6dcr - Revision history

OCA at 06:02, 11 October 2023

OCA — Wed, 11 Oct 2023 06:02:43 GMT

←Older revision		Revision as of 06:02, 11 October 2023
Line 3:		Line 3:
	<StructureSection load='6dcr' size='340' side='right'caption='[[6dcr]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='6dcr' size='340' side='right'caption='[[6dcr]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dcr]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DCR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6DCR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dcr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DCR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DCR FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=SO4:SULFATE+ION'>SO4</scene~~>, ~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.978Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[4nl4\|4nl4]], [[4nl8\|4nl8]]~~<~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">priA, b3935, JW3906 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])~~</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=6dcr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dcr OCA], [https://pdbe.org/6dcr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dcr RCSB], [https://www.ebi.ac.uk/pdbsum/6dcr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dcr 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=6dcr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dcr OCA], [~~http~~://pdbe.org/6dcr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6dcr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6dcr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6dcr ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PRIA_ECOLI PRIA_ECOLI]] Involved in the restart of stalled replication forks. Recognizes and binds the arrested nascent DNA chain at stalled replication forks. It can open the DNA duplex, via its helicase activity, and promote assembly of the primosome and loading of the major replicative helicase DnaB onto DNA. Is also involved in initiation of normal DNA replication in various plasmids and phages. Binds to branched DNA structures that resemble D-loops or to the primosome assembly site (PAS). Binds to DNA in two distinct modes, either dependent on or independent of the 3' terminus recognition.<ref>PMID:2825188</ref> <ref>PMID:8366072</ref> <ref>PMID:10356325</ref> <ref>PMID:10956036</ref> <ref>PMID:11929519</ref> <ref>PMID:12622722</ref> <ref>PMID:12917421</ref> <ref>PMID:15576682</ref> <ref>PMID:17483094</ref> <ref>PMID:23264623</ref>	+	[https://www.uniprot.org/uniprot/PRIA_ECOLI PRIA_ECOLI] Involved in the restart of stalled replication forks. Recognizes and binds the arrested nascent DNA chain at stalled replication forks. It can open the DNA duplex, via its helicase activity, and promote assembly of the primosome and loading of the major replicative helicase DnaB onto DNA. Is also involved in initiation of normal DNA replication in various plasmids and phages. Binds to branched DNA structures that resemble D-loops or to the primosome assembly site (PAS). Binds to DNA in two distinct modes, either dependent on or independent of the 3' terminus recognition.<ref>PMID:2825188</ref> <ref>PMID:8366072</ref> <ref>PMID:10356325</ref> <ref>PMID:10956036</ref> <ref>PMID:11929519</ref> <ref>PMID:12622722</ref> <ref>PMID:12917421</ref> <ref>PMID:15576682</ref> <ref>PMID:17483094</ref> <ref>PMID:23264623</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Keck~~, J L~~]]	+	[[Category: Keck JL]]
-	[[Category: Satyshur~~, K A~~]]	+	[[Category: Satyshur KA]]
-	[[Category: Windgassen~~, T A]]~~	+	[[Category: Windgassen TA]]
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Dna replication restart]]~~	+
-	~~[[Category: Helicase]]~~	+
-	~~[[Category: Pria~~]]	+

OCA at 10:59, 1 January 2020

OCA — Wed, 01 Jan 2020 10:59:43 GMT

←Older revision		Revision as of 10:59, 1 January 2020
Line 1:		Line 1:

	==E. coli PriA helicase winged helix domain deletion protein==		==E. coli PriA helicase winged helix domain deletion protein==
-	<StructureSection load='6dcr' size='340' side='right' caption='[[6dcr]], [[Resolution\|resolution]] 1.98Å' scene=''>	+	<StructureSection load='6dcr' size='340' side='right'caption='[[6dcr]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6dcr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DCR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DCR FirstGlance]. <br>		<table><tr><td colspan='2'>[[6dcr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DCR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DCR FirstGlance]. <br>
Line 25:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Ecoli]]		[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: Keck, J L]]		[[Category: Keck, J L]]
	[[Category: Satyshur, K A]]		[[Category: Satyshur, K A]]

OCA at 20:18, 19 September 2018

OCA — Wed, 19 Sep 2018 20:18:56 GMT

←Older revision		Revision as of 20:18, 19 September 2018
Line 3:		Line 3:
	<StructureSection load='6dcr' size='340' side='right' caption='[[6dcr]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='6dcr' size='340' side='right' caption='[[6dcr]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dcr]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DCR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DCR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dcr]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DCR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DCR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nl4\|4nl4]], [[4nl8\|4nl8]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nl4\|4nl4]], [[4nl8\|4nl8]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">priA, b3935, JW3906 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=6dcr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dcr OCA], [http://pdbe.org/6dcr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dcr RCSB], [http://www.ebi.ac.uk/pdbsum/6dcr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dcr 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=6dcr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dcr OCA], [http://pdbe.org/6dcr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dcr RCSB], [http://www.ebi.ac.uk/pdbsum/6dcr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dcr ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/PRIA_ECOLI PRIA_ECOLI]] Involved in the restart of stalled replication forks. Recognizes and binds the arrested nascent DNA chain at stalled replication forks. It can open the DNA duplex, via its helicase activity, and promote assembly of the primosome and loading of the major replicative helicase DnaB onto DNA. Is also involved in initiation of normal DNA replication in various plasmids and phages. Binds to branched DNA structures that resemble D-loops or to the primosome assembly site (PAS). Binds to DNA in two distinct modes, either dependent on or independent of the 3' terminus recognition.<ref>PMID:2825188</ref> <ref>PMID:8366072</ref> <ref>PMID:10356325</ref> <ref>PMID:10956036</ref> <ref>PMID:11929519</ref> <ref>PMID:12622722</ref> <ref>PMID:12917421</ref> <ref>PMID:15576682</ref> <ref>PMID:17483094</ref> <ref>PMID:23264623</ref>		[[http://www.uniprot.org/uniprot/PRIA_ECOLI PRIA_ECOLI]] Involved in the restart of stalled replication forks. Recognizes and binds the arrested nascent DNA chain at stalled replication forks. It can open the DNA duplex, via its helicase activity, and promote assembly of the primosome and loading of the major replicative helicase DnaB onto DNA. Is also involved in initiation of normal DNA replication in various plasmids and phages. Binds to branched DNA structures that resemble D-loops or to the primosome assembly site (PAS). Binds to DNA in two distinct modes, either dependent on or independent of the 3' terminus recognition.<ref>PMID:2825188</ref> <ref>PMID:8366072</ref> <ref>PMID:10356325</ref> <ref>PMID:10956036</ref> <ref>PMID:11929519</ref> <ref>PMID:12622722</ref> <ref>PMID:12917421</ref> <ref>PMID:15576682</ref> <ref>PMID:17483094</ref> <ref>PMID:23264623</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	DNA replication restart, the essential process that reinitiates prematurely terminated genome replication reactions, relies on exquisitely specific recognition of abandoned DNA replication-fork structures. The PriA DNA helicase mediates this process in bacteria through mechanisms that remain poorly defined. We report the crystal structure of a PriA/replication-fork complex, which resolves leading-strand duplex DNA bound to the protein. Interaction with PriA unpairs one end of the DNA and sequesters the 3'-most nucleotide from the nascent leading strand into a conserved protein pocket. Cross-linking studies reveal a surface on the winged-helix domain of PriA that binds to parental duplex DNA. Deleting the winged-helix domain alters PriA's structure-specific DNA unwinding properties and impairs its activity in vivo. Our observations lead to a model in which coordinated parental-, leading-, and lagging-strand DNA binding provide PriA with the structural specificity needed to act on abandoned DNA replication forks.
		+
		+	Structure-specific DNA replication-fork recognition directs helicase and replication restart activities of the PriA helicase.,Windgassen TA, Leroux M, Satyshur KA, Sandler SJ, Keck JL Proc Natl Acad Sci U S A. 2018 Sep 10. pii: 1809842115. doi:, 10.1073/pnas.1809842115. PMID:30201718<ref>PMID:30201718</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6dcr" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ecoli]]
	[[Category: Keck, J L]]		[[Category: Keck, J L]]
	[[Category: Satyshur, K A]]		[[Category: Satyshur, K A]]

OCA at 10:08, 5 September 2018

OCA — Wed, 05 Sep 2018 10:08:10 GMT

←Older revision		Revision as of 10:08, 5 September 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6dcr is ~~ON HOLD until Paper Publication~~	+	==E. coli PriA helicase winged helix domain deletion protein==
-		+	<StructureSection load='6dcr' size='340' side='right' caption='[[6dcr]], [[Resolution\|resolution]] 1.98Å' scene=''>
-	~~Authors~~: ~~Satyshur~~, K.A., ~~Windgassen~~, T.A., ~~Keck~~, J.L.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6dcr]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DCR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DCR FirstGlance]. <br>
-	~~Description~~: E. ~~coli PriA~~ helicase ~~winged helix domain deletion protein~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4nl4\|4nl4]], [[4nl8\|4nl8]]</td></tr>
-	[[Category: ~~Keck~~, ~~J.L~~]]	+	<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=6dcr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dcr OCA], [http://pdbe.org/6dcr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dcr RCSB], [http://www.ebi.ac.uk/pdbsum/6dcr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dcr ProSAT]</span></td></tr>
-	[[Category: Windgassen, T.A]]	+	</table>
-	[[Category: ~~Satyshur, K.A~~]]	+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PRIA_ECOLI PRIA_ECOLI]] Involved in the restart of stalled replication forks. Recognizes and binds the arrested nascent DNA chain at stalled replication forks. It can open the DNA duplex, via its helicase activity, and promote assembly of the primosome and loading of the major replicative helicase DnaB onto DNA. Is also involved in initiation of normal DNA replication in various plasmids and phages. Binds to branched DNA structures that resemble D-loops or to the primosome assembly site (PAS). Binds to DNA in two distinct modes, either dependent on or independent of the 3' terminus recognition.<ref>PMID:2825188</ref> <ref>PMID:8366072</ref> <ref>PMID:10356325</ref> <ref>PMID:10956036</ref> <ref>PMID:11929519</ref> <ref>PMID:12622722</ref> <ref>PMID:12917421</ref> <ref>PMID:15576682</ref> <ref>PMID:17483094</ref> <ref>PMID:23264623</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Keck, J L]]
		+	[[Category: Satyshur, K A]]
		+	[[Category: Windgassen, T A]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Dna replication restart]]
		+	[[Category: Helicase]]
		+	[[Category: Pria]]

OCA at 04:03, 30 May 2018

OCA — Wed, 30 May 2018 04:03:32 GMT

←Older revision		Revision as of 04:03, 30 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Satyshur, K.A., Windgassen, T.A., Keck, J.L.		Authors: Satyshur, K.A., Windgassen, T.A., Keck, J.L.

OCA at 05:59, 23 May 2018

OCA — Wed, 23 May 2018 05:59:12 GMT

←Older revision		Revision as of 05:59, 23 May 2018
Line 5:		Line 5:
	Authors: Satyshur, K.A., Windgassen, T.A., Keck, J.L.		Authors: Satyshur, K.A., Windgassen, T.A., Keck, J.L.

-	Description: ~~1.9 A resolution structure of~~ E. coli PriA helicase ~~with the~~ winged helix domain ~~removed~~	+	Description: E. coli PriA helicase winged helix domain deletion protein
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Keck, J.L]]		[[Category: Keck, J.L]]
	[[Category: Windgassen, T.A]]		[[Category: Windgassen, T.A]]
	[[Category: Satyshur, K.A]]		[[Category: Satyshur, K.A]]

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

OCA — Wed, 16 May 2018 04:07:23 GMT

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

←Older revision

Revision as of 04:07, 16 May 2018

OCA: New page: '''Unreleased structure''' The entry 6dcr is ON HOLD Authors: Satyshur, K.A., Windgassen, T.A., Keck, J.L. Description: 1.9 A resolution structure of E. coli PriA helicase with the win...

OCA — Wed, 16 May 2018 04:07:22 GMT

New page: '''Unreleased structure''' The entry 6dcr is ON HOLD Authors: Satyshur, K.A., Windgassen, T.A., Keck, J.L. Description: 1.9 A resolution structure of E. coli PriA helicase with the win...

New page

'''Unreleased structure'''

The entry 6dcr is ON HOLD

Authors: Satyshur, K.A., Windgassen, T.A., Keck, J.L.

Description: 1.9 A resolution structure of E. coli PriA helicase with the winged helix domain removed
[[Category: Unreleased Structures]]
[[Category: Keck, J.L]]
[[Category: Windgassen, T.A]]
[[Category: Satyshur, K.A]]