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==Dpo4 extension ternary complex with 3'-terminal primer T base opposite the 1-methylguanine (M1G) lesion==
==Dpo4 extension ternary complex with 3'-terminal primer T base opposite the 1-methylguanine (M1G) lesion==
<StructureSection load='3rax' size='340' side='right' caption='[[3rax]], [[Resolution|resolution]] 1.89&Aring;' scene=''>
<StructureSection load='3rax' size='340' side='right' caption='[[3rax]], [[Resolution|resolution]] 1.89&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3rax]] is a 6 chain structure with 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=3RAX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RAX FirstGlance]. <br>
<table><tr><td colspan='2'>[[3rax]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RAX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RAX FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene></td></tr>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DGT:2-DEOXYGUANOSINE-5-TRIPHOSPHATE'>DGT</scene></td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2DT:3-DEOXYTHYMIDINE-5-MONOPHOSPHATE'>2DT</scene>, <scene name='pdbligand=MG1:2-DEOXY-1-METHYLGUANOSINE+5-(DIHYDROGEN+PHOSPHATE)'>MG1</scene></td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2DT:3-DEOXYTHYMIDINE-5-MONOPHOSPHATE'>2DT</scene>, <scene name='pdbligand=MG1:2-DEOXY-1-METHYLGUANOSINE+5-(DIHYDROGEN+PHOSPHATE)'>MG1</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3raq|3raq]]</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3raq|3raq]]</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dbh, dpo4, SSO2448 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2287 Sulfolobus solfataricus])</td></tr>
<tr id='activity'><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'>[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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3rax FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rax OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rax RCSB], [http://www.ebi.ac.uk/pdbsum/3rax PDBsum]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3rax FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rax OCA], [http://pdbe.org/3rax PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3rax RCSB], [http://www.ebi.ac.uk/pdbsum/3rax PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3rax ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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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 3rax" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
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</StructureSection>
</StructureSection>
[[Category: DNA-directed DNA polymerase]]
[[Category: DNA-directed DNA polymerase]]
[[Category: Sulfolobus solfataricus]]
[[Category: Patel, D J]]
[[Category: Patel, D J]]
[[Category: Rechkoblit, O]]
[[Category: Rechkoblit, O]]

Latest revision as of 07:02, 5 August 2016

Dpo4 extension ternary complex with 3'-terminal primer T base opposite the 1-methylguanine (M1G) lesionDpo4 extension ternary complex with 3'-terminal primer T base opposite the 1-methylguanine (M1G) lesion

Structural highlights

3rax is a 6 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:,
NonStd Res:,
Activity:DNA-directed DNA polymerase, with EC number 2.7.7.7
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[DPO4_SULSO] 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.[HAMAP-Rule:MF_01113]

Publication Abstract from PubMed

DNA is susceptible to alkylation damage by a number of environmental agents that modify the Watson-Crick edge of the bases. Such lesions, if not repaired, may be bypassed by Y-family DNA polymerases. The bypass polymerase Dpo4 is strongly inhibited by 1-methylguanine (m1G) and 3-methylcytosine (m3C), with nucleotide incorporation opposite these lesions being predominantly mutagenic. Further, extension after insertion of both correct and incorrect bases, introduces additional base substitution and deletion errors. Crystal structures of the Dpo4 ternary extension complexes with correct and mismatched 3'-terminal primer bases opposite the lesions reveal that both m1G and m3C remain positioned within the DNA template/primer helix. However, both correct and incorrect pairing partners exhibit pronounced primer terminal nucleotide distortion, being primarily evicted from the DNA helix when opposite m1G or misaligned when pairing with m3C. Our studies provide insights into mechanisms related to hindered and mutagenic bypass of methylated lesions and models associated with damage recognition by repair demethylases.

Implications for damage recognition during Dpo4-mediated mutagenic bypass of m1G and m3C lesions.,Rechkoblit O, Delaney JC, Essigmann JM, Patel DJ Structure. 2011 Jun 8;19(6):821-32. doi: 10.1016/j.str.2011.03.020. PMID:21645853[1]

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

See Also

References

  1. Rechkoblit O, Delaney JC, Essigmann JM, Patel DJ. Implications for damage recognition during Dpo4-mediated mutagenic bypass of m1G and m3C lesions. Structure. 2011 Jun 8;19(6):821-32. doi: 10.1016/j.str.2011.03.020. PMID:21645853 doi:10.1016/j.str.2011.03.020

3rax, resolution 1.89Å

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