7wie - Revision history

OCA at 19:44, 29 May 2024

OCA — Wed, 29 May 2024 19:44:27 GMT

←Older revision		Revision as of 19:44, 29 May 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7wie]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mesorhizobium_loti Mesorhizobium loti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7WIE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7WIE FirstGlance]. <br>		<table><tr><td colspan='2'>[[7wie]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mesorhizobium_loti Mesorhizobium loti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7WIE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7WIE FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7DG:7-DEAZAGUANINE'>7DG</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</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]] 2.9Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7DG:7-DEAZAGUANINE'>7DG</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</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=7wie FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7wie OCA], [https://pdbe.org/7wie PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7wie RCSB], [https://www.ebi.ac.uk/pdbsum/7wie PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7wie 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=7wie FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7wie OCA], [https://pdbe.org/7wie PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7wie RCSB], [https://www.ebi.ac.uk/pdbsum/7wie PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7wie ProSAT]</span></td></tr>
	</table>		</table>
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	In bacteria, expression of folate-related genes is controlled by the tetrahydrofolate (THF) riboswitch in response to specific binding of THF and its derivatives. Recently, a second class of THF riboswitches, named THF-II, was identified in Gram-negative bacteria, which exhibit distinct architecture from the previously characterized THF-I riboswitches found in Gram-positive bacteria. Here, we present the crystal structures of the ligand-bound THF-II riboswitch from Mesorhizobium loti. These structures exhibit a long rod-like fold stabilized by continuous base pair and base triplet stacking across two helices of P1 and P2 and their interconnecting ligand-bound binding pocket. The pterin moiety of the ligand docks into the binding pocket by forming hydrogen bonds with two highly conserved pyrimidines in J12 and J21, which resembles the hydrogen-bonding pattern at the ligand-binding site FAPK in the THF-I riboswitch. Using small-angle X-ray scattering and isothermal titration calorimetry, we further characterized the riboswitch in solution and reveal that Mg2+ is essential for pre-organization of the binding pocket for efficient ligand binding. RNase H cleavage assay indicates that ligand binding reduces accessibility of the ribosome binding site in the right arm of P1, thus down-regulating the expression of downstream genes. Together, these results provide mechanistic insights into translation regulation by the THF-II riboswitch.		In bacteria, expression of folate-related genes is controlled by the tetrahydrofolate (THF) riboswitch in response to specific binding of THF and its derivatives. Recently, a second class of THF riboswitches, named THF-II, was identified in Gram-negative bacteria, which exhibit distinct architecture from the previously characterized THF-I riboswitches found in Gram-positive bacteria. Here, we present the crystal structures of the ligand-bound THF-II riboswitch from Mesorhizobium loti. These structures exhibit a long rod-like fold stabilized by continuous base pair and base triplet stacking across two helices of P1 and P2 and their interconnecting ligand-bound binding pocket. The pterin moiety of the ligand docks into the binding pocket by forming hydrogen bonds with two highly conserved pyrimidines in J12 and J21, which resembles the hydrogen-bonding pattern at the ligand-binding site FAPK in the THF-I riboswitch. Using small-angle X-ray scattering and isothermal titration calorimetry, we further characterized the riboswitch in solution and reveal that Mg2+ is essential for pre-organization of the binding pocket for efficient ligand binding. RNase H cleavage assay indicates that ligand binding reduces accessibility of the ribosome binding site in the right arm of P1, thus down-regulating the expression of downstream genes. Together, these results provide mechanistic insights into translation regulation by the THF-II riboswitch.

-	Structural insights into translation regulation by the THF-II riboswitch.,Xu L, Xiao Y, Zhang J, Fang X Nucleic Acids Res. 2023 Jan 9:~~gkac1257~~. doi: 10.1093/nar/gkac1257. PMID:36620887<ref>PMID:36620887</ref>	+	Structural insights into translation regulation by the THF-II riboswitch.,Xu L, Xiao Y, Zhang J, Fang X Nucleic Acids Res. 2023 Jan 25;51(2):952-965. doi: 10.1093/nar/gkac1257. PMID:36620887<ref>PMID:36620887</ref>

	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 7wie" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7wie" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Riboswitch 3D structures\|Riboswitch 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:19, 18 January 2023

OCA — Wed, 18 Jan 2023 07:19:21 GMT

←Older revision		Revision as of 07:19, 18 January 2023
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-	'''Unreleased structure'''

-	The ~~entry~~ 7wie is ~~ON HOLD until 2024~~-04-03	+	==The THF-II riboswitch bound to 7DG==
		+	<StructureSection load='7wie' size='340' side='right'caption='[[7wie]], [[Resolution\|resolution]] 2.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[7wie]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mesorhizobium_loti Mesorhizobium loti]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7WIE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7WIE FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=7DG:7-DEAZAGUANINE'>7DG</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</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=7wie FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7wie OCA], [https://pdbe.org/7wie PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7wie RCSB], [https://www.ebi.ac.uk/pdbsum/7wie PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7wie ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In bacteria, expression of folate-related genes is controlled by the tetrahydrofolate (THF) riboswitch in response to specific binding of THF and its derivatives. Recently, a second class of THF riboswitches, named THF-II, was identified in Gram-negative bacteria, which exhibit distinct architecture from the previously characterized THF-I riboswitches found in Gram-positive bacteria. Here, we present the crystal structures of the ligand-bound THF-II riboswitch from Mesorhizobium loti. These structures exhibit a long rod-like fold stabilized by continuous base pair and base triplet stacking across two helices of P1 and P2 and their interconnecting ligand-bound binding pocket. The pterin moiety of the ligand docks into the binding pocket by forming hydrogen bonds with two highly conserved pyrimidines in J12 and J21, which resembles the hydrogen-bonding pattern at the ligand-binding site FAPK in the THF-I riboswitch. Using small-angle X-ray scattering and isothermal titration calorimetry, we further characterized the riboswitch in solution and reveal that Mg2+ is essential for pre-organization of the binding pocket for efficient ligand binding. RNase H cleavage assay indicates that ligand binding reduces accessibility of the ribosome binding site in the right arm of P1, thus down-regulating the expression of downstream genes. Together, these results provide mechanistic insights into translation regulation by the THF-II riboswitch.

-	~~Authors~~:	+	Structural insights into translation regulation by the THF-II riboswitch.,Xu L, Xiao Y, Zhang J, Fang X Nucleic Acids Res. 2023 Jan 9:gkac1257. doi: 10.1093/nar/gkac1257. PMID:36620887<ref>PMID:36620887</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 7wie" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Mesorhizobium loti]]
		+	[[Category: Fang X]]
		+	[[Category: Xiao Y]]
		+	[[Category: Xu L]]

OCA at 07:07, 14 December 2022

OCA — Wed, 14 Dec 2022 07:07:57 GMT

←Older revision		Revision as of 07:07, 14 December 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7wie is ON HOLD	+	The entry 7wie is ON HOLD until 2024-04-03

	Authors:		Authors:

OCA at 04:57, 7 December 2022

OCA — Wed, 07 Dec 2022 04:57:33 GMT

←Older revision		Revision as of 04:57, 7 December 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7wie is ON HOLD ~~until Paper Publication~~	+	The entry 7wie is ON HOLD

	Authors:		Authors:

OCA at 04:24, 28 September 2022

OCA — Wed, 28 Sep 2022 04:24:52 GMT

←Older revision		Revision as of 04:24, 28 September 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7wie is ON HOLD until ~~00 0001~~	+	The entry 7wie is ON HOLD until Paper Publication

	Authors:		Authors:

OCA at 06:22, 21 September 2022

OCA — Wed, 21 Sep 2022 06:22:58 GMT

←Older revision		Revision as of 06:22, 21 September 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7wie is ON HOLD	+	The entry 7wie is ON HOLD until 00 0001

	Authors:		Authors:

OCA at 05:30, 14 September 2022

OCA — Wed, 14 Sep 2022 05:30:48 GMT

←Older revision		Revision as of 05:30, 14 September 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7wie is ON HOLD ~~until Paper Publication~~	+	The entry 7wie is ON HOLD

	Authors:		Authors:

OCA at 06:26, 9 February 2022

OCA — Wed, 09 Feb 2022 06:26:05 GMT

←Older revision		Revision as of 06:26, 9 February 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7wie is ON HOLD	+	The entry 7wie is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7wie" [edit=sysop:move=sysop]

OCA — Wed, 12 Jan 2022 08:46:03 GMT

Protected "7wie" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:46, 12 January 2022

OCA: New page: '''Unreleased structure''' The entry 7wie is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 12 Jan 2022 08:46:01 GMT

New page: '''Unreleased structure''' The entry 7wie is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7wie is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]