3or3: Difference between revisions

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[[Image:3or3.png|left|200px]]


{{STRUCTURE_3or3| PDB=3or3 | SCENE= }}
==Restriction endonuclease HPY188I in complex with product DNA==
<StructureSection load='3or3' size='340' side='right'caption='[[3or3]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3or3]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori_118 Helicobacter pylori 118]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OR3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OR3 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]] 1.95&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=3or3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3or3 OCA], [https://pdbe.org/3or3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3or3 RCSB], [https://www.ebi.ac.uk/pdbsum/3or3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3or3 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q9KJ88_HELPX Q9KJ88_HELPX]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The GIY-YIG nuclease domain is present in all kingdoms of life and has diverse functions. It is found in the eukaryotic flap endonuclease and Holliday junction resolvase Slx1-Slx4, the prokaryotic nucleotide excision repair proteins UvrC and Cho, and in proteins of 'selfish' genetic elements. Here we present the structures of the ternary pre- and post-cleavage complexes of the type II GIY-YIG restriction endonuclease Hpy188I with DNA and a surrogate or catalytic metal ion, respectively. Our structures suggest that GIY-YIG nucleases catalyze DNA hydrolysis by a single substitution reaction. They are consistent with a previous proposal that a tyrosine residue (which we expect to occur in its phenolate form) acts as a general base for the attacking water molecule. In contrast to the earlier proposal, our data identify the general base with the GIY and not the YIG tyrosine. A conserved glutamate residue (Glu149 provided in trans in Hpy188I) anchors a single metal cation in the active site. This metal ion contacts the phosphate proS oxygen atom and the leaving group 3'-oxygen atom, presumably to facilitate its departure. Taken together, our data reveal striking analogy in the absence of homology between GIY-YIG and betabetaalpha-Me nucleases.


===Restriction endonuclease HPY188I in complex with product DNA===
Hpy188I-DNA pre- and post-cleavage complexes--snapshots of the GIY-YIG nuclease mediated catalysis.,Sokolowska M, Czapinska H, Bochtler M Nucleic Acids Res. 2010 Oct 8. PMID:20935048<ref>PMID:20935048</ref>


{{ABSTRACT_PUBMED_20935048}}
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
</div>
==About this Structure==
<div class="pdbe-citations 3or3" style="background-color:#fffaf0;"></div>
[[3or3]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OR3 OCA].


==See Also==
==See Also==
*[[Endonuclease|Endonuclease]]
*[[Endonuclease 3D structures|Endonuclease 3D structures]]
 
== References ==
==Reference==
<references/>
<ref group="xtra">PMID:020935048</ref><references group="xtra"/>
__TOC__
[[Category: Helicobacter pylori]]
</StructureSection>
[[Category: Bochtler, M.]]
[[Category: Helicobacter pylori 118]]
[[Category: Czapinska, H.]]
[[Category: Large Structures]]
[[Category: Sokolowska, M.]]
[[Category: Bochtler M]]
[[Category: Catalytic mechanism]]
[[Category: Czapinska H]]
[[Category: Dna]]
[[Category: Sokolowska M]]
[[Category: Endonuclease-dna complex]]
[[Category: Giy-yig nuclease]]
[[Category: Hpy188i]]
[[Category: Hydrolase-dna complex]]
[[Category: Intercalation]]
[[Category: Pseudopalindrome]]
[[Category: Restriction endonuclease]]
[[Category: Restriction enzyme]]
Retrieved from "https://proteopedia.org/3or3"