4a8q: Difference between revisions
New page: '''Unreleased structure''' The entry 4a8q is ON HOLD Authors: Wright, S., Poranen, M.M., Bamford, D.H., Stuart, D.I., Grimes, J.M. Description: Non-Catalytic Ions Direct the RNA-Depend... |
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==Non-Catalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial dsRNA virus phi6 from De Novo Initiation to Elongation== | |||
<StructureSection load='4a8q' size='340' side='right'caption='[[4a8q]], [[Resolution|resolution]] 3.06Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4a8q]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_virus_phi6 Pseudomonas virus phi6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4A8Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4A8Q FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.06Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=4a8q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4a8q OCA], [https://pdbe.org/4a8q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4a8q RCSB], [https://www.ebi.ac.uk/pdbsum/4a8q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4a8q ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/RDRP_BPPH6 RDRP_BPPH6] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
RNA-dependent RNA polymerases (RdRps) are key to the replication of RNA viruses. A common divalent cation binding site, distinct from the positions of catalytic ions, has been identified in many viral RdRps. We have applied biochemical, biophysical, and structural approaches to show how the RdRp from bacteriophage varphi6 uses the bound noncatalytic Mn(2+) to facilitate the displacement of the C-terminal domain during the transition from initiation to elongation. We find that this displacement releases the noncatalytic Mn(2+), which must be replaced for elongation to occur. By inserting a dysfunctional Mg(2+) at this site, we captured two nucleoside triphosphates within the active site in the absence of Watson-Crick base pairing with template and mapped movements of divalent cations during preinitiation. These structures refine the pathway from preinitiation through initiation to elongation for the RNA-dependent RNA polymerization reaction, explain the role of the noncatalytic divalent cation in 6 RdRp, and pinpoint the previously unresolved Mn(2+)-dependent step in replication. | |||
Noncatalytic ions direct the RNA-dependent RNA polymerase of bacterial double-stranded RNA virus varphi6 from de novo initiation to elongation.,Wright S, Poranen MM, Bamford DH, Stuart DI, Grimes JM J Virol. 2012 Mar;86(5):2837-49. Epub 2011 Dec 28. PMID:22205747<ref>PMID:22205747</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4a8q" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[RNA polymerase 3D structures|RNA polymerase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Pseudomonas virus phi6]] | |||
[[Category: Bamford DH]] | |||
[[Category: Grimes JM]] | |||
[[Category: Poranen MM]] | |||
[[Category: Stuart DI]] | |||
[[Category: Wright S]] | |||
Latest revision as of 13:48, 9 May 2024
Non-Catalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial dsRNA virus phi6 from De Novo Initiation to ElongationNon-Catalytic Ions Direct the RNA-Dependent RNA Polymerase of Bacterial dsRNA virus phi6 from De Novo Initiation to Elongation
Structural highlights
FunctionPublication Abstract from PubMedRNA-dependent RNA polymerases (RdRps) are key to the replication of RNA viruses. A common divalent cation binding site, distinct from the positions of catalytic ions, has been identified in many viral RdRps. We have applied biochemical, biophysical, and structural approaches to show how the RdRp from bacteriophage varphi6 uses the bound noncatalytic Mn(2+) to facilitate the displacement of the C-terminal domain during the transition from initiation to elongation. We find that this displacement releases the noncatalytic Mn(2+), which must be replaced for elongation to occur. By inserting a dysfunctional Mg(2+) at this site, we captured two nucleoside triphosphates within the active site in the absence of Watson-Crick base pairing with template and mapped movements of divalent cations during preinitiation. These structures refine the pathway from preinitiation through initiation to elongation for the RNA-dependent RNA polymerization reaction, explain the role of the noncatalytic divalent cation in 6 RdRp, and pinpoint the previously unresolved Mn(2+)-dependent step in replication. Noncatalytic ions direct the RNA-dependent RNA polymerase of bacterial double-stranded RNA virus varphi6 from de novo initiation to elongation.,Wright S, Poranen MM, Bamford DH, Stuart DI, Grimes JM J Virol. 2012 Mar;86(5):2837-49. Epub 2011 Dec 28. PMID:22205747[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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