2jl9: Difference between revisions

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-{{Seed}}
-[[Image:2jl9.png|left|200px]]
-<!--
+==Structural explanation for the role of Mn in the activity of phi6 RNA- dependent RNA polymerase==
-The line below this paragraph, containing "STRUCTURE_2jl9", creates the "Structure Box" on the page.
+<StructureSection load='2jl9' size='340' side='right'caption='[[2jl9]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2jl9]] is a 3 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=2JL9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JL9 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.2&#8491;</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=2jl9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jl9 OCA], [https://pdbe.org/2jl9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jl9 RCSB], [https://www.ebi.ac.uk/pdbsum/2jl9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jl9 ProSAT]</span></td></tr>
-{{STRUCTURE_2jl9|  PDB=2jl9  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RDRP_BPPH6 RDRP_BPPH6]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The biological role of manganese (Mn(2+)) has been a long-standing puzzle, since at low concentrations it activates several polymerases whilst at higher concentrations it inhibits. Viral RNA polymerases possess a common architecture, reminiscent of a closed right hand. The RNA-dependent RNA polymerase (RdRp) of bacteriophage 6 is one of the best understood examples of this important class of polymerases. We have probed the role of Mn(2+) by biochemical, biophysical and structural analyses of the wild-type enzyme and of a mutant form with an altered Mn(2+)-binding site (E491 to Q). The E491Q mutant has much reduced affinity for Mn(2+), reduced RNA binding and a compromised elongation rate. Loss of Mn(2+) binding structurally stabilizes the enzyme. These data and a re-examination of the structures of other viral RNA polymerases clarify the role of manganese in the activation of polymerization: Mn(2+) coordination of a catalytic aspartate is necessary to allow the active site to properly engage with the triphosphates of the incoming NTPs. The structural flexibility caused by Mn(2+) is also important for the enzyme dynamics, explaining the requirement for manganese throughout RNA polymerization.
-===STRUCTURAL EXPLANATION FOR THE ROLE OF MN IN THE ACTIVITY OF PHI6 RNA-DEPENDENT RNA POLYMERASE===
+Structural explanation for the role of Mn2+ in the activity of {phi}6 RNA-dependent RNA polymerase.,Poranen MM, Salgado PS, Koivunen MR, Wright S, Bamford DH, Stuart DI, Grimes JM Nucleic Acids Res. 2008 Oct 21. PMID:18940872<ref>PMID:18940872</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2jl9" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18940872}}, adds the Publication Abstract to the page
+*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18940872 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18940872}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-JL9 is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Pseudomonas_phage_phi6 Pseudomonas phage phi6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JL9 OCA].
+[[Category: Pseudomonas virus phi6]]
+[[Category: Bamford DH]]
-==Reference==
+[[Category: Grimes JM]]
-Structural explanation for the role of Mn2+ in the activity of {phi}6 RNA-dependent RNA polymerase., Poranen MM, Salgado PS, Koivunen MR, Wright S, Bamford DH, Stuart DI, Grimes JM, Nucleic Acids Res. 2008 Oct 21. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18940872 18940872]
+[[Category: Koivunen MRL]]
-[[Category: Pseudomonas phage phi6]]
+[[Category: Poranen MM]]
-[[Category: RNA-directed RNA polymerase]]
+[[Category: Salgado PS]]
-[[Category: Bamford, D H.]]
+[[Category: Stuart DI]]
-[[Category: Grimes, J M.]]
+[[Category: Wright S]]
-[[Category: Koivunen, M R.L.]]
-[[Category: Poranen, M M.]]
-[[Category: Salgado, P S.]]
-[[Category: Stuart, D I.]]
-[[Category: Wright, S.]]
-[[Category: Magnesium]]
-[[Category: Manganese]]
-[[Category: Metal-binding]]
-[[Category: Nucleotide-binding]]
-[[Category: Nucleotidyltransferase]]
-[[Category: Oligonucleotide]]
-[[Category: Polymerase]]
-[[Category: Polymerase/complex]]
-[[Category: Rna replication]]
-[[Category: Rna-dependent rna polymerase]]
-[[Category: Rna-directed rna polymerase]]
-[[Category: Transferase]]
-[[Category: Virion]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Nov 26 20:05:50 2008''