6yjb: Difference between revisions
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==== | ==VcaM4I restriction endonuclease 5hmC-ssDNA complex== | ||
<StructureSection load='6yjb' size='340' side='right'caption='[[6yjb]]' scene=''> | <StructureSection load='6yjb' size='340' side='right'caption='[[6yjb]], [[Resolution|resolution]] 1.55Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br> | <table><tr><td colspan='2'>[[6yjb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_campbellii Vibrio campbellii] 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=6YJB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YJB FirstGlance]. <br> | ||
</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=6yjb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yjb OCA], [https://pdbe.org/6yjb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yjb RCSB], [https://www.ebi.ac.uk/pdbsum/6yjb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yjb ProSAT]</span></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]] 1.55Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5HC:2-DEOXY-5-(HYDROXYMETHYL)CYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>5HC</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6yjb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yjb OCA], [https://pdbe.org/6yjb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yjb RCSB], [https://www.ebi.ac.uk/pdbsum/6yjb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yjb ProSAT]</span></td></tr> | |||
</table> | </table> | ||
== Function == | |||
[https://www.uniprot.org/uniprot/A0A344KQF3_9VIBR A0A344KQF3_9VIBR] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Many modification-dependent restriction endonucleases (MDREs) are fusions of a PUA superfamily modification sensor domain and a nuclease catalytic domain. EVE domains belong to the PUA superfamily, and are present in MDREs in combination with HNH nuclease domains. Here, we present a biochemical characterization of the EVE-HNH endonuclease VcaM4I and crystal structures of the protein alone, with EVE domain bound to either 5mC modified dsDNA or to 5mC/5hmC containing ssDNA. The EVE domain is moderately specific for 5mC/5hmC containing DNA according to EMSA experiments. It flips the modified nucleotide, to accommodate it in a hydrophobic pocket of the enzyme, primarily formed by P24, W82 and Y130 residues. In the crystallized conformation, the EVE domain and linker helix between the two domains block DNA binding to the catalytic domain. Removal of the EVE domain and inter-domain linker, but not of the EVE domain alone converts VcaM4I into a non-specific toxic nuclease. The role of the key residues in the EVE and HNH domains of VcaM4I is confirmed by digestion and restriction assays with the enzyme variants that differ from the wild-type by changes to the base binding pocket or to the catalytic residues. | |||
Crystal structures of the EVE-HNH endonuclease VcaM4I in the presence and absence of DNA.,Pastor M, Czapinska H, Helbrecht I, Krakowska K, Lutz T, Xu SY, Bochtler M Nucleic Acids Res. 2021 Feb 22;49(3):1708-1723. doi: 10.1093/nar/gkaa1218. PMID:33450012<ref>PMID:33450012</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 6yjb" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Endonuclease 3D structures|Endonuclease 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: | [[Category: Synthetic construct]] | ||
[[Category: Vibrio campbellii]] | |||
[[Category: Bochtler M]] | |||
[[Category: Czapinska H]] | |||
[[Category: Helbrecht I]] | |||
[[Category: Lutz T]] | |||
[[Category: Pastor M]] | |||
[[Category: Xu S]] | |||
Latest revision as of 16:28, 24 January 2024
VcaM4I restriction endonuclease 5hmC-ssDNA complexVcaM4I restriction endonuclease 5hmC-ssDNA complex
Structural highlights
FunctionPublication Abstract from PubMedMany modification-dependent restriction endonucleases (MDREs) are fusions of a PUA superfamily modification sensor domain and a nuclease catalytic domain. EVE domains belong to the PUA superfamily, and are present in MDREs in combination with HNH nuclease domains. Here, we present a biochemical characterization of the EVE-HNH endonuclease VcaM4I and crystal structures of the protein alone, with EVE domain bound to either 5mC modified dsDNA or to 5mC/5hmC containing ssDNA. The EVE domain is moderately specific for 5mC/5hmC containing DNA according to EMSA experiments. It flips the modified nucleotide, to accommodate it in a hydrophobic pocket of the enzyme, primarily formed by P24, W82 and Y130 residues. In the crystallized conformation, the EVE domain and linker helix between the two domains block DNA binding to the catalytic domain. Removal of the EVE domain and inter-domain linker, but not of the EVE domain alone converts VcaM4I into a non-specific toxic nuclease. The role of the key residues in the EVE and HNH domains of VcaM4I is confirmed by digestion and restriction assays with the enzyme variants that differ from the wild-type by changes to the base binding pocket or to the catalytic residues. Crystal structures of the EVE-HNH endonuclease VcaM4I in the presence and absence of DNA.,Pastor M, Czapinska H, Helbrecht I, Krakowska K, Lutz T, Xu SY, Bochtler M Nucleic Acids Res. 2021 Feb 22;49(3):1708-1723. doi: 10.1093/nar/gkaa1218. PMID:33450012[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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