5u3g - Revision history

OCA at 14:24, 6 March 2024

2024-03-06T14:24:56Z

←Older revision		Revision as of 14:24, 6 March 2024
Line 3:		Line 3:
	<StructureSection load='5u3g' size='340' side='right'caption='[[5u3g]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='5u3g' size='340' side='right'caption='[[5u3g]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5u3g]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U3G OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5U3G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5u3g]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Dickeya_dadantii Dickeya dadantii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U3G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5U3G FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=GAI:GUANIDINE'>GAI</scene~~>, ~~<scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.3Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GAI:GUANIDINE'>GAI</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=5u3g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u3g OCA], [~~http~~://pdbe.org/5u3g PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5u3g RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5u3g PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5u3g 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=5u3g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u3g OCA], [https://pdbe.org/5u3g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5u3g RCSB], [https://www.ebi.ac.uk/pdbsum/5u3g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5u3g ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Regulation of gene expression by cis-encoded riboswitches is a prevalent theme in bacteria. Of the hundreds of riboswitch families identified, the majority of them remain as orphans, without a clear ligand assignment. The ykkC orphan family was recently characterized as guanidine-sensing riboswitches. Herein we present a 2.04 A crystal structure of the guanidine-bound ykkC riboswitch from Dickeya dadantii. The riboswitch folds into a boot-shaped structure, with a co-axially stacked P1/P2 stem forming the boot, and a 3'-P3 stem-loop forming the heel. Sophisticated base-pairing and cross-helix tertiary contacts give rise to the ligand-binding pocket between the boot and the heel. The guanidine is recognized in its positively charged guanidinium form, in its sp2 hybridization state, through a network of coplanar hydrogen bonds and by a cation-pi stacking contact on top of a conserved guanosine residue. Disruption of these contacts resulted in severe guanidinium binding defects. These results provide the structural basis for specific guanidine sensing by ykkC riboswitches, and pave the way for a deeper understanding of guanidine detoxification - a previously unappreciated aspect of bacterial physiology.
-
-	Structural Basis for Guanidine Sensing by the ykkC Family of Riboswitches.,Battaglia RA, Price IR, Ke A RNA. 2017 Jan 17. pii: rna.060186.116. doi: 10.1261/rna.060186.116. PMID:28096518<ref>PMID:28096518</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5u3g" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Riboswitch\|Riboswitch]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Dickeya dadantii]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Battaglia~~, R A~~]]	+	[[Category: Battaglia RA]]
-	[[Category: Ke, A]]	+	[[Category: Ke A]]
-	[[Category: Price~~, I R]]~~	+	[[Category: Price IR]]
-	~~[[Category: Guanidine]]~~	+
-	~~[[Category: Guanidinium]]~~	+
-	~~[[Category: Riboswitch]]~~	+
-	~~[[Category: Rna]]~~	+
-	~~[[Category: Ykkc~~]]	+

OCA at 09:27, 4 December 2019

2019-12-04T09:27:57Z

←Older revision		Revision as of 09:27, 4 December 2019
Line 1:		Line 1:

	==Structure of the Dickeya dadantii ykkC riboswitch bound to guanidinium==		==Structure of the Dickeya dadantii ykkC riboswitch bound to guanidinium==
-	<StructureSection load='5u3g' size='340' side='right' caption='[[5u3g]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='5u3g' size='340' side='right'caption='[[5u3g]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5u3g]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U3G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5U3G FirstGlance]. <br>		<table><tr><td colspan='2'>[[5u3g]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U3G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5U3G FirstGlance]. <br>
Line 24:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Battaglia, R A]]		[[Category: Battaglia, R A]]
	[[Category: Ke, A]]		[[Category: Ke, A]]

OCA at 14:30, 6 November 2017

2017-11-06T14:30:08Z

←Older revision		Revision as of 14:30, 6 November 2017
Line 17:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 5u3g" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5u3g" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Riboswitch\|Riboswitch]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:08, 9 March 2017

2017-03-09T07:08:52Z

←Older revision		Revision as of 07:08, 9 March 2017
Line 8:		Line 8:
	<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=5u3g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u3g OCA], [http://pdbe.org/5u3g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u3g RCSB], [http://www.ebi.ac.uk/pdbsum/5u3g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u3g 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=5u3g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u3g OCA], [http://pdbe.org/5u3g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u3g RCSB], [http://www.ebi.ac.uk/pdbsum/5u3g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u3g ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Regulation of gene expression by cis-encoded riboswitches is a prevalent theme in bacteria. Of the hundreds of riboswitch families identified, the majority of them remain as orphans, without a clear ligand assignment. The ykkC orphan family was recently characterized as guanidine-sensing riboswitches. Herein we present a 2.04 A crystal structure of the guanidine-bound ykkC riboswitch from Dickeya dadantii. The riboswitch folds into a boot-shaped structure, with a co-axially stacked P1/P2 stem forming the boot, and a 3'-P3 stem-loop forming the heel. Sophisticated base-pairing and cross-helix tertiary contacts give rise to the ligand-binding pocket between the boot and the heel. The guanidine is recognized in its positively charged guanidinium form, in its sp2 hybridization state, through a network of coplanar hydrogen bonds and by a cation-pi stacking contact on top of a conserved guanosine residue. Disruption of these contacts resulted in severe guanidinium binding defects. These results provide the structural basis for specific guanidine sensing by ykkC riboswitches, and pave the way for a deeper understanding of guanidine detoxification - a previously unappreciated aspect of bacterial physiology.
		+
		+	Structural Basis for Guanidine Sensing by the ykkC Family of Riboswitches.,Battaglia RA, Price IR, Ke A RNA. 2017 Jan 17. pii: rna.060186.116. doi: 10.1261/rna.060186.116. PMID:28096518<ref>PMID:28096518</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5u3g" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 18:10, 1 February 2017

2017-02-01T18:10:23Z

←Older revision		Revision as of 18:10, 1 February 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5u3g ~~is ON HOLD~~	+	==Structure of the Dickeya dadantii ykkC riboswitch bound to guanidinium==
-		+	<StructureSection load='5u3g' size='340' side='right' caption='[[5u3g]], [[Resolution\|resolution]] 2.30Å' scene=''>
-	~~Authors~~: ~~Battaglia, R~~.A.~~, Price, I~~.R., Ke, A.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5u3g]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U3G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5U3G FirstGlance]. <br>
-	~~Description~~: ~~Structure of the Dickeya dadantii ykkC riboswitch bound to guanidinium~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GAI:GUANIDINE'>GAI</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>
-	[[Category: Battaglia, R.A]]	+	<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=5u3g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u3g OCA], [http://pdbe.org/5u3g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u3g RCSB], [http://www.ebi.ac.uk/pdbsum/5u3g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u3g ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Battaglia, R A]]
	[[Category: Ke, A]]		[[Category: Ke, A]]
-	[[Category: Price, I.R]]	+	[[Category: Price, I R]]
		+	[[Category: Guanidine]]
		+	[[Category: Guanidinium]]
		+	[[Category: Riboswitch]]
		+	[[Category: Rna]]
		+	[[Category: Ykkc]]

OCA: Protected "5u3g" [edit=sysop:move=sysop]

2016-12-15T17:37:05Z

Protected "5u3g" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:37, 15 December 2016

OCA: New page: '''Unreleased structure''' The entry 5u3g is ON HOLD Authors: Battaglia, R.A., Price, I.R., Ke, A. Description: Structure of the Dickeya dadantii ykkC riboswitch bound to guanidinium [...

2016-12-15T17:37:03Z

New page: '''Unreleased structure''' The entry 5u3g is ON HOLD Authors: Battaglia, R.A., Price, I.R., Ke, A. Description: Structure of the Dickeya dadantii ykkC riboswitch bound to guanidinium [...

New page

'''Unreleased structure'''

The entry 5u3g is ON HOLD

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

Description: Structure of the Dickeya dadantii ykkC riboswitch bound to guanidinium
[[Category: Unreleased Structures]]
[[Category: Battaglia, R.A]]
[[Category: Ke, A]]
[[Category: Price, I.R]]