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====
==Sequence impact in DNA duplex opening by the Rad4/XPC nucleotide excision repair complex==
<StructureSection load='6ug1' size='340' side='right'caption='[[6ug1]]' scene=''>
<StructureSection load='6ug1' size='340' side='right'caption='[[6ug1]], [[Resolution|resolution]] 2.83&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
<table><tr><td colspan='2'>[[6ug1]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] and [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UG1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6UG1 FirstGlance]. <br>
</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=6ug1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ug1 OCA], [https://pdbe.org/6ug1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ug1 RCSB], [https://www.ebi.ac.uk/pdbsum/6ug1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ug1 ProSAT]</span></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.833&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=G47:N2-ETHANETHIOL-2-DEOXY-GUANOSINE-5-MONOPHOSPHATE'>G47</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=6ug1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ug1 OCA], [https://pdbe.org/6ug1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ug1 RCSB], [https://www.ebi.ac.uk/pdbsum/6ug1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ug1 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RAD4_YEAST RAD4_YEAST] Involved in nucleotide excision repair of DNA damaged with UV light, bulky adducts, or cross-linking agents.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Rad4/XPC recognizes diverse DNA lesions to initiate nucleotide excision repair (NER). However, NER propensities among lesions vary widely and repair-resistant lesions are persistent and thus highly mutagenic. Rad4 recognizes repair-proficient lesions by unwinding ('opening') the damaged DNA site. Such 'opening' is also observed on a normal DNA sequence containing consecutive C/G's (CCC/GGG) when tethered to Rad4 to prevent protein diffusion. However, it was unknown if such tethering-facilitated DNA 'opening' could occur on any DNA or if certain structures/sequences would resist being 'opened'. Here, we report that DNA containing alternating C/G's (CGC/GCG) failed to be opened even when tethered; instead, Rad4 bound in a 180 degrees -reversed manner, capping the DNA end. Fluorescence lifetime studies of DNA conformations in solution showed that CCC/GGG exhibits local pre-melting that is absent in CGC/GCG. In MD simulations, CGC/GCG failed to engage Rad4 to promote 'opening' contrary to CCC/GGG. Altogether, our study illustrates how local sequences can impact DNA recognition by Rad4/XPC and how certain DNA sites resist being 'opened' even with Rad4 held at that site indefinitely. The contrast between CCC/GGG and CGC/GCG sequences in Rad4-DNA recognition may help decipher a lesion's mutagenicity in various genomic sequence contexts to explain lesion-determined mutational hot and cold spots.
Impact of DNA sequences on DNA 'opening' by the Rad4/XPC nucleotide excision repair complex.,Paul D, Mu H, Tavakoli A, Dai Q, Chakraborty S, He C, Ansari A, Broyde S, Min JH DNA Repair (Amst). 2021 Nov;107:103194. doi: 10.1016/j.dnarep.2021.103194. Epub , 2021 Jul 29. PMID:34428697<ref>PMID:34428697</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6ug1" style="background-color:#fffaf0;"></div>
==See Also==
*[[DNA repair protein Rad4|DNA repair protein Rad4]]
*[[UV excision repair protein 3D structures|UV excision repair protein 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Z-disk]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae S288C]]
[[Category: Min J-H]]
[[Category: Paul D]]
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