1q8f - Revision history

OCA at 09:59, 16 August 2023

2023-08-16T09:59:52Z

←Older revision		Revision as of 09:59, 16 August 2023
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	<StructureSection load='1q8f' size='340' side='right'caption='[[1q8f]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1q8f' size='340' side='right'caption='[[1q8f]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1q8f]] is a 4 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=1Q8F OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1Q8F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1q8f]] is a 4 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=1Q8F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q8F FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>~~, ~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.7Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[1mas\|1mas]], [[2mas\|2mas]], [[1hp0\|1hp0]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>YEIK ([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'>[https://proteopedia.org/fgij/fg.htm?mol=1q8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q8f OCA], [https://pdbe.org/1q8f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q8f RCSB], [https://www.ebi.ac.uk/pdbsum/1q8f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q8f ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Ribosylpyrimidine_nucleosidase Ribosylpyrimidine nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.8 3.2.2.8]~~ </~~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=1q8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q8f OCA], [~~http~~://pdbe.org/1q8f PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1q8f RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1q8f PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1q8f ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RIHB_ECOLI RIHB_ECOLI]] Hydrolyzes cytidine or uridine to ribose and cytosine or uracil, respectively. Has a clear preference for cytidine over uridine. Strictly specific for ribonucleosides. Has a low but significant activity for the purine nucleoside xanthosine.[HAMAP-Rule:MF_01433]	+	[https://www.uniprot.org/uniprot/RIHB_ECOLI RIHB_ECOLI] Hydrolyzes cytidine or uridine to ribose and cytosine or uracil, respectively. Has a clear preference for cytidine over uridine. Strictly specific for ribonucleosides. Has a low but significant activity for the purine nucleoside xanthosine.[HAMAP-Rule:MF_01433]
	== 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: Ribosylpyrimidine nucleosidase]]~~	+	[[Category: Degano M]]
-	[[Category: Degano, M]]	+	[[Category: Giabbai B]]
-	[[Category: Giabbai, B]]	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Nh-fold]]~~	+
-	~~[[Category: Open alpha-beta structure~~]]	+

OCA at 07:45, 9 December 2020

2020-12-09T07:45:39Z

←Older revision		Revision as of 07:45, 9 December 2020
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	==Crystal Structure of the E.coli pyrimidine nucleoside hydrolase yeiK==		==Crystal Structure of the E.coli pyrimidine nucleoside hydrolase yeiK==
-	<StructureSection load='1q8f' size='340' side='right' caption='[[1q8f]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='1q8f' size='340' side='right'caption='[[1q8f]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1q8f]] is a 4 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=1Q8F OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1Q8F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1q8f]] is a 4 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=1Q8F OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1Q8F FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1mas\|1mas]], [[2mas\|2mas]], [[1hp0\|1hp0]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1mas\|1mas]], [[2mas\|2mas]], [[1hp0\|1hp0]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YEIK ([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">YEIK ([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/Ribosylpyrimidine_nucleosidase Ribosylpyrimidine nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.8 3.2.2.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribosylpyrimidine_nucleosidase Ribosylpyrimidine nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.8 3.2.2.8] </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=1q8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q8f OCA], [http://pdbe.org/1q8f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q8f RCSB], [http://www.ebi.ac.uk/pdbsum/1q8f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1q8f 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=1q8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q8f OCA], [http://pdbe.org/1q8f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q8f RCSB], [http://www.ebi.ac.uk/pdbsum/1q8f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1q8f ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Ribosylpyrimidine nucleosidase]]		[[Category: Ribosylpyrimidine nucleosidase]]
	[[Category: Degano, M]]		[[Category: Degano, M]]

OCA at 08:24, 24 February 2018

2018-02-24T08:24:43Z

←Older revision		Revision as of 08:24, 24 February 2018
Line 1:		Line 1:
		+
	==Crystal Structure of the E.coli pyrimidine nucleoside hydrolase yeiK==		==Crystal Structure of the E.coli pyrimidine nucleoside hydrolase yeiK==
	<StructureSection load='1q8f' size='340' side='right' caption='[[1q8f]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='1q8f' size='340' side='right' caption='[[1q8f]], [[Resolution\|resolution]] 1.70Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YEIK ([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">YEIK ([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/Ribosylpyrimidine_nucleosidase Ribosylpyrimidine nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.8 3.2.2.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribosylpyrimidine_nucleosidase Ribosylpyrimidine nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.8 3.2.2.8] </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=1q8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q8f OCA], [http://pdbe.org/1q8f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q8f RCSB], [http://www.ebi.ac.uk/pdbsum/1q8f 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=1q8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q8f OCA], [http://pdbe.org/1q8f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q8f RCSB], [http://www.ebi.ac.uk/pdbsum/1q8f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1q8f ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q8/1q8f_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q8/1q8f_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>
	</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=1q8f ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:11, 11 September 2015

2015-09-11T07:11:58Z

←Older revision		Revision as of 07:11, 11 September 2015
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YEIK ([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">YEIK ([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/Ribosylpyrimidine_nucleosidase Ribosylpyrimidine nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.8 3.2.2.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribosylpyrimidine_nucleosidase Ribosylpyrimidine nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.8 3.2.2.8] </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=1q8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q8f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1q8f RCSB], [http://www.ebi.ac.uk/pdbsum/1q8f 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=1q8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q8f OCA], [http://pdbe.org/1q8f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q8f RCSB], [http://www.ebi.ac.uk/pdbsum/1q8f PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RIHB_ECOLI RIHB_ECOLI]] Hydrolyzes cytidine or uridine to ribose and cytosine or uracil, respectively. Has a clear preference for cytidine over uridine. Strictly specific for ribonucleosides. Has a low but significant activity for the purine nucleoside xanthosine.[HAMAP-Rule:MF_01433]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 27:		Line 29:
	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 1q8f" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:21, 6 January 2015

2015-01-06T08:21:33Z

←Older revision		Revision as of 08:21, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1q8f]] is a 4 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=1Q8F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q8F FirstGlance]. <br>		<table><tr><td colspan='2'>[[1q8f]] is a 4 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=1Q8F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q8F FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1mas\|1mas]], [[2mas\|2mas]], [[1hp0\|1hp0]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1mas\|1mas]], [[2mas\|2mas]], [[1hp0\|1hp0]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YEIK ([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">YEIK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribosylpyrimidine_nucleosidase Ribosylpyrimidine nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.8 3.2.2.8] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribosylpyrimidine_nucleosidase Ribosylpyrimidine nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.8 3.2.2.8] </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=1q8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q8f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1q8f RCSB], [http://www.ebi.ac.uk/pdbsum/1q8f 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=1q8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q8f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1q8f RCSB], [http://www.ebi.ac.uk/pdbsum/1q8f PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
	[[Category: Ribosylpyrimidine nucleosidase]]		[[Category: Ribosylpyrimidine nucleosidase]]
-	[[Category: Degano, M.]]	+	[[Category: Degano, M]]
-	[[Category: Giabbai, B.]]	+	[[Category: Giabbai, B]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Nh-fold]]		[[Category: Nh-fold]]
	[[Category: Open alpha-beta structure]]		[[Category: Open alpha-beta structure]]

OCA at 10:04, 3 October 2014

2014-10-03T10:04:15Z

←Older revision		Revision as of 10:04, 3 October 2014
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-	~~{{STRUCTURE_1q8f\| PDB=1q8f \| SCENE= }}~~	+	==Crystal Structure of the E.coli pyrimidine nucleoside hydrolase yeiK==
-	===Crystal Structure of the E.coli pyrimidine nucleoside hydrolase yeiK===	+	<StructureSection load='1q8f' size='340' side='right' caption='[[1q8f]], [[Resolution\|resolution]] 1.70Å' scene=''>
-	~~{{ABSTRACT_PUBMED_15130467}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1q8f]] is a 4 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=1Q8F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q8F FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1mas\|1mas]], [[2mas\|2mas]], [[1hp0\|1hp0]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">YEIK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribosylpyrimidine_nucleosidase Ribosylpyrimidine nucleosidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.2.8 3.2.2.8] </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=1q8f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q8f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1q8f RCSB], [http://www.ebi.ac.uk/pdbsum/1q8f 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/q8/1q8f_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 ==
		+	Enzymes with nucleoside hydrolase (NH) activity are crucial for salvaging nucleic acid components in purine auxotrophic protozoan parasites, but are also present in prokaryotes and higher eukaryotes. Here we analyze the distribution of genes encoding for putative NH proteins and characterize the yeiK gene product from Escherichia coli as a pyrimidine-specific NH. The crystal structure of YeiK to 1.7 A defines the structural basis for its substrate specificity and identifies residues involved in the catalytic mechanism that differ from both nonspecific and purine-specific NHs. Large differences in the tetrameric quaternary structure compared to nonspecific protozoan NHs are brought forth by minor differences in the interacting surfaces. The first structural and functional characterization of a nonparasitic, pyrimidine nucleoside-specific NH suggests a possible role for these enzymes in the metabolism of tRNA nucleosides. The high catalytic efficiency of YeiK toward 5-fluorouridine could be exploited for suicide gene therapy in cancer treatment.

-	~~==About this Structure==~~	+	Crystal structure to 1.7 a of the Escherichia coli pyrimidine nucleoside hydrolase YeiK, a novel candidate for cancer gene therapy.,Giabbai B, Degano M Structure. 2004 May;12(5):739-49. PMID:15130467<ref>PMID:15130467</ref>
-	~~[[1q8f]] is a 4 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=1Q8F OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:015130467</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
	[[Category: Ribosylpyrimidine nucleosidase]]		[[Category: Ribosylpyrimidine nucleosidase]]

OCA: Protected "1q8f" [edit=sysop:move=sysop]

2014-04-16T10:50:26Z

Protected "1q8f" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:50, 16 April 2014

OCA at 10:50, 16 April 2014

2014-04-16T10:50:25Z

←Older revision		Revision as of 10:50, 16 April 2014
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-	{{Seed}}
-	[[Image:1q8f.png\|left\|200px]]
-
-	<!--
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-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
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	{{STRUCTURE_1q8f\| PDB=1q8f \| SCENE= }}		{{STRUCTURE_1q8f\| PDB=1q8f \| SCENE= }}
-
	===Crystal Structure of the E.coli pyrimidine nucleoside hydrolase yeiK===		===Crystal Structure of the E.coli pyrimidine nucleoside hydrolase yeiK===
-
-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15130467}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15130467 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_15130467}}		{{ABSTRACT_PUBMED_15130467}}

	==About this Structure==		==About this Structure==
-	~~1Q8F~~ is a 4 ~~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=1Q8F OCA].	+	[[1q8f]] is a 4 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=1Q8F OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15130467~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015130467</ref><references group="xtra"/><references/>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Ribosylpyrimidine nucleosidase]]		[[Category: Ribosylpyrimidine nucleosidase]]
	[[Category: Degano, M.]]		[[Category: Degano, M.]]
	[[Category: Giabbai, B.]]		[[Category: Giabbai, B.]]
		+	[[Category: Hydrolase]]
	[[Category: Nh-fold]]		[[Category: Nh-fold]]
	[[Category: Open alpha-beta structure]]		[[Category: Open alpha-beta structure]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 16:55:03 2009''

OCA at 14:55, 17 February 2009

2009-02-17T14:55:03Z

←Older revision		Revision as of 14:55, 17 February 2009
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	==About this Structure==		==About this Structure==
-	1Q8F 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=1Q8F OCA].	+	1Q8F is a 4 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=1Q8F OCA].

	==Reference==		==Reference==
-	~~Crystal structure to 1.7 a of the Escherichia coli pyrimidine nucleoside hydrolase YeiK, a novel candidate for cancer gene therapy., Giabbai B, Degano M, Structure. 2004 May;12(5):739-49.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/15130467 15130467]~~	+	<ref group="xtra">PMID:15130467</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Ribosylpyrimidine nucleosidase]]		[[Category: Ribosylpyrimidine nucleosidase]]
-	[[Category: Single protein]]
	[[Category: Degano, M.]]		[[Category: Degano, M.]]
	[[Category: Giabbai, B.]]		[[Category: Giabbai, B.]]
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	[[Category: Open alpha-beta structure]]		[[Category: Open alpha-beta structure]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 23~~:43:~~54 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 16:55:03 2009''

OCA at 20:43, 28 July 2008

2008-07-28T20:43:57Z

←Older revision		Revision as of 20:43, 28 July 2008
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-	[[Image:1q8f.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:1q8f.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_1q8f\| PDB=1q8f \| SCENE= }}		{{STRUCTURE_1q8f\| PDB=1q8f \| SCENE= }}

-	~~'''~~Crystal Structure of the E.coli pyrimidine nucleoside hydrolase yeiK~~'''~~	+	===Crystal Structure of the E.coli pyrimidine nucleoside hydrolase yeiK===


-	~~==Overview==~~	+	<!--
-	~~Enzymes with nucleoside hydrolase (NH) activity are crucial for salvaging nucleic acid components in purine auxotrophic protozoan parasites~~, ~~but are also present in prokaryotes and higher eukaryotes. Here we analyze~~ the ~~distribution of genes encoding for putative NH proteins and characterize~~ the ~~yeiK gene product from Escherichia coli~~ as ~~a pyrimidine-specific NH~~. ~~The crystal structure of YeiK to 1~~.7 A defines the structural basis for its substrate specificity and identifies residues involved in the catalytic mechanism that differ from both nonspecific and purine-specific NHs. Large differences in the tetrameric quaternary structure compared to nonspecific protozoan NHs are brought forth by minor differences in the interacting surfaces. The first structural and functional characterization of a nonparasitic, ~~pyrimidine nucleoside-specific NH suggests a possible role for these enzymes in~~ the ~~metabolism of tRNA nucleosides~~. ~~The high catalytic efficiency of YeiK toward 5~~-~~fluorouridine could be exploited for suicide gene therapy in cancer treatment.~~	+	The line below this paragraph, {{ABSTRACT_PUBMED_15130467}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 15130467 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_15130467}}

	==About this Structure==		==About this Structure==
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	[[Category: Nh-fold]]		[[Category: Nh-fold]]
	[[Category: Open alpha-beta structure]]		[[Category: Open alpha-beta structure]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sat May 3 05~~:59:30 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 23:43:54 2008''