1s9f

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(New page: 200px<br /><applet load="1s9f" size="450" color="white" frame="true" align="right" spinBox="true" caption="1s9f, resolution 2.00&Aring;" /> '''DPO with AT matched'...)
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[[Image:1s9f.gif|left|200px]]<br /><applet load="1s9f" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1s9f, resolution 2.00&Aring;" />
 
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'''DPO with AT matched'''<br />
 
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==Overview==
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==DPO with AT matched==
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The ability or inability of a DNA polymerase to extend a mispair directly, affects the establishment of genomic mutations. We report here kinetic, analyses of the ability of Dpo4, a Y-family polymerase from Sulfolobus, solfataricus, to extend from all mispairs opposite a template G or T. Dpo4, is equally inefficient at extending these mispairs, which include, surprisingly, a G.T mispair expected to conform closely to Watson-Crick, geometry. To elucidate the basis of this, we solved the structure of Dpo4, bound to G.T-mispaired primer template in the presence of an incoming, nucleotide. As a control, we also determined the structure of Dpo4 bound, to a matched A-T base pair at the primer terminus. The structures offer a, basis for the low efficiency of Dpo4 in extending a G.T mispair: a reverse, wobble that deflects the primer 3'-OH away from the incoming nucleotide.
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<StructureSection load='1s9f' size='340' side='right'caption='[[1s9f]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1s9f]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus Saccharolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S9F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S9F FirstGlance]. <br>
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</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&#8491;</td></tr>
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<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=DDY:2,3-DIDEOXYCYTOSINE-5-DIPHOSPHATE'>DDY</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1s9f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s9f OCA], [https://pdbe.org/1s9f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s9f RCSB], [https://www.ebi.ac.uk/pdbsum/1s9f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s9f ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/DPO4_SACS2 DPO4_SACS2] Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. It is involved in translesional synthesis.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/s9/1s9f_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1s9f ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The ability or inability of a DNA polymerase to extend a mispair directly affects the establishment of genomic mutations. We report here kinetic analyses of the ability of Dpo4, a Y-family polymerase from Sulfolobus solfataricus, to extend from all mispairs opposite a template G or T. Dpo4 is equally inefficient at extending these mispairs, which include, surprisingly, a G.T mispair expected to conform closely to Watson-Crick geometry. To elucidate the basis of this, we solved the structure of Dpo4 bound to G.T-mispaired primer template in the presence of an incoming nucleotide. As a control, we also determined the structure of Dpo4 bound to a matched A-T base pair at the primer terminus. The structures offer a basis for the low efficiency of Dpo4 in extending a G.T mispair: a reverse wobble that deflects the primer 3'-OH away from the incoming nucleotide.
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==About this Structure==
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Dpo4 is hindered in extending a G.T mismatch by a reverse wobble.,Trincao J, Johnson RE, Wolfle WT, Escalante CR, Prakash S, Prakash L, Aggarwal AK Nat Struct Mol Biol. 2004 May;11(5):457-62. Epub 2004 Apr 11. PMID:15077104<ref>PMID:15077104</ref>
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1S9F is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus] with CA, MG and DDY as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1S9F OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Dpo4 is hindered in extending a G.T mismatch by a reverse wobble., Trincao J, Johnson RE, Wolfle WT, Escalante CR, Prakash S, Prakash L, Aggarwal AK, Nat Struct Mol Biol. 2004 May;11(5):457-62. Epub 2004 Apr 11. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15077104 15077104]
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</div>
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[[Category: DNA-directed DNA polymerase]]
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<div class="pdbe-citations 1s9f" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: Sulfolobus solfataricus]]
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[[Category: Aggarwal, A.K.]]
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[[Category: Escalante, C.R.]]
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[[Category: Johnson, R.E.]]
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[[Category: Prakash, L.]]
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[[Category: Prakash, S.]]
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[[Category: Trincao, J.]]
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[[Category: Wolfle, W.T.]]
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[[Category: CA]]
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[[Category: DDY]]
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[[Category: MG]]
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[[Category: protein-dna complex]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 02:12:55 2007''
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==See Also==
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*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Saccharolobus solfataricus]]
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[[Category: Aggarwal AK]]
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[[Category: Escalante CR]]
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[[Category: Johnson RE]]
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[[Category: Prakash L]]
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[[Category: Prakash S]]
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[[Category: Trincao J]]
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[[Category: Wolfle WT]]

Current revision

DPO with AT matched

PDB ID 1s9f

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