5c94

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Revision as of 06:24, 7 June 2023

Infectious bronchitis virus nsp9

Structural highlights

5c94 is a 1 chain structure with sequence from Avian infectious bronchitis virus (strain M41). Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

R1AB_IBVM 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. 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). 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. Also contains an ADP-ribose-1-phosphate (ADRP)-binding function (By similarity).[PROSITE-ProRule:PRU00772] The peptide p16 might be involved in the EGF signaling pathway. 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). The exoribonuclease acts on both ssRNA and dsRNA in a 3' to 5' direction. Nsp7-nsp8 hexadecamer may possibly confer processivity to the polymerase, maybe by binding to dsRNA or by producing primers utilized by the latter. Nsp9 is a ssRNA-binding protein. NendoU is a Mn(2+)-dependent, uridylate-specific enzyme, which leaves 2'-3'-cyclic phosphates 5' to the cleaved bond.

Publication Abstract from PubMed

The potential for infection by coronaviruses (CoVs) has become a serious concern with the recent emergence of Middle East respiratory syndrome and severe acute respiratory syndrome (SARS) in the human population. CoVs encode two large polyproteins, which are then processed into 15-16 nonstructural proteins (nsps) that make significant contributions to viral replication and transcription by assembling the RNA replicase complex. Among them, nsp9 plays an essential role in viral replication by forming a homodimer that binds single-stranded RNA. Thus, disrupting nsp9 dimerization is a potential anti-CoV therapy. However, different nsp9 dimer forms have been reported for alpha- and beta-CoVs, and no structural information is available for gamma-CoVs. Here we determined the crystal structure of nsp9 from the avian infectious bronchitis virus (IBV), a representative gamma-CoV that affects the economy of the poultry industry because it can infect domestic fowl. IBV nsp9 forms a homodimer via interactions across a hydrophobic interface, which consists of two parallel alpha helices near the carboxy terminus of the protein. The IBV nsp9 dimer resembles that of SARS-CoV nsp9, indicating that this type of dimerization is conserved among all CoVs. This makes disruption of the dimeric interface an excellent strategy for developing anti-CoV therapies. To facilitate this effort, we characterized the roles of six conserved residues on this interface using site-directed mutagenesis and a multitude of biochemical and biophysical methods. We found that three residues are critical for nsp9 dimerization and its abitlity to bind RNA.

Structural basis for dimerization and RNA binding of avian infectious bronchitis virus nsp9.,Hu T, Chen C, Li H, Dou Y, Zhou M, Lu D, Zong Q, Li Y, Yang C, Zhong Z, Singh N, Hu H, Zhang R, Yang H, Su D Protein Sci. 2017 May;26(5):1037-1048. doi: 10.1002/pro.3150. Epub 2017 Apr 20. PMID:28257598^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Hu T, Chen C, Li H, Dou Y, Zhou M, Lu D, Zong Q, Li Y, Yang C, Zhong Z, Singh N, Hu H, Zhang R, Yang H, Su D. Structural basis for dimerization and RNA binding of avian infectious bronchitis virus nsp9. Protein Sci. 2017 May;26(5):1037-1048. doi: 10.1002/pro.3150. Epub 2017 Apr 20. PMID:28257598 doi:http://dx.doi.org/10.1002/pro.3150

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5c94"

Categories: Large Structures | Chen C | Dou Y | Su D | Yang H

@@ Line 3: / Line 3: @@
 <StructureSection load='5c94' size='340' side='right'caption='[[5c94]], [[Resolution|resolution]] 2.44&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5c94]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Avian_infectious_bronchitis_virus_(strain_m41) Avian infectious bronchitis virus (strain m41)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C94 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5C94 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5c94]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Avian_infectious_bronchitis_virus_(strain_M41) Avian infectious bronchitis virus (strain M41)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C94 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5C94 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></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=11127 Avian infectious bronchitis virus (strain M41)])</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=5c94 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c94 OCA], [https://pdbe.org/5c94 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5c94 RCSB], [https://www.ebi.ac.uk/pdbsum/5c94 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5c94 ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5c94 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c94 OCA], [http://pdbe.org/5c94 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5c94 RCSB], [http://www.ebi.ac.uk/pdbsum/5c94 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5c94 ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/R1AB_IBVM R1AB_IBVM]] 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.  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).  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. Also contains an ADP-ribose-1''-phosphate (ADRP)-binding function (By similarity).[PROSITE-ProRule:PRU00772]  The peptide p16 might be involved in the EGF signaling pathway.  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).  The exoribonuclease acts on both ssRNA and dsRNA in a 3' to 5' direction.  Nsp7-nsp8 hexadecamer may possibly confer processivity to the polymerase, maybe by binding to dsRNA or by producing primers utilized by the latter.  Nsp9 is a ssRNA-binding protein.  NendoU is a Mn(2+)-dependent, uridylate-specific enzyme, which leaves 2'-3'-cyclic phosphates 5' to the cleaved bond.
+[https://www.uniprot.org/uniprot/R1AB_IBVM R1AB_IBVM] 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.  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).  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. Also contains an ADP-ribose-1''-phosphate (ADRP)-binding function (By similarity).[PROSITE-ProRule:PRU00772]  The peptide p16 might be involved in the EGF signaling pathway.  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).  The exoribonuclease acts on both ssRNA and dsRNA in a 3' to 5' direction.  Nsp7-nsp8 hexadecamer may possibly confer processivity to the polymerase, maybe by binding to dsRNA or by producing primers utilized by the latter.  Nsp9 is a ssRNA-binding protein.  NendoU is a Mn(2+)-dependent, uridylate-specific enzyme, which leaves 2'-3'-cyclic phosphates 5' to the cleaved bond.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 23: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Chen, C]]
+[[Category: Chen C]]
-[[Category: Dou, Y]]
+[[Category: Dou Y]]
-[[Category: Su, D]]
+[[Category: Su D]]
-[[Category: Yang, H]]
+[[Category: Yang H]]
-[[Category: Coronaviurs rna replicase]]
-[[Category: Homodimer]]
-[[Category: Hydrolase]]
-[[Category: Nsp]]
-[[Category: Rna binding protein]]

5c94

From Proteopedia

Revision as of 06:24, 7 June 2023

Infectious bronchitis virus nsp9

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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