2yrf - Revision history

OCA at 09:04, 25 October 2023

OCA — Wed, 25 Oct 2023 09:04:57 GMT

←Older revision		Revision as of 09:04, 25 October 2023
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	<StructureSection load='2yrf' size='340' side='right'caption='[[2yrf]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='2yrf' size='340' side='right'caption='[[2yrf]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2yrf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"vibrio_subtilis"_ehrenberg_1835 "vibrio~~ subtilis~~" ehrenberg 1835~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YRF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YRF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2yrf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YRF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YRF 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]] 2.7Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>mtnA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~1423~~ "~~Vibrio subtilis~~" ~~Ehrenberg 1835])</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~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>[https://en.wikipedia.org/wiki/S-methyl-5-thioribose-1-phosphate_isomerase S-methyl-5-thioribose-1-phosphate isomerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.23 5.3.1.23] </~~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=2yrf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yrf OCA], [https://pdbe.org/2yrf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yrf RCSB], [https://www.ebi.ac.uk/pdbsum/2yrf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yrf 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=2yrf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yrf OCA], [https://pdbe.org/2yrf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yrf RCSB], [https://www.ebi.ac.uk/pdbsum/2yrf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yrf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/MTNA_BACSU MTNA_BACSU]] Catalyzes the interconversion of methylthioribose-1-phosphate (MTR-1-P) into methylthioribulose-1-phosphate (MTRu-1-P).<ref>PMID:14551435</ref>	+	[https://www.uniprot.org/uniprot/MTNA_BACSU MTNA_BACSU] Catalyzes the interconversion of methylthioribose-1-phosphate (MTR-1-P) into methylthioribulose-1-phosphate (MTRu-1-P).<ref>PMID:14551435</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: ~~Vibrio~~ subtilis ~~ehrenberg 1835~~]]	+	[[Category: Bacillus subtilis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: S-methyl-5-thioribose-1-phosphate isomerase]]~~	+	[[Category: Inoue T]]
-	[[Category: Inoue, T]]	+	[[Category: Kai Y]]
-	[[Category: Kai, Y]]	+	[[Category: Matsumura H]]
-	[[Category: Matsumura, H]]	+	[[Category: Tamura H]]
-	[[Category: Tamura, H]]	+
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Methionine salvage pathway~~]]	+

OCA at 13:36, 24 November 2021

OCA — Wed, 24 Nov 2021 13:36:00 GMT

←Older revision		Revision as of 13:36, 24 November 2021
Line 1:		Line 1:

	==Crystal structure of 5-methylthioribose 1-phosphate isomerase from Bacillus subtilis complexed with sulfate ion==		==Crystal structure of 5-methylthioribose 1-phosphate isomerase from Bacillus subtilis complexed with sulfate ion==
-	<StructureSection load='2yrf' size='340' side='right' caption='[[2yrf]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='2yrf' size='340' side='right'caption='[[2yrf]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2yrf]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YRF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2YRF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2yrf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YRF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YRF 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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mtnA ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mtnA ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/S-methyl-5-thioribose-1-phosphate_isomerase S-methyl-5-thioribose-1-phosphate isomerase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.23 5.3.1.23] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/S-methyl-5-thioribose-1-phosphate_isomerase S-methyl-5-thioribose-1-phosphate isomerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.23 5.3.1.23] </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=2yrf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yrf OCA], [~~http~~://pdbe.org/2yrf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2yrf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2yrf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2yrf 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=2yrf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yrf OCA], [https://pdbe.org/2yrf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yrf RCSB], [https://www.ebi.ac.uk/pdbsum/2yrf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yrf ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/MTNA_BACSU MTNA_BACSU]] Catalyzes the interconversion of methylthioribose-1-phosphate (MTR-1-P) into methylthioribulose-1-phosphate (MTRu-1-P).<ref>PMID:14551435</ref>	+	[[https://www.uniprot.org/uniprot/MTNA_BACSU MTNA_BACSU]] Catalyzes the interconversion of methylthioribose-1-phosphate (MTR-1-P) into methylthioribulose-1-phosphate (MTRu-1-P).<ref>PMID:14551435</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Vibrio subtilis ehrenberg 1835]]		[[Category: Vibrio subtilis ehrenberg 1835]]
		+	[[Category: Large Structures]]
	[[Category: S-methyl-5-thioribose-1-phosphate isomerase]]		[[Category: S-methyl-5-thioribose-1-phosphate isomerase]]
	[[Category: Inoue, T]]		[[Category: Inoue, T]]

OCA at 09:07, 17 October 2018

OCA — Wed, 17 Oct 2018 09:07:01 GMT

←Older revision		Revision as of 09:07, 17 October 2018
Line 1:		Line 1:
		+
	==Crystal structure of 5-methylthioribose 1-phosphate isomerase from Bacillus subtilis complexed with sulfate ion==		==Crystal structure of 5-methylthioribose 1-phosphate isomerase from Bacillus subtilis complexed with sulfate ion==
	<StructureSection load='2yrf' size='340' side='right' caption='[[2yrf]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='2yrf' size='340' side='right' caption='[[2yrf]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2yrf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"~~bacillus_globigii~~"~~_migula_1900~~ "~~bacillus globigii~~" ~~migula 1900~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YRF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YRF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2yrf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YRF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YRF 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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mtnA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "~~Bacillus globigii~~" ~~Migula 1900~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mtnA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/S-methyl-5-thioribose-1-phosphate_isomerase S-methyl-5-thioribose-1-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.23 5.3.1.23] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/S-methyl-5-thioribose-1-phosphate_isomerase S-methyl-5-thioribose-1-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.23 5.3.1.23] </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=2yrf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yrf OCA], [http://pdbe.org/2yrf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2yrf RCSB], [http://www.ebi.ac.uk/pdbsum/2yrf 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=2yrf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yrf OCA], [http://pdbe.org/2yrf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2yrf RCSB], [http://www.ebi.ac.uk/pdbsum/2yrf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2yrf 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/yr/2yrf_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yr/2yrf_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 33:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus globigii migula 1900~~]]	+	[[Category: Vibrio subtilis ehrenberg 1835]]
	[[Category: S-methyl-5-thioribose-1-phosphate isomerase]]		[[Category: S-methyl-5-thioribose-1-phosphate isomerase]]
	[[Category: Inoue, T]]		[[Category: Inoue, T]]

OCA at 09:26, 8 February 2016

OCA — Mon, 08 Feb 2016 09:26:26 GMT

←Older revision		Revision as of 09:26, 8 February 2016
Line 2:		Line 2:
	<StructureSection load='2yrf' size='340' side='right' caption='[[2yrf]], [[Resolution\|resolution]] 2.70Å' scene=''>		<StructureSection load='2yrf' size='340' side='right' caption='[[2yrf]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2yrf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bacillus_subtilis Bacillus subtilis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YRF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YRF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2yrf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YRF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YRF 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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mtnA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus ~~subtilis~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mtnA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/S-methyl-5-thioribose-1-phosphate_isomerase S-methyl-5-thioribose-1-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.23 5.3.1.23] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/S-methyl-5-thioribose-1-phosphate_isomerase S-methyl-5-thioribose-1-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.23 5.3.1.23] </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=2yrf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yrf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2yrf RCSB], [http://www.ebi.ac.uk/pdbsum/2yrf 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=2yrf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yrf OCA], [http://pdbe.org/2yrf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2yrf RCSB], [http://www.ebi.ac.uk/pdbsum/2yrf PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 18:
	<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=2yrf ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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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 2yrf" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus ~~subtilis~~]]	+	[[Category: Bacillus globigii migula 1900]]
	[[Category: S-methyl-5-thioribose-1-phosphate isomerase]]		[[Category: S-methyl-5-thioribose-1-phosphate isomerase]]
	[[Category: Inoue, T]]		[[Category: Inoue, T]]

OCA at 22:18, 24 December 2014

OCA — Wed, 24 Dec 2014 22:18:05 GMT

←Older revision		Revision as of 22:18, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2yrf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YRF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YRF FirstGlance]. <br>		<table><tr><td colspan='2'>[[2yrf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YRF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YRF 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>[[Gene\|Gene:]]</b></td><td class="sblockDat">mtnA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mtnA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/S-methyl-5-thioribose-1-phosphate_isomerase S-methyl-5-thioribose-1-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.23 5.3.1.23] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/S-methyl-5-thioribose-1-phosphate_isomerase S-methyl-5-thioribose-1-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.23 5.3.1.23] </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=2yrf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yrf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2yrf RCSB], [http://www.ebi.ac.uk/pdbsum/2yrf 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=2yrf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yrf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2yrf RCSB], [http://www.ebi.ac.uk/pdbsum/2yrf PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MTNA_BACSU MTNA_BACSU]] Catalyzes the interconversion of methylthioribose-1-phosphate (MTR-1-P) into methylthioribulose-1-phosphate (MTRu-1-P).<ref>PMID:14551435</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 34:
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: S-methyl-5-thioribose-1-phosphate isomerase]]		[[Category: S-methyl-5-thioribose-1-phosphate isomerase]]
-	[[Category: Inoue, T.]]	+	[[Category: Inoue, T]]
-	[[Category: Kai, Y.]]	+	[[Category: Kai, Y]]
-	[[Category: Matsumura, H.]]	+	[[Category: Matsumura, H]]
-	[[Category: Tamura, H.]]	+	[[Category: Tamura, H]]
	[[Category: Isomerase]]		[[Category: Isomerase]]
	[[Category: Methionine salvage pathway]]		[[Category: Methionine salvage pathway]]

OCA at 04:55, 2 October 2014

OCA — Thu, 02 Oct 2014 04:55:20 GMT

←Older revision		Revision as of 04:55, 2 October 2014
Line 1:		Line 1:
-	[[~~Image:~~2yrf.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of 5-methylthioribose 1-phosphate isomerase from Bacillus subtilis complexed with sulfate ion==
		+	<StructureSection load='2yrf' size='340' side='right' caption='[[2yrf]], [[Resolution\|resolution]] 2.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2yrf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YRF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YRF 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>[[Gene\|Gene:]]</b></td><td class="sblockDat">mtnA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/S-methyl-5-thioribose-1-phosphate_isomerase S-methyl-5-thioribose-1-phosphate isomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.3.1.23 5.3.1.23] </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=2yrf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yrf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2yrf RCSB], [http://www.ebi.ac.uk/pdbsum/2yrf 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/yr/2yrf_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 methionine salvage pathway (MSP) plays a crucial role in recycling a sulphahydryl derivative of the nucleoside. Recently, the genes and reactions in MSP from Bacillus subtilis have been identified, where 5-methylthioribose 1-phosphate isomerase (M1Pi) catalyzes a conversion of 5-methylthioribose 1-phosphate (MTR-1-P) to 5-methylthioribulose 1-phosphate (MTRu-1-P). Herein, we report the crystal structures of B. subtilis M1Pi (Bs-M1Pi) in complex with its product MTRu-1-P, and a sulfate at 2.4 and 2.7 A resolution, respectively. The electron density clearly shows the presence of each compound in the active site. The structural comparison with other homologous proteins explains how the substrate uptake of Bs-M1Pi may be induced by an open/closed transition of the active site. The highly conserved residues at the active site, namely, Cys160 and Asp240 are most likely to be involved in catalysis. The structural analysis sheds light on its catalytic mechanism of M1Pi.

-	~~{{STRUCTURE_2yrf\| PDB=2yrf \| SCENE= }}~~	+	Crystal structure of 5-methylthioribose 1-phosphate isomerase product complex from Bacillus subtilis: implications for catalytic mechanism.,Tamura H, Saito Y, Ashida H, Inoue T, Kai Y, Yokota A, Matsumura H Protein Sci. 2008 Jan;17(1):126-35. PMID:18156470<ref>PMID:18156470</ref>

-	~~===Crystal structure~~ of ~~5-methylthioribose 1-phosphate isomerase from Bacillus subtilis complexed with sulfate ion===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18156470}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2yrf]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Bacillus_subtilis Bacillus subtilis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2YRF OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:018156470<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: S-methyl-5-thioribose-1-phosphate isomerase]]		[[Category: S-methyl-5-thioribose-1-phosphate isomerase]]

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

OCA — Mon, 07 Jan 2013 17:59:45 GMT

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

←Older revision

Revision as of 17:59, 7 January 2013

OCA at 17:59, 7 January 2013

OCA — Mon, 07 Jan 2013 17:59:43 GMT

←Older revision		Revision as of 17:59, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2yrf.png\|left\|200px]]		[[Image:2yrf.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2yrf", 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_2yrf\| PDB=2yrf \| SCENE= }}		{{STRUCTURE_2yrf\| PDB=2yrf \| SCENE= }}

	===Crystal structure of 5-methylthioribose 1-phosphate isomerase from Bacillus subtilis complexed with sulfate ion===		===Crystal structure of 5-methylthioribose 1-phosphate isomerase from Bacillus subtilis complexed with sulfate ion===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18156470}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18156470 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18156470}}		{{ABSTRACT_PUBMED_18156470}}

	==About this Structure==		==About this Structure==
-	~~2YRF~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YRF OCA].	+	[[2yrf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YRF OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18156470~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018156470</ref><references group="xtra"/>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: S-methyl-5-thioribose-1-phosphate isomerase]]		[[Category: S-methyl-5-thioribose-1-phosphate isomerase]]
Line 30:		Line 18:
	[[Category: Matsumura, H.]]		[[Category: Matsumura, H.]]
	[[Category: Tamura, H.]]		[[Category: Tamura, H.]]
-	[[Category: Crystal structure]]
	[[Category: Isomerase]]		[[Category: Isomerase]]
	[[Category: Methionine salvage pathway]]		[[Category: Methionine salvage pathway]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 20:58:06 2009''

OCA at 18:58, 16 February 2009

OCA — Mon, 16 Feb 2009 18:58:08 GMT

←Older revision		Revision as of 18:58, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2YRF is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YRF OCA].	+	2YRF is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YRF OCA].

	==Reference==		==Reference==
-	Crystal structure of 5-methylthioribose 1-phosphate isomerase product complex from Bacillus subtilis: implications for catalytic mechanism., Tamura H, Saito Y, Ashida H, Inoue T, Kai Y, Yokota A, Matsumura H, Protein Sci. 2008 Jan;17(1):126-35. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18156470 18156470]~~	+	<ref group="xtra">PMID:18156470</ref><references group="xtra"/>
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: S-methyl-5-thioribose-1-phosphate isomerase]]		[[Category: S-methyl-5-thioribose-1-phosphate isomerase]]
-	[[Category: Single protein]]
	[[Category: Inoue, T.]]		[[Category: Inoue, T.]]
	[[Category: Kai, Y.]]		[[Category: Kai, Y.]]
Line 35:		Line 34:
	[[Category: Methionine salvage pathway]]		[[Category: Methionine salvage pathway]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon ~~Jul 28 01~~:31:~~31 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 20:58:06 2009''

OCA at 22:31, 27 July 2008

OCA — Sun, 27 Jul 2008 22:31:39 GMT

←Older revision		Revision as of 22:31, 27 July 2008
Line 1:		Line 1:
-	[[Image:2yrf.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2yrf.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_2yrf\| PDB=2yrf \| SCENE= }}		{{STRUCTURE_2yrf\| PDB=2yrf \| SCENE= }}

-	~~'''~~Crystal structure of 5-methylthioribose 1-phosphate isomerase from Bacillus subtilis complexed with sulfate ion~~'''~~	+	===Crystal structure of 5-methylthioribose 1-phosphate isomerase from Bacillus subtilis complexed with sulfate ion===


-	~~==Overview==~~	+	<!--
-	The ~~methionine salvage pathway (MSP) plays a crucial role in recycling a sulphahydryl derivative of the nucleoside. Recently~~, the ~~genes and reactions in MSP from Bacillus subtilis have been identified, where 5-methylthioribose 1-phosphate isomerase (M1Pi) catalyzes a conversion of 5-methylthioribose 1-phosphate (MTR-1-P)~~ to ~~5-methylthioribulose 1-phosphate (MTRu-1-P). Herein, we report~~ the ~~crystal structures of B. subtilis M1Pi~~ (~~Bs-M1Pi) in complex with its product MTRu-1-P, and a sulfate~~ at 2.~~4 and 2~~.~~7 A resolution~~, ~~respectively. The electron density clearly shows~~ the ~~presence of each compound in the active site~~. ~~The structural comparison with other homologous proteins explains how the substrate uptake of Bs~~-M1Pi may be induced by an open/closed transition of the active site. The highly conserved residues at the active site, namely, Cys160 and Asp240 are most likely to be involved in catalysis. The structural analysis sheds light on its catalytic mechanism of M1Pi.	+	The line below this paragraph, {{ABSTRACT_PUBMED_18156470}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 18156470 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_18156470}}

	==About this Structure==		==About this Structure==
Line 30:		Line 34:
	[[Category: Isomerase]]		[[Category: Isomerase]]
	[[Category: Methionine salvage pathway]]		[[Category: Methionine salvage pathway]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 19~~:15:08 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 01:31:31 2008''