1yoe - Revision history

OCA at 08:12, 25 October 2023

OCA — Wed, 25 Oct 2023 08:12:09 GMT

←Older revision		Revision as of 08:12, 25 October 2023
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	<StructureSection load='1yoe' size='340' side='right'caption='[[1yoe]], [[Resolution\|resolution]] 1.78Å' scene=''>		<StructureSection load='1yoe' size='340' side='right'caption='[[1yoe]], [[Resolution\|resolution]] 1.78Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1yoe]] is a 1 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=1YOE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1YOE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1yoe]] is a 1 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=1YOE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YOE 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=RIB:RIBOSE'>RIB</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]] 1.78Å</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]], [[1ezr\|1ezr]], [[1q8f\|1q8f]], [[1hoz\|1hoz]], [[1kie\|1kie]]</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=RIB:RIBOSE'>RIB</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>ybeK/rihA ([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=1yoe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yoe OCA], [https://pdbe.org/1yoe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yoe RCSB], [https://www.ebi.ac.uk/pdbsum/1yoe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yoe 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=1yoe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yoe OCA], [~~http~~://pdbe.org/1yoe PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1yoe RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1yoe PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1yoe ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RIHA_ECOLI RIHA_ECOLI]] Hydrolyzes with equal efficiency cytidine or uridine to ribose and cytosine or uracil, respectively.	+	[https://www.uniprot.org/uniprot/RIHA_ECOLI RIHA_ECOLI] Hydrolyzes with equal efficiency cytidine or uridine to ribose and cytosine or uracil, respectively.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=1yoe 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=1yoe ConSurf].
	<div style="clear:both"></div>		<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.
-
-	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>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1yoe" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__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: Muzzolini L]]
-	[[Category: Muzzolini, L]]	+	[[Category: Steyaert J]]
-	[[Category: Steyaert, J]]	+	[[Category: Versees W]]
-	[[Category: Versees, W]]	+
-	~~[[Category: Bacterial nucleosidase]]~~	+
-	~~[[Category: Enzyme-product complex]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Pyrimidine nucleoside hydrolase]]~~	+
-	~~[[Category: Ribose~~]]	+

OCA at 08:49, 20 January 2021

OCA — Wed, 20 Jan 2021 08:49:42 GMT

←Older revision		Revision as of 08:49, 20 January 2021
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	==Crystal structure of a the E. coli pyrimidine nucleoside hydrolase YbeK with bound ribose==		==Crystal structure of a the E. coli pyrimidine nucleoside hydrolase YbeK with bound ribose==
-	<StructureSection load='1yoe' size='340' side='right' caption='[[1yoe]], [[Resolution\|resolution]] 1.78Å' scene=''>	+	<StructureSection load='1yoe' size='340' side='right'caption='[[1yoe]], [[Resolution\|resolution]] 1.78Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1yoe]] is a 1 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=1YOE OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1YOE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1yoe]] is a 1 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=1YOE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1YOE 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=RIB:RIBOSE'>RIB</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=RIB:RIBOSE'>RIB</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1mas\|1mas]], [[2mas\|2mas]], [[1ezr\|1ezr]], [[1q8f\|1q8f]], [[1hoz\|1hoz]], [[1kie\|1kie]]</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]], [[1ezr\|1ezr]], [[1q8f\|1q8f]], [[1hoz\|1hoz]], [[1kie\|1kie]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ybeK/rihA ([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">ybeK/rihA ([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=1yoe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yoe OCA], [http://pdbe.org/1yoe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yoe RCSB], [http://www.ebi.ac.uk/pdbsum/1yoe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yoe 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=1yoe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yoe OCA], [http://pdbe.org/1yoe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yoe RCSB], [http://www.ebi.ac.uk/pdbsum/1yoe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yoe 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 07:03, 25 April 2018

OCA — Wed, 25 Apr 2018 07:03:48 GMT

←Older revision		Revision as of 07:03, 25 April 2018
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		+
	==Crystal structure of a the E. coli pyrimidine nucleoside hydrolase YbeK with bound ribose==		==Crystal structure of a the E. coli pyrimidine nucleoside hydrolase YbeK with bound ribose==
	<StructureSection load='1yoe' size='340' side='right' caption='[[1yoe]], [[Resolution\|resolution]] 1.78Å' scene=''>		<StructureSection load='1yoe' size='340' side='right' caption='[[1yoe]], [[Resolution\|resolution]] 1.78Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ybeK/rihA ([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">ybeK/rihA ([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=1yoe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yoe OCA], [http://pdbe.org/1yoe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yoe RCSB], [http://www.ebi.ac.uk/pdbsum/1yoe 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=1yoe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yoe OCA], [http://pdbe.org/1yoe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yoe RCSB], [http://www.ebi.ac.uk/pdbsum/1yoe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yoe 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/yo/1yoe_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yo/1yoe_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 01:37, 8 February 2016

OCA — Mon, 08 Feb 2016 01:37:52 GMT

←Older revision		Revision as of 01:37, 8 February 2016
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	<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=1yoe ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 06:40, 10 September 2015

OCA — Thu, 10 Sep 2015 06:40:11 GMT

←Older revision		Revision as of 06:40, 10 September 2015
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	<StructureSection load='1yoe' size='340' side='right' caption='[[1yoe]], [[Resolution\|resolution]] 1.78Å' scene=''>		<StructureSection load='1yoe' size='340' side='right' caption='[[1yoe]], [[Resolution\|resolution]] 1.78Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1yoe]] is a 1 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=1YOE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YOE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1yoe]] is a 1 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=1YOE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YOE 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=RIB:RIBOSE'>RIB</scene></td></tr>		</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=RIB:RIBOSE'>RIB</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1mas\|1mas]], [[2mas\|2mas]], [[1ezr\|1ezr]], [[1q8f\|1q8f]], [[1hoz\|1hoz]], [[1kie\|1kie]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1mas\|1mas]], [[2mas\|2mas]], [[1ezr\|1ezr]], [[1q8f\|1q8f]], [[1hoz\|1hoz]], [[1kie\|1kie]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ybeK/rihA ([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">ybeK/rihA ([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=1yoe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yoe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yoe RCSB], [http://www.ebi.ac.uk/pdbsum/1yoe 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=1yoe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yoe OCA], [http://pdbe.org/1yoe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yoe RCSB], [http://www.ebi.ac.uk/pdbsum/1yoe PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RIHA_ECOLI RIHA_ECOLI]] Hydrolyzes with equal efficiency cytidine or uridine to ribose and cytosine or uracil, respectively.
	== 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 1yoe" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Ribosylpyrimidine nucleosidase]]		[[Category: Ribosylpyrimidine nucleosidase]]
	[[Category: Degano, M]]		[[Category: Degano, M]]

OCA at 10:40, 8 January 2015

OCA — Thu, 08 Jan 2015 10:40:49 GMT

←Older revision		Revision as of 10:40, 8 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1yoe]] is a 1 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=1YOE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YOE FirstGlance]. <br>		<table><tr><td colspan='2'>[[1yoe]] is a 1 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=1YOE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YOE 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=RIB:RIBOSE'>RIB</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=RIB:RIBOSE'>RIB</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1mas\|1mas]], [[2mas\|2mas]], [[1ezr\|1ezr]], [[1q8f\|1q8f]], [[1hoz\|1hoz]], [[1kie\|1kie]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1mas\|1mas]], [[2mas\|2mas]], [[1ezr\|1ezr]], [[1q8f\|1q8f]], [[1hoz\|1hoz]], [[1kie\|1kie]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ybeK/rihA ([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">ybeK/rihA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/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=1yoe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yoe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yoe RCSB], [http://www.ebi.ac.uk/pdbsum/1yoe 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=1yoe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yoe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yoe RCSB], [http://www.ebi.ac.uk/pdbsum/1yoe PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 33:
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Ribosylpyrimidine nucleosidase]]		[[Category: Ribosylpyrimidine nucleosidase]]
-	[[Category: Degano, M.]]	+	[[Category: Degano, M]]
-	[[Category: Muzzolini, L.]]	+	[[Category: Muzzolini, L]]
-	[[Category: Steyaert, J.]]	+	[[Category: Steyaert, J]]
-	[[Category: Versees, W.]]	+	[[Category: Versees, W]]
	[[Category: Bacterial nucleosidase]]		[[Category: Bacterial nucleosidase]]
	[[Category: Enzyme-product complex]]		[[Category: Enzyme-product complex]]

OCA at 10:07, 3 October 2014

OCA — Fri, 03 Oct 2014 10:07:29 GMT

←Older revision		Revision as of 10:07, 3 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_1yoe\| PDB=1yoe \| SCENE= }}~~	+	==Crystal structure of a the E. coli pyrimidine nucleoside hydrolase YbeK with bound ribose==
-	===Crystal structure of a the E. coli pyrimidine nucleoside hydrolase YbeK with bound ribose===	+	<StructureSection load='1yoe' size='340' side='right' caption='[[1yoe]], [[Resolution\|resolution]] 1.78Å' scene=''>
-	~~{{ABSTRACT_PUBMED_15130467}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1yoe]] is a 1 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=1YOE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YOE 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=RIB:RIBOSE'>RIB</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1mas\|1mas]], [[2mas\|2mas]], [[1ezr\|1ezr]], [[1q8f\|1q8f]], [[1hoz\|1hoz]], [[1kie\|1kie]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ybeK/rihA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/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=1yoe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yoe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1yoe RCSB], [http://www.ebi.ac.uk/pdbsum/1yoe 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/yo/1yoe_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>
-	~~[[1yoe]] is a~~ 1 ~~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=1YOE 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: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Ribosylpyrimidine nucleosidase]]		[[Category: Ribosylpyrimidine nucleosidase]]

OCA at 08:43, 23 April 2014

OCA — Wed, 23 Apr 2014 08:43:03 GMT

←Older revision		Revision as of 08:43, 23 April 2014
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-	[[Image:1yoe.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_1yoe", 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_1yoe\| PDB=1yoe \| SCENE= }}		{{STRUCTURE_1yoe\| PDB=1yoe \| SCENE= }}
-
	===Crystal structure of a the E. coli pyrimidine nucleoside hydrolase YbeK with bound ribose===		===Crystal structure of a the E. coli pyrimidine nucleoside hydrolase YbeK with bound ribose===
-
-
-	<!--
-	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}}		{{ABSTRACT_PUBMED_15130467}}

Line 22:		Line 7:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15130467~~</ref><~~ref~~ group="xtra"~~>PMID:11292348<~~/~~ref><ref group="xtra">PMID:9572842</ref~~><references ~~group="xtra"~~/>	+	<ref group="xtra">PMID:015130467</ref><references group="xtra"/><references/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Ribosylpyrimidine nucleosidase]]		[[Category: Ribosylpyrimidine nucleosidase]]
Line 30:		Line 15:
	[[Category: Versees, W.]]		[[Category: Versees, W.]]
	[[Category: Bacterial nucleosidase]]		[[Category: Bacterial nucleosidase]]
-	[[Category: Enzyme/product complex]]	+	[[Category: Enzyme-product complex]]
		+	[[Category: Hydrolase]]
	[[Category: Pyrimidine nucleoside hydrolase]]		[[Category: Pyrimidine nucleoside hydrolase]]
	[[Category: Ribose]]		[[Category: Ribose]]

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

OCA — Tue, 15 Mar 2011 00:35:41 GMT

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

←Older revision

Revision as of 00:35, 15 March 2011

OCA at 00:35, 15 March 2011

OCA — Tue, 15 Mar 2011 00:35:40 GMT

←Older revision		Revision as of 00:35, 15 March 2011
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1yoe.png\|left\|200px]]		[[Image:1yoe.png\|left\|200px]]

Line 12:		Line 11:
	===Crystal structure of a the E. coli pyrimidine nucleoside hydrolase YbeK with bound ribose===		===Crystal structure of a the E. coli pyrimidine nucleoside hydrolase YbeK with bound ribose===

		+
		+	<!--
		+	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==
-	~~1YOE~~ is a 1 chain 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=1YOE OCA].	+	[[1yoe]] is a 1 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=1YOE OCA].

	==Reference==		==Reference==
Line 28:		Line 33:
	[[Category: Pyrimidine nucleoside hydrolase]]		[[Category: Pyrimidine nucleoside hydrolase]]
	[[Category: Ribose]]		[[Category: Ribose]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 17:52:23 2009''