3kvy - Revision history

OCA at 10:18, 21 February 2024

OCA — Wed, 21 Feb 2024 10:18:36 GMT

←Older revision		Revision as of 10:18, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='3kvy' size='340' side='right'caption='[[3kvy]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='3kvy' size='340' side='right'caption='[[3kvy]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3kvy]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bovin Bovin~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KVY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=3KVY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3kvy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KVY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KVY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=R2B:1,4-ANHYDRO-D-ERYTHRO-PENT-1-ENITOL'>R2B</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=URA:URACIL'>URA</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]] 2.3Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ku4\|3ku4]], [[3kuk\|3kuk]], [[3kvr\|3kvr]], [[3kvv\|3kvv]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=R2B:1,4-ANHYDRO-D-ERYTHRO-PENT-1-ENITOL'>R2B</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=URA:URACIL'>URA</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UPP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9913 BOVIN])~~</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=3kvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kvy OCA], [https://pdbe.org/3kvy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kvy RCSB], [https://www.ebi.ac.uk/pdbsum/3kvy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kvy 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=3kvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kvy OCA], [~~http~~://pdbe.org/3kvy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3kvy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3kvy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3kvy ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A5PJH9_BOVIN A5PJH9_BOVIN]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 20:
	</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=3kvy 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=3kvy ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Uridine phosphorylase is a key enzyme in the pyrimidine salvage pathway. This enzyme catalyzes the reversible phosphorolysis of uridine to uracil and ribose 1-phosphate (or 2'-deoxyuridine to 2'-deoxyribose 1-phosphate). Here we report the structure of hexameric Escherichia coli uridine phosphorylase treated with 5-fluorouridine and sulfate and dimeric bovine uridine phosphorylase treated with 5-fluoro-2'-deoxyuridine or uridine, plus sulfate. In each case the electron density shows three separate species corresponding to the pyrimidine base, sulfate, and a ribosyl species, which can be modeled as a glycal. In the structures of the glycal complexes, the fluorouracil O2 atom is appropriately positioned to act as the base required for glycal formation via deprotonation at C2'. Crystals of bovine uridine phosphorylase treated with 2'-deoxyuridine and sulfate show intact nucleoside. NMR time course studies demonstrate that uridine phosphorylase can catalyze the hydrolysis of the fluorinated nucleosides in the absence of phosphate or sulfate, without the release of intermediates or enzyme inactivation. These results add a previously unencountered mechanistic motif to the body of information on glycal formation by enzymes catalyzing the cleavage of glycosyl bonds.
-
-	Glycal formation in crystals of uridine phosphorylase.,Paul D, O'Leary SE, Rajashankar K, Bu W, Toms A, Settembre EC, Sanders JM, Begley TP, Ealick SE Biochemistry. 2010 Apr 27;49(16):3499-509. PMID:20364833<ref>PMID:20364833</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3kvy" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Uridine phosphorylase 3D structures\|Uridine phosphorylase 3D structures]]		*[[Uridine phosphorylase 3D structures\|Uridine phosphorylase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bovin~~]]	+	[[Category: Bos taurus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Begley~~, T P~~]]	+	[[Category: Begley TP]]
-	[[Category: Bu, W]]	+	[[Category: Bu W]]
-	[[Category: Ealick~~, S E~~]]	+	[[Category: Ealick SE]]
-	[[Category: Leary, S O]]	+	[[Category: O'Leary S]]
-	[[Category: Paul, D]]	+	[[Category: Paul D]]
-	[[Category: Rajashankar, K]]	+	[[Category: Rajashankar K]]
-	[[Category: Sanders, J]]	+	[[Category: Sanders J]]
-	[[Category: Settembre, E]]	+	[[Category: Settembre E]]
-	[[Category: Toms, A]]	+	[[Category: Toms A]]
-	~~[[Category: Glycal]]~~	+
-	~~[[Category: Oxocarbenium ion]]~~	+
-	~~[[Category: Pyrimidine salvage]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Uridine phosphorylase~~]]	+

OCA at 05:51, 22 April 2020

OCA — Wed, 22 Apr 2020 05:51:41 GMT

←Older revision		Revision as of 05:51, 22 April 2020
Line 1:		Line 1:

	==Trapping of an oxocarbenium ion intermediate in UP crystals==		==Trapping of an oxocarbenium ion intermediate in UP crystals==
-	<StructureSection load='3kvy' size='340' side='right' caption='[[3kvy]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='3kvy' size='340' side='right'caption='[[3kvy]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3kvy]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bovin Bovin]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KVY OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3KVY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3kvy]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bovin Bovin]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KVY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3KVY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=R2B:1,4-ANHYDRO-D-ERYTHRO-PENT-1-ENITOL'>R2B</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=URA:URACIL'>URA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=R2B:1,4-ANHYDRO-D-ERYTHRO-PENT-1-ENITOL'>R2B</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=URA:URACIL'>URA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ku4\|3ku4]], [[3kuk\|3kuk]], [[3kvr\|3kvr]], [[3kvv\|3kvv]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ku4\|3ku4]], [[3kuk\|3kuk]], [[3kvr\|3kvr]], [[3kvv\|3kvv]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UPP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9913 BOVIN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UPP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9913 BOVIN])</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=3kvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kvy OCA], [http://pdbe.org/3kvy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3kvy RCSB], [http://www.ebi.ac.uk/pdbsum/3kvy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3kvy 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=3kvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kvy OCA], [http://pdbe.org/3kvy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3kvy RCSB], [http://www.ebi.ac.uk/pdbsum/3kvy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3kvy ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 30:		Line 30:

	==See Also==		==See Also==
-	*[[Uridine phosphorylase\|Uridine phosphorylase]]	+	*[[Uridine phosphorylase 3D structures\|Uridine phosphorylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 36:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Bovin]]		[[Category: Bovin]]
		+	[[Category: Large Structures]]
	[[Category: Begley, T P]]		[[Category: Begley, T P]]
	[[Category: Bu, W]]		[[Category: Bu, W]]

OCA at 06:41, 2 January 2019

OCA — Wed, 02 Jan 2019 06:41:49 GMT

←Older revision		Revision as of 06:41, 2 January 2019
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kv/3kvy_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kv/3kvy_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 01:30, 5 August 2016

OCA — Fri, 05 Aug 2016 01:30:30 GMT

←Older revision		Revision as of 01:30, 5 August 2016
Line 1:		Line 1:
		+
	==Trapping of an oxocarbenium ion intermediate in UP crystals==		==Trapping of an oxocarbenium ion intermediate in UP crystals==
	<StructureSection load='3kvy' size='340' side='right' caption='[[3kvy]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='3kvy' size='340' side='right' caption='[[3kvy]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3kvy]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bos_taurus Bos taurus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KVY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KVY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3kvy]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bovin Bovin]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KVY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KVY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=R2B:1,4-ANHYDRO-D-ERYTHRO-PENT-1-ENITOL'>R2B</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=URA:URACIL'>URA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=R2B:1,4-ANHYDRO-D-ERYTHRO-PENT-1-ENITOL'>R2B</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=URA:URACIL'>URA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ku4\|3ku4]], [[3kuk\|3kuk]], [[3kvr\|3kvr]], [[3kvv\|3kvv]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ku4\|3ku4]], [[3kuk\|3kuk]], [[3kvr\|3kvr]], [[3kvv\|3kvv]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UPP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9913 ~~Bos taurus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UPP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9913 BOVIN])</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=3kvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kvy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kvy RCSB], [http://www.ebi.ac.uk/pdbsum/3kvy 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=3kvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kvy OCA], [http://pdbe.org/3kvy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3kvy RCSB], [http://www.ebi.ac.uk/pdbsum/3kvy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3kvy ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		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=3kvy ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		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 3kvy" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 33:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bos taurus~~]]	+	[[Category: Bovin]]
	[[Category: Begley, T P]]		[[Category: Begley, T P]]
	[[Category: Bu, W]]		[[Category: Bu, W]]

OCA at 17:30, 18 December 2014

OCA — Thu, 18 Dec 2014 17:30:22 GMT

←Older revision		Revision as of 17:30, 18 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3kvy\| PDB=3kvy \| SCENE= }}~~	+	==Trapping of an oxocarbenium ion intermediate in UP crystals==
-	===Trapping of an oxocarbenium ion intermediate in UP crystals===	+	<StructureSection load='3kvy' size='340' side='right' caption='[[3kvy]], [[Resolution\|resolution]] 2.30Å' scene=''>
-	~~{{ABSTRACT_PUBMED_20364833}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3kvy]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KVY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KVY FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=R2B:1,4-ANHYDRO-D-ERYTHRO-PENT-1-ENITOL'>R2B</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=URA:URACIL'>URA</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ku4\|3ku4]], [[3kuk\|3kuk]], [[3kvr\|3kvr]], [[3kvv\|3kvv]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UPP1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9913 Bos taurus])</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=3kvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kvy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kvy RCSB], [http://www.ebi.ac.uk/pdbsum/3kvy 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/kv/3kvy_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 ==
		+	Uridine phosphorylase is a key enzyme in the pyrimidine salvage pathway. This enzyme catalyzes the reversible phosphorolysis of uridine to uracil and ribose 1-phosphate (or 2'-deoxyuridine to 2'-deoxyribose 1-phosphate). Here we report the structure of hexameric Escherichia coli uridine phosphorylase treated with 5-fluorouridine and sulfate and dimeric bovine uridine phosphorylase treated with 5-fluoro-2'-deoxyuridine or uridine, plus sulfate. In each case the electron density shows three separate species corresponding to the pyrimidine base, sulfate, and a ribosyl species, which can be modeled as a glycal. In the structures of the glycal complexes, the fluorouracil O2 atom is appropriately positioned to act as the base required for glycal formation via deprotonation at C2'. Crystals of bovine uridine phosphorylase treated with 2'-deoxyuridine and sulfate show intact nucleoside. NMR time course studies demonstrate that uridine phosphorylase can catalyze the hydrolysis of the fluorinated nucleosides in the absence of phosphate or sulfate, without the release of intermediates or enzyme inactivation. These results add a previously unencountered mechanistic motif to the body of information on glycal formation by enzymes catalyzing the cleavage of glycosyl bonds.

-	~~==About this Structure==~~	+	Glycal formation in crystals of uridine phosphorylase.,Paul D, O'Leary SE, Rajashankar K, Bu W, Toms A, Settembre EC, Sanders JM, Begley TP, Ealick SE Biochemistry. 2010 Apr 27;49(16):3499-509. PMID:20364833<ref>PMID:20364833</ref>
-	~~[[3kvy]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Bos_taurus Bos taurus]~~. ~~Full crystallographic information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3KVY OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group~~=~~"xtra">PMID:020364833</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+
		+	==See Also==
		+	*[[Uridine phosphorylase\|Uridine phosphorylase]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Bos taurus]]		[[Category: Bos taurus]]
-	[[Category: Begley, T P.]]	+	[[Category: Begley, T P]]
-	[[Category: Bu, W.]]	+	[[Category: Bu, W]]
-	[[Category: Ealick, S E.]]	+	[[Category: Ealick, S E]]
-	[[Category: Leary, S O.]]	+	[[Category: Leary, S O]]
-	[[Category: Paul, D.]]	+	[[Category: Paul, D]]
-	[[Category: Rajashankar, K.]]	+	[[Category: Rajashankar, K]]
-	[[Category: Sanders, J.]]	+	[[Category: Sanders, J]]
-	[[Category: Settembre, E.]]	+	[[Category: Settembre, E]]
-	[[Category: Toms, A.]]	+	[[Category: Toms, A]]
	[[Category: Glycal]]		[[Category: Glycal]]
	[[Category: Oxocarbenium ion]]		[[Category: Oxocarbenium ion]]

OCA: Protected "3kvy" [edit=sysop:move=sysop]

OCA — Thu, 04 Apr 2013 20:17:18 GMT

Protected "3kvy" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:17, 4 April 2013

OCA at 20:17, 4 April 2013

OCA — Thu, 04 Apr 2013 20:17:16 GMT

←Older revision		Revision as of 20:17, 4 April 2013
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-	{{Seed}}
-	[[Image:3kvy.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3kvy", 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_3kvy\| PDB=3kvy \| SCENE= }}		{{STRUCTURE_3kvy\| PDB=3kvy \| SCENE= }}
-
	===Trapping of an oxocarbenium ion intermediate in UP crystals===		===Trapping of an oxocarbenium ion intermediate in UP crystals===
-
-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_20364833}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 20364833 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_20364833}}		{{ABSTRACT_PUBMED_20364833}}

	==About this Structure==		==About this Structure==
-	~~3KVY~~ is a 2 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KVY OCA].	+	[[3kvy]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KVY OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20364833~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020364833</ref><references group="xtra"/><references/>
	[[Category: Bos taurus]]		[[Category: Bos taurus]]
	[[Category: Begley, T P.]]		[[Category: Begley, T P.]]
Line 39:		Line 23:
	[[Category: Transferase]]		[[Category: Transferase]]
	[[Category: Uridine phosphorylase]]		[[Category: Uridine phosphorylase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 5 11:26:18 2010''

OCA at 08:26, 5 May 2010

OCA — Wed, 05 May 2010 08:26:19 GMT

←Older revision		Revision as of 08:26, 5 May 2010
Line 1:		Line 1:
	{{Seed}}		{{Seed}}
-	[[Image:3kvy.~~jpg~~\|left\|200px]]	+	[[Image:3kvy.png\|left\|200px]]

	<!--		<!--
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	[[Category: Uridine phosphorylase]]		[[Category: Uridine phosphorylase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Apr 28 10~~:57:07 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 5 11:26:18 2010''

OCA at 07:57, 28 April 2010

OCA — Wed, 28 Apr 2010 07:57:09 GMT

←Older revision		Revision as of 07:57, 28 April 2010
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3kvy.jpg\|left\|200px]]

-	The ~~entry 3kvy~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3kvy", 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_3kvy\| PDB=3kvy \| SCENE= }}

-	~~Authors: Paul, D., O'Leary, S., Rajashankar, K., Bu, W., Toms, A., Settembre, E., Sanders, J., Begley, T.P., Ealick, S.E.~~	+	===Trapping of an oxocarbenium ion intermediate in UP crystals===

-	Description: Trapping of an oxocarbenium ion intermediate in UP crystals

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Dec 9 14~~:45:~~16 2009~~''	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_20364833}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 20364833 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_20364833}}
		+
		+	==About this Structure==
		+	3KVY is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KVY OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:20364833</ref><references group="xtra"/>
		+	[[Category: Bos taurus]]
		+	[[Category: Begley, T P.]]
		+	[[Category: Bu, W.]]
		+	[[Category: Ealick, S E.]]
		+	[[Category: Leary, S O.]]
		+	[[Category: Paul, D.]]
		+	[[Category: Rajashankar, K.]]
		+	[[Category: Sanders, J.]]
		+	[[Category: Settembre, E.]]
		+	[[Category: Toms, A.]]
		+	[[Category: Glycal]]
		+	[[Category: Oxocarbenium ion]]
		+	[[Category: Pyrimidine salvage]]
		+	[[Category: Transferase]]
		+	[[Category: Uridine phosphorylase]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 28 10:57:07 2010''

OCA: New page: '''Unreleased structure''' The entry 3kvy is ON HOLD Authors: Paul, D., O'Leary, S., Rajashankar, K., Bu, W., Toms, A., Settembre, E., Sanders, J., Begley, T.P., Ealick, S.E. Descripti...

OCA — Wed, 09 Dec 2009 12:45:17 GMT

New page: '''Unreleased structure''' The entry 3kvy is ON HOLD Authors: Paul, D., O'Leary, S., Rajashankar, K., Bu, W., Toms, A., Settembre, E., Sanders, J., Begley, T.P., Ealick, S.E. Descripti...

New page

'''Unreleased structure'''

The entry 3kvy is ON HOLD

Authors: Paul, D., O'Leary, S., Rajashankar, K., Bu, W., Toms, A., Settembre, E., Sanders, J., Begley, T.P., Ealick, S.E.

Description: Trapping of an oxocarbenium ion intermediate in UP crystals

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 9 14:45:16 2009''