VPg Impact on Ryegrass Mottle Virus Serine-like 3C Protease Proteolysis and Structure

Sobemoviruses encode serine-like 3C proteases (Pro) that participate in the processing and maturation of other virus-encoded proteins. Its cis and trans activity is mediated by the naturally unfolded virus-genome-linked protein (VPg). Nuclear magnetic resonance studies show a Pro–VPg complex interac...

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Vydané v:	International journal of molecular sciences Ročník 24; číslo 6; s. 5347
Hlavní autori:	Kalnins, Gints, Ludviga, Rebeka, Kalnciema, Ieva, Resevica, Gunta, Zeltina, Vilija, Bogans, Janis, Tars, Kaspars, Zeltins, Andris, Balke, Ina
Médium:	Journal Article
Jazyk:	English
Vydavateľské údaje:	Switzerland MDPI AG 10.03.2023 MDPI
Predmet:	3C Viral Proteases Amino Acid Sequence Endopeptidases - metabolism Enzymes Genomes Genomics Gram-positive bacteria Lolium - metabolism NMR Nuclear magnetic resonance Peptide Hydrolases - metabolism Peptides Proteins Proteolysis RNA polymerase RNA Viruses - metabolism Scientific equipment and supplies industry Serine Serine - metabolism Viral Proteins - metabolism Viruses Latvia United States Massachusetts Germany ryegrass mottle virus serine-like 3C proteases Sobemovirus VPg
ISSN:	1422-0067, 1661-6596, 1422-0067
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Abstract	Sobemoviruses encode serine-like 3C proteases (Pro) that participate in the processing and maturation of other virus-encoded proteins. Its cis and trans activity is mediated by the naturally unfolded virus-genome-linked protein (VPg). Nuclear magnetic resonance studies show a Pro–VPg complex interaction and VPg tertiary structure; however, information regarding structural changes of the Pro–VPg complex during interaction is lacking. Here, we solved a full Pro–VPg 3D structure of ryegrass mottle virus (RGMoV) that demonstrates the structural changes in three different conformations due to VPg interaction with Pro. We identified a unique site of VPg interaction with Pro that was not observed in other sobemoviruses, and observed different conformations of the Pro β2 barrel. This is the first report of a full plant Pro crystal structure with its VPg cofactor. We also confirmed the existence of an unusual previously unmapped cleavage site for sobemovirus Pro in the transmembrane domain: E/A. We demonstrated that RGMoV Pro in cis activity is not regulated by VPg and that in trans, VPg can also mediate Pro in free form. Additionally, we observed Ca2+ and Zn2+ inhibitory effects on the Pro cleavage activity.
AbstractList	Sobemoviruses encode serine-like 3C proteases (Pro) that participate in the processing and maturation of other virus-encoded proteins. Its cis and trans activity is mediated by the naturally unfolded virus-genome-linked protein (VPg). Nuclear magnetic resonance studies show a Pro–VPg complex interaction and VPg tertiary structure; however, information regarding structural changes of the Pro–VPg complex during interaction is lacking. Here, we solved a full Pro–VPg 3D structure of ryegrass mottle virus (RGMoV) that demonstrates the structural changes in three different conformations due to VPg interaction with Pro. We identified a unique site of VPg interaction with Pro that was not observed in other sobemoviruses, and observed different conformations of the Pro β2 barrel. This is the first report of a full plant Pro crystal structure with its VPg cofactor. We also confirmed the existence of an unusual previously unmapped cleavage site for sobemovirus Pro in the transmembrane domain: E/A. We demonstrated that RGMoV Pro in cis activity is not regulated by VPg and that in trans, VPg can also mediate Pro in free form. Additionally, we observed Ca2+ and Zn2+ inhibitory effects on the Pro cleavage activity. Sobemoviruses encode serine-like 3C proteases (Pro) that participate in the processing and maturation of other virus-encoded proteins. Its and activity is mediated by the naturally unfolded virus-genome-linked protein (VPg). Nuclear magnetic resonance studies show a Pro-VPg complex interaction and VPg tertiary structure; however, information regarding structural changes of the Pro-VPg complex during interaction is lacking. Here, we solved a full Pro-VPg 3D structure of ryegrass mottle virus (RGMoV) that demonstrates the structural changes in three different conformations due to VPg interaction with Pro. We identified a unique site of VPg interaction with Pro that was not observed in other sobemoviruses, and observed different conformations of the Pro β2 barrel. This is the first report of a full plant Pro crystal structure with its VPg cofactor. We also confirmed the existence of an unusual previously unmapped cleavage site for sobemovirus Pro in the transmembrane domain: E/A. We demonstrated that RGMoV Pro activity is not regulated by VPg and that , VPg can also mediate Pro in free form. Additionally, we observed Ca and Zn inhibitory effects on the Pro cleavage activity. Sobemoviruses encode serine-like 3C proteases (Pro) that participate in the processing and maturation of other virus-encoded proteins. Its cis and trans activity is mediated by the naturally unfolded virus-genome-linked protein (VPg). Nuclear magnetic resonance studies show a Pro-VPg complex interaction and VPg tertiary structure; however, information regarding structural changes of the Pro-VPg complex during interaction is lacking. Here, we solved a full Pro-VPg 3D structure of ryegrass mottle virus (RGMoV) that demonstrates the structural changes in three different conformations due to VPg interaction with Pro. We identified a unique site of VPg interaction with Pro that was not observed in other sobemoviruses, and observed different conformations of the Pro β2 barrel. This is the first report of a full plant Pro crystal structure with its VPg cofactor. We also confirmed the existence of an unusual previously unmapped cleavage site for sobemovirus Pro in the transmembrane domain: E/A. We demonstrated that RGMoV Pro in cis activity is not regulated by VPg and that in trans, VPg can also mediate Pro in free form. Additionally, we observed Ca[sup.2+] and Zn[sup.2+] inhibitory effects on the Pro cleavage activity. Sobemoviruses encode serine-like 3C proteases (Pro) that participate in the processing and maturation of other virus-encoded proteins. Its cis and trans activity is mediated by the naturally unfolded virus-genome-linked protein (VPg). Nuclear magnetic resonance studies show a Pro-VPg complex interaction and VPg tertiary structure; however, information regarding structural changes of the Pro-VPg complex during interaction is lacking. Here, we solved a full Pro-VPg 3D structure of ryegrass mottle virus (RGMoV) that demonstrates the structural changes in three different conformations due to VPg interaction with Pro. We identified a unique site of VPg interaction with Pro that was not observed in other sobemoviruses, and observed different conformations of the Pro β2 barrel. This is the first report of a full plant Pro crystal structure with its VPg cofactor. We also confirmed the existence of an unusual previously unmapped cleavage site for sobemovirus Pro in the transmembrane domain: E/A. We demonstrated that RGMoV Pro in cis activity is not regulated by VPg and that in trans, VPg can also mediate Pro in free form. Additionally, we observed Ca2+ and Zn2+ inhibitory effects on the Pro cleavage activity.Sobemoviruses encode serine-like 3C proteases (Pro) that participate in the processing and maturation of other virus-encoded proteins. Its cis and trans activity is mediated by the naturally unfolded virus-genome-linked protein (VPg). Nuclear magnetic resonance studies show a Pro-VPg complex interaction and VPg tertiary structure; however, information regarding structural changes of the Pro-VPg complex during interaction is lacking. Here, we solved a full Pro-VPg 3D structure of ryegrass mottle virus (RGMoV) that demonstrates the structural changes in three different conformations due to VPg interaction with Pro. We identified a unique site of VPg interaction with Pro that was not observed in other sobemoviruses, and observed different conformations of the Pro β2 barrel. This is the first report of a full plant Pro crystal structure with its VPg cofactor. We also confirmed the existence of an unusual previously unmapped cleavage site for sobemovirus Pro in the transmembrane domain: E/A. We demonstrated that RGMoV Pro in cis activity is not regulated by VPg and that in trans, VPg can also mediate Pro in free form. Additionally, we observed Ca2+ and Zn2+ inhibitory effects on the Pro cleavage activity.
Audience	Academic
Author	Zeltins, Andris Kalnciema, Ieva Bogans, Janis Tars, Kaspars Ludviga, Rebeka Resevica, Gunta Kalnins, Gints Zeltina, Vilija Balke, Ina
AuthorAffiliation	2 Plant Virus Protein Research Group, Latvian Biomedical Research and Study Centre, Ratsupites Street 1, k-1, LV-1067 Riga, Latvia 4 Biotechnology Core Facility, Latvian Biomedical Research and Study Centre, Ratsupites Street 1, k-1, LV-1067 Riga, Latvia 3 Plant Virology Group, Latvian Biomedical Research and Study Centre, Ratsupites Street 1, k-1, LV-1067 Riga, Latvia 1 Structural Biology Group, Latvian Biomedical Research and Study Centre, Ratsupites Street 1, k-1, LV-1067 Riga, Latvia
AuthorAffiliation_xml	– name: 1 Structural Biology Group, Latvian Biomedical Research and Study Centre, Ratsupites Street 1, k-1, LV-1067 Riga, Latvia – name: 4 Biotechnology Core Facility, Latvian Biomedical Research and Study Centre, Ratsupites Street 1, k-1, LV-1067 Riga, Latvia – name: 3 Plant Virology Group, Latvian Biomedical Research and Study Centre, Ratsupites Street 1, k-1, LV-1067 Riga, Latvia – name: 2 Plant Virus Protein Research Group, Latvian Biomedical Research and Study Centre, Ratsupites Street 1, k-1, LV-1067 Riga, Latvia
Author_xml	– sequence: 1 givenname: Gints surname: Kalnins fullname: Kalnins, Gints – sequence: 2 givenname: Rebeka surname: Ludviga fullname: Ludviga, Rebeka – sequence: 3 givenname: Ieva surname: Kalnciema fullname: Kalnciema, Ieva – sequence: 4 givenname: Gunta surname: Resevica fullname: Resevica, Gunta – sequence: 5 givenname: Vilija surname: Zeltina fullname: Zeltina, Vilija – sequence: 6 givenname: Janis surname: Bogans fullname: Bogans, Janis – sequence: 7 givenname: Kaspars surname: Tars fullname: Tars, Kaspars – sequence: 8 givenname: Andris surname: Zeltins fullname: Zeltins, Andris – sequence: 9 givenname: Ina orcidid: 0000-0002-5171-7744 surname: Balke fullname: Balke, Ina
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Cites_doi	10.1038/s41586-021-03819-2 10.1140/epjp/i2015-15141-2 10.1006/viro.1998.9100 10.4161/psb.5.3.10740 10.1038/sj.emboj.7600971 10.1099/0022-1317-72-9-2197 10.1016/j.virol.2003.09.035 10.1107/S0907444905036693 10.1128/MRA.00037-21 10.1107/S0907444910045749 10.1074/jbc.M504122200 10.1099/0022-1317-81-11-2783 10.1093/nar/7.8.2137 10.1007/s00705-012-1519-0 10.1073/pnas.86.21.8247 10.3186/jjphytopath.49.610 10.1107/S0021889897006766 10.1107/S0907444904019158 10.1007/s11262-007-0087-y 10.3390/v7062761 10.1016/j.virol.2009.09.025 10.1016/j.jbiotec.2005.11.013 10.1016/j.jmb.2022.167715 10.1111/j.1432-1033.1990.tb15613.x 10.1007/s00705-006-0867-z 10.1099/vir.0.026476-0 10.1016/j.febslet.2009.12.003 10.1016/j.peptides.2006.01.018 10.1107/S0907444996012255 10.1128/JVI.03151-12 10.1016/j.febslet.2011.08.009 10.1007/978-1-4939-7808-3_2 10.1002/prot.20750 10.1016/j.jmb.2013.03.028 10.1016/j.virol.2008.08.034 10.1107/S0907444912001308 10.1016/j.virol.2013.05.033 10.3389/fmicb.2018.01466 10.1111/j.1365-313X.2009.04062.x 10.1023/A:1008044715899 10.32607/20758251-2017-9-2-17-33 10.1016/j.virol.2007.07.028 10.1006/jmbi.1999.3091 10.1006/jmbi.2000.4315 10.1021/acs.biochem.0c00721 10.1128/JVI.00631-08 10.1107/S0907444910048675 10.1093/nar/gky427 10.1371/journal.ppat.0030180 10.1128/JVI.02733-12 10.3389/fpls.2019.01171 10.1074/jbc.M705666200 10.1016/j.virol.2008.04.025 10.1016/0014-5793(88)80039-5 10.1186/1743-422X-6-23 10.1016/j.virol.2005.11.011
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Keywords	ryegrass mottle virus serine-like 3C proteases Sobemovirus VPg
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References	Olspert (ref_8) 2011; 585 Ghosh (ref_7) 1979; 7 Olspert (ref_13) 2011; 92 Nair (ref_10) 2010; 584 Meier (ref_6) 2007; 152 Gayathri (ref_32) 2006; 346 Jones (ref_50) 1999; 292 Gorbalenya (ref_9) 1988; 236 Leen (ref_27) 2013; 87 Kader (ref_43) 2010; 5 ref_19 Satheshkumar (ref_14) 2005; 280 Gruez (ref_26) 2008; 82 Toriyama (ref_1) 1983; 49 Freivalds (ref_37) 2006; 123 Emsley (ref_58) 2004; D60 Chen (ref_25) 2013; 87 Hebrard (ref_16) 2009; 6 (ref_17) 2010; 64 Dixit (ref_20) 2020; 59 Schein (ref_24) 2006; 27 Demidyuk (ref_31) 2017; 9 Grzela (ref_18) 2008; 283 Lee (ref_28) 2018; 9 Lacombe (ref_47) 2010; 61 Satheshkumar (ref_12) 2004; 318 Makinen (ref_39) 2000; 81 Gillet (ref_46) 2013; 425 Bourhis (ref_40) 2006; 62 Afonine (ref_60) 2012; 68 Ling (ref_5) 2013; 446 Waterhouse (ref_57) 2018; 46 Jumper (ref_51) 2021; 596 Mueller (ref_52) 2015; 130 Nair (ref_41) 2010; 396 Balke (ref_4) 2007; 35 Verbeek (ref_42) 1998; 17 Koonin (ref_33) 1991; 72 Balke (ref_38) 2018; Volume 1776 Nair (ref_15) 2008; 382 Lycksell (ref_22) 1990; 190 Plevka (ref_44) 2007; 369 Demidiuk (ref_29) 1999; 33 Sarmiento (ref_11) 2015; 7 Bonneau (ref_48) 1998; 244 Evans (ref_54) 2006; 62 Rantalainen (ref_21) 2008; 377 Somera (ref_34) 2013; 158 Poignavent (ref_49) 2022; 434 Battye (ref_53) 2011; 67 Krogh (ref_35) 2001; 305 Vagin (ref_56) 1997; 30 Voiushina (ref_30) 2003; 29 ref_3 ref_2 Murshudov (ref_59) 1997; 53 Winn (ref_55) 2011; 67 Hirel (ref_36) 1989; 86 Arias (ref_23) 2006; 25 Cabot (ref_45) 2019; 10
References_xml	– volume: 596 start-page: 583 year: 2021 ident: ref_51 article-title: Highly accurate protein structure prediction with AlphaFold publication-title: Nature doi: 10.1038/s41586-021-03819-2 – volume: 130 start-page: 141 year: 2015 ident: ref_52 article-title: The macromolecular crystallography beamlines at BESSY II of the Helmholtz-Zentrum Berlin: Current status and perspectives publication-title: Eur. Phys. J. Plus doi: 10.1140/epjp/i2015-15141-2 – volume: 244 start-page: 79 year: 1998 ident: ref_48 article-title: Expression of the rice yellow mottle virus P1 protein in vitro and in vivo and its involvement in virus spread publication-title: Virology doi: 10.1006/viro.1998.9100 – volume: 5 start-page: 233 year: 2010 ident: ref_43 article-title: Cytosolic calcium and pH signaling in plants under salinity stress publication-title: Plant Signal. Behav. doi: 10.4161/psb.5.3.10740 – volume: 33 start-page: 100 year: 1999 ident: ref_29 article-title: Features of the functional organization of glutamyl endopeptidase publication-title: Mol. Biol. – volume: 25 start-page: 880 year: 2006 ident: ref_23 article-title: The structure of a protein primer—polymerase complex in the initiation of genome replication publication-title: EMBO J. doi: 10.1038/sj.emboj.7600971 – volume: 72 start-page: 2197 year: 1991 ident: ref_33 article-title: The phylogeny of RNA-dependent RNA polymerases of positive-strand RNA viruses publication-title: J. Gen. Virol. doi: 10.1099/0022-1317-72-9-2197 – volume: 318 start-page: 429 year: 2004 ident: ref_12 article-title: Polyprotein processing: Cis and trans proteolytic activities of Sesbania mosaic virus serine protease publication-title: Virology doi: 10.1016/j.virol.2003.09.035 – volume: 62 start-page: 72 year: 2006 ident: ref_54 article-title: Scaling and assessment of data quality publication-title: Acta Crystallogr. Sect. D Biol. Crystallogr. doi: 10.1107/S0907444905036693 – ident: ref_3 doi: 10.1128/MRA.00037-21 – volume: 67 start-page: 235 year: 2011 ident: ref_55 article-title: Overview of the CCP4 suite and current developments publication-title: Acta Crystallogr. Sect. D Biol. Crystallogr. doi: 10.1107/S0907444910045749 – volume: 280 start-page: 30291 year: 2005 ident: ref_14 article-title: “Natively unfolded” VPg is essential for Sesbania mosaic virus serine protease activity publication-title: J. Biol. Chem. doi: 10.1074/jbc.M504122200 – volume: 81 start-page: 2783 year: 2000 ident: ref_39 article-title: Characterization of VPg and the polyprotein processing of cocksfoot mottle virus (genus Sobemovirus) publication-title: J. Gen. Virol. doi: 10.1099/0022-1317-81-11-2783 – volume: 7 start-page: 2137 year: 1979 ident: ref_7 article-title: Southern bean mosaic viral RNA has a 5′-linked protein but lacks 3′ terminal poly(A) publication-title: Nucleic Acids Res. doi: 10.1093/nar/7.8.2137 – volume: 29 start-page: 563 year: 2003 ident: ref_30 article-title: Glutamyl endopeptidase. Structure, function, practical use publication-title: Bioorg. Khim. – volume: 158 start-page: 673 year: 2013 ident: ref_34 article-title: The genome organization of lucerne transient streak and turnip rosette sobemoviruses revisited publication-title: Arch. Virol. doi: 10.1007/s00705-012-1519-0 – volume: 86 start-page: 8247 year: 1989 ident: ref_36 article-title: Extent of N-terminal methionine excision from Escherichia coli proteins is governed by the side-chain length of the penultimate amino acid publication-title: Proc. Natl. Acad. Sci. USA doi: 10.1073/pnas.86.21.8247 – volume: 49 start-page: 610 year: 1983 ident: ref_1 article-title: Ryegrass mottle virus, a new virus from Lolium multiflorum in Japan publication-title: Jpn. J. Phytopathol. doi: 10.3186/jjphytopath.49.610 – volume: 30 start-page: 1022 year: 1997 ident: ref_56 article-title: MOLREP: An automated program for molecular replacement publication-title: J. Appl. Crystallogr. doi: 10.1107/S0021889897006766 – volume: D60 start-page: 2126 year: 2004 ident: ref_58 article-title: Coot: Model-building tools for molecular graphics publication-title: Acta Crystallogr. Sect. D Struct. Biol. Crystallogr. doi: 10.1107/S0907444904019158 – volume: 35 start-page: 395 year: 2007 ident: ref_4 article-title: The ryegrass mottle virus genome codes for a sobemovirus 3C-like serine protease and RNA-dependent RNA polymerase translated via −1 ribosomal frameshifting publication-title: Virus Genes doi: 10.1007/s11262-007-0087-y – volume: 7 start-page: 3076 year: 2015 ident: ref_11 article-title: Overview on sobemoviruses and a proposal for the creation of the family Sobemoviridae publication-title: Viruses doi: 10.3390/v7062761 – volume: 396 start-page: 106 year: 2010 ident: ref_41 article-title: Processing of SeMV polyproteins revisited publication-title: Virology doi: 10.1016/j.virol.2009.09.025 – volume: 123 start-page: 297 year: 2006 ident: ref_37 article-title: Assembly of bacteriophage Qbeta virus-like particles in yeast Saccharomyces cerevisiae and Pichia pastoris publication-title: J. Biotechnol. doi: 10.1016/j.jbiotec.2005.11.013 – volume: 434 start-page: 167715 year: 2022 ident: ref_49 article-title: A flexible and original architecture of two unrelated zinc fingers underlies the role of the multitask P1 in RYMV spread publication-title: J. Mol. Biol. doi: 10.1016/j.jmb.2022.167715 – volume: 190 start-page: 583 year: 1990 ident: ref_22 article-title: Computer-aided assignment of the 1H-NMR spectrum of the viral-protein-genome-linked polypeptide from cowpea mosaic virus publication-title: Eur. J. Biochem. doi: 10.1111/j.1432-1033.1990.tb15613.x – volume: 152 start-page: 635 year: 2007 ident: ref_6 article-title: Sobemoviruses possess a common CfMV-like genomic organization publication-title: Arch. Virol. doi: 10.1007/s00705-006-0867-z – volume: 92 start-page: 445 year: 2011 ident: ref_13 article-title: Protein-RNA linkage and post-translational modifications of two sobemovirus VPgs publication-title: J. Gen. Virol. doi: 10.1099/vir.0.026476-0 – volume: 584 start-page: 571 year: 2010 ident: ref_10 article-title: Natively unfolded nucleic acid binding P8 domain of SeMV polyprotein 2a affects the novel ATPase activity of the preceding P10 domain publication-title: FEBS Lett. doi: 10.1016/j.febslet.2009.12.003 – volume: 27 start-page: 1676 year: 2006 ident: ref_24 article-title: NMR structure of the viral peptide linked to the genome (VPg) of poliovirus publication-title: Peptides doi: 10.1016/j.peptides.2006.01.018 – volume: 53 start-page: 240 year: 1997 ident: ref_59 article-title: Refinement of macromolecular structures by the maximum-likelihood method publication-title: Acta Crystallogr. Sect. D Biol. Crystallogr. doi: 10.1107/S0907444996012255 – volume: 87 start-page: 5318 year: 2013 ident: ref_27 article-title: Structures of the compact helical core domains of feline calicivirus and murine norovirus VPg proteins publication-title: J. Virol. doi: 10.1128/JVI.03151-12 – volume: 585 start-page: 2979 year: 2011 ident: ref_8 article-title: Sobemovirus RNA linked to VPg over a threonine residue publication-title: FEBS Lett. doi: 10.1016/j.febslet.2011.08.009 – volume: Volume 1776 start-page: 19 year: 2018 ident: ref_38 article-title: Isolation and characterization of two distinct types of unmodified spherical plant sobemovirus-like particles for diagnostic and technical uses publication-title: Virus-Derived Nanoparticles for Advanced Technologies Methods and Protocols doi: 10.1007/978-1-4939-7808-3_2 – volume: 62 start-page: 24 year: 2006 ident: ref_40 article-title: Assessing protein disorder and induced folding publication-title: Proteins: Struct. Funct. Bioinform. doi: 10.1002/prot.20750 – volume: 425 start-page: 2423 year: 2013 ident: ref_46 article-title: The RYMV-encoded viral suppressor of RNA silencing P1 is a zinc-binding protein with redox-dependent flexibility publication-title: J. Mol. Biol. doi: 10.1016/j.jmb.2013.03.028 – volume: 382 start-page: 83 year: 2008 ident: ref_15 article-title: Stacking interactions of W271 and H275 of SeMV serine protease with W43 of natively unfolded VPg confer catalytic activity to protease publication-title: Virology doi: 10.1016/j.virol.2008.08.034 – volume: 68 start-page: 352 year: 2012 ident: ref_60 article-title: Towards automated crystallographic structure refinement with phenix.refine publication-title: Acta Crystallogr. Sect. D Biol. Crystallogr. doi: 10.1107/S0907444912001308 – volume: 446 start-page: 397 year: 2013 ident: ref_5 article-title: An essential fifth coding ORF in the sobemoviruses publication-title: Virology doi: 10.1016/j.virol.2013.05.033 – volume: 9 start-page: 1466 year: 2018 ident: ref_28 article-title: Insight into the interaction between RNA polymerase and VPg for murine norovirus replication publication-title: Front. Microbiol. doi: 10.3389/fmicb.2018.01466 – volume: 61 start-page: 371 year: 2010 ident: ref_47 article-title: The rice yellow mottle virus P1 protein exhibits dual functions to suppress and activate gene silencing publication-title: Plant J. doi: 10.1111/j.1365-313X.2009.04062.x – volume: 17 start-page: 21 year: 1998 ident: ref_42 article-title: The genome-linked protein (VPg) of southern bean mosaic virus is encoded by the ORF2 publication-title: Virus Genes doi: 10.1023/A:1008044715899 – volume: 9 start-page: 17 year: 2017 ident: ref_31 article-title: Glutamyl endopeptidases: The puzzle of substrate specificity publication-title: Acta Naturae doi: 10.32607/20758251-2017-9-2-17-33 – volume: 369 start-page: 364 year: 2007 ident: ref_44 article-title: The three-dimensional structure of ryegrass mottle virus at 2.9 Å resolution publication-title: Virology doi: 10.1016/j.virol.2007.07.028 – volume: 292 start-page: 195 year: 1999 ident: ref_50 article-title: Protein secondary structure prediction based on position-specific scoring matrices publication-title: J. Mol. Biol. doi: 10.1006/jmbi.1999.3091 – volume: 64 start-page: 215 year: 2010 ident: ref_17 article-title: Expression and characterisation of the ryegrass mottle virus non-structural proteins publication-title: Latv. Acad. Sciences. Sect. B. Nat. Exact Appl. Sci. – ident: ref_2 – volume: 305 start-page: 567 year: 2001 ident: ref_35 article-title: Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes publication-title: J. Mol. Biol. doi: 10.1006/jmbi.2000.4315 – volume: 59 start-page: 4663 year: 2020 ident: ref_20 article-title: Aromatic interactions drive the coupled folding and binding of the intrinsically disordered Sesbania mosaic virus VPg protein publication-title: Biochemistry doi: 10.1021/acs.biochem.0c00721 – volume: 82 start-page: 9577 year: 2008 ident: ref_26 article-title: The crystal structure of coxsackievirus B3 RNA-dependent RNA polymerase in complex with its protein primer VPg confirms the existence of a second VPg binding site on Picornaviridae polymerases publication-title: J. Virol. doi: 10.1128/JVI.00631-08 – volume: 67 start-page: 271 year: 2011 ident: ref_53 article-title: iMOSFLM: A new graphical interface for diffraction-image processing with MOSFLM publication-title: Acta Crystallogr. Sect. D Biol. Crystallogr. doi: 10.1107/S0907444910048675 – volume: 46 start-page: W296 year: 2018 ident: ref_57 article-title: Swiss-model: Homology modelling of protein structures and complexes publication-title: Nucleic Acids Res. doi: 10.1093/nar/gky427 – ident: ref_19 doi: 10.1371/journal.ppat.0030180 – volume: 87 start-page: 5755 year: 2013 ident: ref_25 article-title: Crystal structure of enterovirus 71 RNA-dependent RNA polymerase complexed with its protein primer VPg: Implication for a trans mechanism of VPg uridylylation publication-title: J. Virol. doi: 10.1128/JVI.02733-12 – volume: 10 start-page: 1171 year: 2019 ident: ref_45 article-title: A role for zinc in plant defense against pathogens and herbivores publication-title: Front. Plant Sci. doi: 10.3389/fpls.2019.01171 – volume: 283 start-page: 213 year: 2008 ident: ref_18 article-title: Virulence factor of potato virus y, genome-attached terminal protein VPg, is a highly disordered protein publication-title: J. Biol. Chem. doi: 10.1074/jbc.M705666200 – volume: 377 start-page: 280 year: 2008 ident: ref_21 article-title: Potato virus a genome-linked protein VPg is an intrinsically disordered molten globule-like protein with a hydrophobic core publication-title: Virology doi: 10.1016/j.virol.2008.04.025 – volume: 236 start-page: 287 year: 1988 ident: ref_9 article-title: Sobemovirus genome appears to encode a serine protease related to cysteine proteases of picornaviruses publication-title: FEBS Lett. doi: 10.1016/0014-5793(88)80039-5 – volume: 6 start-page: 23 year: 2009 ident: ref_16 article-title: Intrinsic disorder in viral proteins genome-linked: Experimental and predictive analyses publication-title: Virol. J. doi: 10.1186/1743-422X-6-23 – volume: 346 start-page: 440 year: 2006 ident: ref_32 article-title: Crystal structure of the serine protease domain of Sesbania mosaic virus polyprotein and mutational analysis of residues forming the S1-binding pocket publication-title: Virology doi: 10.1016/j.virol.2005.11.011
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Snippet	Sobemoviruses encode serine-like 3C proteases (Pro) that participate in the processing and maturation of other virus-encoded proteins. Its cis and trans... Sobemoviruses encode serine-like 3C proteases (Pro) that participate in the processing and maturation of other virus-encoded proteins. Its and activity is...
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SubjectTerms	3C Viral Proteases Amino Acid Sequence Endopeptidases - metabolism Enzymes Genomes Genomics Gram-positive bacteria Lolium - metabolism NMR Nuclear magnetic resonance Peptide Hydrolases - metabolism Peptides Proteins Proteolysis RNA polymerase RNA Viruses - metabolism Scientific equipment and supplies industry Serine Serine - metabolism Viral Proteins - metabolism Viruses
Title	VPg Impact on Ryegrass Mottle Virus Serine-like 3C Protease Proteolysis and Structure
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