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[[Image:1n56.gif|left|200px]]


{{Structure
==Y-family DNA polymerase Dpo4 in complex with DNA containing abasic lesion==
|PDB= 1n56 |SIZE=350|CAPTION= <scene name='initialview01'>1n56</scene>, resolution 2.4&Aring;
<StructureSection load='1n56' size='340' side='right'caption='[[1n56]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=3DR:1&#39;,2&#39;-DIDEOXYRIBOFURANOSE-5&#39;-PHOSPHATE'>3DR</scene>, <scene name='pdbligand=ATP:ADENOSINE-5&#39;-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>
<table><tr><td colspan='2'>[[1n56]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus Saccharolobus solfataricus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N56 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N56 FirstGlance]. <br>
|ACTIVITY=  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
|GENE= dpo4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 Sulfolobus solfataricus])
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
|DOMAIN=
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1n56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n56 OCA], [https://pdbe.org/1n56 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n56 RCSB], [https://www.ebi.ac.uk/pdbsum/1n56 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n56 ProSAT]</span></td></tr>
|RELATEDENTRY=[[1jx4|1JX4]], [[1jxl|1JXL]], [[1n48|1N48]]
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1n56 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n56 OCA], [http://www.ebi.ac.uk/pdbsum/1n56 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1n56 RCSB]</span>
== Function ==
}}
[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.
== 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/n5/1n56_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=1n56 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.


'''Y-family DNA polymerase Dpo4 in complex with DNA containing abasic lesion'''
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>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1n56" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
Studies on several recently discovered error-prone DNA polymerases reveal novel structures that may explain the low fidelity of this general class of enzymes, a number of which are involved in the replicative bypass (translesion synthesis) of base damage in DNA.
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
 
== References ==
==About this Structure==
<references/>
1N56 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=1N56 OCA].
__TOC__
 
</StructureSection>
==Reference==
[[Category: Large Structures]]
Error-prone DNA polymerases: novel structures and the benefits of infidelity., Friedberg EC, Fischhaber PL, Kisker C, Cell. 2001 Oct 5;107(1):9-12. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11595180 11595180]
[[Category: Saccharolobus solfataricus]]
[[Category: Single protein]]
[[Category: Synthetic construct]]
[[Category: Sulfolobus solfataricus]]
[[Category: Boudsocq F]]
[[Category: Boudsocq, F.]]
[[Category: Ling H]]
[[Category: Ling, H.]]
[[Category: Woodgate R]]
[[Category: Woodgate, R.]]
[[Category: Yang W]]
[[Category: Yang, W.]]
[[Category: dna lesion bypass]]
[[Category: dna polymerase]]
[[Category: protein-dna complex]]
[[Category: y-family]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:25:33 2008''

Latest revision as of 10:19, 25 October 2023

Y-family DNA polymerase Dpo4 in complex with DNA containing abasic lesionY-family DNA polymerase Dpo4 in complex with DNA containing abasic lesion

Structural highlights

1n56 is a 6 chain structure with sequence from Saccharolobus solfataricus and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.4Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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.

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[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Ling H, Boudsocq F, Woodgate R, Yang W. Snapshots of replication through an abasic lesion; structural basis for base substitutions and frameshifts. Mol Cell. 2004 Mar 12;13(5):751-62. PMID:15023344

1n56, resolution 2.40Å

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