4fjh: Difference between revisions

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 ==RB69 DNA polymerase ternary complex with dGTP/dC==
-<StructureSection load='4fjh' size='340' side='right' caption='[[4fjh]], [[Resolution|resolution]] 2.11&Aring;' scene=''>
+<StructureSection load='4fjh' size='340' side='right'caption='[[4fjh]], [[Resolution|resolution]] 2.11&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4fjh]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpr69 Bpr69]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4FJH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4FJH FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4fjh]] 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=4FJH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4FJH 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=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.11&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4fj5|4fj5]], [[4fj7|4fj7]], [[4fj8|4fj8]], [[4fj9|4fj9]], [[4fjg|4fjg]], [[4fji|4fji]], [[4fjj|4fjj]], [[4fjk|4fjk]], [[4fjl|4fjl]], [[4fjm|4fjm]], [[4fjn|4fjn]], [[4fjx|4fjx]], [[4fk0|4fk0]], [[4fk2|4fk2]], [[4fk4|4fk4]]</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=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">43 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12353 BPR69])</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=4fjh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fjh OCA], [https://pdbe.org/4fjh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4fjh RCSB], [https://www.ebi.ac.uk/pdbsum/4fjh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4fjh ProSAT]</span></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=4fjh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4fjh OCA], [http://pdbe.org/4fjh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4fjh RCSB], [http://www.ebi.ac.uk/pdbsum/4fjh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4fjh ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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.
+[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 ==
-Current hypotheses that attempt to rationalize the high degree of base selectivity exhibited by replicative DNA polymerases (pols) concur that ternary complexes formed with incorrect dNTPs are destabilized. Knowing what accounts for this destabilization is likely to be the key to understanding base discrimination. To address this issue, we have determined crystal structures of ternary complexes with all twelve mismatches using an engineered RB69 pol quadruple mutant (qm, L415A/L561A/S565G/Y567A) that enabled us to capture nascent mispaired dNTPs. These structures show that mismatches in the Nascent base-pair Binding Pocket (NBP) of the qm pol differ markedly from mismatches embedded in binary pol-DNA complexes. Surprisingly only 3 of 12 mismatches clash with the NBP when they are modeled into the wt pol. The remaining can fit into a wt pol ternary complex but deviate from normal Watson-Crick base-pairs. Repositioning of the templating nucleotide residue and the enlarged NBP in qm ternary complex play important roles in accommodating incorrect incoming dNTPs. From these structures, we propose additional reasons as to why incorrect dNTP are incorporated so inefficiently by wild type RB69 pol: (i) steric clashes with side chains in the NBP after Fingers closing; (ii) weak interactions or large gaps between the incoming dNTP and the templating base; (iii) burying a protonated base in the hydrophobic environment of the NBP. All of these possibilities would be expected to destabilize the closed ternary complex so that incorporation of incorrect dNTP would be a rare event.
-DNA Mismatch Synthesis Complexes Provide Insights into Base Selectivity of a B Family DNA Polymerase.,Xia S, Wang J, Konigsberg WH J Am Chem Soc. 2012 Dec 6. PMID:23214497<ref>PMID:23214497</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 4fjh" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[DNA polymerase|DNA polymerase]]
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Bpr69]]
+[[Category: Escherichia phage RB69]]
-[[Category: DNA-directed DNA polymerase]]
+[[Category: Large Structures]]
-[[Category: Konigsberg, W H]]
+[[Category: Konigsberg WH]]
-[[Category: Wang, J]]
+[[Category: Wang J]]
-[[Category: Xia, S]]
+[[Category: Xia S]]
-[[Category: Dgtp/dc]]
-[[Category: Quadruple]]
-[[Category: Rb69]]
-[[Category: Rb69pol]]
-[[Category: Transferase-dna complex]]