3kvr - Revision history

OCA at 10:18, 21 February 2024

2024-02-21T10:18:30Z

←Older revision		Revision as of 10:18, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='3kvr' size='340' side='right'caption='[[3kvr]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='3kvr' size='340' side='right'caption='[[3kvr]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3kvr]] 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=3KVR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=3KVR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3kvr]] 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=3KVR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KVR FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=R2G:2,5~~-~~ANHYDRO-4-DEOXY-D-ERYTHRO-PENT-4-ENITOL'>R2G</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=URF:5-FLUOROURACIL'>URF</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]] 2.6Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[3ku4\|3ku4]], [[3kuk\|3kuk]], [[3kvv\|3kvv]], [[3kvy\|3kvy]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=R2G:2,5-ANHYDRO-4-DEOXY-D-ERYTHRO-PENT-4-ENITOL'>R2G</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=URF:5-FLUOROURACIL'>URF</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=3kvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kvr OCA], [https://pdbe.org/3kvr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kvr RCSB], [https://www.ebi.ac.uk/pdbsum/3kvr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kvr 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/Uridine_phosphorylase Uridine phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.3 2.4.2.3]~~ </~~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=3kvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kvr OCA], [~~http~~://pdbe.org/3kvr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3kvr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3kvr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3kvr 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 20:		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=3kvr 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=3kvr 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 3kvr" 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: Uridine phosphorylase]]~~	+	[[Category: Begley TP]]
-	[[Category: Begley~~, T P~~]]	+	[[Category: Bu W]]
-	[[Category: Bu, W]]	+	[[Category: Ealick SE]]
-	[[Category: Ealick~~, S E~~]]	+	[[Category: O'Leary S]]
-	[[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: Oxocarbenium ion]]~~	+
-	~~[[Category: Pyrimidine salvage]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 05:51, 22 April 2020

2020-04-22T05:51:34Z

←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='3kvr' size='340' side='right' caption='[[3kvr]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='3kvr' size='340' side='right'caption='[[3kvr]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3kvr]] 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=3KVR OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3KVR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3kvr]] 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=3KVR OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3KVR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=R2G:2,5-ANHYDRO-4-DEOXY-D-ERYTHRO-PENT-4-ENITOL'>R2G</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=URF:5-FLUOROURACIL'>URF</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=R2G:2,5-ANHYDRO-4-DEOXY-D-ERYTHRO-PENT-4-ENITOL'>R2G</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=URF:5-FLUOROURACIL'>URF</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ku4\|3ku4]], [[3kuk\|3kuk]], [[3kvv\|3kvv]], [[3kvy\|3kvy]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ku4\|3ku4]], [[3kuk\|3kuk]], [[3kvv\|3kvv]], [[3kvy\|3kvy]]</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uridine_phosphorylase Uridine phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.3 2.4.2.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uridine_phosphorylase Uridine phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.3 2.4.2.3] </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=3kvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kvr OCA], [http://pdbe.org/3kvr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3kvr RCSB], [http://www.ebi.ac.uk/pdbsum/3kvr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3kvr 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=3kvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kvr OCA], [http://pdbe.org/3kvr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3kvr RCSB], [http://www.ebi.ac.uk/pdbsum/3kvr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3kvr ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[Uridine phosphorylase\|Uridine phosphorylase]]	+	*[[Uridine phosphorylase 3D structures\|Uridine phosphorylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 37:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Bovin]]		[[Category: Bovin]]
		+	[[Category: Large Structures]]
	[[Category: Uridine phosphorylase]]		[[Category: Uridine phosphorylase]]
	[[Category: Begley, T P]]		[[Category: Begley, T P]]

OCA at 06:31, 2 January 2019

2019-01-02T06:31:20Z

←Older revision		Revision as of 06:31, 2 January 2019
Line 14:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kv/3kvr_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kv/3kvr_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 10:55, 4 August 2016

2016-08-04T10:55:42Z

←Older revision		Revision as of 10:55, 4 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='3kvr' size='340' side='right' caption='[[3kvr]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='3kvr' size='340' side='right' caption='[[3kvr]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3kvr]] 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=3KVR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KVR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3kvr]] 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=3KVR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KVR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=R2G:2,5-ANHYDRO-4-DEOXY-D-ERYTHRO-PENT-4-ENITOL'>R2G</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=URF:5-FLUOROURACIL'>URF</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=R2G:2,5-ANHYDRO-4-DEOXY-D-ERYTHRO-PENT-4-ENITOL'>R2G</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=URF:5-FLUOROURACIL'>URF</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ku4\|3ku4]], [[3kuk\|3kuk]], [[3kvv\|3kvv]], [[3kvy\|3kvy]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ku4\|3ku4]], [[3kuk\|3kuk]], [[3kvv\|3kvv]], [[3kvy\|3kvy]]</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uridine_phosphorylase Uridine phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.3 2.4.2.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uridine_phosphorylase Uridine phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.3 2.4.2.3] </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=3kvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kvr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kvr RCSB], [http://www.ebi.ac.uk/pdbsum/3kvr 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=3kvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kvr OCA], [http://pdbe.org/3kvr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3kvr RCSB], [http://www.ebi.ac.uk/pdbsum/3kvr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3kvr ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 17:		Line 18:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3kvr ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 27:		Line 28:
	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 3kvr" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bos taurus~~]]	+	[[Category: Bovin]]
	[[Category: Uridine phosphorylase]]		[[Category: Uridine phosphorylase]]
	[[Category: Begley, T P]]		[[Category: Begley, T P]]

OCA at 17:21, 18 December 2014

2014-12-18T17:21:51Z

←Older revision		Revision as of 17:21, 18 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3kvr\| PDB=3kvr \| SCENE= }}~~	+	==Trapping of an oxocarbenium ion intermediate in UP crystals==
-	===Trapping of an oxocarbenium ion intermediate in UP crystals===	+	<StructureSection load='3kvr' size='340' side='right' caption='[[3kvr]], [[Resolution\|resolution]] 2.60Å' scene=''>
-	~~{{ABSTRACT_PUBMED_20364833}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3kvr]] 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=3KVR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3KVR FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=R2G:2,5-ANHYDRO-4-DEOXY-D-ERYTHRO-PENT-4-ENITOL'>R2G</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=URF:5-FLUOROURACIL'>URF</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ku4\|3ku4]], [[3kuk\|3kuk]], [[3kvv\|3kvv]], [[3kvy\|3kvy]]</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='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Uridine_phosphorylase Uridine phosphorylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.3 2.4.2.3] </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=3kvr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kvr OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3kvr RCSB], [http://www.ebi.ac.uk/pdbsum/3kvr 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/3kvr_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>
-	~~[[3kvr]] 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=3KVR 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: Uridine phosphorylase]]		[[Category: Uridine phosphorylase]]
-	[[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]]
	[[Category: Pyrimidine salvage]]		[[Category: Pyrimidine salvage]]
	[[Category: Transferase]]		[[Category: Transferase]]
-	[[Category: Uridine phosphorylase]]

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

2013-04-04T19:58:03Z

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

←Older revision

Revision as of 19:58, 4 April 2013

OCA at 19:58, 4 April 2013

2013-04-04T19:58:01Z

←Older revision		Revision as of 19:58, 4 April 2013
Line 1:		Line 1:
-	{{Seed}}
-	[[Image:3kvr.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3kvr", 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_3kvr\| PDB=3kvr \| SCENE= }}		{{STRUCTURE_3kvr\| PDB=3kvr \| 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==
-	~~3KVR~~ 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=3KVR OCA].	+	[[3kvr]] 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=3KVR 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: Uridine phosphorylase]]		[[Category: Uridine phosphorylase]]
Line 40:		Line 24:
	[[Category: Transferase]]		[[Category: Transferase]]
	[[Category: Uridine phosphorylase]]		[[Category: Uridine phosphorylase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 5 11:07:51 2010''

OCA at 08:07, 5 May 2010

2010-05-05T08:07:52Z

←Older revision		Revision as of 08:07, 5 May 2010
Line 1:		Line 1:
	{{Seed}}		{{Seed}}
-	[[Image:3kvr.~~jpg~~\|left\|200px]]	+	[[Image:3kvr.png\|left\|200px]]

	<!--		<!--
Line 41:		Line 41:
	[[Category: Uridine phosphorylase]]		[[Category: Uridine phosphorylase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Apr 28 10~~:43:36 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 5 11:07:51 2010''

OCA at 07:43, 28 April 2010

2010-04-28T07:43:40Z

←Older revision		Revision as of 07:43, 28 April 2010
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3kvr.jpg\|left\|200px]]

-	The ~~entry 3kvr~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3kvr", 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_3kvr\| PDB=3kvr \| 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 ~~Mar 31 13~~:20:18 2010''	+	<!--
		+	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==
		+	3KVR 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=3KVR OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:20364833</ref><references group="xtra"/>
		+	[[Category: Bos taurus]]
		+	[[Category: Uridine phosphorylase]]
		+	[[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 10:43:36 2010''

OCA at 10:20, 31 March 2010

2010-03-31T10:20:19Z

←Older revision		Revision as of 10:20, 31 March 2010
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3kvr is ON HOLD	+	The entry 3kvr is ON HOLD until Paper Publication

	Authors: Paul, D., O'Leary, S., Rajashankar, K., Bu, W., Toms, A., Settembre, E., Sanders, J., Begley, T.P., Ealick, S.E.		Authors: Paul, D., O'Leary, S., Rajashankar, K., Bu, W., Toms, A., Settembre, E., Sanders, J., Begley, T.P., Ealick, S.E.
Line 7:		Line 7:
	Description: 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:~~13 2009~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 31 13:20:18 2010''