6njw: Difference between revisions

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<StructureSection load='6njw' size='340' side='right'caption='[[6njw]], [[Resolution|resolution]] 1.86&Aring;' scene=''>
<StructureSection load='6njw' size='340' side='right'caption='[[6njw]], [[Resolution|resolution]] 1.86&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6njw]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Xancb Xancb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NJW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NJW FirstGlance]. <br>
<table><tr><td colspan='2'>[[6njw]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Xanthomonas_campestris_pv._campestris_str._B100 Xanthomonas campestris pv. campestris str. B100]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NJW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6NJW FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</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]] 1.86&#8491;</td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">XCCB100_2436 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=509169 XANCB])</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</scene></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=6njw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6njw OCA], [http://pdbe.org/6njw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6njw RCSB], [http://www.ebi.ac.uk/pdbsum/6njw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6njw 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=6njw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6njw OCA], [https://pdbe.org/6njw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6njw RCSB], [https://www.ebi.ac.uk/pdbsum/6njw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6njw ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/B0RTN2_XANCB B0RTN2_XANCB]
Overcoming lysogenization defect (OLD) proteins constitute a family of uncharacterized nucleases present in bacteria, archaea, and some viruses. These enzymes contain an N-terminal ATPase domain and a C-terminal Toprim domain common amongst replication, recombination, and repair proteins. The in vivo activities of OLD proteins remain poorly understood and no definitive structural information exists. Here we identify and define two classes of OLD proteins based on differences in gene neighborhood and amino acid sequence conservation and present the crystal structures of the catalytic C-terminal regions from the Burkholderia pseudomallei and Xanthamonas campestris p.v. campestris Class 2 OLD proteins at 2.24 A and 1.86 A resolution respectively. The structures reveal a two-domain architecture containing a Toprim domain with altered architecture and a unique helical domain. Conserved side chains contributed by both domains coordinate two bound magnesium ions in the active site of B. pseudomallei OLD in a geometry that supports a two-metal catalysis mechanism for cleavage. The spatial organization of these domains additionally suggests a novel mode of DNA binding that is distinct from other Toprim containing proteins. Together, these findings define the fundamental structural properties of the OLD family catalytic core and the underlying mechanism controlling nuclease activity.
 
Structural characterization of Class 2 OLD family nucleases supports a two-metal catalysis mechanism for cleavage.,Schiltz CJ, Lee A, Partlow EA, Hosford CJ, Chappie JS Nucleic Acids Res. 2019 Aug 10. pii: 5545734. doi: 10.1093/nar/gkz703. PMID:31400118<ref>PMID:31400118</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6njw" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Xancb]]
[[Category: Xanthomonas campestris pv. campestris str. B100]]
[[Category: Chappie, J S]]
[[Category: Chappie JS]]
[[Category: Hosford, C J]]
[[Category: Hosford CJ]]
[[Category: Lee, A]]
[[Category: Lee A]]
[[Category: Partlow, E A]]
[[Category: Partlow EA]]
[[Category: Schiltz, C J]]
[[Category: Schiltz CJ]]
[[Category: Nuclease]]
[[Category: Toprim]]
[[Category: Unknown function]]
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