2rgk - Revision history

OCA at 09:03, 25 October 2023

2023-10-25T09:03:55Z

←Older revision		Revision as of 09:03, 25 October 2023
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	<StructureSection load='2rgk' size='340' side='right'caption='[[2rgk]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2rgk' size='340' side='right'caption='[[2rgk]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rgk]] is a 6 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=2RGK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RGK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rgk]] is a 6 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=2RGK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RGK FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=EPE:4~~-(2~~-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</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]] 2.5Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>yihS ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~562~~ "~~Bacillus coli~~" ~~Migula 1895]~~)</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene></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=2rgk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rgk OCA], [https://pdbe.org/2rgk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rgk RCSB], [https://www.ebi.ac.uk/pdbsum/2rgk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rgk 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=2rgk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rgk OCA], [https://pdbe.org/2rgk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rgk RCSB], [https://www.ebi.ac.uk/pdbsum/2rgk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rgk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/SQUS_ECOLI SQUS_ECOLI]] Catalyzes the isomerization of sulfoquinovose (SQ) to 6-deoxy-6-sulfo-D-fructose (SF). In vitro, can also catalyze the interconversion of mannose, fructose and glucose, or lyxose and xylulose, but has extremely low activity with glucose.[HAMAP-Rule:MF_00998]<ref>PMID:18328504</ref> <ref>PMID:24463506</ref>	+	[https://www.uniprot.org/uniprot/SQUS_ECOLI SQUS_ECOLI] Catalyzes the isomerization of sulfoquinovose (SQ) to 6-deoxy-6-sulfo-D-fructose (SF). In vitro, can also catalyze the interconversion of mannose, fructose and glucose, or lyxose and xylulose, but has extremely low activity with glucose.[HAMAP-Rule:MF_00998]<ref>PMID:18328504</ref> <ref>PMID:24463506</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hashimoto, W]]	+	[[Category: Hashimoto W]]
-	[[Category: Itoh, T]]	+	[[Category: Itoh T]]
-	[[Category: Mikami, B]]	+	[[Category: Mikami B]]
-	[[Category: Murata, K]]	+	[[Category: Murata K]]
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: N-acyl-d-glucosamine 2-epimerase protein family~~]]	+

OCA at 04:24, 2 July 2021

2021-07-02T04:24:53Z

←Older revision		Revision as of 04:24, 2 July 2021
Line 1:		Line 1:

	==Functional annotation of Escherichia coli yihS-encoded protein==		==Functional annotation of Escherichia coli yihS-encoded protein==
-	<StructureSection load='2rgk' size='340' side='right' caption='[[2rgk]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='2rgk' size='340' side='right'caption='[[2rgk]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rgk]] is a 6 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=2RGK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2RGK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rgk]] is a 6 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=2RGK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RGK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yihS ([~~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">yihS ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=2rgk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rgk OCA], [~~http~~://pdbe.org/2rgk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2rgk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2rgk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2rgk 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=2rgk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rgk OCA], [https://pdbe.org/2rgk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rgk RCSB], [https://www.ebi.ac.uk/pdbsum/2rgk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rgk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/SQUS_ECOLI SQUS_ECOLI]] Catalyzes the isomerization of sulfoquinovose (SQ) to 6-deoxy-6-sulfo-D-fructose (SF). In vitro, can also catalyze the interconversion of mannose, fructose and glucose, or lyxose and xylulose, but has extremely low activity with glucose.[HAMAP-Rule:MF_00998]<ref>PMID:18328504</ref> <ref>PMID:24463506</ref>	+	[[https://www.uniprot.org/uniprot/SQUS_ECOLI SQUS_ECOLI]] Catalyzes the isomerization of sulfoquinovose (SQ) to 6-deoxy-6-sulfo-D-fructose (SF). In vitro, can also catalyze the interconversion of mannose, fructose and glucose, or lyxose and xylulose, but has extremely low activity with glucose.[HAMAP-Rule:MF_00998]<ref>PMID:18328504</ref> <ref>PMID:24463506</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Hashimoto, W]]		[[Category: Hashimoto, W]]
	[[Category: Itoh, T]]		[[Category: Itoh, T]]

OCA at 11:23, 5 September 2018

2018-09-05T11:23:43Z

←Older revision		Revision as of 11:23, 5 September 2018
Line 1:		Line 1:
		+
	==Functional annotation of Escherichia coli yihS-encoded protein==		==Functional annotation of Escherichia coli yihS-encoded protein==
	<StructureSection load='2rgk' size='340' side='right' caption='[[2rgk]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2rgk' size='340' side='right' caption='[[2rgk]], [[Resolution\|resolution]] 2.50Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yihS ([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">yihS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=2rgk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rgk OCA], [http://pdbe.org/2rgk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rgk RCSB], [http://www.ebi.ac.uk/pdbsum/2rgk 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=2rgk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rgk OCA], [http://pdbe.org/2rgk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rgk RCSB], [http://www.ebi.ac.uk/pdbsum/2rgk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2rgk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rg/2rgk_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rg/2rgk_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 00:04, 9 February 2016

2016-02-09T00:04:12Z

←Older revision		Revision as of 00:04, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='2rgk' size='340' side='right' caption='[[2rgk]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2rgk' size='340' side='right' caption='[[2rgk]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2rgk]] is a 6 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=2RGK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RGK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2rgk]] is a 6 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=2RGK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RGK FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yihS ([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">yihS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</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=2rgk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rgk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rgk RCSB], [http://www.ebi.ac.uk/pdbsum/2rgk 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=2rgk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rgk OCA], [http://pdbe.org/2rgk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rgk RCSB], [http://www.ebi.ac.uk/pdbsum/2rgk PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~YIHS_ECOLI YIHS_ECOLI~~]] Catalyzes the isomerization of sulfoquinovose (SQ) to 6-deoxy-6-sulfo-D-fructose (SF). In vitro, can also catalyze the interconversion of mannose, fructose and glucose, or lyxose and xylulose, but has extremely low activity with glucose.<ref>PMID:~~24463506~~</ref> <ref>PMID:~~18328504~~</ref>	+	[[http://www.uniprot.org/uniprot/SQUS_ECOLI SQUS_ECOLI]] Catalyzes the isomerization of sulfoquinovose (SQ) to 6-deoxy-6-sulfo-D-fructose (SF). In vitro, can also catalyze the interconversion of mannose, fructose and glucose, or lyxose and xylulose, but has extremely low activity with glucose.[HAMAP-Rule:MF_00998]<ref>PMID:18328504</ref> <ref>PMID:24463506</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 17:		Line 17:
	<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=2rgk ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 27:		Line 27:
	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 2rgk" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Hashimoto, W]]		[[Category: Hashimoto, W]]
	[[Category: Itoh, T]]		[[Category: Itoh, T]]

OCA at 03:04, 25 December 2014

2014-12-25T03:04:53Z

←Older revision		Revision as of 03:04, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2rgk]] is a 6 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=2RGK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RGK FirstGlance]. <br>		<table><tr><td colspan='2'>[[2rgk]] is a 6 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=2RGK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RGK FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yihS ([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">yihS ([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>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2rgk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rgk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rgk RCSB], [http://www.ebi.ac.uk/pdbsum/2rgk 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=2rgk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rgk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rgk RCSB], [http://www.ebi.ac.uk/pdbsum/2rgk PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/YIHS_ECOLI YIHS_ECOLI]] Catalyzes the isomerization of sulfoquinovose (SQ) to 6-deoxy-6-sulfo-D-fructose (SF). In vitro, can also catalyze the interconversion of mannose, fructose and glucose, or lyxose and xylulose, but has extremely low activity with glucose.<ref>PMID:24463506</ref> <ref>PMID:18328504</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Hashimoto, W.]]	+	[[Category: Hashimoto, W]]
-	[[Category: Itoh, T.]]	+	[[Category: Itoh, T]]
-	[[Category: Mikami, B.]]	+	[[Category: Mikami, B]]
-	[[Category: Murata, K.]]	+	[[Category: Murata, K]]
	[[Category: Isomerase]]		[[Category: Isomerase]]
	[[Category: N-acyl-d-glucosamine 2-epimerase protein family]]		[[Category: N-acyl-d-glucosamine 2-epimerase protein family]]

OCA at 18:25, 30 September 2014

2014-09-30T18:25:54Z

←Older revision		Revision as of 18:25, 30 September 2014
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-	[[~~Image:~~2rgk.~~png~~\|~~left~~\|200px]]	+	==Functional annotation of Escherichia coli yihS-encoded protein==
		+	<StructureSection load='2rgk' size='340' side='right' caption='[[2rgk]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2rgk]] is a 6 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=2RGK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RGK FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yihS ([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>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2rgk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rgk OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2rgk RCSB], [http://www.ebi.ac.uk/pdbsum/2rgk 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/rg/2rgk_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 three-dimensional structure of a Salmonella enterica hypothetical protein YihS is significantly similar to that of N-acyl-D-glucosamine 2-epimerase (AGE) with respect to a common scaffold, an alpha6/alpha6-barrel, although the function of YihS remains to be clarified. To identify the function of YihS, Escherichia coli and S. enterica YihS proteins were overexpressed in E. coli, purified, and characterized. Both proteins were found to show no AGE activity but showed cofactor-independent aldose-ketose isomerase activity involved in the interconversion of monosaccharides, mannose, fructose, and glucose, or lyxose and xylulose. In order to clarify the structure/function relationship of YihS, we determined the crystal structure of S. enterica YihS mutant (H248A) in complex with a substrate (D-mannose) at 1.6 A resolution. This enzyme-substrate complex structure is the first demonstration in the AGE structural family, and it enables us to identify active-site residues and postulate a reaction mechanism for YihS. The substrate, beta-d-mannose, fits well in the active site and is specifically recognized by the enzyme. The substrate-binding site of YihS for the mannose C1 and O5 atoms is architecturally similar to those of mutarotases, suggesting that YihS adopts the pyranose ring-opening process by His383 and acidifies the C2 position, forming an aldehyde at the C1 position. In the isomerization step, His248 functions as a base catalyst responsible for transferring the proton from the C2 to C1 positions through a cis-enediol intermediate. On the other hand, in AGE, His248 is thought to abstract and re-adduct the proton at the C2 position of the substrate. These findings provide not only molecular insights into the YihS reaction mechanism but also useful information for the molecular design of novel carbohydrate-active enzymes with the common scaffold, alpha6/alpha6-barrel.

-	~~{{STRUCTURE_2rgk\| PDB=2rgk \| SCENE= }}~~	+	Crystal structure of YihS in complex with D-mannose: structural annotation of Escherichia coli and Salmonella enterica yihS-encoded proteins to an aldose-ketose isomerase.,Itoh T, Mikami B, Hashimoto W, Murata K J Mol Biol. 2008 Apr 11;377(5):1443-59. Epub 2008 Feb 12. PMID:18328504<ref>PMID:18328504</ref>

-	~~===Functional annotation~~ of ~~Escherichia coli yihS-encoded protein===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18328504}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2rgk]] is a 6 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=2RGK OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:018328504<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Hashimoto, W.]]		[[Category: Hashimoto, W.]]

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

2013-01-07T18:19:30Z

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

←Older revision

Revision as of 18:19, 7 January 2013

OCA at 18:19, 7 January 2013

2013-01-07T18:19:28Z

←Older revision		Revision as of 18:19, 7 January 2013
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-	{{Seed}}
	[[Image:2rgk.png\|left\|200px]]		[[Image:2rgk.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2rgk", 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_2rgk\| PDB=2rgk \| SCENE= }}		{{STRUCTURE_2rgk\| PDB=2rgk \| SCENE= }}

	===Functional annotation of Escherichia coli yihS-encoded protein===		===Functional annotation of Escherichia coli yihS-encoded protein===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18328504}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18328504 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_18328504}}		{{ABSTRACT_PUBMED_18328504}}

	==About this Structure==		==About this Structure==
-	~~2RGK~~ is a 6 ~~chains~~ structure ~~of sequences~~ 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=2RGK OCA].	+	[[2rgk]] is a 6 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=2RGK OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18328504~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018328504</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Hashimoto, W.]]		[[Category: Hashimoto, W.]]
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	[[Category: Isomerase]]		[[Category: Isomerase]]
	[[Category: N-acyl-d-glucosamine 2-epimerase protein family]]		[[Category: N-acyl-d-glucosamine 2-epimerase protein family]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 04:43:33 2009''

OCA at 02:43, 17 February 2009

2009-02-17T02:43:34Z

←Older revision		Revision as of 02:43, 17 February 2009
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	{{Seed}}		{{Seed}}
-	[[Image:2rgk.~~jpg~~\|left\|200px]]	+	[[Image:2rgk.png\|left\|200px]]

	<!--		<!--
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	==About this Structure==		==About this Structure==
-	2RGK is a ~~[[Single protein]]~~ structure of ~~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=2RGK OCA].	+	2RGK is a 6 chains structure of sequences 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=2RGK OCA].

	==Reference==		==Reference==
-	Crystal structure of YihS in complex with D-mannose: structural annotation of Escherichia coli and Salmonella enterica yihS-encoded proteins to an aldose-ketose isomerase., Itoh T, Mikami B, Hashimoto W, Murata K, J Mol Biol. 2008 Apr 11;377(5):1443-59. Epub 2008 Feb 12. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18328504 18328504]~~	+	<ref group="xtra">PMID:18328504</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Single protein]]
	[[Category: Hashimoto, W.]]		[[Category: Hashimoto, W.]]
	[[Category: Itoh, T.]]		[[Category: Itoh, T.]]
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	[[Category: N-acyl-d-glucosamine 2-epimerase protein family]]		[[Category: N-acyl-d-glucosamine 2-epimerase protein family]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Aug 27 11~~:08:~~57 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 04:43:33 2009''

OCA at 08:08, 27 August 2008

2008-08-27T08:08:58Z

←Older revision		Revision as of 08:08, 27 August 2008
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-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:2rgk.jpg\|left\|200px]]

-	The ~~entry 2rgk~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_2rgk", 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_2rgk\| PDB=2rgk \| SCENE= }}

-	~~Authors: Itoh, T., Mikami, B., Hashimoto, W., Murata, K.~~	+	===Functional annotation of Escherichia coli yihS-encoded protein===

-	Description: Functional annotation of Escherichia coli yihS-encoded protein

		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_18328504}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 18328504 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_18328504}}

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Jun~~ 11 08:48:52 2008''	+	==About this Structure==
		+	2RGK is a [[Single protein]] structure of 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=2RGK OCA].
		+
		+	==Reference==
		+	Crystal structure of YihS in complex with D-mannose: structural annotation of Escherichia coli and Salmonella enterica yihS-encoded proteins to an aldose-ketose isomerase., Itoh T, Mikami B, Hashimoto W, Murata K, J Mol Biol. 2008 Apr 11;377(5):1443-59. Epub 2008 Feb 12. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18328504 18328504]
		+	[[Category: Escherichia coli]]
		+	[[Category: Single protein]]
		+	[[Category: Hashimoto, W.]]
		+	[[Category: Itoh, T.]]
		+	[[Category: Mikami, B.]]
		+	[[Category: Murata, K.]]
		+	[[Category: Isomerase]]
		+	[[Category: N-acyl-d-glucosamine 2-epimerase protein family]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 27 11:08:57 2008''