2vs1 - Revision history

OCA at 11:45, 30 March 2022

OCA — Wed, 30 Mar 2022 11:45:17 GMT

←Older revision		Revision as of 11:45, 30 March 2022
Line 3:		Line 3:
	<StructureSection load='2vs1' size='340' side='right'caption='[[2vs1]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2vs1' size='340' side='right'caption='[[2vs1]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2vs1]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"pyrococcus_abyssi"_erauso_et_al._1993 "pyrococcus abyssi" erauso et al. 1993]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VS1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2VS1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2vs1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"pyrococcus_abyssi"_erauso_et_al._1993 "pyrococcus abyssi" erauso et al. 1993]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VS1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VS1 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <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" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <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=CSS:S-MERCAPTOCYSTEINE'>CSS</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSS:S-MERCAPTOCYSTEINE'>CSS</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2jjq\|2jjq]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2jjq\|2jjq]]</div></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=2vs1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vs1 OCA], [~~http~~://pdbe.org/2vs1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2vs1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2vs1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2vs1 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=2vs1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vs1 OCA], [https://pdbe.org/2vs1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vs1 RCSB], [https://www.ebi.ac.uk/pdbsum/2vs1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vs1 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 08:27, 25 June 2020

OCA — Thu, 25 Jun 2020 08:27:09 GMT

←Older revision		Revision as of 08:27, 25 June 2020
Line 1:		Line 1:

	==The crystal structure of Pyrococcus abyssi tRNA (uracil-54, C5)- methyltransferase in complex with S-adenosyl-L-homocysteine==		==The crystal structure of Pyrococcus abyssi tRNA (uracil-54, C5)- methyltransferase in complex with S-adenosyl-L-homocysteine==
-	<StructureSection load='2vs1' size='340' side='right' caption='[[2vs1]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='2vs1' size='340' side='right'caption='[[2vs1]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2vs1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"pyrococcus_abyssi"_erauso_et_al._1993 "pyrococcus abyssi" erauso et al. 1993]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VS1 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2VS1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2vs1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"pyrococcus_abyssi"_erauso_et_al._1993 "pyrococcus abyssi" erauso et al. 1993]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VS1 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2VS1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <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" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <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=CSS:S-MERCAPTOCYSTEINE'>CSS</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSS:S-MERCAPTOCYSTEINE'>CSS</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2jjq\|2jjq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2jjq\|2jjq]]</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=2vs1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vs1 OCA], [http://pdbe.org/2vs1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vs1 RCSB], [http://www.ebi.ac.uk/pdbsum/2vs1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vs1 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=2vs1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vs1 OCA], [http://pdbe.org/2vs1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vs1 RCSB], [http://www.ebi.ac.uk/pdbsum/2vs1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vs1 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Pyrococcus abyssi erauso et al. 1993]]		[[Category: Pyrococcus abyssi erauso et al. 1993]]
		+	[[Category: Large Structures]]
	[[Category: Golinelli-Pimpaneau, B]]		[[Category: Golinelli-Pimpaneau, B]]
	[[Category: Grosjean, H]]		[[Category: Grosjean, H]]

OCA at 21:05, 19 September 2018

OCA — Wed, 19 Sep 2018 21:05:31 GMT

←Older revision		Revision as of 21:05, 19 September 2018
Line 1:		Line 1:
-	==~~THE CRYSTAL STRUCTURE OF PYROCOCCUS ABYSSI TRNA~~ (~~URACIL~~-54, C5)-~~METHYLTRANSFERASE IN COMPLEX WITH~~ S-~~ADENOSYL~~-L-~~HOMOCYSTEINE~~==	+
		+	==The crystal structure of Pyrococcus abyssi tRNA (uracil-54, C5)- methyltransferase in complex with S-adenosyl-L-homocysteine==
	<StructureSection load='2vs1' size='340' side='right' caption='[[2vs1]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2vs1' size='340' side='right' caption='[[2vs1]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
Line 6:		Line 7:
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSS:S-MERCAPTOCYSTEINE'>CSS</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSS:S-MERCAPTOCYSTEINE'>CSS</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2jjq\|2jjq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2jjq\|2jjq]]</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=2vs1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vs1 OCA], [http://pdbe.org/2vs1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vs1 RCSB], [http://www.ebi.ac.uk/pdbsum/2vs1 PDBsum]</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=2vs1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vs1 OCA], [http://pdbe.org/2vs1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vs1 RCSB], [http://www.ebi.ac.uk/pdbsum/2vs1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2vs1 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vs/2vs1_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vs/2vs1_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 03:04, 9 February 2016

OCA — Tue, 09 Feb 2016 03:04:41 GMT

←Older revision		Revision as of 03:04, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='2vs1' size='340' side='right' caption='[[2vs1]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='2vs1' size='340' side='right' caption='[[2vs1]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2vs1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pyrococcus_abyssi Pyrococcus~~ abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VS1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VS1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2vs1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"pyrococcus_abyssi"_erauso_et_al._1993 "pyrococcus abyssi" erauso et al. 1993]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VS1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VS1 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <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=PO4:PHOSPHATE+ION'>PO4</scene>, <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=CSS:S-MERCAPTOCYSTEINE'>CSS</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSS:S-MERCAPTOCYSTEINE'>CSS</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2jjq\|2jjq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2jjq\|2jjq]]</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=2vs1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vs1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vs1 RCSB], [http://www.ebi.ac.uk/pdbsum/2vs1 PDBsum]</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=2vs1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vs1 OCA], [http://pdbe.org/2vs1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2vs1 RCSB], [http://www.ebi.ac.uk/pdbsum/2vs1 PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		Line 16:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2vs1 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		Line 26:
	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 2vs1" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Pyrococcus abyssi]]	+	[[Category: Pyrococcus abyssi erauso et al. 1993]]
	[[Category: Golinelli-Pimpaneau, B]]		[[Category: Golinelli-Pimpaneau, B]]
	[[Category: Grosjean, H]]		[[Category: Grosjean, H]]

OCA at 16:51, 19 January 2015

OCA — Mon, 19 Jan 2015 16:51:55 GMT

←Older revision		Revision as of 16:51, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2vs1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VS1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VS1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2vs1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VS1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VS1 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSS:S-MERCAPTOCYSTEINE'>CSS</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSS:S-MERCAPTOCYSTEINE'>CSS</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2jjq\|2jjq]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2jjq\|2jjq]]</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2vs1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vs1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vs1 RCSB], [http://www.ebi.ac.uk/pdbsum/2vs1 PDBsum]</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=2vs1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vs1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vs1 RCSB], [http://www.ebi.ac.uk/pdbsum/2vs1 PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Pyrococcus abyssi]]		[[Category: Pyrococcus abyssi]]
-	[[Category: Golinelli-Pimpaneau, B.]]	+	[[Category: Golinelli-Pimpaneau, B]]
-	[[Category: Grosjean, H.]]	+	[[Category: Grosjean, H]]
-	[[Category: Leulliot, N.]]	+	[[Category: Leulliot, N]]
-	[[Category: Walbott, H.]]	+	[[Category: Walbott, H]]
	[[Category: Iron]]		[[Category: Iron]]
	[[Category: Iron-sulfur]]		[[Category: Iron-sulfur]]

OCA: Protected "2vs1" [edit=sysop:move=sysop]

OCA — Wed, 01 Oct 2014 01:34:25 GMT

Protected "2vs1" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:34, 1 October 2014

OCA at 01:34, 1 October 2014

OCA — Wed, 01 Oct 2014 01:34:23 GMT

←Older revision		Revision as of 01:34, 1 October 2014
Line 1:		Line 1:
-	~~{{Seed}}~~	+	==THE CRYSTAL STRUCTURE OF PYROCOCCUS ABYSSI TRNA (URACIL-54, C5)-METHYLTRANSFERASE IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE==
-	[[~~Image:~~2vs1.~~png~~\|~~left~~\|200px]]	+	<StructureSection load='2vs1' size='340' side='right' caption='[[2vs1]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2vs1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VS1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2VS1 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSS:S-MERCAPTOCYSTEINE'>CSS</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2jjq\|2jjq]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2vs1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vs1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2vs1 RCSB], [http://www.ebi.ac.uk/pdbsum/2vs1 PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vs/2vs1_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The 5-methyluridine is invariably found at position 54 in the TPsiC loop of tRNAs of most organisms. In Pyrococcus abyssi, its formation is catalyzed by the S-adenosyl-l-methionine-dependent tRNA (uracil-54, C5)-methyltransferase ((Pab)TrmU54), an enzyme that emerged through an ancient horizontal transfer of an RNA (uracil, C5)-methyltransferase-like gene from bacteria to archaea. The crystal structure of (Pab)TrmU54 in complex with S-adenosyl-l-homocysteine at 1.9 A resolution shows the protein organized into three domains like Escherichia coli RumA, which catalyzes the same reaction at position 1939 of 23S rRNA. A positively charged groove at the interface between the three domains probably locates part of the tRNA-binding site of (Pab)TrmU54. We show that a mini-tRNA lacking both the D and anticodon stem-loops is recognized by (Pab)TrmU54. These results were used to model yeast tRNA(Asp) in the (Pab)TrmU54 structure to get further insights into the different RNA specificities of RumA and (Pab)TrmU54. Interestingly, the presence of two flexible loops in the central domain, unique to (Pab)TrmU54, may explain the different substrate selectivities of both enzymes. We also predict that a large TPsiC loop conformational change has to occur for the flipping of the target uridine into the (Pab)TrmU54 active site during catalysis.

-	<!--	+	The crystal structure of Pyrococcus abyssi tRNA (uracil-54, C5)-methyltransferase provides insights into its tRNA specificity.,Walbott H, Leulliot N, Grosjean H, Golinelli-Pimpaneau B Nucleic Acids Res. 2008 Sep;36(15):4929-40. Epub 2008 Jul 24. PMID:18653523<ref>PMID:18653523</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_2vs1"~~, ~~creates the "Structure Box" on the page~~.	+
-	~~You may change the PDB parameter~~ (~~which sets the PDB file loaded into the applet~~)	+
-	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~	+
-	~~or leave the SCENE parameter empty for the default display.~~	+
-	-->	+
-	~~{{STRUCTURE_2vs1\| PDB=2vs1 \| SCENE= }}~~	+

-	~~===THE CRYSTAL STRUCTURE OF PYROCOCCUS ABYSSI TRNA (URACIL-54~~, ~~C5)-METHYLTRANSFERASE IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_18653523}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 18653523 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_18653523}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~2VS1 is a 1 chain structure of sequence from [http:~~/~~/en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VS1 OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:18653523<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Pyrococcus abyssi]]		[[Category: Pyrococcus abyssi]]
	[[Category: Golinelli-Pimpaneau, B.]]		[[Category: Golinelli-Pimpaneau, B.]]
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	[[Category: Leulliot, N.]]		[[Category: Leulliot, N.]]
	[[Category: Walbott, H.]]		[[Category: Walbott, H.]]
-	[[Category: 4fe-4]]
	[[Category: Iron]]		[[Category: Iron]]
	[[Category: Iron-sulfur]]		[[Category: Iron-sulfur]]
Line 37:		Line 42:
	[[Category: Transferase]]		[[Category: Transferase]]
	[[Category: Trna methyltransferase]]		[[Category: Trna methyltransferase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 05:57:21 2009''

OCA at 03:57, 17 February 2009

OCA — Tue, 17 Feb 2009 03:57:23 GMT

←Older revision		Revision as of 03:57, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2VS1 is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VS1 OCA].	+	2VS1 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VS1 OCA].

	==Reference==		==Reference==
-	The crystal structure of Pyrococcus abyssi tRNA (uracil-54, C5)-methyltransferase provides insights into its tRNA specificity., Walbott H, Leulliot N, Grosjean H, Golinelli-Pimpaneau B, Nucleic Acids Res. 2008 Jul 24. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18653523 18653523]~~	+	<ref group="xtra">PMID:18653523</ref><references group="xtra"/>
	[[Category: Pyrococcus abyssi]]		[[Category: Pyrococcus abyssi]]
-	[[Category: Single protein]]
	[[Category: Golinelli-Pimpaneau, B.]]		[[Category: Golinelli-Pimpaneau, B.]]
	[[Category: Grosjean, H.]]		[[Category: Grosjean, H.]]
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	[[Category: Trna methyltransferase]]		[[Category: Trna methyltransferase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Sep 10 09~~:12:~~45 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 05:57:21 2009''

OCA at 06:12, 10 September 2008

OCA — Wed, 10 Sep 2008 06:12:45 GMT

←Older revision		Revision as of 06:12, 10 September 2008
Line 1:		Line 1:
	{{Seed}}		{{Seed}}
-	[[Image:2vs1.~~jpg~~\|left\|200px]]	+	[[Image:2vs1.png\|left\|200px]]

	<!--		<!--
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	[[Category: Trna methyltransferase]]		[[Category: Trna methyltransferase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Aug 6 12~~:49:58 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 10 09:12:45 2008''

OCA at 09:50, 6 August 2008

OCA — Wed, 06 Aug 2008 09:50:00 GMT

←Older revision		Revision as of 09:50, 6 August 2008
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-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:2vs1.jpg\|left\|200px]]

-	The ~~entry 2vs1~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_2vs1", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_2vs1\| PDB=2vs1 \| SCENE= }}

-	~~Authors: Walbott~~, ~~H., Leulliot, N., Grosjean, H., Golinelli~~-~~Pimpaneau, B.~~	+	===THE CRYSTAL STRUCTURE OF PYROCOCCUS ABYSSI TRNA (URACIL-54, C5)-METHYLTRANSFERASE IN COMPLEX WITH S-ADENOSYL-L-HOMOCYSTEINE===

-	Description: The crystal structure of Pyrococcus abyssi tRNA (uracil-54, C5)-methyltransferase in complex with S-adenosyl-L-homocysteine

		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_18653523}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 18653523 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_18653523}}

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Jun 11 08~~:55:13 2008''	+	==About this Structure==
		+	2VS1 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VS1 OCA].
		+
		+	==Reference==
		+	The crystal structure of Pyrococcus abyssi tRNA (uracil-54, C5)-methyltransferase provides insights into its tRNA specificity., Walbott H, Leulliot N, Grosjean H, Golinelli-Pimpaneau B, Nucleic Acids Res. 2008 Jul 24. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18653523 18653523]
		+	[[Category: Pyrococcus abyssi]]
		+	[[Category: Single protein]]
		+	[[Category: Golinelli-Pimpaneau, B.]]
		+	[[Category: Grosjean, H.]]
		+	[[Category: Leulliot, N.]]
		+	[[Category: Walbott, H.]]
		+	[[Category: 4fe-4]]
		+	[[Category: Iron]]
		+	[[Category: Iron-sulfur]]
		+	[[Category: Metal-binding]]
		+	[[Category: Methyltransferase]]
		+	[[Category: S-adenosyl-l-methionine]]
		+	[[Category: Transferase]]
		+	[[Category: Trna methyltransferase]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 6 12:49:58 2008''