View source for 5gkg


==Structure of EndoMS-dsDNA1'' complex==
<StructureSection load='5gkg' size='340' side='right'caption='[[5gkg]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5gkg]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis_KOD1 Thermococcus kodakarensis KOD1] 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=5GKG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5GKG 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]] 2.6&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=5gkg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5gkg OCA], [https://pdbe.org/5gkg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5gkg RCSB], [https://www.ebi.ac.uk/pdbsum/5gkg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5gkg ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/NUCS_THEKO NUCS_THEKO] Cleaves both 3' and 5' ssDNA extremities of branched DNA structures.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Archaeal NucS nuclease was thought to degrade the single-stranded region of branched DNA, which contains flapped and splayed DNA. However, recent findings indicated that EndoMS, the orthologous enzyme of NucS, specifically cleaves double-stranded DNA (dsDNA) containing mismatched bases. In this study, we determined the structure of the EndoMS-DNA complex. The complex structure of the EndoMS dimer with dsDNA unexpectedly revealed that the mismatched bases were flipped out into binding sites, and the overall architecture most resembled that of restriction enzymes. The structure of the apo form was similar to the reported structure of Pyrococcus abyssi NucS, indicating that movement of the C-terminal domain from the resting state was required for activity. In addition, a model of the EndoMS-PCNA-DNA complex was preliminarily verified with electron microscopy. The structures strongly support the idea that EndoMS acts in a mismatch repair pathway.

Structure of the EndoMS-DNA Complex as Mismatch Restriction Endonuclease.,Nakae S, Hijikata A, Tsuji T, Yonezawa K, Kouyama KI, Mayanagi K, Ishino S, Ishino Y, Shirai T Structure. 2016 Oct 17. pii: S0969-2126(16)30294-5. doi:, 10.1016/j.str.2016.09.005. PMID:27773688<ref>PMID:27773688</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5gkg" style="background-color:#fffaf0;"></div>

==See Also==
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Synthetic construct]]
[[Category: Thermococcus kodakarensis KOD1]]
[[Category: Hijikata A]]
[[Category: Ishino S]]
[[Category: Ishino Y]]
[[Category: Kouyama K]]
[[Category: Mayanagi K]]
[[Category: Nakae S]]
[[Category: Shirai T]]
[[Category: Tsuji T]]
[[Category: Yonezawa K]]