View source for 9yhv


==DNA ligase 1 E346A/E592A in complex with nick containing 3'-8oxorG:C captured at pre-catalytic stage==
<StructureSection load='9yhv' size='340' side='right'caption='[[9yhv]], [[Resolution|resolution]] 2.81&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[9yhv]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] 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=9YHV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9YHV FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.81&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=8GM:[(2R,3S,4R,5R)-5-[2-AZANYL-6,8-BIS(OXIDANYLIDENE)-1,7-DIHYDROPURIN-9-YL]-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYL+DIHYDROGEN+PHOSPHATE'>8GM</scene>, <scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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=9yhv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9yhv OCA], [https://pdbe.org/9yhv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9yhv RCSB], [https://www.ebi.ac.uk/pdbsum/9yhv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9yhv ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/DNLI1_HUMAN DNLI1_HUMAN] DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
DNA ligase 1 (LIG1) seals broken strand breaks by joining two adjacent ends during DNA replication and repair transactions. We previously reported atomic-level insight into the strategies that LIG1 uses to discriminate mismatches or ribonucleotides. However, how LIG1 processes strand breaks with oxidatively damaged ends in the absence and presence of a "wrong" sugar remains unknown. Here, we determined the crystal structures of LIG1/nick DNA complexes with 3'-8-oxodG and 3'-8-oxorG templating A or C during the pre- and post-catalytic steps of the ligation reaction. Our structures demonstrated differences in the distances at the +1 and +2 nucleotides relative to the 3'-end of the nick and a shift in the template base position to accommodate the oxidative lesion depending on the dual coding potential of 8-oxoG, which forms Hoogsteen or Watson-Crick base pairing in -syn or -anti conformation. Furthermore, these structural adjustments lead to mutagenic ligation or non-mutagenic end joining of the nick substrates. Overall, our findings provide mechanistic insight into how LIG1 processes nicks harboring oxidative damage and ribonucleotides to ensure fidelity at the final ligation step of DNA repair and replication to maintain genome integrity.

Processing of DNA single-strand breaks with oxidatively damaged ends by LIG1.,Balu KE, Almohdar D, Lerner C, Ratcliffe J, Tang Q, Parwal T, Lee KM, Prakash A, Caglayan M Nucleic Acids Res. 2025 Nov 26;53(22):gkaf1344. doi: 10.1093/nar/gkaf1344. PMID:41370201<ref>PMID:41370201</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 9yhv" style="background-color:#fffaf0;"></div>
== References ==
<references/>
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</StructureSection>
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Synthetic construct]]
[[Category: Caglayan M]]
[[Category: KanalElamparithi B]]