5c15 - Revision history

OCA at 09:31, 15 November 2023

OCA — Wed, 15 Nov 2023 09:31:36 GMT

←Older revision		Revision as of 09:31, 15 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5c15]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Shigella_virus_Sf6 Shigella virus Sf6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C15 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5C15 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5c15]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Shigella_virus_Sf6 Shigella virus Sf6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C15 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5C15 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 1.57Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=5c15 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c15 OCA], [https://pdbe.org/5c15 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5c15 RCSB], [https://www.ebi.ac.uk/pdbsum/5c15 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5c15 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=5c15 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c15 OCA], [https://pdbe.org/5c15 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5c15 RCSB], [https://www.ebi.ac.uk/pdbsum/5c15 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5c15 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:15, 7 June 2023

OCA — Wed, 07 Jun 2023 06:15:46 GMT

←Older revision		Revision as of 06:15, 7 June 2023
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	<StructureSection load='5c15' size='340' side='right'caption='[[5c15]], [[Resolution\|resolution]] 1.57Å' scene=''>		<StructureSection load='5c15' size='340' side='right'caption='[[5c15]], [[Resolution\|resolution]] 1.57Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5c15]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bpsfv Bpsfv~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C15 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5C15 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5c15]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Shigella_virus_Sf6 Shigella virus Sf6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C15 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5C15 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4idh\|4idh]], [[5c10\|5c10]], [[5c12\|5c12]], [[5c2d\|5c2d]], [[5c2f\|5c2f]]~~</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=5c15 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c15 OCA], [https://pdbe.org/5c15 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5c15 RCSB], [https://www.ebi.ac.uk/pdbsum/5c15 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5c15 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=5c15 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c15 OCA], [~~http~~://pdbe.org/5c15 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5c15 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5c15 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5c15 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q716H3_BPSFV Q716H3_BPSFV]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
-	*[[Terminase\|Terminase]]	+	*[[Terminase 3D Structures\|Terminase 3D Structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bpsfv]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Tang, L~~]]	+	[[Category: Shigella virus Sf6]]
-	[[Category: ~~Zhao, H~~]]	+	[[Category: Tang L]]
-	[[Category: ~~Metal binding protein]]~~	+	[[Category: Zhao H]]
-	~~[[Category: Metal binding site]]~~	+
-	~~[[Category: Nuclease domain~~]]	+

OCA at 11:08, 25 December 2019

OCA — Wed, 25 Dec 2019 11:08:43 GMT

←Older revision		Revision as of 11:08, 25 December 2019
Line 1:		Line 1:

	==K428A muntant nuclease domain of the large terminase subunit gp2 of bacterial virus Sf6 with Manganese==		==K428A muntant nuclease domain of the large terminase subunit gp2 of bacterial virus Sf6 with Manganese==
-	<StructureSection load='5c15' size='340' side='right' caption='[[5c15]], [[Resolution\|resolution]] 1.57Å' scene=''>	+	<StructureSection load='5c15' size='340' side='right'caption='[[5c15]], [[Resolution\|resolution]] 1.57Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5c15]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpsfv Bpsfv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C15 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5C15 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5c15]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpsfv Bpsfv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C15 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5C15 FirstGlance]. <br>
Line 17:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 5c15" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5c15" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Terminase\|Terminase]]
	== References ==		== References ==
	<references/>		<references/>
Line 22:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Bpsfv]]		[[Category: Bpsfv]]
		+	[[Category: Large Structures]]
	[[Category: Tang, L]]		[[Category: Tang, L]]
	[[Category: Zhao, H]]		[[Category: Zhao, H]]

OCA at 12:24, 6 November 2017

OCA — Mon, 06 Nov 2017 12:24:29 GMT

←Older revision		Revision as of 12:24, 6 November 2017
Line 1:		Line 1:
		+
	==K428A muntant nuclease domain of the large terminase subunit gp2 of bacterial virus Sf6 with Manganese==		==K428A muntant nuclease domain of the large terminase subunit gp2 of bacterial virus Sf6 with Manganese==
	<StructureSection load='5c15' size='340' side='right' caption='[[5c15]], [[Resolution\|resolution]] 1.57Å' scene=''>		<StructureSection load='5c15' size='340' side='right' caption='[[5c15]], [[Resolution\|resolution]] 1.57Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5c15]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C15 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5C15 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5c15]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpsfv Bpsfv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C15 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5C15 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4idh\|4idh]], [[5c10\|5c10]], [[5c12\|5c12]], [[5c2d\|5c2d]], [[5c2f\|5c2f]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4idh\|4idh]], [[5c10\|5c10]], [[5c12\|5c12]], [[5c2d\|5c2d]], [[5c2f\|5c2f]]</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=5c15 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c15 OCA], [http://pdbe.org/5c15 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5c15 RCSB], [http://www.ebi.ac.uk/pdbsum/5c15 PDBsum]</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=5c15 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c15 OCA], [http://pdbe.org/5c15 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5c15 RCSB], [http://www.ebi.ac.uk/pdbsum/5c15 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5c15 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bpsfv]]
	[[Category: Tang, L]]		[[Category: Tang, L]]
	[[Category: Zhao, H]]		[[Category: Zhao, H]]

OCA at 05:25, 22 October 2015

OCA — Thu, 22 Oct 2015 05:25:11 GMT

←Older revision		Revision as of 05:25, 22 October 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==K428A muntant nuclease domain of the large terminase subunit gp2 of bacterial virus Sf6 with Manganese==
		+	<StructureSection load='5c15' size='340' side='right' caption='[[5c15]], [[Resolution\|resolution]] 1.57Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5c15]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5C15 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5C15 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4idh\|4idh]], [[5c10\|5c10]], [[5c12\|5c12]], [[5c2d\|5c2d]], [[5c2f\|5c2f]]</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=5c15 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5c15 OCA], [http://pdbe.org/5c15 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5c15 RCSB], [http://www.ebi.ac.uk/pdbsum/5c15 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Many dsDNA viruses encode DNA-packaging terminases, each containing a nuclease domain that resolves concatemeric DNA into genome-length units. Terminase nucleases resemble the RNase H-superfamily nucleotidyltransferases in folds, and share a two-metal-ion catalytic mechanism. Here we show that residue K428 of a bacteriophage terminase gp2 nuclease domain mediates binding of the metal cofactor Mg2+. A K428A mutation allows visualization, at high resolution, of a metal ion binding mode with a coupled-octahedral configuration at the active site, exhibiting an unusually short metal-metal distance of 2.42 A. Such proximity of the two metal ions may play an essential role in catalysis by generating a highly positive electrostatic niche to enable formation of the negatively charged pentacovalent phosphate transition state, and provides the structural basis for distinguishing Mg2+ from Ca2+. Using a metal ion chelator beta-thujaplicinol as a molecular probe, we observed a second mode of metal ion binding at the active site, mimicking the DNA binding state. Arrangement of the active site residues differs drastically from those in RNase H-like nucleases, suggesting a drifting of the active site configuration during evolution. The two distinct metal ion binding modes unveiled mechanistic details of the two-metal-ion catalysis at atomic resolution.

-	~~The entry 5c15 is ON HOLD until Paper Publication~~	+	Two distinct modes of metal ion binding in the nuclease active site of a viral DNA-packaging terminase: insight into the two-metal-ion catalytic mechanism.,Zhao H, Lin Z, Lynn AY, Varnado B, Beutler JA, Murelli RP, Le Grice SF, Tang L Nucleic Acids Res. 2015 Oct 7. pii: gkv1018. PMID:26450964<ref>PMID:26450964</ref>

-	~~Authors: Zhao~~, H.~~, Tang, L~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~K428A muntant nuclease domain of the large terminase subunit gp2 of bacterial virus Sf6 with Manganese~~	+	<div class="pdbe-citations 5c15" style="background-color:#fffaf0;"></div>
-	~~[[Category: Unreleased Structures]]~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Tang, L]]		[[Category: Tang, L]]
	[[Category: Zhao, H]]		[[Category: Zhao, H]]
		+	[[Category: Metal binding protein]]
		+	[[Category: Metal binding site]]
		+	[[Category: Nuclease domain]]

OCA at 11:29, 26 August 2015

OCA — Wed, 26 Aug 2015 11:29:04 GMT

←Older revision		Revision as of 11:29, 26 August 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5c15 is ON HOLD	+	The entry 5c15 is ON HOLD until Paper Publication

	Authors: Zhao, H., Tang, L.		Authors: Zhao, H., Tang, L.

OCA: Protected "5c15" [edit=sysop:move=sysop]

OCA — Wed, 24 Jun 2015 11:54:13 GMT

Protected "5c15" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:54, 24 June 2015

OCA: New page: '''Unreleased structure''' The entry 5c15 is ON HOLD Authors: Zhao, H., Tang, L. Description: K428A muntant nuclease domain of the large terminase subunit gp2 of bacterial virus Sf6 wi...

OCA — Wed, 24 Jun 2015 11:54:12 GMT

New page: '''Unreleased structure''' The entry 5c15 is ON HOLD Authors: Zhao, H., Tang, L. Description: K428A muntant nuclease domain of the large terminase subunit gp2 of bacterial virus Sf6 wi...

New page

'''Unreleased structure'''

The entry 5c15 is ON HOLD

Authors: Zhao, H., Tang, L.

Description: K428A muntant nuclease domain of the large terminase subunit gp2 of bacterial virus Sf6 with Manganese
[[Category: Unreleased Structures]]
[[Category: Tang, L]]
[[Category: Zhao, H]]