavage sites.
Journal of VirologyCharacterization of a second cleavage site and demonstration of activity in trans by the papain-like proteinase of the murine coronavirus mouse hepatitis virus strain A59
67 Citations1997Pedro J. Bonilla, Scott Hughes +1 more
Journal of VirologyA 100-kilodalton polypeptide encoded by open reading frame (ORF) 1b of the coronavirus infectious bronchitis virus is processed by ORF 1a products
58 Citations1994Ding Xiang Liu, Ian Brierley +2 more
In vitro translation and in vivo transfection studies also indicate that the ORF 1a region between nucleotides 8763 and 10720 contains elements that down-regulate the expression of OrF 1b, suggesting that deletion of the picornavirus 3C-like proteinase domain and surrounding regions abolishes processing of the 1b polyprotein.
Journal of VirologyProteolytic processing of the coronavirus infectious bronchitis virus 1a polyprotein: identification of a 10-kilodalton polypeptide and determination of its cleavage sites
57 Citations1997Ding Xiang Liu, Hanqing Xu +1 more
Coexpression, deletion, and mutagenesis studies showed that this novel polypeptide was encoded by ORF 1a from nucleotide 11545 to 11878 and was cleaved from the 1a polyprotein by the 3C-like proteinase domain.
Journal of VirologyProteolytic Processing at the Amino Terminus of Human Coronavirus 229E Gene 1-Encoded Polyproteins: Identification of a Papain-Like Proteinase and Its Substrate
57 Citations1998Jens Herold, Alexander E. Gorbalenya +3 more
Transfection and immunoprecipitation assays and a comparative sequence analysis suggest that substrate positions P1 and P5 seem to be the major determinants of the PCP1 cleavage site and that the latter can occupy a variable position at the amino terminus of the coronavirus pp1a and pp1ab polyproteins.
VirologyFurther Characterization of the Coronavirus Infectious Bronchitis Virus 3C-like Proteinase and Determination of a New Cleavage Site
56 Citations2000Lisa F. P. Ng, Ding Xiang Liu
Analysis of the autoprocessing kinetics in vitro reveals that proteolysis at the Q2779–S2780 site is the first cleavage event mediated by this proteinase, and this is followed by cleavage at theQ3086–S3087 site.
VirologyIntracellular andin Vitro-Translated 27-kDa Proteins Contain the 3C-like Proteinase Activity of the Coronavirus MHV-A59
56 Citations1996Xiaotao Lu, Yiqi Lu +1 more
Results indicate that the 27-kDa protein is a mature proteinase in MHV-A59-infected cells, and that appropriate processing of this molecule occurs in vitro.
Journal of VirologyMouse Hepatitis Virus 3C-Like Protease Cleaves a 22-Kilodalton Protein from the Open Reading Frame 1a Polyprotein in Virus-Infected Cells and In Vitro
54 Citations1998Xiao Lu, Amy Sims +1 more
It is predicted that at least seven mature proteins are processed from the ORF 1a polyprotein by 3CLpro and suggested that additional noncanonical cleavage sites may be used by3CLpro during processing of the gene 1 polyprotein.
Journal of VirologyCharacterization in vitro of an autocatalytic processing activity associated with the predicted 3C-like proteinase domain of the coronavirus avian infectious bronchitis virus
50 Citations1996K. W. Tibbles, Ian Brierley +2 more
Processed products of the wild-type protein were active in trans cleavage assays, which were used to demonstrate that the IBV 3CLP is sensitive to inhibition by both serine and cysteine protease class-specific inhibitors.
Journal of VirologyIdentification of an ATPase activity associated with a 71-kilodalton polypeptide encoded in gene 1 of the human coronavirus 229E
42 Citations1997Gerhard Heusipp, Ute Harms +2 more
A 71-kDa polypeptide in virus-infected cells that is released from pp1ab by the virus-encoded 3C-like proteinase and that has been predicted to contain both metal-binding and helicase domains is detected.
Journal of General VirologyIdentification and subcellular localization of a 41 kDa, polyprotein 1ab processing product in human coronavirus 229E-infected cells.
37 Citations1997Gerhard Heusipp, Jens Herold +3 more
This study has identified an ORF 1b-encoded, 41 kDa processing product in HCV 229E-infected cells by using a monoclonal antibody with defined specificity and shows that this polypeptide is released from polyprotein 1ab by 3C-like proteinase-mediated cleavage of the peptide bonds Gln-6110/Gly-6111 and GlN-6458/Ser-6459.
VirologyProteolytic Mapping of the Coronavirus Infectious Bronchitis Virus 1b Polyprotein: Evidence for the Presence of Four Cleavage Sites of the 3C-like Proteinase and Identification of Two Novel Cleavage Products
37 Citations1998Ding Xiang Liu, Shuo Shen +2 more
Results suggest that the ORF 1b region of IBV mRNA1 may be able to encode five mature products, including the 100-kDa protein previously identified.
VirologyDeterminants of Mouse Hepatitis Virus 3C-like Proteinase Activity
37 Citations1997Yiqi Lu, Mark R. Denison
These studies suggest that the coronavirus 3CL-proteinases may have a substantially different structure and catalytic mechanism than other 3C-like proteinases.
VirologyCharacterization of a 105-kDa Polypeptide Encoded in Gene 1 of the Human Coronavirus HCV 229E
32 Citations1996Carsten Grötzinger, Gerhard Heusipp +4 more
These data contribute to the characterization of coronavirus 3C-like proteinase-mediated processing of pp1ab and provide the first identification of an HCV 229E ORF 1ab-encoded polypeptide in virus-infected cells.
Journal of General VirologyExpression and characterization of a recombinant murine coronavirus 3C-like proteinase.
31 Citations1997Anja Seybert, Stuart G. Siddell +1 more
A bacterial system that has allowed us to express and characterize a recombinant murine coronavirus (MHV-JHM) 3C-like proteinase is described, which has been shown to exhibit proteolytic activity in trans and mutation analysis and the effect of class-specific proteinase inhibitors on the trans cleavage activity has been used to demonstrate the functional and structural homology of this enzyme to the picornavirus 3C proteinases.
Methods in enzymology on CD-ROM/Methods in enzymology[5] Characterization of coronavirus RNA polymerase gene products
22 Citations1996Jens Herold, Stuart G. Siddell +1 more