1snh: Difference between revisions
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==Solution structure of the DNA Decamer Duplex Containing Double TG Mismatches of Cis-syn Cyclobutane Pyrimidine Dimer== | |||
<StructureSection load='1snh' size='340' side='right'caption='[[1snh]]' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[1snh]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SNH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SNH 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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1snh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1snh OCA], [https://pdbe.org/1snh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1snh RCSB], [https://www.ebi.ac.uk/pdbsum/1snh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1snh ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The cis-syn cyclobutane pyrimidine dimer (CPD) is a cytotoxic, mutagenic and carcinogenic DNA photoproduct and is repaired by the nucleotide excision repair (NER) pathway in mammalian cells. The XPC-hHR23B complex as the initiator of global genomic NER binds to sites of certain kinds of DNA damage. Although CPDs are rarely recognized by the XPC-hHR23B complex, the presence of mismatched bases opposite a CPD significantly increased the binding affinity of the XPC-hHR23B complex to the CPD. In order to decipher the properties of the DNA structures that determine the binding affinity for XPC-hHR23B to DNA, we carried out structural analyses of the various types of CPDs by NMR spectroscopy. The DNA duplex which contains a single 3' T*G wobble pair in a CPD (CPD/GA duplex) induces little conformational distortion. However, severe distortion of the helical conformation occurs when a CPD contains double T*G wobble pairs (CPD/GG duplex) even though the T residues of the CPD form stable hydrogen bonds with the opposite G residues. The helical bending angle of the CPD/GG duplex was larger than those of the CPD/GA duplex and properly matched CPD/AA duplex. The fluctuation of the backbone conformation and significant changes in the widths of the major and minor grooves at the double T*G wobble paired site were also observed in the CPD/GG duplex. These structural features were also found in a duplex that contains the (6-4) adduct, which is efficiently recognized by the XPC-hHR23B complex. Thus, we suggest that the unique structural features of the DNA double helix (that is, helical bending, flexible backbone conformation, and significant changes of the major and/or minor grooves) might be important factors in determining the binding affinity of the XPC-hHR23B complex to DNA. | |||
NMR structure of the DNA decamer duplex containing double T*G mismatches of cis-syn cyclobutane pyrimidine dimer: implications for DNA damage recognition by the XPC-hHR23B complex.,Lee JH, Park CJ, Shin JS, Ikegami T, Akutsu H, Choi BS Nucleic Acids Res. 2004 Apr 30;32(8):2474-81. Print 2004. PMID:15121904<ref>PMID:15121904</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
== | <div class="pdbe-citations 1snh" style="background-color:#fffaf0;"></div> | ||
[[ | == References == | ||
[[Category: Akutsu | <references/> | ||
[[Category: Choi | __TOC__ | ||
[[Category: Ikegami | </StructureSection> | ||
[[Category: Lee | [[Category: Large Structures]] | ||
[[Category: Park | [[Category: Akutsu H]] | ||
[[Category: Shin | [[Category: Choi BS]] | ||
[[Category: Ikegami T]] | |||
[[Category: Lee JH]] | |||
[[Category: Park CJ]] | |||
[[Category: Shin JS]] | |||
Latest revision as of 12:24, 6 December 2023
Solution structure of the DNA Decamer Duplex Containing Double TG Mismatches of Cis-syn Cyclobutane Pyrimidine DimerSolution structure of the DNA Decamer Duplex Containing Double TG Mismatches of Cis-syn Cyclobutane Pyrimidine Dimer
Structural highlights
Publication Abstract from PubMedThe cis-syn cyclobutane pyrimidine dimer (CPD) is a cytotoxic, mutagenic and carcinogenic DNA photoproduct and is repaired by the nucleotide excision repair (NER) pathway in mammalian cells. The XPC-hHR23B complex as the initiator of global genomic NER binds to sites of certain kinds of DNA damage. Although CPDs are rarely recognized by the XPC-hHR23B complex, the presence of mismatched bases opposite a CPD significantly increased the binding affinity of the XPC-hHR23B complex to the CPD. In order to decipher the properties of the DNA structures that determine the binding affinity for XPC-hHR23B to DNA, we carried out structural analyses of the various types of CPDs by NMR spectroscopy. The DNA duplex which contains a single 3' T*G wobble pair in a CPD (CPD/GA duplex) induces little conformational distortion. However, severe distortion of the helical conformation occurs when a CPD contains double T*G wobble pairs (CPD/GG duplex) even though the T residues of the CPD form stable hydrogen bonds with the opposite G residues. The helical bending angle of the CPD/GG duplex was larger than those of the CPD/GA duplex and properly matched CPD/AA duplex. The fluctuation of the backbone conformation and significant changes in the widths of the major and minor grooves at the double T*G wobble paired site were also observed in the CPD/GG duplex. These structural features were also found in a duplex that contains the (6-4) adduct, which is efficiently recognized by the XPC-hHR23B complex. Thus, we suggest that the unique structural features of the DNA double helix (that is, helical bending, flexible backbone conformation, and significant changes of the major and/or minor grooves) might be important factors in determining the binding affinity of the XPC-hHR23B complex to DNA. NMR structure of the DNA decamer duplex containing double T*G mismatches of cis-syn cyclobutane pyrimidine dimer: implications for DNA damage recognition by the XPC-hHR23B complex.,Lee JH, Park CJ, Shin JS, Ikegami T, Akutsu H, Choi BS Nucleic Acids Res. 2004 Apr 30;32(8):2474-81. Print 2004. PMID:15121904[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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