View source for 8ka3


==Arabidopsis AP endonuclease ARP complex with 22bp THF-containing DNA==
<StructureSection load='8ka3' size='340' side='right'caption='[[8ka3]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[8ka3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] 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=8KA3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8KA3 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]] 3&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</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=8ka3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ka3 OCA], [https://pdbe.org/8ka3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8ka3 RCSB], [https://www.ebi.ac.uk/pdbsum/8ka3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8ka3 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/ARP_ARATH ARP_ARATH] Repairs oxidative DNA damages, seems also to act as a redox factor (PubMed:7512729). Is multifunctional and may be involved both in DNA repair and in the regulation of transcription (PubMed:7512729). Exhibits apurinic/apyrimidinic (AP) endonuclease activity (PubMed:21781197, PubMed:25228464, PubMed:25569774). Catalyzes the conversion of 3'-phosphor-alpha,beta-unsaturated aldehyde (3'-PUA) to 3'-OH (PubMed:25228464). May be involved in base excision repair in chloroplasts (PubMed:19372224). According to a report, has a significant in vitro 3'-phosphatase activity (PubMed:25228464). According to another report, has no in vitro 3'-phosphatase activity (PubMed:25569774). Has a strong non-specific affinity to DNA (PubMed:25228464).<ref>PMID:19372224</ref> <ref>PMID:21781197</ref> <ref>PMID:25228464</ref> <ref>PMID:25569774</ref> <ref>PMID:7512729</ref> <ref>PMID:19172180</ref> 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Base excision repair (BER) is a critical genome defense pathway that copes with a broad range of DNA lesions induced by endogenous or exogenous genotoxic agents. AP endonucleases in the BER pathway are responsible for removing the damaged bases and nicking the abasic sites. In plants, the BER pathway plays a critical role in the active demethylation of 5-methylcytosine (5mC) DNA modification. Here, we have determined the crystal structures of Arabidopsis AP endonuclease AtARP in complex with the double-stranded DNA containing tetrahydrofuran (THF) that mimics the abasic site. We identified the critical residues in AtARP for binding and removing the abasic site and the unique residues for interacting with the orphan base. Additionally, we investigated the differences among the three plant AP endonucleases and evaluated the general DNA repair capacity of AtARP in a mammalian cell line. Our studies provide further mechanistic insights into the BER pathway in plants.

Structural insights into the catalytic mechanism of the AP endonuclease AtARP.,Guo W, Wu W, Wen Y, Gao Y, Zhuang S, Meng C, Chen H, Zhao Z, Hu K, Wu B Structure. 2024 Mar 8:S0969-2126(24)00053-4. doi: 10.1016/j.str.2024.02.014. PMID:38503293<ref>PMID:38503293</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 8ka3" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Arabidopsis thaliana]]
[[Category: Large Structures]]
[[Category: Synthetic construct]]
[[Category: Guo WT]]
[[Category: Wu BX]]