1rxs - Revision history

OCA at 13:29, 13 March 2024

OCA — Wed, 13 Mar 2024 13:29:36 GMT

←Older revision		Revision as of 13:29, 13 March 2024
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	<StructureSection load='1rxs' size='340' side='right'caption='[[1rxs]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1rxs' size='340' side='right'caption='[[1rxs]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1rxs]] is a 30 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=1RXS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1RXS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1rxs]] is a 30 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=1RXS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RXS FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=DUR:2~~-~~DEOXYURIDINE'>DUR</scene>~~, ~~<scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=V7O:META+VANADATE'>V7O</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]] 2.8Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[1lgg\|1lgg]], [[1rxc\|1rxc]], [[1rxy\|1rxy]], [[1rxu\|1rxu]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DUR:2-DEOXYURIDINE'>DUR</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=V7O:META+VANADATE'>V7O</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td><~~td class~~=~~"sblockDat">UDP ([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=1rxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rxs OCA], [https://pdbe.org/1rxs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rxs RCSB], [https://www.ebi.ac.uk/pdbsum/1rxs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rxs 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=1rxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rxs OCA], [~~http~~://pdbe.org/1rxs PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1rxs RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1rxs PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1rxs ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/UDP_ECOLI UDP_ECOLI]] Catalyzes the reversible phosphorylytic cleavage of uridine and deoxyuridine to uracil and ribose- or deoxyribose-1-phosphate. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis.	+	[https://www.uniprot.org/uniprot/UDP_ECOLI UDP_ECOLI] Catalyzes the reversible phosphorylytic cleavage of uridine and deoxyuridine to uracil and ribose- or deoxyribose-1-phosphate. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis.
	== 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=1rxs 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=1rxs ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Uridine phosphorylase (UP) is a key enzyme in the pyrimidine salvage pathway that catalyses the reversible phosphorolysis of uridine to uracil and ribose 1-phosphate. Inhibiting liver UP in humans raises blood uridine levels and produces a protective effect ("uridine rescue") against the toxicity of the chemotherapeutic agent 5-fluorouracil without reducing its antitumour activity. We have investigated UP-substrate interactions by determining the crystal structures of native Escherichia coli UP (two forms), and complexes with 5-fluorouracil/ribose 1-phosphate, 2-deoxyuridine/phosphate and thymidine/phosphate. These hexameric structures confirm the overall structural similarity of UP to E.coli purine nucleoside phosphorylase (PNP) whereby, in the presence of substrate, each displays a closed conformation resulting from a concerted movement that closes the active site cleft. However, in contrast to PNP where helix segmentation is the major conformational change between the open and closed forms, in UP more extensive changes are observed. In particular a swinging movement of a flap region consisting of residues 224-234 seals the active site. This overall change in conformation results in compression of the active site cleft. Gln166 and Arg168, part of an inserted segment not seen in PNP, are key residues in the uracil binding pocket and together with a tightly bound water molecule are seen to be involved in the substrate specificity of UP. Enzyme activity shows a twofold dependence on potassium ion concentration. The presence of a potassium ion at the monomer/monomer interface induces some local rearrangement, which results in dimer stabilisation. The conservation of key residues and interactions with substrate in the phosphate and ribose binding pockets suggest that ribooxocarbenium ion formation during catalysis of UP may be similar to that proposed for E.coli PNP.
-
-	Crystal structures of Escherichia coli uridine phosphorylase in two native and three complexed forms reveal basis of substrate specificity, induced conformational changes and influence of potassium.,Caradoc-Davies TT, Cutfield SM, Lamont IL, Cutfield JF J Mol Biol. 2004 Mar 19;337(2):337-54. PMID:15003451<ref>PMID:15003451</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1rxs" 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: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Uridine phosphorylase]]~~	+	[[Category: Caradoc-Davies TT]]
-	[[Category: Caradoc-Davies~~, T T~~]]	+	[[Category: Cutfield JF]]
-	[[Category: Cutfield~~, J F~~]]	+	[[Category: Cutfield SM]]
-	[[Category: Cutfield~~, S M~~]]	+	[[Category: Lamont IL]]
-	[[Category: Lamont~~, I L]]~~	+
-	~~[[Category: 2'-deoxyuridine]]~~	+
-	~~[[Category: Induced fit]]~~	+
-	~~[[Category: Pentosyltransferase]]~~	+
-	~~[[Category: Potassium]]~~	+
-	~~[[Category: Specificity]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 13:35, 16 December 2020

OCA — Wed, 16 Dec 2020 13:35:38 GMT

←Older revision		Revision as of 13:35, 16 December 2020
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	==E. coli uridine phosphorylase: 2'-deoxyuridine phosphate complex==		==E. coli uridine phosphorylase: 2'-deoxyuridine phosphate complex==
-	<StructureSection load='1rxs' size='340' side='right' caption='[[1rxs]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='1rxs' size='340' side='right'caption='[[1rxs]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1rxs]] is a 30 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=1RXS OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1RXS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1rxs]] is a 30 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=1RXS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1RXS FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DUR:2-DEOXYURIDINE'>DUR</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=V7O:META+VANADATE'>V7O</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DUR:2-DEOXYURIDINE'>DUR</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=V7O:META+VANADATE'>V7O</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lgg\|1lgg]], [[1rxc\|1rxc]], [[1rxy\|1rxy]], [[1rxu\|1rxu]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1lgg\|1lgg]], [[1rxc\|1rxc]], [[1rxy\|1rxy]], [[1rxu\|1rxu]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UDP ([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">UDP ([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/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=1rxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rxs OCA], [http://pdbe.org/1rxs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rxs RCSB], [http://www.ebi.ac.uk/pdbsum/1rxs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1rxs 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=1rxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rxs OCA], [http://pdbe.org/1rxs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rxs RCSB], [http://www.ebi.ac.uk/pdbsum/1rxs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1rxs ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	==See Also==		==See Also==
-	*[[Uridine phosphorylase\|Uridine phosphorylase]]	+	*[[Uridine phosphorylase 3D structures\|Uridine phosphorylase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Uridine phosphorylase]]		[[Category: Uridine phosphorylase]]
	[[Category: Caradoc-Davies, T T]]		[[Category: Caradoc-Davies, T T]]

OCA at 06:41, 8 March 2018

OCA — Thu, 08 Mar 2018 06:41:59 GMT

←Older revision		Revision as of 06:41, 8 March 2018
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		+
	==E. coli uridine phosphorylase: 2'-deoxyuridine phosphate complex==		==E. coli uridine phosphorylase: 2'-deoxyuridine phosphate complex==
	<StructureSection load='1rxs' size='340' side='right' caption='[[1rxs]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1rxs' size='340' side='right' caption='[[1rxs]], [[Resolution\|resolution]] 2.80Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UDP ([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">UDP ([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/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=1rxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rxs OCA], [http://pdbe.org/1rxs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rxs RCSB], [http://www.ebi.ac.uk/pdbsum/1rxs 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=1rxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rxs OCA], [http://pdbe.org/1rxs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rxs RCSB], [http://www.ebi.ac.uk/pdbsum/1rxs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1rxs ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rx/1rxs_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rx/1rxs_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 08:22, 7 February 2016

OCA — Sun, 07 Feb 2016 08:22:32 GMT

←Older revision		Revision as of 08:22, 7 February 2016
Line 19:		Line 19:
	<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=1rxs ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 23:35, 9 September 2015

OCA — Wed, 09 Sep 2015 23:35:32 GMT

←Older revision		Revision as of 23:35, 9 September 2015
Line 2:		Line 2:
	<StructureSection load='1rxs' size='340' side='right' caption='[[1rxs]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1rxs' size='340' side='right' caption='[[1rxs]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1rxs]] is a 30 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=1RXS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RXS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1rxs]] is a 30 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=1RXS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RXS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DUR:2-DEOXYURIDINE'>DUR</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=V7O:META+VANADATE'>V7O</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DUR:2-DEOXYURIDINE'>DUR</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=V7O:META+VANADATE'>V7O</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lgg\|1lgg]], [[1rxc\|1rxc]], [[1rxy\|1rxy]], [[1rxu\|1rxu]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lgg\|1lgg]], [[1rxc\|1rxc]], [[1rxy\|1rxy]], [[1rxu\|1rxu]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UDP ([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">UDP ([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/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=1rxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rxs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rxs RCSB], [http://www.ebi.ac.uk/pdbsum/1rxs 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=1rxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rxs OCA], [http://pdbe.org/1rxs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1rxs RCSB], [http://www.ebi.ac.uk/pdbsum/1rxs PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 29:		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 1rxs" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Uridine phosphorylase]]		[[Category: Uridine phosphorylase]]
	[[Category: Caradoc-Davies, T T]]		[[Category: Caradoc-Davies, T T]]

OCA at 13:38, 24 December 2014

OCA — Wed, 24 Dec 2014 13:38:01 GMT

←Older revision		Revision as of 13:38, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1rxs]] is a 30 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=1RXS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RXS FirstGlance]. <br>		<table><tr><td colspan='2'>[[1rxs]] is a 30 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=1RXS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RXS FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DUR:2-DEOXYURIDINE'>DUR</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=V7O:META+VANADATE'>V7O</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DUR:2-DEOXYURIDINE'>DUR</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=V7O:META+VANADATE'>V7O</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lgg\|1lgg]], [[1rxc\|1rxc]], [[1rxy\|1rxy]], [[1rxu\|1rxu]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lgg\|1lgg]], [[1rxc\|1rxc]], [[1rxy\|1rxy]], [[1rxu\|1rxu]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UDP ([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">UDP ([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/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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1rxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rxs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rxs RCSB], [http://www.ebi.ac.uk/pdbsum/1rxs 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=1rxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rxs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rxs RCSB], [http://www.ebi.ac.uk/pdbsum/1rxs PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/UDP_ECOLI UDP_ECOLI]] Catalyzes the reversible phosphorylytic cleavage of uridine and deoxyuridine to uracil and ribose- or deoxyribose-1-phosphate. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 38:
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Uridine phosphorylase]]		[[Category: Uridine phosphorylase]]
-	[[Category: Caradoc-Davies, T T.]]	+	[[Category: Caradoc-Davies, T T]]
-	[[Category: Cutfield, J F.]]	+	[[Category: Cutfield, J F]]
-	[[Category: Cutfield, S M.]]	+	[[Category: Cutfield, S M]]
-	[[Category: Lamont, I L.]]	+	[[Category: Lamont, I L]]
	[[Category: 2'-deoxyuridine]]		[[Category: 2'-deoxyuridine]]
	[[Category: Induced fit]]		[[Category: Induced fit]]
Line 46:		Line 48:
	[[Category: Specificity]]		[[Category: Specificity]]
	[[Category: Transferase]]		[[Category: Transferase]]
-	[[Category: Uridine phosphorylase]]

OCA at 15:24, 29 September 2014

OCA — Mon, 29 Sep 2014 15:24:40 GMT

←Older revision		Revision as of 15:24, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1rxs.~~png~~\|~~left~~\|200px]]	+	==E. coli uridine phosphorylase: 2'-deoxyuridine phosphate complex==
		+	<StructureSection load='1rxs' size='340' side='right' caption='[[1rxs]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1rxs]] is a 30 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=1RXS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RXS FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DUR:2-DEOXYURIDINE'>DUR</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=V7O:META+VANADATE'>V7O</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1lgg\|1lgg]], [[1rxc\|1rxc]], [[1rxy\|1rxy]], [[1rxu\|1rxu]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">UDP ([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/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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1rxs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rxs OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1rxs RCSB], [http://www.ebi.ac.uk/pdbsum/1rxs 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/rx/1rxs_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 (UP) is a key enzyme in the pyrimidine salvage pathway that catalyses the reversible phosphorolysis of uridine to uracil and ribose 1-phosphate. Inhibiting liver UP in humans raises blood uridine levels and produces a protective effect ("uridine rescue") against the toxicity of the chemotherapeutic agent 5-fluorouracil without reducing its antitumour activity. We have investigated UP-substrate interactions by determining the crystal structures of native Escherichia coli UP (two forms), and complexes with 5-fluorouracil/ribose 1-phosphate, 2-deoxyuridine/phosphate and thymidine/phosphate. These hexameric structures confirm the overall structural similarity of UP to E.coli purine nucleoside phosphorylase (PNP) whereby, in the presence of substrate, each displays a closed conformation resulting from a concerted movement that closes the active site cleft. However, in contrast to PNP where helix segmentation is the major conformational change between the open and closed forms, in UP more extensive changes are observed. In particular a swinging movement of a flap region consisting of residues 224-234 seals the active site. This overall change in conformation results in compression of the active site cleft. Gln166 and Arg168, part of an inserted segment not seen in PNP, are key residues in the uracil binding pocket and together with a tightly bound water molecule are seen to be involved in the substrate specificity of UP. Enzyme activity shows a twofold dependence on potassium ion concentration. The presence of a potassium ion at the monomer/monomer interface induces some local rearrangement, which results in dimer stabilisation. The conservation of key residues and interactions with substrate in the phosphate and ribose binding pockets suggest that ribooxocarbenium ion formation during catalysis of UP may be similar to that proposed for E.coli PNP.

-	~~{{STRUCTURE_1rxs\| PDB=1rxs \| SCENE= }}~~	+	Crystal structures of Escherichia coli uridine phosphorylase in two native and three complexed forms reveal basis of substrate specificity, induced conformational changes and influence of potassium.,Caradoc-Davies TT, Cutfield SM, Lamont IL, Cutfield JF J Mol Biol. 2004 Mar 19;337(2):337-54. PMID:15003451<ref>PMID:15003451</ref>

-	~~===E~~. ~~coli uridine phosphorylase: 2'-deoxyuridine phosphate complex===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_15003451}}~~	+	==See Also==
-		+	*[[Uridine phosphorylase\|Uridine phosphorylase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~1rxs~~]] is a 30 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=1RXS OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:015003451<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Uridine phosphorylase]]		[[Category: Uridine phosphorylase]]

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

OCA — Fri, 04 Jan 2013 10:06:25 GMT

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

←Older revision

Revision as of 10:06, 4 January 2013

OCA at 10:06, 4 January 2013

OCA — Fri, 04 Jan 2013 10:06:22 GMT

←Older revision		Revision as of 10:06, 4 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1rxs.png\|left\|200px]]		[[Image:1rxs.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1rxs", 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_1rxs\| PDB=1rxs \| SCENE= }}		{{STRUCTURE_1rxs\| PDB=1rxs \| SCENE= }}

	===E. coli uridine phosphorylase: 2'-deoxyuridine phosphate complex===		===E. coli uridine phosphorylase: 2'-deoxyuridine phosphate complex===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15003451}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15003451 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15003451}}		{{ABSTRACT_PUBMED_15003451}}

	==About this Structure==		==About this Structure==
-	~~1RXS~~ is a 30 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RXS OCA].	+	[[1rxs]] is a 30 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=1RXS OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15003451~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015003451</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Uridine phosphorylase]]		[[Category: Uridine phosphorylase]]
Line 35:		Line 23:
	[[Category: Potassium]]		[[Category: Potassium]]
	[[Category: Specificity]]		[[Category: Specificity]]
		+	[[Category: Transferase]]
	[[Category: Uridine phosphorylase]]		[[Category: Uridine phosphorylase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 12:33:09 2009''

OCA at 10:33, 16 February 2009

OCA — Mon, 16 Feb 2009 10:33:10 GMT

←Older revision		Revision as of 10:33, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1RXS is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RXS OCA].	+	1RXS is a 30 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RXS OCA].

	==Reference==		==Reference==
-	Crystal structures of Escherichia coli uridine phosphorylase in two native and three complexed forms reveal basis of substrate specificity, induced conformational changes and influence of potassium., Caradoc-Davies TT, Cutfield SM, Lamont IL, Cutfield JF, J Mol Biol. 2004 Mar 19;337(2):337-54. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/15003451 15003451]~~	+	<ref group="xtra">PMID:15003451</ref><references group="xtra"/>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Single protein]]
	[[Category: Uridine phosphorylase]]		[[Category: Uridine phosphorylase]]
	[[Category: Caradoc-Davies, T T.]]		[[Category: Caradoc-Davies, T T.]]
Line 38:		Line 37:
	[[Category: Uridine phosphorylase]]		[[Category: Uridine phosphorylase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Jul 27 14~~:47:~~43 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 12:33:09 2009''