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| | ==Crystal structure of IBV X-domain at pH 5.6== | | ==Crystal structure of IBV X-domain at pH 5.6== |
| - | <StructureSection load='3eke' size='340' side='right' caption='[[3eke]], [[Resolution|resolution]] 2.10Å' scene=''> | + | <StructureSection load='3eke' size='340' side='right'caption='[[3eke]], [[Resolution|resolution]] 2.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3eke]] 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=3EKE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EKE FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3eke]] 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=3EKE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EKE FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ejf|3ejf]], [[3ejg|3ejg]]</td></tr> | + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ejf|3ejf]], [[3ejg|3ejg]]</div></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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rep, 1a-1b ([https://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=3eke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eke OCA], [http://pdbe.org/3eke PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3eke RCSB], [http://www.ebi.ac.uk/pdbsum/3eke PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3eke ProSAT]</span></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=3eke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eke OCA], [https://pdbe.org/3eke PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3eke RCSB], [https://www.ebi.ac.uk/pdbsum/3eke PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3eke 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> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | + | [[Category: Large Structures]] |
| | [[Category: Hansen, G]] | | [[Category: Hansen, G]] |
| | [[Category: Hilgenfeld, R]] | | [[Category: Hilgenfeld, R]] |
| 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]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
The polyproteins of coronaviruses are cleaved by viral proteases into at least 15 nonstructural proteins (Nsps). Consisting of five domains, Nsp3 is the largest of these (180-210 kDa). Among these domains, the so-called X-domain is believed to act as ADP-ribose-1-phosphate phosphatase or to bind poly(ADP-ribose). However, here we show that the X-domain of Infectious Bronchitis Virus (strain Beaudette), a Group-3 coronavirus, fails to bind ADP-ribose. This is explained on the basis of the crystal structure of the protein, determined at two different pH values. For comparison, we also describe the crystal structure of the homologous X-domain from Human Coronavirus 229E, a Group-1 coronavirus, which does bind ADP-ribose.
Crystal structures of the X-domains of a Group-1 and a Group-3 coronavirus reveal that ADP-ribose-binding may not be a conserved property.,Piotrowski Y, Hansen G, Boomaars-van der Zanden AL, Snijder EJ, Gorbalenya AE, Hilgenfeld R Protein Sci. 2009 Jan;18(1):6-16. PMID:19177346[10]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
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
- ↑ Piotrowski Y, Hansen G, Boomaars-van der Zanden AL, Snijder EJ, Gorbalenya AE, Hilgenfeld R. Crystal structures of the X-domains of a Group-1 and a Group-3 coronavirus reveal that ADP-ribose-binding may not be a conserved property. Protein Sci. 2009 Jan;18(1):6-16. PMID:19177346 doi:10.1002/pro.15
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