1zl3 - Revision history

OCA at 07:10, 23 August 2023

OCA — Wed, 23 Aug 2023 07:10:10 GMT

←Older revision		Revision as of 07:10, 23 August 2023
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	<StructureSection load='1zl3' size='340' side='right'caption='[[1zl3]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1zl3' size='340' side='right'caption='[[1zl3]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1zl3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZL3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZL3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1zl3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZL3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZL3 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.8Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>~~[[~~Non-Standard_Residue~~\|~~NonStd Res:~~]]~~</b></td><td class="sblockDat"><scene name='pdbligand=UD5:5-FLUOROURIDINE'>UD5</scene>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UD5:5-FLUOROURIDINE'>UD5</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>truB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~562~~ "~~Bacillus coli~~" ~~Migula 1895])</td~~><~~/tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Pseudouridylate_synthase Pseudouridylate synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.70 4.2.1.70]~~ </~~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=1zl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zl3 OCA], [https://pdbe.org/1zl3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zl3 RCSB], [https://www.ebi.ac.uk/pdbsum/1zl3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zl3 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=1zl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zl3 OCA], [https://pdbe.org/1zl3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zl3 RCSB], [https://www.ebi.ac.uk/pdbsum/1zl3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zl3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/TRUB_ECOLI TRUB_ECOLI]] Responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs.<ref>PMID:7489483</ref> <ref>PMID:11142385</ref>	+	[https://www.uniprot.org/uniprot/TRUB_ECOLI TRUB_ECOLI] Responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs.<ref>PMID:7489483</ref> <ref>PMID:11142385</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pseudouridylate synthase]]~~	+	[[Category: Ferre-D'Amare AR]]
-	~~[[Category: Amare, A R.~~Ferre-D]]	+	[[Category: Hamilton CS]]
-	[[Category: Hamilton~~, C S~~]]	+	[[Category: Hoang C]]
-	[[Category: Hoang, C]]	+	[[Category: Mueller EG]]
-	[[Category: Mueller~~, E G]]~~	+
-	~~[[Category: Inter-domain coupling]]~~	+
-	~~[[Category: Lyase-rna complex]]~~	+
-	~~[[Category: Product release]]~~	+
-	~~[[Category: Rna-modification~~]]	+

OCA at 17:01, 20 October 2021

OCA — Wed, 20 Oct 2021 17:01:34 GMT

OCA at 09:06, 20 January 2021

OCA — Wed, 20 Jan 2021 09:06:07 GMT

←Older revision		Revision as of 09:06, 20 January 2021
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	==Coupling of active site motions and RNA binding==		==Coupling of active site motions and RNA binding==
-	<StructureSection load='1zl3' size='340' side='right' caption='[[1zl3]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='1zl3' size='340' side='right'caption='[[1zl3]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1zl3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZL3 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1ZL3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1zl3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZL3 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1ZL3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UD5:5-FLUOROURIDINE'>UD5</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UD5:5-FLUOROURIDINE'>UD5</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">truB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">truB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pseudouridylate_synthase Pseudouridylate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.70 4.2.1.70] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pseudouridylate_synthase Pseudouridylate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.70 4.2.1.70] </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=1zl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zl3 OCA], [http://pdbe.org/1zl3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1zl3 RCSB], [http://www.ebi.ac.uk/pdbsum/1zl3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1zl3 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=1zl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zl3 OCA], [http://pdbe.org/1zl3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1zl3 RCSB], [http://www.ebi.ac.uk/pdbsum/1zl3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1zl3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 1zl3" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1zl3" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Guide-independent Pseudouridine synthase\|Guide-independent Pseudouridine synthase]]
		+	*[[Pseudouridine synthase 3D structures\|Pseudouridine synthase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 36:		Line 40:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Pseudouridylate synthase]]		[[Category: Pseudouridylate synthase]]
	[[Category: Amare, A R.Ferre-D]]		[[Category: Amare, A R.Ferre-D]]

OCA at 09:04, 2 May 2018

OCA — Wed, 02 May 2018 09:04:56 GMT

←Older revision		Revision as of 09:04, 2 May 2018
Line 1:		Line 1:
		+
	==Coupling of active site motions and RNA binding==		==Coupling of active site motions and RNA binding==
	<StructureSection load='1zl3' size='340' side='right' caption='[[1zl3]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1zl3' size='340' side='right' caption='[[1zl3]], [[Resolution\|resolution]] 2.80Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">truB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">truB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pseudouridylate_synthase Pseudouridylate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.70 4.2.1.70] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pseudouridylate_synthase Pseudouridylate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.70 4.2.1.70] </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=1zl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zl3 OCA], [http://pdbe.org/1zl3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1zl3 RCSB], [http://www.ebi.ac.uk/pdbsum/1zl3 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=1zl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zl3 OCA], [http://pdbe.org/1zl3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1zl3 RCSB], [http://www.ebi.ac.uk/pdbsum/1zl3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1zl3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zl/1zl3_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zl/1zl3_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>
Line 30:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 1zl3" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1zl3" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[TRNA pseudouridine synthase\|TRNA pseudouridine synthase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:12, 9 February 2016

OCA — Tue, 09 Feb 2016 06:12:53 GMT

←Older revision		Revision as of 06:12, 9 February 2016
Line 19:		Line 19:
	<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=1zl3 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 19:23, 10 September 2015

OCA — Thu, 10 Sep 2015 19:23:39 GMT

←Older revision		Revision as of 19:23, 10 September 2015
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	<StructureSection load='1zl3' size='340' side='right' caption='[[1zl3]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1zl3' size='340' side='right' caption='[[1zl3]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1zl3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZL3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ZL3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1zl3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZL3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ZL3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UD5:5-FLUOROURIDINE'>UD5</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UD5:5-FLUOROURIDINE'>UD5</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">truB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 ~~Escherichia~~ coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">truB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pseudouridylate_synthase Pseudouridylate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.70 4.2.1.70] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pseudouridylate_synthase Pseudouridylate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.70 4.2.1.70] </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=1zl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zl3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1zl3 RCSB], [http://www.ebi.ac.uk/pdbsum/1zl3 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=1zl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zl3 OCA], [http://pdbe.org/1zl3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1zl3 RCSB], [http://www.ebi.ac.uk/pdbsum/1zl3 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	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 1zl3" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Pseudouridylate synthase]]		[[Category: Pseudouridylate synthase]]
	[[Category: Amare, A R.Ferre-D]]		[[Category: Amare, A R.Ferre-D]]

OCA at 04:56, 25 December 2014

OCA — Thu, 25 Dec 2014 04:56:55 GMT

←Older revision		Revision as of 04:56, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1zl3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZL3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ZL3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1zl3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZL3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ZL3 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UD5:5-FLUOROURIDINE'>UD5</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UD5:5-FLUOROURIDINE'>UD5</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">truB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">truB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pseudouridylate_synthase Pseudouridylate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.70 4.2.1.70] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pseudouridylate_synthase Pseudouridylate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.70 4.2.1.70] </span></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=1zl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zl3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1zl3 RCSB], [http://www.ebi.ac.uk/pdbsum/1zl3 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=1zl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zl3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1zl3 RCSB], [http://www.ebi.ac.uk/pdbsum/1zl3 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TRUB_ECOLI TRUB_ECOLI]] Responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs.<ref>PMID:7489483</ref> <ref>PMID:11142385</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 38:
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Pseudouridylate synthase]]		[[Category: Pseudouridylate synthase]]
-	[[Category: Amare, A R.Ferre-D.]]	+	[[Category: Amare, A R.Ferre-D]]
-	[[Category: Hamilton, C S.]]	+	[[Category: Hamilton, C S]]
-	[[Category: Hoang, C.]]	+	[[Category: Hoang, C]]
-	[[Category: Mueller, E G.]]	+	[[Category: Mueller, E G]]
	[[Category: Inter-domain coupling]]		[[Category: Inter-domain coupling]]
	[[Category: Lyase-rna complex]]		[[Category: Lyase-rna complex]]
	[[Category: Product release]]		[[Category: Product release]]
	[[Category: Rna-modification]]		[[Category: Rna-modification]]

OCA at 04:38, 29 September 2014

OCA — Mon, 29 Sep 2014 04:38:50 GMT

←Older revision		Revision as of 04:38, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1zl3.~~png~~\|~~left~~\|200px]]	+	==Coupling of active site motions and RNA binding==
		+	<StructureSection load='1zl3' size='340' side='right' caption='[[1zl3]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1zl3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZL3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ZL3 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UD5:5-FLUOROURIDINE'>UD5</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">truB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pseudouridylate_synthase Pseudouridylate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.70 4.2.1.70] </span></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=1zl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zl3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1zl3 RCSB], [http://www.ebi.ac.uk/pdbsum/1zl3 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/zl/1zl3_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 pseudouridine synthase TruB is responsible for the universally conserved post-transcriptional modification of residue 55 of elongator tRNAs. In addition to the active site, the "thumb", a peripheral domain unique to the TruB family of enzymes, makes extensive interactions with the substrate. To coordinate RNA binding and release with catalysis, the thumb may be able to sense progress of the reaction in the active site. To establish whether there is a structural correlate of communication between the active site and the RNA-sequestering thumb, we have solved the structure of a catalytically inactive point mutant of TruB in complex with a substrate RNA, and compared it to the previously determined structure of an active TruB bound to a reaction product. Superposition of the two structures shows that they are extremely similar, except in the active site and, intriguingly, in the relative position of the thumb. Because the two structures were solved using isomorphous crystals, and because the thumb is very well ordered in both structures, the displacement of the thumb we observe likely reflects preferential propagation of active site perturbations to this RNA-binding domain. One of the interactions between the active site and the thumb involves an active site residue whose hydrogen-bonding status changes during the reaction. This may allow the peripheral RNA-binding domain to monitor progress of the pseudouridylation reaction.

-	~~{{STRUCTURE_1zl3\| PDB=1zl3 \| SCENE= }}~~	+	Precursor complex structure of pseudouridine synthase TruB suggests coupling of active site perturbations to an RNA-sequestering peripheral protein domain.,Hoang C, Hamilton CS, Mueller EG, Ferre-D'Amare AR Protein Sci. 2005 Aug;14(8):2201-6. Epub 2005 Jun 29. PMID:15987897<ref>PMID:15987897</ref>

-	~~===Coupling~~ of ~~active site motions and RNA binding===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15987897}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1zl3]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli Escherichia coli]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1ZL3 OCA].~~	+

	==See Also==		==See Also==
	*[[TRNA pseudouridine synthase\|TRNA pseudouridine synthase]]		*[[TRNA pseudouridine synthase\|TRNA pseudouridine synthase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:015987897<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Pseudouridylate synthase]]		[[Category: Pseudouridylate synthase]]

OCA at 12:55, 20 October 2012

OCA — Sat, 20 Oct 2012 12:55:11 GMT

←Older revision		Revision as of 12:55, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1zl3]] is a 2 chain structure ~~of [[TRNA pseudouridine synthase]]~~ with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZL3 OCA].	+	[[1zl3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZL3 OCA].

	==See Also==		==See Also==

OCA: Protected "1zl3" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 10:19:21 GMT

Protected "1zl3" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:19, 26 July 2012

←Older revision		Revision as of 17:01, 20 October 2021
Line 3:		Line 3:
	<StructureSection load='1zl3' size='340' side='right'caption='[[1zl3]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1zl3' size='340' side='right'caption='[[1zl3]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1zl3]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZL3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1ZL3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1zl3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZL3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZL3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UD5:5-FLUOROURIDINE'>UD5</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UD5:5-FLUOROURIDINE'>UD5</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">truB ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">truB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Pseudouridylate_synthase Pseudouridylate synthase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.70 4.2.1.70] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Pseudouridylate_synthase Pseudouridylate synthase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.70 4.2.1.70] </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=1zl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zl3 OCA], [~~http~~://pdbe.org/1zl3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1zl3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1zl3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1zl3 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=1zl3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zl3 OCA], [https://pdbe.org/1zl3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zl3 RCSB], [https://www.ebi.ac.uk/pdbsum/1zl3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zl3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/TRUB_ECOLI TRUB_ECOLI]] Responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs.<ref>PMID:7489483</ref> <ref>PMID:11142385</ref>	+	[[https://www.uniprot.org/uniprot/TRUB_ECOLI TRUB_ECOLI]] Responsible for synthesis of pseudouridine from uracil-55 in the psi GC loop of transfer RNAs.<ref>PMID:7489483</ref> <ref>PMID:11142385</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]