6vte - Revision history

OCA at 08:19, 11 October 2023

2023-10-11T08:19:23Z

←Older revision		Revision as of 08:19, 11 October 2023
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	<StructureSection load='6vte' size='340' side='right'caption='[[6vte]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='6vte' size='340' side='right'caption='[[6vte]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6vte]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Amoeba Amoeba~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VTE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6VTE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6vte]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Naegleria_gruberi Naegleria gruberi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VTE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VTE FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>~~, ~~<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]] 2.1Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~NAEGRDRAFT_82186 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=5762 Amoeba]~~)</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</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~~://proteopedia.org/fgij/fg.htm?mol=6vte FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vte OCA], [~~http~~://pdbe.org/6vte PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6vte RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6vte PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6vte 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=6vte FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vte OCA], [https://pdbe.org/6vte PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vte RCSB], [https://www.ebi.ac.uk/pdbsum/6vte PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vte ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/D2W2Z5_NAEGR D2W2Z5_NAEGR]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6vte" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6vte" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[RNA ligase\|RNA ligase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Amoeba]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Goldgur, Y~~]]	+	[[Category: Naegleria gruberi]]
-	[[Category: ~~Shuman, S~~]]	+	[[Category: Goldgur Y]]
-	[[Category: ~~Unciuleac, M C~~]]	+	[[Category: Shuman S]]
-	[[Category: ~~Adenylyltransferase]]~~	+	[[Category: Unciuleac MC]]
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Rna repair~~]]	+

OCA at 06:41, 6 May 2020

2020-05-06T06:41:47Z

←Older revision		Revision as of 06:41, 6 May 2020
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	<StructureSection load='6vte' size='340' side='right'caption='[[6vte]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='6vte' size='340' side='right'caption='[[6vte]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6vte]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VTE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VTE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6vte]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Amoeba Amoeba]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VTE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VTE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NAEGRDRAFT_82186 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5762 Amoeba])</td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6vte FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vte OCA], [http://pdbe.org/6vte PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vte RCSB], [http://www.ebi.ac.uk/pdbsum/6vte PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vte ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6vte FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vte OCA], [http://pdbe.org/6vte PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vte RCSB], [http://www.ebi.ac.uk/pdbsum/6vte PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vte ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Naegleria gruberi RNA ligase (NgrRnl) exemplifies the Rnl5 family of adenosine triphosphate (ATP)-dependent polynucleotide ligases that seal 3'-OH RNA strands in the context of 3'-OH/5'-PO4 nicked duplexes. Like all classic ligases, NgrRnl forms a covalent lysyl-AMP intermediate. A two-metal mechanism of lysine adenylylation was established via a crystal structure of the NgrRnlATP(Mn2+)2 Michaelis complex. Here we conducted an alanine scan of active site constituents that engage the ATP phosphates and the metal cofactors. We then determined crystal structures of ligase-defective NgrRnl-Ala mutants in complexes with ATP/Mn2+. The unexpected findings were that mutations K170A, E227A, K326A and R149A (none of which impacted overall enzyme structure) triggered adverse secondary changes in the active site entailing dislocations of the ATP phosphates, altered contacts to ATP, and variations in the numbers and positions of the metal ions that perverted the active sites into off-pathway states incompatible with lysine adenylylation. Each alanine mutation elicited a distinctive off-pathway distortion of the ligase active site. Our results illuminate a surprising plasticity of the ligase active site in its interactions with ATP and metals. More broadly, they underscore a valuable caveat when interpreting mutational data in the course of enzyme structure-function studies.
		+
		+	Caveat mutator: alanine substitutions for conserved amino acids in RNA ligase elicit unexpected rearrangements of the active site for lysine adenylylation.,Unciuleac MC, Goldgur Y, Shuman S Nucleic Acids Res. 2020 Apr 21. pii: 5823197. doi: 10.1093/nar/gkaa238. PMID:32315072<ref>PMID:32315072</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6vte" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Amoeba]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Goldgur, Y]]		[[Category: Goldgur, Y]]

OCA at 06:59, 8 April 2020

2020-04-08T06:59:48Z

←Older revision		Revision as of 06:59, 8 April 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6vte is ~~ON HOLD until Paper Publication~~	+	==Naegleria gruberi RNA Ligase K170M mutant with AMP and Mn==
-		+	<StructureSection load='6vte' size='340' side='right'caption='[[6vte]], [[Resolution\|resolution]] 2.10Å' scene=''>
-	~~Authors~~: ~~Unciuleac~~, M.C., ~~Goldgur~~, Y., ~~Shuman~~, S.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6vte]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VTE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VTE FirstGlance]. <br>
-	~~Description: Naegleria gruberi RNA Ligase K170M mutant with AMP and Mn~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6vte FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vte OCA], [http://pdbe.org/6vte PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vte RCSB], [http://www.ebi.ac.uk/pdbsum/6vte PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vte ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Goldgur, Y]]		[[Category: Goldgur, Y]]
-	[[Category: Unciuleac, M.C]]
	[[Category: Shuman, S]]		[[Category: Shuman, S]]
		+	[[Category: Unciuleac, M C]]
		+	[[Category: Adenylyltransferase]]
		+	[[Category: Ligase]]
		+	[[Category: Rna repair]]

OCA at 05:36, 4 March 2020

2020-03-04T05:36:19Z

←Older revision		Revision as of 05:36, 4 March 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Unciuleac, M.C., Goldgur, Y., Shuman, S.		Authors: Unciuleac, M.C., Goldgur, Y., Shuman, S.
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	Description: Naegleria gruberi RNA Ligase K170M mutant with AMP and Mn		Description: Naegleria gruberi RNA Ligase K170M mutant with AMP and Mn
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Goldgur, Y]]
	[[Category: Unciuleac, M.C]]		[[Category: Unciuleac, M.C]]
	[[Category: Shuman, S]]		[[Category: Shuman, S]]
-	[[Category: Goldgur, Y]]

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

2020-02-19T05:22:27Z

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

←Older revision

Revision as of 05:22, 19 February 2020

OCA: New page: '''Unreleased structure''' The entry 6vte is ON HOLD Authors: Unciuleac, M.C., Goldgur, Y., Shuman, S. Description: Naegleria gruberi RNA Ligase K170M mutant with AMP and Mn [[Category...

2020-02-19T05:22:26Z

New page: '''Unreleased structure''' The entry 6vte is ON HOLD Authors: Unciuleac, M.C., Goldgur, Y., Shuman, S. Description: Naegleria gruberi RNA Ligase K170M mutant with AMP and Mn [[Category...

New page

'''Unreleased structure'''

The entry 6vte is ON HOLD

Authors: Unciuleac, M.C., Goldgur, Y., Shuman, S.

Description: Naegleria gruberi RNA Ligase K170M mutant with AMP and Mn
[[Category: Unreleased Structures]]
[[Category: Unciuleac, M.C]]
[[Category: Shuman, S]]
[[Category: Goldgur, Y]]