3or3: Difference between revisions

Latest revision as of 09:43, 6 September 2023

Restriction endonuclease HPY188I in complex with product DNA

Structural highlights

3or3 is a 6 chain structure with sequence from Helicobacter pylori 118. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.95Å
Ligands:	CA, CL, MSE
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q9KJ88_HELPX

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Sokolowska M, Czapinska H, Bochtler M. Hpy188I-DNA pre- and post-cleavage complexes--snapshots of the GIY-YIG nuclease mediated catalysis. Nucleic Acids Res. 2010 Oct 8. PMID:20935048 doi:10.1093/nar/gkq821

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Sokolowska M, Czapinska H, Bochtler M. Hpy188I-DNA pre- and post-cleavage complexes--snapshots of the GIY-YIG nuclease mediated catalysis. Nucleic Acids Res. 2010 Oct 8. PMID:20935048 doi:10.1093/nar/gkq821

[1]

@@ Line 1: / Line 1: @@
-[[Image:3or3.png|left|200px]]
-<!--
+==Restriction endonuclease HPY188I in complex with product DNA==
-The line below this paragraph, containing "STRUCTURE_3or3", creates the "Structure Box" on the page.
+<StructureSection load='3or3' size='340' side='right'caption='[[3or3]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<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>
-or leave the SCENE parameter empty for the default display.
+</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>
-{{STRUCTURE_3or3|  PDB=3or3  |  SCENE=  }}
+<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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3or3" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_20935048}}, adds the Publication Abstract to the page
+*[[Endonuclease 3D structures|Endonuclease 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 20935048 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_20935048}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Helicobacter pylori 118]]
-[[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].
+[[Category: Large Structures]]
+[[Category: Bochtler M]]
-==Reference==
+[[Category: Czapinska H]]
-<ref group="xtra">PMID:20935048</ref><references group="xtra"/>
+[[Category: Sokolowska M]]
-[[Category: Helicobacter pylori]]
-[[Category: Bochtler, M.]]
-[[Category: Czapinska, H.]]
-[[Category: Sokolowska, M.]]

3or3: Difference between revisions

Latest revision as of 09:43, 6 September 2023

Restriction endonuclease HPY188I in complex with product DNA

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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