View source for 6ozg


==Crystal structure of Thermotoga maritima (Tm) Endonuclease V (E89Q) in complex with a 12mer DNA containing an inosine followed by a ribo-adenosine==
<StructureSection load='6ozg' size='340' side='right'caption='[[6ozg]], [[Resolution|resolution]] 1.93&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6ozg]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima] 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=6OZG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6OZG 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]] 1.93&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=N:ANY+5-MONOPHOSPHATE+NUCLEOTIDE'>N</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=6ozg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ozg OCA], [https://pdbe.org/6ozg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ozg RCSB], [https://www.ebi.ac.uk/pdbsum/6ozg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ozg ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/NFI_THEMA NFI_THEMA] Selectively cleaves double-stranded DNA at the second phosphodiester bond 3' to a deoxyinosine leaving behind the intact lesion on the nicked DNA. Acts in DNA repair. In vitro, can also cleave single-stranded substrates with inosine, double-stranded DNA with apurinic sites, or DNA sites with uracil or a mismatched base. When present in molar excess, two protein molecules can bind to the same DNA substrate and effect cleavage of both strands (in vitro).<ref>PMID:12081482</ref> 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Endonuclease V (EndoV) cleaves the second phosphodiester bond 3' to a deaminated adenosine (inosine). Although highly conserved, EndoV homologs change substrate preference from DNA in bacteria to RNA in eukaryotes. We have characterized EndoV from six different species and determined crystal structures of human EndoV and three EndoV homologs from bacteria to mouse in complex with inosine-containing DNA/RNA hybrid or double-stranded RNA (dsRNA). Inosine recognition is conserved, but changes in several connecting loops in eukaryotic EndoV confer recognition of 3 ribonucleotides upstream and 7 or 8 bp of dsRNA downstream of the cleavage site, and bacterial EndoV binds only 2 or 3 nt flanking the scissile phosphate. In addition to the two canonical metal ions in the active site, a third Mn(2+) that coordinates the nucleophilic water appears necessary for product formation. Comparison of EndoV with its homologs RNase H1 and Argonaute reveals the principles by which these enzymes recognize RNA versus DNA.

Evolution of Inosine-Specific Endonuclease V from Bacterial DNase to Eukaryotic RNase.,Wu J, Samara NL, Kuraoka I, Yang W Mol Cell. 2019 Oct 3;76(1):44-56.e3. doi: 10.1016/j.molcel.2019.06.046. Epub 2019, Aug 20. PMID:31444105<ref>PMID:31444105</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6ozg" style="background-color:#fffaf0;"></div>

==See Also==
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Synthetic construct]]
[[Category: Thermotoga maritima]]
[[Category: Samara NL]]
[[Category: Yang W]]