View source for 9bgj


==SgrAI mutant K242A endonuclease DNA-bound dimer with Mg2+ and intact primary site DNA==
<StructureSection load='9bgj' size='340' side='right'caption='[[9bgj]], [[Resolution|resolution]] 3.34&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[9bgj]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_griseus Streptomyces griseus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9BGJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9BGJ FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.34&#8491;</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></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=9bgj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9bgj OCA], [https://pdbe.org/9bgj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9bgj RCSB], [https://www.ebi.ac.uk/pdbsum/9bgj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9bgj ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q9F6L0_STRGR Q9F6L0_STRGR] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Enzymes that form filamentous assemblies with modulated enzymatic activities have gained increasing attention in recent years. SgrAI is a sequence specific type II restriction endonuclease that forms polymeric filaments with accelerated DNA cleavage activity and expanded DNA sequence specificity. Prior studies have suggested a mechanistic model linking the structural changes accompanying SgrAI filamentation to its accelerated DNA cleavage activity. In this model, the conformational changes that are specific to filamentous SgrAI maximize contacts between different copies of the enzyme within the filament and create a second divalent cation binding site in each subunit, which in turn facilitates the DNA cleavage reaction. However, our understanding of the atomic mechanism of catalysis is incomplete. Herein, we present two new structures of filamentous SgrAI solved using cryo-EM. The first structure, resolved to 3.3 A, is of filamentous SgrAI containing an active site mutation that is designed to stall the DNA cleavage reaction, which reveals the enzymatic configuration prior to DNA cleavage. The second structure, resolved to 3.1 A, is of WT filamentous SgrAI containing cleaved substrate DNA, which reveals the enzymatic configuration at the end of the enzymatic cleavage reaction. Both structures contain the phosphate moiety at the cleavage site and the biologically relevant divalent cation cofactor Mg(2+) and define how the Mg(2+) cation reconfigures during enzymatic catalysis. The data support a model for the activation mechanism that involves binding of a second Mg(2+) in the SgrAI active site as a direct result of filamentation induced conformational changes.

Two-metal ion mechanism of DNA cleavage by activated, filamentous SgrAI.,Shan Z, Rivero-Gamez A, Lyumkis D, Horton NC J Biol Chem. 2024 Aug;300(8):107576. doi: 10.1016/j.jbc.2024.107576. Epub 2024 , Jul 14. PMID:39009341<ref>PMID:39009341</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 9bgj" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Streptomyces griseus]]
[[Category: Horton NC]]
[[Category: Lyumkis D]]
[[Category: Shan Z]]