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==Structure of the 1,N2-ethenodeoxyguanosine lesion opposite a one-base deletion in duplex DNA==
<StructureSection load='2ktp' size='340' side='right'caption='[[2ktp]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2ktp]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KTP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KTP FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GNE:1,N2-ETHENOGUANINE'>GNE</scene></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=2ktp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ktp OCA], [https://pdbe.org/2ktp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ktp RCSB], [https://www.ebi.ac.uk/pdbsum/2ktp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ktp ProSAT]</span></td></tr>
</table>
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== Publication Abstract from PubMed ==
The structure of the 1,N(2)-ethenodeoxyguanosine lesion (1,N(2)-epsilondG) has been characterized in 5'-d(CGCATXGAATCC)-3'.5'-d(GGATTCATGCG)-3' (X = 1,N(2)-epsilondG), in which there is no dC opposite the lesion. This duplex (named the 1-BD duplex) models the product of translesion bypass of 1,N(2)-epsilondG by Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) [Zang, H., Goodenough, A. K., Choi, J. Y., Irimia, A., Loukachevitch, L. V., Kozekov, I. D., Angel, K. C., Rizzo, C. J., Egli, M., and Guengerich, F. P. (2005) J. Biol. Chem. 280, 29750-29764], leading to a one-base deletion. The T(m) of this duplex is 6 degrees C higher than that of the duplex in which dC is present opposite the 1,N(2)-epsilondG lesion and 8 degrees C higher than that of the unmodified 1-BD duplex. Analysis of NOEs between the 1,N(2)-epsilondG imidazole and deoxyribose H1' protons and between the 1,N(2)-epsilondG etheno H6 and H7 protons and DNA protons establishes that 1,N(2)-epsilondG adopts the anti conformation about the glycosyl bond and that the etheno moiety is accommodated within the helix. The resonances of the 1,N(2)-epsilondG H6 and H7 etheno protons shift upfield relative to the monomer 1,N(2)-epsilondG, attributed to ring current shielding, consistent with their intrahelical location. NMR data reveal that Watson-Crick base pairing is maintained at both the 5' and 3' neighbor base pairs. The structure of the 1-BD duplex has been refined using molecular dynamics calculations restrained by NMR-derived distance and dihedral angle restraints. The increased stability of the 1,N(2)-epsilondG lesion in the absence of the complementary dC correlates with the one-base deletion extension product observed during the bypass of the 1,N(2)-epsilondG lesion by the Dpo4 polymerase, suggesting that stabilization of this bulged intermediate may be significant with regard to the biological processing of the lesion.

Structure of the 1,N(2)-Etheno-2'-deoxyguanosine Lesion in the 3'-G(epsilondG)T-5' Sequence Opposite a One-Base Deletion.,Shanmugam G, Kozekov ID, Guengerich FP, Rizzo CJ, Stone MP Biochemistry. 2010 Mar 30;49(12):2615-26. PMID:20201499<ref>PMID:20201499</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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== References ==
<references/>
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</StructureSection>
[[Category: Large Structures]]
[[Category: Guengerich PF]]
[[Category: Kozekov ID]]
[[Category: Rizzo CJ]]
[[Category: Shanmugam G]]
[[Category: Stone MP]]