3scx: Difference between revisions

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-[[Image:3scx.png|left|200px]]
+==RB69 DNA Polymerase Triple Mutant(L561A/S565G/Y567A) Ternary Complex with dUpNpp and a Deoxy-terminated Primer in the Presence of Ca2+==
+<StructureSection load='3scx' size='340' side='right' caption='[[3scx]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3scx]] 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=3SCX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SCX FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DUP:2-DEOXYURIDINE+5-ALPHA,BETA-IMIDO-TRIPHOSPHATE'>DUP</scene></td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3nci|3nci]], [[3cfo|3cfo]], [[3cfp|3cfp]], [[3cfr|3cfr]], [[3s9h|3s9h]], [[3si6|3si6]], [[3sjj|3sjj]], [[3snn|3snn]]</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">43, gp43 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12353 Enterobacteria phage RB69])</td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></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=3scx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3scx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3scx RCSB], [http://www.ebi.ac.uk/pdbsum/3scx PDBsum]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+We have captured a preinsertion ternary complex of RB69 DNA polymerase (RB69pol) containing the 3' hydroxyl group at the terminus of an extendable primer (ptO3') and a nonhydrolyzable 2'-deoxyuridine 5'-alpha,beta-substituted triphosphate, dUpXpp, where X is either NH or CH(2), opposite a complementary templating dA nucleotide residue. Here we report four structures of these complexes formed by three different RB69pol variants with catalytically inert Ca(2+) and four other structures with catalytically competent Mn(2+) or Mg(2+). These structures provide new insights into why the complete divalent metal-ion coordination complexes at the A and B sites are required for nucleotidyl transfer. They show that the metal ion in the A site brings ptO3' close to the alpha-phosphorus atom (Palpha) of the incoming dNTP to enable phosphodiester bond formation through simultaneous coordination of both ptO3' and the nonbridging Sp oxygen of the dNTP's alpha-phosphate. The coordination bond length of metal ion A as well as its ionic radius determines how close ptO3' can approach Palpha. These variables are expected to affect the rate of bond formation. The metal ion in the B site brings the pyrophosphate product close enough to Palpha to enable pyrophosphorolysis and assist in the departure of the pyrophosphate. In these dUpXpp-containing complexes, ptO3' occupies the vertex of a distorted metal ion A coordination octahedron. When ptO3' is placed at the vertex of an undistorted, idealized metal ion A octahedron, it is within bond formation distance to Palpha. This geometric relationship appears to be conserved among DNA polymerases of known structure.
-{{STRUCTURE_3scx|  PDB=3scx  |  SCENE=  }}
+Structural Insights into Complete Metal Ion Coordination from Ternary Complexes of B Family RB69 DNA Polymerase.,Xia S, Wang M, Blaha G, Konigsberg WH, Wang J Biochemistry. 2011 Oct 25;50(42):9114-24. Epub 2011 Sep 29. PMID:21923197<ref>PMID:21923197</ref>
-===RB69 DNA Polymerase Triple Mutant(L561A/S565G/Y567A) Ternary Complex with dUpNpp and a Deoxy-terminated Primer in the Presence of Ca2+===
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-{{ABSTRACT_PUBMED_21923197}}
-==About this Structure==
-[[3scx]] 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=3SCX OCA].
 ==See Also==
 *[[DNA polymerase|DNA polymerase]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:021923197</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: DNA-directed DNA polymerase]]
 [[Category: Enterobacteria phage rb69]]
-[[Category: Konigsberg, W H.]]
+[[Category: Konigsberg, W H]]
-[[Category: Wang, J.]]
+[[Category: Wang, J]]
-[[Category: Wang, M.]]
+[[Category: Wang, M]]
 [[Category: Dna binding]]
 [[Category: Transferase-dna complex]]