3oqg: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3oqg]] is a 4 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=3OQG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OQG FirstGlance]. <br>
<table><tr><td colspan='2'>[[3oqg]] is a 4 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=3OQG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OQG FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.75&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3or3|3or3]], [[3mx1|3mx1]], [[3mx4|3mx4]], [[3nic|3nic]], [[2wsh|2wsh]], [[1mk0|1mk0]], [[1yd1|1yd1]]</div></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">hpy188IR ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=585532 Helicobacter pylori 118])</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=3oqg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3oqg OCA], [https://pdbe.org/3oqg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3oqg RCSB], [https://www.ebi.ac.uk/pdbsum/3oqg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3oqg ProSAT]</span></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=3oqg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3oqg OCA], [https://pdbe.org/3oqg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3oqg RCSB], [https://www.ebi.ac.uk/pdbsum/3oqg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3oqg ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/Q9KJ88_HELPX Q9KJ88_HELPX]
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.
 
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>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3oqg" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Helicobacter pylori 118]]
[[Category: Helicobacter pylori 118]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Bochtler, M]]
[[Category: Bochtler M]]
[[Category: Czapinska, H]]
[[Category: Czapinska H]]
[[Category: Sokolowska, M]]
[[Category: Sokolowska M]]
[[Category: Catalytic mechanism]]
[[Category: Endonuclease-dna complex]]
[[Category: Giy-yig nuclease]]
[[Category: Hpy188i]]
[[Category: Hydrolase-dna complex]]
[[Category: Intercalation]]
[[Category: Pseudopalindrome]]
[[Category: Restriction enzyme]]

Revision as of 11:18, 21 February 2024

Restriction endonuclease HPY188I in complex with substrate DNA

3oqg, resolution 1.75Å

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