6xjy - Revision history

OCA at 14:53, 18 October 2023

2023-10-18T14:53:55Z

←Older revision		Revision as of 14:53, 18 October 2023
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-	====	+	==Crystal structure of a self-alkylating ribozyme - short time incubation with the epoxide substrate==
-	<StructureSection load='6xjy' size='340' side='right'caption='[[6xjy]]' scene=''>	+	<StructureSection load='6xjy' size='340' side='right'caption='[[6xjy]], [[Resolution\|resolution]] 2.16Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6xjy]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeropyrum_pernix Aeropyrum pernix] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XJY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XJY FirstGlance]. <br>
-	</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=6xjy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xjy OCA], [https://pdbe.org/6xjy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xjy RCSB], [https://www.ebi.ac.uk/pdbsum/6xjy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xjy ProSAT]</span></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]] 2.156Å</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=6xjy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xjy OCA], [https://pdbe.org/6xjy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xjy RCSB], [https://www.ebi.ac.uk/pdbsum/6xjy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xjy ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ribozymes that react with small-molecule probes have important applications in transcriptomics and chemical biology, such as RNA labeling and imaging. Understanding the structural basis for these RNA-modifying reactions will enable the development of better tools for studying RNA. Nevertheless, high-resolution structures and underlying catalytic mechanisms for members of this ribozyme class remain elusive. Here, we focus on a self-alkylating ribozyme that catalyzes nitrogen-carbon bond formation between a specific guanine and a 2,3-disubstituted epoxide substrate and report the crystal structures of a self-alkylating ribozyme, including both alkylated and apo forms, at 1.71-A and 2.49-A resolution, respectively. The ribozyme assumes an elongated hairpin-like architecture preorganized to accommodate the epoxide substrate in a hook-shaped conformation. Observed reactivity of substrate analogs together with an inverse, log-linear pH dependence of the reaction rate suggests a requirement for epoxide protonation, possibly assisted by the ether oxygens within the substrate.
		+
		+	Structural basis for substrate binding and catalysis by a self-alkylating ribozyme.,Krochmal D, Shao Y, Li NS, DasGupta S, Shelke SA, Koirala D, Piccirilli JA Nat Chem Biol. 2022 Apr;18(4):376-384. doi: 10.1038/s41589-021-00950-z. Epub 2022 , Jan 20. PMID:35058645<ref>PMID:35058645</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6xjy" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribozyme 3D structures\|Ribozyme 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aeropyrum pernix]]
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Koirala D]]
		+	[[Category: Piccirilli JA]]

OCA at 07:26, 19 January 2022

2022-01-19T07:26:20Z

←Older revision		Revision as of 07:26, 19 January 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 6xjy ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='6xjy' size='340' side='right'caption='[[6xjy]]' scene=''>
-	~~Authors~~: ~~Koirala, D~~.~~, Piccirilli, J~~.A.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description: Crystal structure of a self~~-~~alkylating ribozyme -short time incubation with~~ the ~~epoxide substrate~~	+	</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=6xjy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xjy OCA], [https://pdbe.org/6xjy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xjy RCSB], [https://www.ebi.ac.uk/pdbsum/6xjy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xjy ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[Category: ~~Koirala, D~~]]	+	__TOC__
-	[[Category: ~~Piccirilli, J.A~~]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 06:42, 22 July 2020

2020-07-22T06:42:39Z

←Older revision		Revision as of 06:42, 22 July 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6xjy is ON HOLD	+	The entry 6xjy is ON HOLD until Paper Publication

	Authors: Koirala, D., Piccirilli, J.A.		Authors: Koirala, D., Piccirilli, J.A.

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

2020-07-08T10:53:04Z

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

←Older revision

Revision as of 10:53, 8 July 2020

OCA: New page: '''Unreleased structure''' The entry 6xjy is ON HOLD Authors: Koirala, D., Piccirilli, J.A. Description: Crystal structure of a self-alkylating ribozyme -short time incubation with the...

2020-07-08T10:53:03Z

New page: '''Unreleased structure''' The entry 6xjy is ON HOLD Authors: Koirala, D., Piccirilli, J.A. Description: Crystal structure of a self-alkylating ribozyme -short time incubation with the...

New page

'''Unreleased structure'''

The entry 6xjy is ON HOLD

Authors: Koirala, D., Piccirilli, J.A.

Description: Crystal structure of a self-alkylating ribozyme -short time incubation with the epoxide substrate
[[Category: Unreleased Structures]]
[[Category: Koirala, D]]
[[Category: Piccirilli, J.A]]