5zb8

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Current revision (10:27, 27 March 2024) (edit) (undo)
 
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<StructureSection load='5zb8' size='340' side='right'caption='[[5zb8]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
<StructureSection load='5zb8' size='340' side='right'caption='[[5zb8]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5zb8]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43587 Atcc 43587]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZB8 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5ZB8 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5zb8]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZB8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZB8 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SM:SAMARIUM+(III)+ION'>SM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5zb8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zb8 OCA], [http://pdbe.org/5zb8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zb8 RCSB], [http://www.ebi.ac.uk/pdbsum/5zb8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zb8 ProSAT]</span></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SM:SAMARIUM+(III)+ION'>SM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5zb8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zb8 OCA], [https://pdbe.org/5zb8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zb8 RCSB], [https://www.ebi.ac.uk/pdbsum/5zb8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zb8 ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/Q8U0N5_PYRFU Q8U0N5_PYRFU]
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Because base deaminations, which are promoted by high temperature, ionizing radiation, aerobic respiration and nitrosative stress, produce mutations during replication, deaminated bases must be repaired quickly to maintain genome integrity. Recently, we identified a novel lesion-specific endonuclease, PfuEndoQ, from Pyrococcus furiosus, and PfuEndoQ may be involved in the DNA repair pathway in Thermococcales of Archaea. PfuEndoQ recognizes a deaminated base and cleaves the phosphodiester bond 5' of the lesion site. To elucidate the structural basis of the substrate recognition and DNA cleavage mechanisms of PfuEndoQ, we determined the structure of PfuEndoQ using X-ray crystallography. The PfuEndoQ structure and the accompanying biochemical data suggest that PfuEndoQ recognizes a deaminated base using a highly conserved pocket adjacent to a Zn2+-binding site and hydrolyses a phosphodiester bond using two Zn2+ ions. The PfuEndoQ-DNA complex is stabilized by a Zn-binding domain and a C-terminal helical domain, and the complex may recruit downstream proteins in the DNA repair pathway.
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Crystal structure of the novel lesion-specific endonuclease PfuEndoQ from Pyrococcus furiosus.,Miyazono KI, Ishino S, Makita N, Ito T, Ishino Y, Tanokura M Nucleic Acids Res. 2018 Apr 12. pii: 4969244. doi: 10.1093/nar/gky261. PMID:29660024<ref>PMID:29660024</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 5zb8" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Atcc 43587]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Ito, T]]
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[[Category: Pyrococcus furiosus]]
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[[Category: Miyazono, K]]
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[[Category: Ito T]]
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[[Category: Tanokura, M]]
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[[Category: Miyazono K]]
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[[Category: Dna binding protein]]
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[[Category: Tanokura M]]
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[[Category: Dna repair]]
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[[Category: Endonuclease]]
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Current revision

Crystal structure of the novel lesion-specific endonuclease PfuEndoQ from Pyrococcus furiosus

PDB ID 5zb8

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