4psl - Revision history

OCA at 07:28, 8 February 2023

OCA — Wed, 08 Feb 2023 07:28:36 GMT

←Older revision		Revision as of 07:28, 8 February 2023
Line 1:		Line 1:

	==Crystal structure of pfuThermo-DBP-RP1 (crystal form I)==		==Crystal structure of pfuThermo-DBP-RP1 (crystal form I)==
-	<StructureSection load='4psl' size='340' side='right' caption='[[4psl]], [[Resolution\|resolution]] 3.50Å' scene=''>	+	<StructureSection load='4psl' size='340' side='right'caption='[[4psl]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4psl]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pyrfu Pyrfu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PSL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4PSL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4psl]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus_DSM_3638 Pyrococcus furiosus DSM 3638]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PSL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4PSL 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></td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=4psl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4psl OCA], [https://pdbe.org/4psl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4psl RCSB], [https://www.ebi.ac.uk/pdbsum/4psl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4psl ProSAT]</span></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat">[[4psm\|4psm]], [[4psn\|4psn]], [[4pso\|4pso]]</td></tr>~~	+
-	~~<tr id='gene~~'>~~<td class="sblockLbl"><b>[[Gene\|Gene:]]~~</b>~~</td><td class="sblockDat">PF1044 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])~~</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=4psl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4psl OCA], [~~http~~://pdbe.org/4psl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4psl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4psl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4psl ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8U208_PYRFU Q8U208_PYRFU]
	<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: ~~Pyrfu~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Eppers, D~~]]	+	[[Category: Pyrococcus furiosus DSM 3638]]
-	[[Category: ~~Gahlei, H~~]]	+	[[Category: Eppers D]]
-	[[Category: ~~Loll, B~~]]	+	[[Category: Gahlei H]]
-	[[Category: ~~Moeller, H von~~]]	+	[[Category: Loll B]]
-	[[Category: Sohmen, D]]	+	[[Category: Sohmen D]]
-	[[Category: Wahl~~, M C~~]]	+	[[Category: Wahl MC]]
-	[[Category: Wilson~~, D N~~]]	+	[[Category: Wilson DN]]
-	[[Category: ~~Dna binding protein]]~~	+	[[Category: Von Moeller H]]
-	~~[[Category: Ssdna binding protein~~]]	+

OCA at 10:49, 11 August 2016

OCA — Thu, 11 Aug 2016 10:49:19 GMT

←Older revision		Revision as of 10:49, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of pfuThermo-DBP-RP1 (crystal form I)==		==Crystal structure of pfuThermo-DBP-RP1 (crystal form I)==
	<StructureSection load='4psl' size='340' side='right' caption='[[4psl]], [[Resolution\|resolution]] 3.50Å' scene=''>		<StructureSection load='4psl' size='340' side='right' caption='[[4psl]], [[Resolution\|resolution]] 3.50Å' scene=''>
Line 7:		Line 8:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4psm\|4psm]], [[4psn\|4psn]], [[4pso\|4pso]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4psm\|4psm]], [[4psn\|4psn]], [[4pso\|4pso]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF1044 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF1044 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</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=4psl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4psl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4psl RCSB], [http://www.ebi.ac.uk/pdbsum/4psl 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=4psl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4psl OCA], [http://pdbe.org/4psl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4psl RCSB], [http://www.ebi.ac.uk/pdbsum/4psl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4psl ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 18:
	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 4psl" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:34, 5 January 2015

OCA — Mon, 05 Jan 2015 08:34:53 GMT

←Older revision		Revision as of 08:34, 5 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4psl]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrfu Pyrfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PSL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PSL FirstGlance]. <br>		<table><tr><td colspan='2'>[[4psl]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrfu Pyrfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PSL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PSL FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><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></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">[[4psm\|4psm]], [[4psn\|4psn]], [[4pso\|4pso]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4psm\|4psm]], [[4psn\|4psn]], [[4pso\|4pso]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF1044 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF1044 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</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=4psl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4psl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4psl RCSB], [http://www.ebi.ac.uk/pdbsum/4psl 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=4psl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4psl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4psl RCSB], [http://www.ebi.ac.uk/pdbsum/4psl 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 22:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Pyrfu]]		[[Category: Pyrfu]]
-	[[Category: Eppers, D.]]	+	[[Category: Eppers, D]]
-	[[Category: Gahlei, H.]]	+	[[Category: Gahlei, H]]
-	[[Category: Loll, B.]]	+	[[Category: Loll, B]]
-	[[Category: Moeller, H von.]]	+	[[Category: Moeller, H von]]
-	[[Category: Sohmen, D.]]	+	[[Category: Sohmen, D]]
-	[[Category: Wahl, M C.]]	+	[[Category: Wahl, M C]]
-	[[Category: Wilson, D N.]]	+	[[Category: Wilson, D N]]
	[[Category: Dna binding protein]]		[[Category: Dna binding protein]]
	[[Category: Ssdna binding protein]]		[[Category: Ssdna binding protein]]

OCA at 05:21, 25 June 2014

OCA — Wed, 25 Jun 2014 05:21:21 GMT

←Older revision		Revision as of 05:21, 25 June 2014
Line 2:		Line 2:
	<StructureSection load='4psl' size='340' side='right' caption='[[4psl]], [[Resolution\|resolution]] 3.50Å' scene=''>		<StructureSection load='4psl' size='340' side='right' caption='[[4psl]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4psl]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PSL OCA]. <br>	+	<table><tr><td colspan='2'>[[4psl]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrfu Pyrfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PSL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4PSL FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>		</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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>[[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">[[4psm\|4psm]], [[4psn\|4psn]], [[4pso\|4pso]]</td></tr>		<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4psm\|4psm]], [[4psn\|4psn]], [[4pso\|4pso]]</td></tr>
-	<tr><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat">~~<span class='plainlinks'>~~[http://en.~~wikipedia~~.~~org/wiki/Glucokinase Glucokinase], with EC number [http://www~~.~~brenda-enzymes~~.~~info~~/~~php~~/~~result_flat~~.~~php4~~?~~ecno~~=~~2.7.1.2 2.7.1.2~~] ~~</span>~~</td></tr>	+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF1044 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</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=4psl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4psl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4psl RCSB], [http://www.ebi.ac.uk/pdbsum/4psl PDBsum]</span></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=4psl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4psl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4psl RCSB], [http://www.ebi.ac.uk/pdbsum/4psl PDBsum]</span></td></tr>
	<table>		<table>
Line 15:		Line 15:
	Entrapment of DNA in an intersubunit tunnel system of a single-stranded DNA-binding protein.,Ghalei H, Moeller HV, Eppers D, Sohmen D, Wilson DN, Loll B, Wahl MC Nucleic Acids Res. 2014 Apr 17. PMID:24744237<ref>PMID:24744237</ref>		Entrapment of DNA in an intersubunit tunnel system of a single-stranded DNA-binding protein.,Ghalei H, Moeller HV, Eppers D, Sohmen D, Wilson DN, Loll B, Wahl MC Nucleic Acids Res. 2014 Apr 17. PMID:24744237<ref>PMID:24744237</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
	== References ==		== References ==
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Pyrfu]]
	[[Category: Eppers, D.]]		[[Category: Eppers, D.]]
	[[Category: Gahlei, H.]]		[[Category: Gahlei, H.]]

OCA at 09:31, 1 May 2014

OCA — Thu, 01 May 2014 09:31:19 GMT

←Older revision		Revision as of 09:31, 1 May 2014
Line 2:		Line 2:
	<StructureSection load='4psl' size='340' side='right' caption='[[4psl]], [[Resolution\|resolution]] 3.50Å' scene=''>		<StructureSection load='4psl' size='340' side='right' caption='[[4psl]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	[[4psl]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PSL OCA]. <br>	+	<table><tr><td colspan='2'>[[4psl]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PSL OCA]. <br>
-	<b>[[Ligand\|Ligands:]]</b> <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
-	<b>[[Non-Standard_Residue\|NonStd Res:]]</b> <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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>
-	<b>[[Related_structure\|Related:]]</b> [[4psm\|4psm]], [[4psn\|4psn]], [[4pso\|4pso]]<br>	+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4psm\|4psm]], [[4psn\|4psn]], [[4pso\|4pso]]</td></tr>
-	<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>	+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></td></tr>
-	<b>Resources:</b> <span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4psl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4psl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4psl RCSB], [http://www.ebi.ac.uk/pdbsum/4psl PDBsum]</span><br>	+	<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=4psl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4psl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4psl RCSB], [http://www.ebi.ac.uk/pdbsum/4psl PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
	Instead of a classical single-stranded deoxyribonuleic acid (DNA)-binding protein (SSB), some hyperthermophilic crenarchaea harbor a non-canonical SSB termed ThermoDBP. Two related but poorly characterized groups of proteins, which share the ThermoDBP N-terminal DNA-binding domain, have a broader phylogenetic distribution and co-exist with ThermoDBPs and/or other SSBs. We have investigated the nucleic acid binding properties and crystal structures of representatives of these groups of ThermoDBP-related proteins (ThermoDBP-RPs) 1 and 2. ThermoDBP-RP 1 and 2 oligomerize by different mechanisms and only ThermoDBP-RP2 exhibits strong single-stranded DNA affinity in vitro. A crystal structure of ThermoDBP-RP2 in complex with DNA reveals how the NTD common to ThermoDBPs and ThermoDBP-RPs can contact the nucleic acid in a manner that allows a symmetric homotetrameric protein complex to bind single-stranded DNA molecules asymmetrically. While single-stranded DNA wraps around the surface or binds along channels of previously investigated SSBs, it traverses an internal, intersubunit tunnel system of a ThermoDBP-RP2 tetramer. Our results indicate that some archaea have acquired special SSBs for genome maintenance in particularly challenging environments.		Instead of a classical single-stranded deoxyribonuleic acid (DNA)-binding protein (SSB), some hyperthermophilic crenarchaea harbor a non-canonical SSB termed ThermoDBP. Two related but poorly characterized groups of proteins, which share the ThermoDBP N-terminal DNA-binding domain, have a broader phylogenetic distribution and co-exist with ThermoDBPs and/or other SSBs. We have investigated the nucleic acid binding properties and crystal structures of representatives of these groups of ThermoDBP-related proteins (ThermoDBP-RPs) 1 and 2. ThermoDBP-RP 1 and 2 oligomerize by different mechanisms and only ThermoDBP-RP2 exhibits strong single-stranded DNA affinity in vitro. A crystal structure of ThermoDBP-RP2 in complex with DNA reveals how the NTD common to ThermoDBPs and ThermoDBP-RPs can contact the nucleic acid in a manner that allows a symmetric homotetrameric protein complex to bind single-stranded DNA molecules asymmetrically. While single-stranded DNA wraps around the surface or binds along channels of previously investigated SSBs, it traverses an internal, intersubunit tunnel system of a ThermoDBP-RP2 tetramer. Our results indicate that some archaea have acquired special SSBs for genome maintenance in particularly challenging environments.
Line 14:		Line 16:

	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>		From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:06, 30 April 2014

OCA — Wed, 30 Apr 2014 10:06:35 GMT

←Older revision		Revision as of 10:06, 30 April 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	[[4psl]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PSL OCA]. <br>		[[4psl]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PSL OCA]. <br>
-	<b>Related:</b> [[4psm\|4psm]], [[4psn\|4psn]], [[4pso\|4pso]]<br>	+	<b>[[Ligand\|Ligands:]]</b> <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<b>[[Non-Standard_Residue\|NonStd Res:]]</b> <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene><br>
		+	<b>[[Related_structure\|Related:]]</b> [[4psm\|4psm]], [[4psn\|4psn]], [[4pso\|4pso]]<br>
	<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>		<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>
		+	<b>Resources:</b> <span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4psl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4psl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4psl RCSB], [http://www.ebi.ac.uk/pdbsum/4psl PDBsum]</span><br>
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
	Instead of a classical single-stranded deoxyribonuleic acid (DNA)-binding protein (SSB), some hyperthermophilic crenarchaea harbor a non-canonical SSB termed ThermoDBP. Two related but poorly characterized groups of proteins, which share the ThermoDBP N-terminal DNA-binding domain, have a broader phylogenetic distribution and co-exist with ThermoDBPs and/or other SSBs. We have investigated the nucleic acid binding properties and crystal structures of representatives of these groups of ThermoDBP-related proteins (ThermoDBP-RPs) 1 and 2. ThermoDBP-RP 1 and 2 oligomerize by different mechanisms and only ThermoDBP-RP2 exhibits strong single-stranded DNA affinity in vitro. A crystal structure of ThermoDBP-RP2 in complex with DNA reveals how the NTD common to ThermoDBPs and ThermoDBP-RPs can contact the nucleic acid in a manner that allows a symmetric homotetrameric protein complex to bind single-stranded DNA molecules asymmetrically. While single-stranded DNA wraps around the surface or binds along channels of previously investigated SSBs, it traverses an internal, intersubunit tunnel system of a ThermoDBP-RP2 tetramer. Our results indicate that some archaea have acquired special SSBs for genome maintenance in particularly challenging environments.		Instead of a classical single-stranded deoxyribonuleic acid (DNA)-binding protein (SSB), some hyperthermophilic crenarchaea harbor a non-canonical SSB termed ThermoDBP. Two related but poorly characterized groups of proteins, which share the ThermoDBP N-terminal DNA-binding domain, have a broader phylogenetic distribution and co-exist with ThermoDBPs and/or other SSBs. We have investigated the nucleic acid binding properties and crystal structures of representatives of these groups of ThermoDBP-related proteins (ThermoDBP-RPs) 1 and 2. ThermoDBP-RP 1 and 2 oligomerize by different mechanisms and only ThermoDBP-RP2 exhibits strong single-stranded DNA affinity in vitro. A crystal structure of ThermoDBP-RP2 in complex with DNA reveals how the NTD common to ThermoDBPs and ThermoDBP-RPs can contact the nucleic acid in a manner that allows a symmetric homotetrameric protein complex to bind single-stranded DNA molecules asymmetrically. While single-stranded DNA wraps around the surface or binds along channels of previously investigated SSBs, it traverses an internal, intersubunit tunnel system of a ThermoDBP-RP2 tetramer. Our results indicate that some archaea have acquired special SSBs for genome maintenance in particularly challenging environments.

OCA at 07:45, 30 April 2014

OCA — Wed, 30 Apr 2014 07:45:21 GMT

←Older revision		Revision as of 07:45, 30 April 2014
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Crystal structure of pfuThermo-DBP-RP1 (crystal form I)==
		+	<StructureSection load='4psl' size='340' side='right' caption='[[4psl]], [[Resolution\|resolution]] 3.50Å' scene=''>
		+	== Structural highlights ==
		+	[[4psl]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4PSL OCA]. <br>
		+	<b>Related:</b> [[4psm\|4psm]], [[4psn\|4psn]], [[4pso\|4pso]]<br>
		+	<b>Activity:</b> <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span><br>
		+	== Publication Abstract from PubMed ==
		+	Instead of a classical single-stranded deoxyribonuleic acid (DNA)-binding protein (SSB), some hyperthermophilic crenarchaea harbor a non-canonical SSB termed ThermoDBP. Two related but poorly characterized groups of proteins, which share the ThermoDBP N-terminal DNA-binding domain, have a broader phylogenetic distribution and co-exist with ThermoDBPs and/or other SSBs. We have investigated the nucleic acid binding properties and crystal structures of representatives of these groups of ThermoDBP-related proteins (ThermoDBP-RPs) 1 and 2. ThermoDBP-RP 1 and 2 oligomerize by different mechanisms and only ThermoDBP-RP2 exhibits strong single-stranded DNA affinity in vitro. A crystal structure of ThermoDBP-RP2 in complex with DNA reveals how the NTD common to ThermoDBPs and ThermoDBP-RPs can contact the nucleic acid in a manner that allows a symmetric homotetrameric protein complex to bind single-stranded DNA molecules asymmetrically. While single-stranded DNA wraps around the surface or binds along channels of previously investigated SSBs, it traverses an internal, intersubunit tunnel system of a ThermoDBP-RP2 tetramer. Our results indicate that some archaea have acquired special SSBs for genome maintenance in particularly challenging environments.

-	~~The entry 4psl is ON HOLD until Paper Publication~~	+	Entrapment of DNA in an intersubunit tunnel system of a single-stranded DNA-binding protein.,Ghalei H, Moeller HV, Eppers D, Sohmen D, Wilson DN, Loll B, Wahl MC Nucleic Acids Res. 2014 Apr 17. PMID:24744237<ref>PMID:24744237</ref>

-	~~Authors~~: Gahlei, H., ~~von~~ Moeller, H.~~, Eppers, D.,~~ Sohmen, D., Wilson, D.N.~~, Loll, B., Wahl, M.C.~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	== References ==
-	~~Description~~:	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Eppers, D.]]
		+	[[Category: Gahlei, H.]]
		+	[[Category: Loll, B.]]
		+	[[Category: Moeller, H von.]]
		+	[[Category: Sohmen, D.]]
		+	[[Category: Wahl, M C.]]
		+	[[Category: Wilson, D N.]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Ssdna binding protein]]

OCA at 09:06, 16 April 2014

OCA — Wed, 16 Apr 2014 09:06:43 GMT

←Older revision		Revision as of 09:06, 16 April 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4psl is ON HOLD	+	The entry 4psl is ON HOLD until Paper Publication

	Authors: Gahlei, H., von Moeller, H., Eppers, D., Sohmen, D., Wilson, D.N., Loll, B., Wahl, M.C.		Authors: Gahlei, H., von Moeller, H., Eppers, D., Sohmen, D., Wilson, D.N., Loll, B., Wahl, M.C.

-	Description: ~~ssDNA binding protein~~	+	Description:

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

OCA — Wed, 19 Mar 2014 07:41:09 GMT

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

←Older revision

Revision as of 07:41, 19 March 2014

OCA: New page: '''Unreleased structure''' The entry 4psl is ON HOLD Authors: Gahlei, H., von Moeller, H., Eppers, D., Sohmen, D., Wilson, D.N., Loll, B., Wahl, M.C. Description: ssDNA binding protein

OCA — Wed, 19 Mar 2014 07:41:07 GMT

New page: '''Unreleased structure''' The entry 4psl is ON HOLD Authors: Gahlei, H., von Moeller, H., Eppers, D., Sohmen, D., Wilson, D.N., Loll, B., Wahl, M.C. Description: ssDNA binding protein

New page

'''Unreleased structure'''

The entry 4psl is ON HOLD

Authors: Gahlei, H., von Moeller, H., Eppers, D., Sohmen, D., Wilson, D.N., Loll, B., Wahl, M.C.

Description: ssDNA binding protein