2p5o: Difference between revisions

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==Crystal structure of RB69 GP43 in complex with DNA containing an abasic site analog==
==Crystal structure of RB69 GP43 in complex with DNA containing an abasic site analog==
<StructureSection load='2p5o' size='340' side='right' caption='[[2p5o]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
<StructureSection load='2p5o' size='340' side='right'caption='[[2p5o]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[2p5o]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpr69 Bpr69]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rv2 1rv2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P5O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2P5O FirstGlance]. <br>
<table><tr><td colspan='2'>[[2p5o]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Bpr69 Bpr69]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1rv2 1rv2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P5O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2P5O FirstGlance]. <br>
</td></tr><tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ig9|1ig9]], [[1clq|1clq]], [[2dy4|2dy4]], [[2dtu|2dtu]], [[1q9y|1q9y]]</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ig9|1ig9]], [[1clq|1clq]], [[2dy4|2dy4]], [[2dtu|2dtu]], [[1q9y|1q9y]]</div></td></tr>
<tr><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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">43 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=12353 BPR69])</td></tr>
<tr><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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] </span></td></tr>
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2p5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p5o OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2p5o RCSB], [http://www.ebi.ac.uk/pdbsum/2p5o PDBsum]</span></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=2p5o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p5o OCA], [https://pdbe.org/2p5o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2p5o RCSB], [https://www.ebi.ac.uk/pdbsum/2p5o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2p5o ProSAT]</span></td></tr>
<table>
</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 ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/p5/2p5o_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/p5/2p5o_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </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/chain_selection.php?pdb_ID=2ata ConSurf].
</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=2p5o ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
</div>
 
<div class="pdbe-citations 2p5o" style="background-color:#fffaf0;"></div>
==See Also==
*[[DNA polymerase|DNA polymerase]]
== References ==
== References ==
<references/>
<references/>
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[[Category: Bpr69]]
[[Category: Bpr69]]
[[Category: DNA-directed DNA polymerase]]
[[Category: DNA-directed DNA polymerase]]
[[Category: Doublie, S.]]
[[Category: Large Structures]]
[[Category: Hogg, M.]]
[[Category: Doublie, S]]
[[Category: Wallace, S S.]]
[[Category: Hogg, M]]
[[Category: Wallace, S S]]
[[Category: Abasic site]]
[[Category: Abasic site]]
[[Category: Dna lesion]]
[[Category: Dna lesion]]

Latest revision as of 15:16, 17 June 2021

Crystal structure of RB69 GP43 in complex with DNA containing an abasic site analog

2p5o, resolution 2.80Å

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