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| | <StructureSection load='4x2z' size='340' side='right'caption='[[4x2z]], [[Resolution|resolution]] 2.15Å' scene=''> | | <StructureSection load='4x2z' size='340' side='right'caption='[[4x2z]], [[Resolution|resolution]] 2.15Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4x2z]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Avian_infectious_bronchitis_virus_(strain_beaudette) Avian infectious bronchitis virus (strain beaudette)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X2Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4X2Z FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4x2z]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Avian_infectious_bronchitis_virus_(strain_Beaudette) Avian infectious bronchitis virus (strain Beaudette)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4X2Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4X2Z FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4x2z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x2z OCA], [https://pdbe.org/4x2z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4x2z RCSB], [https://www.ebi.ac.uk/pdbsum/4x2z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4x2z ProSAT]</span></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rep, 1a-1b ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11122 Avian infectious bronchitis virus (strain Beaudette)])</td></tr>
| + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4x2z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4x2z OCA], [http://pdbe.org/4x2z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4x2z RCSB], [http://www.ebi.ac.uk/pdbsum/4x2z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4x2z ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/R1AB_IBVB R1AB_IBVB]] The replicase polyprotein of coronaviruses is a multifunctional protein: it contains the activities necessary for the transcription of negative stranded RNA, leader RNA, subgenomic mRNAs and progeny virion RNA as well as proteinases responsible for the cleavage of the polyprotein into functional products.<ref>PMID:11413307</ref> The papain-like proteinase (PL-PRO) is responsible for the cleavages located at the N-terminus of replicase polyprotein. Activity of PL-PRO is dependent on zinc (By similarity).<ref>PMID:11413307</ref> The main proteinase 3CL-PRO is responsible for the majority of cleavages as it cleaves the C-terminus of replicase polyprotein at 11 sites. Recognizes substrates containing the core sequence [ILMVF]-Q-|-[SGACN]. Inhibited by the substrate-analog Cbz-Val-Asn-Ser-Thr-Leu-Gln-CMK (By similarity).<ref>PMID:11413307</ref> The peptide p16 might be involved in the EGF signaling pathway.<ref>PMID:11413307</ref> The helicase which contains a zinc finger structure displays RNA and DNA duplex-unwinding activities with 5' to 3' polarity. Its ATPase activity is strongly stimulated by poly(U), poly(dT), poly(C), poly(dA), but not by poly(G) (By similarity).<ref>PMID:11413307</ref> The exoribonuclease acts on both ssRNA and dsRNA in a 3' to 5' direction (By similarity).<ref>PMID:11413307</ref> Nsp7-nsp8 hexadecamer may possibly confer processivity to the polymerase, maybe by binding to dsRNA or by producing primers utilized by the latter (By similarity).<ref>PMID:11413307</ref> Nsp9 is a ssRNA-binding protein (By similarity).<ref>PMID:11413307</ref> NendoU is a Mn(2+)-dependent, uridylate-specific enzyme, which leaves 2'-3'-cyclic phosphates 5' to the cleaved bond (By similarity).<ref>PMID:11413307</ref> | + | [https://www.uniprot.org/uniprot/R1AB_IBVB R1AB_IBVB] The replicase polyprotein of coronaviruses is a multifunctional protein: it contains the activities necessary for the transcription of negative stranded RNA, leader RNA, subgenomic mRNAs and progeny virion RNA as well as proteinases responsible for the cleavage of the polyprotein into functional products.<ref>PMID:11413307</ref> The papain-like proteinase (PL-PRO) is responsible for the cleavages located at the N-terminus of replicase polyprotein. Activity of PL-PRO is dependent on zinc (By similarity).<ref>PMID:11413307</ref> The main proteinase 3CL-PRO is responsible for the majority of cleavages as it cleaves the C-terminus of replicase polyprotein at 11 sites. Recognizes substrates containing the core sequence [ILMVF]-Q-|-[SGACN]. Inhibited by the substrate-analog Cbz-Val-Asn-Ser-Thr-Leu-Gln-CMK (By similarity).<ref>PMID:11413307</ref> The peptide p16 might be involved in the EGF signaling pathway.<ref>PMID:11413307</ref> The helicase which contains a zinc finger structure displays RNA and DNA duplex-unwinding activities with 5' to 3' polarity. Its ATPase activity is strongly stimulated by poly(U), poly(dT), poly(C), poly(dA), but not by poly(G) (By similarity).<ref>PMID:11413307</ref> The exoribonuclease acts on both ssRNA and dsRNA in a 3' to 5' direction (By similarity).<ref>PMID:11413307</ref> Nsp7-nsp8 hexadecamer may possibly confer processivity to the polymerase, maybe by binding to dsRNA or by producing primers utilized by the latter (By similarity).<ref>PMID:11413307</ref> Nsp9 is a ssRNA-binding protein (By similarity).<ref>PMID:11413307</ref> NendoU is a Mn(2+)-dependent, uridylate-specific enzyme, which leaves 2'-3'-cyclic phosphates 5' to the cleaved bond (By similarity).<ref>PMID:11413307</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Nonstructural protein|Nonstructural protein]] | + | *[[Nonstructural protein 3D structures|Nonstructural protein 3D structures]] |
| - | *[[Virus protease|Virus protease]] | + | *[[Virus protease 3D structures|Virus protease 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Kong, L]] | + | [[Category: Kong L]] |
| - | [[Category: Lou, Z]] | + | [[Category: Lou Z]] |
| - | [[Category: Rao, Z]] | + | [[Category: Rao Z]] |
| - | [[Category: Shaw, N]] | + | [[Category: Shaw N]] |
| - | [[Category: Yan, L]] | + | [[Category: Yan L]] |
| - | [[Category: Coronavirus]]
| + | |
| - | [[Category: De-ubiquitination]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Ibv]]
| + | |
| - | [[Category: Plpro]]
| + | |
| Structural highlights
Function
R1AB_IBVB The replicase polyprotein of coronaviruses is a multifunctional protein: it contains the activities necessary for the transcription of negative stranded RNA, leader RNA, subgenomic mRNAs and progeny virion RNA as well as proteinases responsible for the cleavage of the polyprotein into functional products.[1] The papain-like proteinase (PL-PRO) is responsible for the cleavages located at the N-terminus of replicase polyprotein. Activity of PL-PRO is dependent on zinc (By similarity).[2] The main proteinase 3CL-PRO is responsible for the majority of cleavages as it cleaves the C-terminus of replicase polyprotein at 11 sites. Recognizes substrates containing the core sequence [ILMVF]-Q-|-[SGACN]. Inhibited by the substrate-analog Cbz-Val-Asn-Ser-Thr-Leu-Gln-CMK (By similarity).[3] The peptide p16 might be involved in the EGF signaling pathway.[4] The helicase which contains a zinc finger structure displays RNA and DNA duplex-unwinding activities with 5' to 3' polarity. Its ATPase activity is strongly stimulated by poly(U), poly(dT), poly(C), poly(dA), but not by poly(G) (By similarity).[5] The exoribonuclease acts on both ssRNA and dsRNA in a 3' to 5' direction (By similarity).[6] Nsp7-nsp8 hexadecamer may possibly confer processivity to the polymerase, maybe by binding to dsRNA or by producing primers utilized by the latter (By similarity).[7] Nsp9 is a ssRNA-binding protein (By similarity).[8] NendoU is a Mn(2+)-dependent, uridylate-specific enzyme, which leaves 2'-3'-cyclic phosphates 5' to the cleaved bond (By similarity).[9]
Publication Abstract from PubMed
Papain-like protease (PLpro) of coronaviruses (CoVs) carries out proteolytic maturation of non-structural proteins that play a role in replication of the virus and performs deubiquitination of host cell factors to scuttle antiviral responses. Avian infectious bronchitis virus (IBV), the causative agent of bronchitis in chicken that results in huge economic losses every year in the poultry industry globally, encodes a PLpro. The substrate specificities of this PLpro are not clearly understood. Here, we show that IBV PLpro can degrade Lys(48)- and Lys(63)-linked polyubiquitin chains to monoubiquitin but not linear polyubiquitin. To explain the substrate specificities, we have solved the crystal structure of PLpro from IBV at 2.15-A resolution. The overall structure is reminiscent of the structure of severe acute respiratory syndrome CoV PLpro. However, unlike the severe acute respiratory syndrome CoV PLpro that lacks blocking loop (BL) 1 of deubiquitinating enzymes, the IBV PLpro has a short BL1-like loop. Access to a conserved catalytic triad consisting of Cys(101), His(264), and Asp(275) is regulated by the flexible BL2. A model of ubiquitin-bound IBV CoV PLpro brings out key differences in substrate binding sites of PLpros. In particular, P3 and P4 subsites as well as residues interacting with the beta-barrel of ubiquitin are different, suggesting different catalytic efficiencies and substrate specificities. We show that IBV PLpro cleaves peptide substrates KKAG-7-amino-4-methylcoumarin and LRGG-7-amino-4-methylcoumarin with different catalytic efficiencies. These results demonstrate that substrate specificities of IBV PLpro are different from other PLpros and that IBV PLpro might target different ubiquitinated host factors to aid the propagation of the virus.
Structural View and Substrate Specificity of Papain-like Protease from Avian Infectious Bronchitis Virus.,Kong L, Shaw N, Yan L, Lou Z, Rao Z J Biol Chem. 2015 Mar 13;290(11):7160-8. doi: 10.1074/jbc.M114.628636. Epub 2015 , Jan 21. PMID:25609249[10]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Liu C, Xu HY, Liu DX. Induction of caspase-dependent apoptosis in cultured cells by the avian coronavirus infectious bronchitis virus. J Virol. 2001 Jul;75(14):6402-9. PMID:11413307 doi:http://dx.doi.org/10.1128/JVI.75.14.6402-6409.2001
- ↑ Liu C, Xu HY, Liu DX. Induction of caspase-dependent apoptosis in cultured cells by the avian coronavirus infectious bronchitis virus. J Virol. 2001 Jul;75(14):6402-9. PMID:11413307 doi:http://dx.doi.org/10.1128/JVI.75.14.6402-6409.2001
- ↑ Liu C, Xu HY, Liu DX. Induction of caspase-dependent apoptosis in cultured cells by the avian coronavirus infectious bronchitis virus. J Virol. 2001 Jul;75(14):6402-9. PMID:11413307 doi:http://dx.doi.org/10.1128/JVI.75.14.6402-6409.2001
- ↑ Liu C, Xu HY, Liu DX. Induction of caspase-dependent apoptosis in cultured cells by the avian coronavirus infectious bronchitis virus. J Virol. 2001 Jul;75(14):6402-9. PMID:11413307 doi:http://dx.doi.org/10.1128/JVI.75.14.6402-6409.2001
- ↑ Liu C, Xu HY, Liu DX. Induction of caspase-dependent apoptosis in cultured cells by the avian coronavirus infectious bronchitis virus. J Virol. 2001 Jul;75(14):6402-9. PMID:11413307 doi:http://dx.doi.org/10.1128/JVI.75.14.6402-6409.2001
- ↑ Liu C, Xu HY, Liu DX. Induction of caspase-dependent apoptosis in cultured cells by the avian coronavirus infectious bronchitis virus. J Virol. 2001 Jul;75(14):6402-9. PMID:11413307 doi:http://dx.doi.org/10.1128/JVI.75.14.6402-6409.2001
- ↑ Liu C, Xu HY, Liu DX. Induction of caspase-dependent apoptosis in cultured cells by the avian coronavirus infectious bronchitis virus. J Virol. 2001 Jul;75(14):6402-9. PMID:11413307 doi:http://dx.doi.org/10.1128/JVI.75.14.6402-6409.2001
- ↑ Liu C, Xu HY, Liu DX. Induction of caspase-dependent apoptosis in cultured cells by the avian coronavirus infectious bronchitis virus. J Virol. 2001 Jul;75(14):6402-9. PMID:11413307 doi:http://dx.doi.org/10.1128/JVI.75.14.6402-6409.2001
- ↑ Liu C, Xu HY, Liu DX. Induction of caspase-dependent apoptosis in cultured cells by the avian coronavirus infectious bronchitis virus. J Virol. 2001 Jul;75(14):6402-9. PMID:11413307 doi:http://dx.doi.org/10.1128/JVI.75.14.6402-6409.2001
- ↑ Kong L, Shaw N, Yan L, Lou Z, Rao Z. Structural View and Substrate Specificity of Papain-like Protease from Avian Infectious Bronchitis Virus. J Biol Chem. 2015 Mar 13;290(11):7160-8. doi: 10.1074/jbc.M114.628636. Epub 2015 , Jan 21. PMID:25609249 doi:http://dx.doi.org/10.1074/jbc.M114.628636
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