1s10

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[[Image:1s10.gif|left|200px]]
 
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==Snapshots of replication through an abasic lesion: structural basis for base substitution and frameshift==
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The line below this paragraph, containing "STRUCTURE_1s10", creates the "Structure Box" on the page.
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<StructureSection load='1s10' size='340' side='right'caption='[[1s10]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1s10]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus_P2 Saccharolobus solfataricus P2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S10 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S10 FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 2.1&#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=DCP:2-DEOXYCYTIDINE-5-TRIPHOSPHATE'>DCP</scene></td></tr>
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{{STRUCTURE_1s10| PDB=1s10 | SCENE= }}
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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=1s10 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s10 OCA], [https://pdbe.org/1s10 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s10 RCSB], [https://www.ebi.ac.uk/pdbsum/1s10 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s10 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/s1/1s10_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=1s10 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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Dpo4 from S. Solfataricus, a DinB-like Y family polymerase, efficiently replicates DNA past an abasic lesion. We have determined crystal structures of Dpo4 complexed with five different abasic site-containing DNA substrates and find that translesion synthesis is template directed with the abasic site looped out and the incoming nucleotide is opposite the base 5' to the lesion. The ensuing DNA synthesis generates a -1 frameshift when the abasic site remains extrahelical. Template realignment during primer extension is also observed, resulting in base substitutions or even +1 frameshifts. In the case of a +1 frameshift, the extra nucleotide is accommodated in the solvent-exposed minor groove. In addition, the structure of an unproductive Dpo4 ternary complex suggests that the flexible little finger domain facilitates DNA orientation and translocation during translesion synthesis.
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'''Snapshots of replication through an abasic lesion: structural basis for base substitution and frameshift'''
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Snapshots of replication through an abasic lesion; structural basis for base substitutions and frameshifts.,Ling H, Boudsocq F, Woodgate R, Yang W Mol Cell. 2004 Mar 12;13(5):751-62. PMID:15023344<ref>PMID:15023344</ref>
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==Overview==
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Dpo4 from S. Solfataricus, a DinB-like Y family polymerase, efficiently replicates DNA past an abasic lesion. We have determined crystal structures of Dpo4 complexed with five different abasic site-containing DNA substrates and find that translesion synthesis is template directed with the abasic site looped out and the incoming nucleotide is opposite the base 5' to the lesion. The ensuing DNA synthesis generates a -1 frameshift when the abasic site remains extrahelical. Template realignment during primer extension is also observed, resulting in base substitutions or even +1 frameshifts. In the case of a +1 frameshift, the extra nucleotide is accommodated in the solvent-exposed minor groove. In addition, the structure of an unproductive Dpo4 ternary complex suggests that the flexible little finger domain facilitates DNA orientation and translocation during translesion synthesis.
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==About this Structure==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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1S10 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S10 OCA].
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</div>
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<div class="pdbe-citations 1s10" style="background-color:#fffaf0;"></div>
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==Reference==
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==See Also==
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Snapshots of replication through an abasic lesion; structural basis for base substitutions and frameshifts., Ling H, Boudsocq F, Woodgate R, Yang W, Mol Cell. 2004 Mar 12;13(5):751-62. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15023344 15023344]
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*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
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[[Category: DNA-directed DNA polymerase]]
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== References ==
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[[Category: Single protein]]
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<references/>
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[[Category: Sulfolobus solfataricus]]
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__TOC__
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[[Category: Boudsocq, F.]]
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</StructureSection>
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[[Category: Ling, H.]]
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[[Category: Large Structures]]
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[[Category: Woodgate, R.]]
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[[Category: Saccharolobus solfataricus P2]]
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[[Category: Yang, W.]]
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[[Category: Boudsocq F]]
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[[Category: Abaic lesion]]
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[[Category: Ling H]]
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[[Category: Lesion bypass]]
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[[Category: Woodgate R]]
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[[Category: Polymerase]]
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[[Category: Yang W]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 08:09:35 2008''
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Current revision

Snapshots of replication through an abasic lesion: structural basis for base substitution and frameshift

PDB ID 1s10

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