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| | ==eukaryotic junction-resolving enzyme GEN-1 binding with Sodium== | | ==eukaryotic junction-resolving enzyme GEN-1 binding with Sodium== |
| - | <StructureSection load='6grc' size='340' side='right' caption='[[6grc]], [[Resolution|resolution]] 2.45Å' scene=''> | + | <StructureSection load='6grc' size='340' side='right'caption='[[6grc]], [[Resolution|resolution]] 2.45Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6grc]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"thermofilum_carboxyditrophus"_sokolova_et_al._2009 "thermofilum carboxyditrophus" sokolova et al. 2009]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6GRC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6GRC FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6grc]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Chaetomium_thermophilum_var._thermophilum_DSM_1495 Chaetomium thermophilum var. thermophilum DSM 1495] and [https://en.wikipedia.org/wiki/Pichia_kudriavzevii Pichia kudriavzevii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6GRC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6GRC FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.452Å</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CTHT_0007290 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1483572 "Thermofilum carboxyditrophus" Sokolova et al. 2009])</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=6grc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6grc OCA], [https://pdbe.org/6grc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6grc RCSB], [https://www.ebi.ac.uk/pdbsum/6grc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6grc ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6grc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6grc OCA], [http://pdbe.org/6grc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6grc RCSB], [http://www.ebi.ac.uk/pdbsum/6grc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6grc ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/G0RYN2_CHATD G0RYN2_CHATD] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Thermofilum carboxyditrophus sokolova et al. 2009]] | + | [[Category: Chaetomium thermophilum var. thermophilum DSM 1495]] |
| - | [[Category: Freeman, D J]] | + | [[Category: Large Structures]] |
| - | [[Category: Lilley, D M.J]] | + | [[Category: Pichia kudriavzevii]] |
| - | [[Category: Liu, Y]] | + | [[Category: Freeman DJ]] |
| - | [[Category: 4-way holiday junction]] | + | [[Category: Lilley DMJ]] |
| - | [[Category: Dna]] | + | [[Category: Liu Y]] |
| - | [[Category: Dna recombination]]
| + | |
| - | [[Category: Gen1]]
| + | |
| - | [[Category: H2th]]
| + | |
| - | [[Category: Potassium]]
| + | |
| - | [[Category: Resolvase]]
| + | |
| Structural highlights
Function
G0RYN2_CHATD
Publication Abstract from PubMed
GEN1 is a member of the FEN/EXO family of structure-selective nucleases that cleave 1 nt 3' to a variety of branchpoints. For each, the H2TH motif binds a monovalent ion and plays an important role in binding one helical arm of the substrates. We investigate here the importance of this metal ion on substrate specificity and GEN1 structure. In the presence of K+ ions the substrate specificity is wider than in Na+, yet four-way junctions remain the preferred substrate. In a combination of K+ and Mg2+ second strand cleavage is accelerated 17-fold, ensuring bilateral cleavage of the junction. We have solved crystal structures of Chaetomium thermophilum GEN1 with Cs+, K+ and Na+ bound. With bound Cs+ the loop of the H2TH motif extends toward the active site so that D199 coordinates a Mg2+, buttressed by an interaction of the adjacent Y200. With the lighter ions bound the H2TH loop changes conformation and retracts away from the active site. We hypothesize this conformational change might play a role in second strand cleavage acceleration.
A monovalent ion in the DNA binding interface of the eukaryotic junction-resolving enzyme GEN1.,Liu Y, Freeman ADJ, Declais AC, Lilley DMJ Nucleic Acids Res. 2018 Sep 24. pii: 5106143. doi: 10.1093/nar/gky863. PMID:30247722[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Liu Y, Freeman ADJ, Declais AC, Lilley DMJ. A monovalent ion in the DNA binding interface of the eukaryotic junction-resolving enzyme GEN1. Nucleic Acids Res. 2018 Sep 24. pii: 5106143. doi: 10.1093/nar/gky863. PMID:30247722 doi:http://dx.doi.org/10.1093/nar/gky863
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