5zq0 - Revision history

OCA at 09:03, 22 November 2023

OCA — Wed, 22 Nov 2023 09:03:29 GMT

←Older revision		Revision as of 09:03, 22 November 2023
Line 1:		Line 1:

	==Crystal structure of spRlmCD with U747loop RNA==		==Crystal structure of spRlmCD with U747loop RNA==
-	<StructureSection load='5zq0' size='340' side='right' caption='[[5zq0]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='5zq0' size='340' side='right'caption='[[5zq0]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zq0]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Strpn Strpn~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZQ0 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZQ0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zq0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pneumoniae_TIGR4 Streptococcus pneumoniae TIGR4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZQ0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZQ0 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=SAH:S~~-~~ADENOSYL-L-HOMOCYSTEINE'>SAH</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]] 2Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=MUM:'>MUM</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MUM:5-O-(dihydroxyphosphanyl)-5-methyl-5,6-dihydrouridine'>MUM</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat">[[5xj1\|5xj1]]</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=5zq0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zq0 OCA], [https://pdbe.org/5zq0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zq0 RCSB], [https://www.ebi.ac.uk/pdbsum/5zq0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zq0 ProSAT]</span></td></tr>
-	~~<tr id='gene~~'>~~<td class="sblockLbl"><b>[[Gene\|Gene:]]~~</b>~~</td><td class="sblockDat">SP_1029 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=170187 STRPN])~~</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=5zq0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zq0 OCA], [~~http~~://pdbe.org/5zq0 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zq0 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zq0 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zq0 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Y1029_STRPN Y1029_STRPN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Strpn]]~~	+	[[Category: Large Structures]]
-	~~[[Category: Jiang, Y Y]]~~	+	[[Category: Streptococcus pneumoniae TIGR4]]
-	~~[[Category: Yu, H L]]~~	+	[[Category: Jiang YY]]
-	~~[[Category: 23s rna]]~~	+	[[Category: Yu HL]]
-	~~[[Category: Methyltransferase]]~~	+
-	~~[[Category: Ribosome~~]]	+
-	[[Category: Streptococcus pneumoniae]]	+
-	[[Category: ~~Transferase~~]]	+
-	[[Category: ~~Transferase-rna complex~~]]	+

OCA at 08:54, 14 November 2018

OCA — Wed, 14 Nov 2018 08:54:18 GMT

←Older revision		Revision as of 08:54, 14 November 2018
Line 3:		Line 3:
	<StructureSection load='5zq0' size='340' side='right' caption='[[5zq0]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5zq0' size='340' side='right' caption='[[5zq0]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zq0]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZQ0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZQ0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zq0]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Strpn Strpn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZQ0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZQ0 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MUM:'>MUM</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MUM:'>MUM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xj1\|5xj1]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xj1\|5xj1]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SP_1029 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=170187 STRPN])</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=5zq0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zq0 OCA], [http://pdbe.org/5zq0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zq0 RCSB], [http://www.ebi.ac.uk/pdbsum/5zq0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zq0 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=5zq0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zq0 OCA], [http://pdbe.org/5zq0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zq0 RCSB], [http://www.ebi.ac.uk/pdbsum/5zq0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zq0 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Methyltransferase RlmCD was previously shown to be responsible for the introduction of C5 methylation at both U747 and U1939 of the 23S ribosomal RNA in Streptococcus pneumoniae. Intriguingly, its structural homologue, RumA, can only catalyze the methylation of U1939, while RlmC is the dedicated enzyme for m5U747 in Escherichia coli. In this study, we describe the structure of RlmCD in complex with its cofactor and the RNA substrate containing U747 at 2.00 A or U1939 at 3.10 A. We demonstrate that multiple structural features collaborate to establish the dual enzymatic activities of RlmCD. Of them, the side-chain rearrangement of F145 was observed to be an unusual mechanism through which RlmCD can discriminate between U747- and U1939-containing RNA substrate by switching the intermolecular aromatic stacking between protein and RNA on/off. An in-vitro methyltransferase assay and electrophoretic mobility shift assay were performed to validate these findings. Overall, our complex structures allow for a better understanding of the dual-functional mechanism of RlmCD, suggesting useful implications for the evolution of the RumA-type enzyme and the potential development of antibiotic drugs against S. pneumoniae.
		+
		+	Unveiling the structural features that determine the dual methyltransferase activities of Streptococcus pneumoniae RlmCD.,Jiang Y, Yu H, Li F, Cheng L, Zhu L, Shi Y, Gong Q PLoS Pathog. 2018 Nov 2;14(11):e1007379. doi: 10.1371/journal.ppat.1007379. PMID:30388185<ref>PMID:30388185</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5zq0" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Strpn]]
	[[Category: Jiang, Y Y]]		[[Category: Jiang, Y Y]]
	[[Category: Yu, H L]]		[[Category: Yu, H L]]

OCA at 05:48, 24 October 2018

OCA — Wed, 24 Oct 2018 05:48:26 GMT

←Older revision		Revision as of 05:48, 24 October 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5zq0 is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of spRlmCD with U747loop RNA==
-		+	<StructureSection load='5zq0' size='340' side='right' caption='[[5zq0]], [[Resolution\|resolution]] 2.00Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5zq0]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZQ0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZQ0 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</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=MUM:'>MUM</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5xj1\|5xj1]]</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=5zq0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zq0 OCA], [http://pdbe.org/5zq0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zq0 RCSB], [http://www.ebi.ac.uk/pdbsum/5zq0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zq0 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Jiang, Y Y]]
		+	[[Category: Yu, H L]]
		+	[[Category: 23s rna]]
		+	[[Category: Methyltransferase]]
		+	[[Category: Ribosome]]
		+	[[Category: Streptococcus pneumoniae]]
		+	[[Category: Transferase]]
		+	[[Category: Transferase-rna complex]]

OCA at 06:33, 2 May 2018

OCA — Wed, 02 May 2018 06:33:14 GMT

←Older revision		Revision as of 06:33, 2 May 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5zq0 is ON HOLD	+	The entry 5zq0 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5zq0" [edit=sysop:move=sysop]

OCA — Wed, 25 Apr 2018 03:54:16 GMT

Protected "5zq0" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:54, 25 April 2018

OCA: New page: '''Unreleased structure''' The entry 5zq0 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 25 Apr 2018 03:54:15 GMT

New page: '''Unreleased structure''' The entry 5zq0 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5zq0 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]