6njv - Revision history

OCA at 14:47, 13 March 2024

OCA — Wed, 13 Mar 2024 14:47:53 GMT

←Older revision		Revision as of 14:47, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6njv' size='340' side='right'caption='[[6njv]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='6njv' size='340' side='right'caption='[[6njv]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6njv]] 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=6NJV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6NJV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6njv]] 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=6NJV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6NJV 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>~~</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]] 2.3Å</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></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=6njv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6njv OCA], [~~http~~://pdbe.org/6njv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6njv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6njv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6njv 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=6njv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6njv OCA], [https://pdbe.org/6njv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6njv RCSB], [https://www.ebi.ac.uk/pdbsum/6njv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6njv 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®/PubMed®, a database of the U~~.~~S. National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6njv" 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~~]]	+

OCA at 06:37, 21 August 2019

OCA — Wed, 21 Aug 2019 06:37:28 GMT

←Older revision		Revision as of 06:37, 21 August 2019
Line 3:		Line 3:
	<StructureSection load='6njv' size='340' side='right'caption='[[6njv]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='6njv' size='340' side='right'caption='[[6njv]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6njv]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NJV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NJV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6njv]] 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=6NJV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NJV 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></td></tr>		</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></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='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=6njv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6njv OCA], [http://pdbe.org/6njv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6njv RCSB], [http://www.ebi.ac.uk/pdbsum/6njv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6njv 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=6njv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6njv OCA], [http://pdbe.org/6njv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6njv RCSB], [http://www.ebi.ac.uk/pdbsum/6njv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6njv ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	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®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6njv" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Xancb]]
	[[Category: Chappie, J S]]		[[Category: Chappie, J S]]
	[[Category: Hosford, C J]]		[[Category: Hosford, C J]]

OCA at 05:55, 7 August 2019

OCA — Wed, 07 Aug 2019 05:55:48 GMT

←Older revision		Revision as of 05:55, 7 August 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6njv ~~is ON HOLD until Paper Publication~~	+	==C-terminal region of the Xanthomonas campestris pv. campestris OLD protein phased with iodine==
-		+	<StructureSection load='6njv' size='340' side='right'caption='[[6njv]], [[Resolution\|resolution]] 2.30Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6njv]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NJV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NJV FirstGlance]. <br>
-	~~Description~~:	+	</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></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<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=6njv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6njv OCA], [http://pdbe.org/6njv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6njv RCSB], [http://www.ebi.ac.uk/pdbsum/6njv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6njv ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Chappie, J S]]
		+	[[Category: Hosford, C J]]
		+	[[Category: Lee, A]]
		+	[[Category: Partlow, E A]]
		+	[[Category: Schiltz, C J]]
		+	[[Category: Nuclease]]
		+	[[Category: Toprim]]
		+	[[Category: Unknown function]]

OCA at 05:05, 21 February 2019

OCA — Thu, 21 Feb 2019 05:05:27 GMT

←Older revision		Revision as of 05:05, 21 February 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6njv is ON HOLD	+	The entry 6njv is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6njv" [edit=sysop:move=sysop]

OCA — Wed, 16 Jan 2019 10:40:01 GMT

Protected "6njv" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:40, 16 January 2019

OCA: New page: '''Unreleased structure''' The entry 6njv is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 16 Jan 2019 10:39:59 GMT

New page: '''Unreleased structure''' The entry 6njv is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6njv is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]