6ufk - Revision history

OCA at 14:57, 13 March 2024

2024-03-13T14:57:19Z

← Older revision		Revision as of 14:57, 13 March 2024
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	<StructureSection load='6ufk' size='340' side='right'caption='[[6ufk]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='6ufk' size='340' side='right'caption='[[6ufk]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6ufk]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UFK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6UFK FirstGlance]. <br>		<table><tr><td colspan='2'>[[6ufk]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UFK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6UFK FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 3.2Å</td></tr>
	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=23G:GUANOSINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>23G</scene></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=23G:GUANOSINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>23G</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=6ufk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ufk OCA], [~~http~~://pdbe.org/6ufk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ufk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ufk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ufk 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=6ufk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ufk OCA], [https://pdbe.org/6ufk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ufk RCSB], [https://www.ebi.ac.uk/pdbsum/6ufk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ufk ProSAT]</span></td></tr>
	</table>		</table>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Pistol ribozymes constitute a new class of small self-cleaving RNAs. We have solved crystal structures that provide three-dimensional snapshots along the reaction coordinate of pistol phosphodiester cleavage, corresponding to the pre-catalytic state, a vanadate mimic of the transition state, and the product. The resulting architectonic framework dictates the proposed underlying chemical mechanism, which is corroborated by functional assays that involve atomic mutagenesis of the ribozyme. Importantly, a hydrated Mg2+ ion remains innersphere-coordinated to N7-G33 in all three states. This is consistent with its likely role as acid in general acid base catalysis (delta and ss catalysis), supported further by the observation of a more than 1000-fold rate reduction if its positioning is impaired by deletion of the N7 site. Strikingly, the new structures shed light on a second hydrated Mg2+ ion that approaches the scissile phosphate from its binding site in the pre-cleavage state to reach out for water-mediated H-bonding in the cyclophosphate product. Because this second hydrated Mg2+ ion is also close to the 6-oxygen atom of G40 (general base, gamma catalysis), its potential impact on activation of G40 has been experimentally evaluated, however, the major role of the second Mg2+ ion appears to be the stabilization of product conformation. Together, our study delivers a mechanistic understanding of ribozyme-catalyzed backbone cleavage with unprecedented precision.

	On crucial roles of two hydrated Mg2+ ions in reaction catalysis of the pistol ribozyme.,Teplova M, Falschlunger C, Krasheninina O, Egger M, Ren A, Patel DJ, Micura R Angew Chem Int Ed Engl. 2019 Dec 5. doi: 10.1002/anie.201912522. PMID:31804735<ref>PMID:31804735</ref>		==See Also==
			*[[Ribozyme 3D structures\|Ribozyme 3D structures]]
	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 6ufk" style="background-color:#fffaf0;"></div>~~
	== ~~References~~ ==
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Falschlunger, C]]		[[Category: Synthetic construct]]
	[[Category: Krasheninina, O]]		[[Category: Falschlunger C]]
	[[Category: Micura, R]]		[[Category: Krasheninina O]]
	[[Category: Patel~~, D J~~]]		[[Category: Micura R]]
	[[Category: Teplova, M]]		[[Category: Patel DJ]]
	~~[[Category: Cyclophosphate product]]~~		[[Category: Teplova M]]
	~~[[Category: Pentavalent transition state analog]]~~
	~~[[Category: Pre-catalytic state]]~~
	~~[[Category: Rna]]~~
	~~[[Category: Self-cleaving ribozyme]]~~
	~~[[Category: Transesterification reaction~~]]

OCA at 07:59, 18 December 2019

2019-12-18T07:59:26Z

← Older revision		Revision as of 07:59, 18 December 2019
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 6ufk is ~~ON HOLD until Paper~~ Publication		==Pistol ribozyme product crystal soaked in Mn2+==
			<StructureSection load='6ufk' size='340' side='right'caption='[[6ufk]], [[Resolution\|resolution]] 3.20Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[6ufk]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6UFK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6UFK FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
			<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=23G:GUANOSINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>23G</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=6ufk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ufk OCA], [http://pdbe.org/6ufk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ufk RCSB], [http://www.ebi.ac.uk/pdbsum/6ufk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ufk ProSAT]</span></td></tr>
			</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Pistol ribozymes constitute a new class of small self-cleaving RNAs. We have solved crystal structures that provide three-dimensional snapshots along the reaction coordinate of pistol phosphodiester cleavage, corresponding to the pre-catalytic state, a vanadate mimic of the transition state, and the product. The resulting architectonic framework dictates the proposed underlying chemical mechanism, which is corroborated by functional assays that involve atomic mutagenesis of the ribozyme. Importantly, a hydrated Mg2+ ion remains innersphere-coordinated to N7-G33 in all three states. This is consistent with its likely role as acid in general acid base catalysis (delta and ss catalysis), supported further by the observation of a more than 1000-fold rate reduction if its positioning is impaired by deletion of the N7 site. Strikingly, the new structures shed light on a second hydrated Mg2+ ion that approaches the scissile phosphate from its binding site in the pre-cleavage state to reach out for water-mediated H-bonding in the cyclophosphate product. Because this second hydrated Mg2+ ion is also close to the 6-oxygen atom of G40 (general base, gamma catalysis), its potential impact on activation of G40 has been experimentally evaluated, however, the major role of the second Mg2+ ion appears to be the stabilization of product conformation. Together, our study delivers a mechanistic understanding of ribozyme-catalyzed backbone cleavage with unprecedented precision.

	~~Authors:~~ Teplova, M., Falschlunger, C., Krasheninina, O., Patel, D.J.~~, Micura, R~~.		On crucial roles of two hydrated Mg2+ ions in reaction catalysis of the pistol ribozyme.,Teplova M, Falschlunger C, Krasheninina O, Egger M, Ren A, Patel DJ, Micura R Angew Chem Int Ed Engl. 2019 Dec 5. doi: 10.1002/anie.201912522. PMID:31804735<ref>PMID:31804735</ref>

	~~Description~~: ~~Pistol ribozyme product crystal soaked in Mn2+~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	[[Category: ~~Unreleased~~ Structures]]		</div>
	[[Category: ~~Patel~~, ~~D.J~~]]		<div class="pdbe-citations 6ufk" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
			__TOC__
			</StructureSection>
			[[Category: Large Structures]]
			[[Category: Falschlunger, C]]
	[[Category: Krasheninina, O]]		[[Category: Krasheninina, O]]
			[[Category: Micura, R]]
			[[Category: Patel, D J]]
	[[Category: Teplova, M]]		[[Category: Teplova, M]]
	[[Category: ~~Micura, R~~]]		[[Category: Cyclophosphate product]]
	[[Category: ~~Falschlunger, C~~]]		[[Category: Pentavalent transition state analog]]
			[[Category: Pre-catalytic state]]
			[[Category: Rna]]
			[[Category: Self-cleaving ribozyme]]
			[[Category: Transesterification reaction]]

OCA at 04:33, 16 October 2019

2019-10-16T04:33:13Z

← Older revision		Revision as of 04:33, 16 October 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 6ufk is ON HOLD		The entry 6ufk is ON HOLD until Paper Publication

	Authors: Teplova, M., Falschlunger, C., Krasheninina, O., Patel, D.J., Micura, R.		Authors: Teplova, M., Falschlunger, C., Krasheninina, O., Patel, D.J., Micura, R.

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

2019-10-02T08:46:49Z

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

← Older revision	Revision as of 08:46, 2 October 2019
(No difference)

OCA: New page: '''Unreleased structure''' The entry 6ufk is ON HOLD Authors: Teplova, M., Falschlunger, C., Krasheninina, O., Patel, D.J., Micura, R. Description: Pistol ribozyme product crystal soak...

2019-10-02T08:46:48Z

New page: '''Unreleased structure''' The entry 6ufk is ON HOLD Authors: Teplova, M., Falschlunger, C., Krasheninina, O., Patel, D.J., Micura, R. Description: Pistol ribozyme product crystal soak...

New page

'''Unreleased structure'''

The entry 6ufk is ON HOLD

Authors: Teplova, M., Falschlunger, C., Krasheninina, O., Patel, D.J., Micura, R.

Description: Pistol ribozyme product crystal soaked in Mn2+
[[Category: Unreleased Structures]]
[[Category: Patel, D.J]]
[[Category: Krasheninina, O]]
[[Category: Teplova, M]]
[[Category: Micura, R]]
[[Category: Falschlunger, C]]