3ne6: Difference between revisions

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-[[Image:3ne6.jpg|left|200px]]
-<!--
+==RB69 DNA Polymerase (S565G/Y567A) Ternary Complex with dCTP Opposite dG==
-The line below this paragraph, containing "STRUCTURE_3ne6", creates the "Structure Box" on the page.
+<StructureSection load='3ne6' size='340' side='right'caption='[[3ne6]], [[Resolution|resolution]] 2.00&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'>[[3ne6]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_RB69 Escherichia phage RB69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NE6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NE6 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]] 2.001&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>
-{{STRUCTURE_3ne6|  PDB=3ne6  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ne6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ne6 OCA], [https://pdbe.org/3ne6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ne6 RCSB], [https://www.ebi.ac.uk/pdbsum/3ne6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ne6 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DPOL_BPR69 DPOL_BPR69] This polymerase possesses two enzymatic activities: DNA synthesis (polymerase) and an exonucleolytic activity that degrades single stranded DNA in the 3'- to 5'-direction.
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+We have previously observed that stepwise replacement of amino acid residues in the nascent base-pair binding pocket of RB69 DNA polymerase (RB69pol) with Ala or Gly expanded the space in this pocket, resulting in a progressive increase in misincorporation. However, in vivo results with similar RB69pol nascent base-pair binding pocket mutants showed that mutation rates, as determined by the T4 phage rI forward assay and rII reversion assay, were significantly lower for the RB69pol S565G/Y567A double mutant than for the Y567A single mutant, the opposite of what we would have predicted. To investigate the reasons for this unexpected result, we have determined the pre-steady-state kinetic parameters and crystal structures of relevant ternary complexes. We found that the S565G/Y567A mutant generally had greater base selectivity than the Y567A mutant and that the kinetic parameters for dNMP insertion, excision of the 3'-terminal nucleotide residue, and primer extension beyond a mispair differed not only between these two mutants but also between the two highly mutable sequences in the T4 rI complementary strand. Comparison of the crystal structures of these two mutants with correct and incorrect incoming dNTPs provides insight into the unexpected increase in the fidelity of the S565G/Y567A double mutant. Taken together, the kinetic and structural results provide a basis for integrating and interpreting in vivo and in vitro observations.
-===RB69 DNA Polymerase (S565G/Y567A) Ternary Complex with dCTP Opposite dG===
+Variation in Mutation Rates Caused by RB69pol Fidelity Mutants Can Be Rationalized on the Basis of Their Kinetic Behavior and Crystal Structures.,Xia S, Wang M, Lee HR, Sinha A, Blaha G, Christian T, Wang J, Konigsberg W J Mol Biol. 2011 Jan 7. PMID:21216248<ref>PMID:21216248</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3ne6" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_21216248}}, adds the Publication Abstract to the page
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 21216248 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_21216248}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Escherichia phage RB69]]
-[[3ne6]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_rb69 Enterobacteria phage rb69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NE6 OCA].
+[[Category: Large Structures]]
+[[Category: Konigsberg WH]]
-==Reference==
+[[Category: Wang J]]
-<ref group="xtra">PMID:21216248</ref><references group="xtra"/>
+[[Category: Wang M]]
-[[Category: DNA-directed DNA polymerase]]
-[[Category: Enterobacteria phage rb69]]
-[[Category: Konigsberg, W H.]]
-[[Category: Wang, J.]]
-[[Category: Wang, M.]]