4y1j - Revision history

OCA at 13:02, 1 March 2024

OCA — Fri, 01 Mar 2024 13:02:24 GMT

←Older revision		Revision as of 13:02, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4y1j]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactococcus_lactis_subsp._lactis Lactococcus lactis subsp. lactis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y1J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Y1J FirstGlance]. <br>		<table><tr><td colspan='2'>[[4y1j]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactococcus_lactis_subsp._lactis Lactococcus lactis subsp. lactis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y1J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Y1J FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</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]] 2.24Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</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=4y1j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y1j OCA], [https://pdbe.org/4y1j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4y1j RCSB], [https://www.ebi.ac.uk/pdbsum/4y1j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4y1j 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=4y1j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y1j OCA], [https://pdbe.org/4y1j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4y1j RCSB], [https://www.ebi.ac.uk/pdbsum/4y1j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4y1j ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Gene regulation in cis by riboswitches is prevalent in bacteria. The yybP-ykoY riboswitch family is quite widespread, yet its ligand and function remained unknown. Here, we characterize the Lactococcus lactis yybP-ykoY orphan riboswitch as a Mn(2+)-dependent transcription-ON riboswitch, with a approximately 30-40 muM affinity for Mn(2+). We further determined its crystal structure at 2.7 A to elucidate the metal sensing mechanism. The riboswitch resembles a hairpin, with two coaxially stacked helices tethered by a four-way junction and a tertiary docking interface. The Mn(2+)-sensing region, strategically located at the highly conserved docking interface, has two metal binding sites. Whereas one site tolerates the binding of either Mg(2+) or Mn(2+), the other site strongly prefers Mn(2+) due to a direct contact from the N7 of an invariable adenosine. Mutagenesis and a Mn(2+)-free E. coli yybP-ykoY structure further reveal that Mn(2+) binding is coupled with stabilization of the Mn(2+)-sensing region and the aptamer domain.
-
-	Mn(2+)-Sensing Mechanisms of yybP-ykoY Orphan Riboswitches.,Price IR, Gaballa A, Ding F, Helmann JD, Ke A Mol Cell. 2015 Mar 19;57(6):1110-23. doi: 10.1016/j.molcel.2015.02.016. PMID:25794619<ref>PMID:25794619</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4y1j" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Riboswitch 3D structures\|Riboswitch 3D structures]]		*[[Riboswitch 3D structures\|Riboswitch 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 18:03, 26 April 2023

OCA — Wed, 26 Apr 2023 18:03:02 GMT

←Older revision		Revision as of 18:03, 26 April 2023
Line 3:		Line 3:
	<StructureSection load='4y1j' size='340' side='right'caption='[[4y1j]], [[Resolution\|resolution]] 2.24Å' scene=''>		<StructureSection load='4y1j' size='340' side='right'caption='[[4y1j]], [[Resolution\|resolution]] 2.24Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4y1j]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y1J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4Y1J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4y1j]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactococcus_lactis_subsp._lactis Lactococcus lactis subsp. lactis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y1J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Y1J FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4y1i\|4y1i]], [[4y1m\|4y1m]]~~</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=4y1j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y1j OCA], [https://pdbe.org/4y1j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4y1j RCSB], [https://www.ebi.ac.uk/pdbsum/4y1j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4y1j 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=4y1j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y1j OCA], [~~http~~://pdbe.org/4y1j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4y1j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4y1j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4y1j ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 19:		Line 18:

	==See Also==		==See Also==
-	*[[Riboswitch\|Riboswitch]]	+	*[[Riboswitch 3D structures\|Riboswitch 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Lactococcus lactis subsp. lactis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ke, A]]	+	[[Category: Ke A]]
-	[[Category: Price~~, I R]]~~	+	[[Category: Price IR]]
-	~~[[Category: Manganese-binding]]~~	+
-	~~[[Category: Mutant]]~~	+
-	~~[[Category: Riboswitch]]~~	+
-	~~[[Category: Rna~~]]	+

OCA at 10:42, 25 December 2019

OCA — Wed, 25 Dec 2019 10:42:00 GMT

←Older revision		Revision as of 10:42, 25 December 2019
Line 1:		Line 1:

	==Lactococcus lactis yybP-ykoY Mn riboswitch A41U binding site mutant in presence of Mn2+==		==Lactococcus lactis yybP-ykoY Mn riboswitch A41U binding site mutant in presence of Mn2+==
-	<StructureSection load='4y1j' size='340' side='right' caption='[[4y1j]], [[Resolution\|resolution]] 2.24Å' scene=''>	+	<StructureSection load='4y1j' size='340' side='right'caption='[[4y1j]], [[Resolution\|resolution]] 2.24Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4y1j]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y1J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Y1J FirstGlance]. <br>		<table><tr><td colspan='2'>[[4y1j]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y1J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Y1J FirstGlance]. <br>
Line 24:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Ke, A]]		[[Category: Ke, A]]
	[[Category: Price, I R]]		[[Category: Price, I R]]

OCA at 06:33, 26 July 2016

OCA — Tue, 26 Jul 2016 06:33:17 GMT

←Older revision		Revision as of 06:33, 26 July 2016
Line 1:		Line 1:
		+
	==Lactococcus lactis yybP-ykoY Mn riboswitch A41U binding site mutant in presence of Mn2+==		==Lactococcus lactis yybP-ykoY Mn riboswitch A41U binding site mutant in presence of Mn2+==
	<StructureSection load='4y1j' size='340' side='right' caption='[[4y1j]], [[Resolution\|resolution]] 2.24Å' scene=''>		<StructureSection load='4y1j' size='340' side='right' caption='[[4y1j]], [[Resolution\|resolution]] 2.24Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4y1i\|4y1i]], [[4y1m\|4y1m]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4y1i\|4y1i]], [[4y1m\|4y1m]]</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=4y1j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y1j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4y1j RCSB], [http://www.ebi.ac.uk/pdbsum/4y1j 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=4y1j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y1j OCA], [http://pdbe.org/4y1j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4y1j RCSB], [http://www.ebi.ac.uk/pdbsum/4y1j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4y1j ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	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 4y1j" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Riboswitch\|Riboswitch]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:08, 8 April 2015

OCA — Wed, 08 Apr 2015 11:08:23 GMT

←Older revision		Revision as of 11:08, 8 April 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Lactococcus lactis yybP-ykoY Mn riboswitch A41U binding site mutant in presence of Mn2+==
		+	<StructureSection load='4y1j' size='340' side='right' caption='[[4y1j]], [[Resolution\|resolution]] 2.24Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4y1j]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y1J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Y1J FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4y1i\|4y1i]], [[4y1m\|4y1m]]</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=4y1j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y1j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4y1j RCSB], [http://www.ebi.ac.uk/pdbsum/4y1j PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Gene regulation in cis by riboswitches is prevalent in bacteria. The yybP-ykoY riboswitch family is quite widespread, yet its ligand and function remained unknown. Here, we characterize the Lactococcus lactis yybP-ykoY orphan riboswitch as a Mn(2+)-dependent transcription-ON riboswitch, with a approximately 30-40 muM affinity for Mn(2+). We further determined its crystal structure at 2.7 A to elucidate the metal sensing mechanism. The riboswitch resembles a hairpin, with two coaxially stacked helices tethered by a four-way junction and a tertiary docking interface. The Mn(2+)-sensing region, strategically located at the highly conserved docking interface, has two metal binding sites. Whereas one site tolerates the binding of either Mg(2+) or Mn(2+), the other site strongly prefers Mn(2+) due to a direct contact from the N7 of an invariable adenosine. Mutagenesis and a Mn(2+)-free E. coli yybP-ykoY structure further reveal that Mn(2+) binding is coupled with stabilization of the Mn(2+)-sensing region and the aptamer domain.

-	~~The entry 4y1j is ON HOLD until Paper Publication~~	+	Mn(2+)-Sensing Mechanisms of yybP-ykoY Orphan Riboswitches.,Price IR, Gaballa A, Ding F, Helmann JD, Ke A Mol Cell. 2015 Mar 19;57(6):1110-23. doi: 10.1016/j.molcel.2015.02.016. PMID:25794619<ref>PMID:25794619</ref>

-	~~Authors: Price~~, I.R.~~, Ke, A~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: Lactococcus lactis yybP-ykoY Mn riboswitch A41U binding site mutant in presence of Mn2+~~	+	== References ==
-	~~[[Category: Unreleased Structures]]~~	+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Ke, A]]		[[Category: Ke, A]]
-	[[Category: Price, I.R]]	+	[[Category: Price, I R]]
		+	[[Category: Manganese-binding]]
		+	[[Category: Mutant]]
		+	[[Category: Riboswitch]]
		+	[[Category: Rna]]

OCA at 12:35, 25 February 2015

OCA — Wed, 25 Feb 2015 12:35:16 GMT

←Older revision		Revision as of 12:35, 25 February 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4y1j is ON HOLD	+	The entry 4y1j is ON HOLD until Paper Publication

	Authors: Price, I.R., Ke, A.		Authors: Price, I.R., Ke, A.

OCA: Protected "4y1j" [edit=sysop:move=sysop]

OCA — Wed, 18 Feb 2015 11:54:04 GMT

Protected "4y1j" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:54, 18 February 2015

OCA: New page: '''Unreleased structure''' The entry 4y1j is ON HOLD Authors: Price, I.R., Ke, A. Description: Lactococcus lactis yybP-ykoY Mn riboswitch A41U binding site mutant in presence of Mn2+ [...

OCA — Wed, 18 Feb 2015 11:54:03 GMT

New page: '''Unreleased structure''' The entry 4y1j is ON HOLD Authors: Price, I.R., Ke, A. Description: Lactococcus lactis yybP-ykoY Mn riboswitch A41U binding site mutant in presence of Mn2+ [...

New page

'''Unreleased structure'''

The entry 4y1j is ON HOLD

Authors: Price, I.R., Ke, A.

Description: Lactococcus lactis yybP-ykoY Mn riboswitch A41U binding site mutant in presence of Mn2+
[[Category: Unreleased Structures]]
[[Category: Ke, A]]
[[Category: Price, I.R]]