3lds: Difference between revisions

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-[[Image:3lds.png|left|200px]]
-{{STRUCTURE_3lds|  PDB=3lds  |  SCENE=  }}
+==Crystal structure of RB69 gp43 with DNA and dATP opposite 8-oxoG==
+<StructureSection load='3lds' size='340' side='right'caption='[[3lds]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3lds]] 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=3LDS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LDS 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&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8OG:8-OXO-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>8OG</scene>, <scene name='pdbligand=DDG:2,3-DIDEOXY-GUANOSINE-5-MONOPHOSPHATE'>DDG</scene>, <scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=3lds FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lds OCA], [https://pdbe.org/3lds PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lds RCSB], [https://www.ebi.ac.uk/pdbsum/3lds PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lds 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.
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ld/3lds_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3lds ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The fidelity of DNA replication is under constant threat from the formation of lesions within the genome. Oxidation of DNA bases leads to the formation of altered DNA bases such as 8-oxo-7,8-dihydroguanine, commonly called 8-oxoG, and 2-hydroxyadenine, or 2-OHA. In this work we have examined the incorporation kinetics opposite these two oxidatively derived lesions as well as an abasic site analogue by the replicative DNA polymerase from bacteriophage RB69. We compared the kinetic parameters for both wild type and the low fidelity L561A variant. While nucleotide incorporation rates (k(pol)) were generally higher for the variant, the presence of a lesion in the templating position reduced the ability of both the wild-type and variant DNA polymerases to form ternary enzyme-DNA-dNTP complexes. Thus, the L561A substitution does not significantly affect the ability of the RB69 DNA polymerase to recognize damaged DNA; instead, the mutation increases the probability that nucleotide incorporation will occur. We have also solved the crystal structure of the L561A variant forming an 8-oxoG.dATP mispair and show that the propensity for forming this mispair depends on an enlarged polymerase active site.
-===Crystal structure of RB69 gp43 with DNA and dATP opposite 8-oxoG===
+Kinetics of mismatch formation opposite lesions by the replicative DNA polymerase from bacteriophage RB69.,Hogg M, Rudnicki J, Midkiff J, Reha-Krantz L, Doublie S, Wallace SS Biochemistry. 2010 Mar 23;49(11):2317-25. PMID:20166748<ref>PMID:20166748</ref>
-{{ABSTRACT_PUBMED_20166748}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 3lds" style="background-color:#fffaf0;"></div>
-[[3lds]] is a 3 chain structure of [[DNA polymerase]] 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=3LDS OCA].
 ==See Also==
-*[[DNA polymerase|DNA polymerase]]
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:020166748</ref><references group="xtra"/>
+__TOC__
-[[Category: DNA-directed DNA polymerase]]
+</StructureSection>
-[[Category: Enterobacteria phage rb69]]
+[[Category: Escherichia phage RB69]]
-[[Category: Doublie, S.]]
+[[Category: Large Structures]]
-[[Category: Hogg, M.]]
+[[Category: Doublie S]]
-[[Category: Midkiff, J.]]
+[[Category: Hogg M]]
-[[Category: Reha-Krantz, L]]
+[[Category: Midkiff J]]
-[[Category: Rudnicki, J.]]
+[[Category: Reha-Krantz L]]
-[[Category: Wallace, S S.]]
+[[Category: Rudnicki J]]
-[[Category: Mismatch]]
+[[Category: Wallace SS]]
-[[Category: Protein-dna complex]]
-[[Category: Transferase-dna complex]]