4qbl - Revision history

OCA at 11:22, 15 February 2023

OCA — Wed, 15 Feb 2023 11:22:21 GMT

←Older revision		Revision as of 11:22, 15 February 2023
Line 1:		Line 1:

	==VRR_NUC domain protein==		==VRR_NUC domain protein==
-	<StructureSection load='4qbl' size='340' side='right' caption='[[4qbl]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='4qbl' size='340' side='right'caption='[[4qbl]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4qbl]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Psywf Psywf~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QBL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4QBL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4qbl]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Psychrobacter_sp._PRwf-1 Psychrobacter sp. PRwf-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QBL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4QBL 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='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='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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4qbl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qbl OCA], [https://pdbe.org/4qbl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4qbl RCSB], [https://www.ebi.ac.uk/pdbsum/4qbl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4qbl ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qbn\|4qbn]], [[4qbo\|4qbo]]</td></tr>~~	+
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PsycPRwf_1331 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=349106 PSYWF])~~</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=4qbl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qbl OCA], [~~http~~://pdbe.org/4qbl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4qbl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4qbl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4qbl ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A5WF35_PSYWF A5WF35_PSYWF]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Psywf~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Li, J~~]]	+	[[Category: Psychrobacter sp. PRwf-1]]
-	[[Category: ~~Pennell, S~~]]	+	[[Category: Li J]]
-	[[Category: ~~Smerdon,~~ S J]]	+	[[Category: Pennell S]]
-	[[Category: ~~Hydrolase]]~~	+	[[Category: Smerdon SJ]]
-	~~[[Category: Nuclease~~]]	+

OCA at 08:51, 22 November 2017

OCA — Wed, 22 Nov 2017 08:51:41 GMT

←Older revision		Revision as of 08:51, 22 November 2017
Line 3:		Line 3:
	<StructureSection load='4qbl' size='340' side='right' caption='[[4qbl]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='4qbl' size='340' side='right' caption='[[4qbl]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4qbl]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QBL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QBL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4qbl]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Psywf Psywf]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QBL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QBL 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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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='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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qbn\|4qbn]], [[4qbo\|4qbo]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qbn\|4qbn]], [[4qbo\|4qbo]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PsycPRwf_1331 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=349106 PSYWF])</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=4qbl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qbl OCA], [http://pdbe.org/4qbl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qbl RCSB], [http://www.ebi.ac.uk/pdbsum/4qbl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qbl 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=4qbl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qbl OCA], [http://pdbe.org/4qbl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qbl RCSB], [http://www.ebi.ac.uk/pdbsum/4qbl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qbl ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Psywf]]
	[[Category: Li, J]]		[[Category: Li, J]]
	[[Category: Pennell, S]]		[[Category: Pennell, S]]

OCA at 19:07, 11 August 2016

OCA — Thu, 11 Aug 2016 19:07:59 GMT

←Older revision		Revision as of 19:07, 11 August 2016
Line 1:		Line 1:
		+
	==VRR_NUC domain protein==		==VRR_NUC domain protein==
	<StructureSection load='4qbl' size='340' side='right' caption='[[4qbl]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='4qbl' size='340' side='right' caption='[[4qbl]], [[Resolution\|resolution]] 2.00Å' scene=''>
Line 6:		Line 7:
	<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='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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qbn\|4qbn]], [[4qbo\|4qbo]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qbn\|4qbn]], [[4qbo\|4qbo]]</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=4qbl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qbl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qbl RCSB], [http://www.ebi.ac.uk/pdbsum/4qbl 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=4qbl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qbl OCA], [http://pdbe.org/4qbl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4qbl RCSB], [http://www.ebi.ac.uk/pdbsum/4qbl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4qbl ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4qbl" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:27, 20 January 2015

OCA — Tue, 20 Jan 2015 09:27:46 GMT

←Older revision		Revision as of 09:27, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4qbl]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QBL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QBL FirstGlance]. <br>		<table><tr><td colspan='2'>[[4qbl]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QBL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QBL FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><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>
-	<tr><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='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><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qbn\|4qbn]], [[4qbo\|4qbo]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qbn\|4qbn]], [[4qbo\|4qbo]]</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4qbl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qbl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qbl RCSB], [http://www.ebi.ac.uk/pdbsum/4qbl 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=4qbl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qbl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qbl RCSB], [http://www.ebi.ac.uk/pdbsum/4qbl PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Li, J.]]	+	[[Category: Li, J]]
-	[[Category: Pennell, S.]]	+	[[Category: Pennell, S]]
-	[[Category: Smerdon, S J.]]	+	[[Category: Smerdon, S J]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Nuclease]]		[[Category: Nuclease]]

OCA at 09:52, 10 September 2014

OCA — Wed, 10 Sep 2014 09:52:06 GMT

←Older revision		Revision as of 09:52, 10 September 2014
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==VRR_NUC domain protein==
		+	<StructureSection load='4qbl' size='340' side='right' caption='[[4qbl]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4qbl]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4QBL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4QBL FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4qbn\|4qbn]], [[4qbo\|4qbo]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4qbl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4qbl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4qbl RCSB], [http://www.ebi.ac.uk/pdbsum/4qbl PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	FAN1 is a structure-selective DNA repair nuclease with 5' flap endonuclease activity, involved in the repair of interstrand DNA crosslinks. It is the only eukaryotic protein with a virus-type replication-repair nuclease ("VRR-Nuc") "module" that commonly occurs as a standalone domain in many bacteria and viruses. Crystal structures of three representatives show that they structurally resemble Holliday junction resolvases (HJRs), are dimeric in solution, and are able to cleave symmetric four-way junctions. In contrast, FAN1 orthologs are monomeric and cleave 5' flap structures in vitro, but not Holliday junctions. Modeling of the VRR-Nuc domain of FAN1 reveals that it has an insertion, which packs against the dimerization interface observed in the structures of the viral/bacterial VRR-Nuc proteins. We propose that these additional structural elements in FAN1 prevent dimerization and bias specificity toward flap structures.

-	~~The entry 4qbl~~ is ~~ON HOLD~~	+	FAN1 activity on asymmetric repair intermediates is mediated by an atypical monomeric virus-type replication-repair nuclease domain.,Pennell S, Declais AC, Li J, Haire LF, Berg W, Saldanha JW, Taylor IA, Rouse J, Lilley DM, Smerdon SJ Cell Rep. 2014 Jul 10;8(1):84-93. doi: 10.1016/j.celrep.2014.06.001. Epub 2014, Jun 26. PMID:24981866<ref>PMID:24981866</ref>

-	~~Authors: Smerdon~~, S.J., Pennell, S., ~~Li,~~ J.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~VRR_NUC domain protein~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Li, J.]]
		+	[[Category: Pennell, S.]]
		+	[[Category: Smerdon, S J.]]
		+	[[Category: Hydrolase]]
		+	[[Category: Nuclease]]

OCA at 08:16, 21 May 2014

OCA — Wed, 21 May 2014 08:16:31 GMT

←Older revision		Revision as of 08:16, 21 May 2014
Line 3:		Line 3:
	The entry 4qbl is ON HOLD		The entry 4qbl is ON HOLD

-	Authors: Smerdon, S.J., Pennell, S., Li, J	+	Authors: Smerdon, S.J., Pennell, S., Li, J.

	Description: VRR_NUC domain protein		Description: VRR_NUC domain protein

OCA: Protected "4qbl" [edit=sysop:move=sysop]

OCA — Wed, 14 May 2014 07:11:33 GMT

Protected "4qbl" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:11, 14 May 2014

OCA: New page: '''Unreleased structure''' The entry 4qbl is ON HOLD Authors: Smerdon, S.J., Pennell, S., Li, J Description: VRR_NUC domain protein

OCA — Wed, 14 May 2014 07:11:32 GMT

New page: '''Unreleased structure''' The entry 4qbl is ON HOLD Authors: Smerdon, S.J., Pennell, S., Li, J Description: VRR_NUC domain protein

New page

'''Unreleased structure'''

The entry 4qbl is ON HOLD

Authors: Smerdon, S.J., Pennell, S., Li, J

Description: VRR_NUC domain protein