1dqx - Revision history

OCA at 06:58, 7 February 2024

OCA — Wed, 07 Feb 2024 06:58:05 GMT

←Older revision		Revision as of 06:58, 7 February 2024
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	<StructureSection load='1dqx' size='340' side='right'caption='[[1dqx]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1dqx' size='340' side='right'caption='[[1dqx]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1dqx]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_18824 Atcc 18824~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DQX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DQX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1dqx]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DQX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DQX FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=BMP:6~~-~~HYDROXYURIDINE-5-PHOSPHATE'>BMP</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]] 2.4Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[1dqw\|1dqw]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMP:6-HYDROXYURIDINE-5-PHOSPHATE'>BMP</scene></td></tr>
-	~~<tr~~ id~~='activity'><td class~~="~~sblockLbl~~"><~~b>Activity:</b></td><td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[https~~:~~//en.wikipedia.org/wiki/Orotidine~~-5'-~~phosphate_decarboxylase Orotidine-5~~'~~-phosphate decarboxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.23 4.1.1.23]~~ </~~span~~></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=1dqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dqx OCA], [https://pdbe.org/1dqx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dqx RCSB], [https://www.ebi.ac.uk/pdbsum/1dqx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dqx ProSAT]</span></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=1dqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dqx OCA], [https://pdbe.org/1dqx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dqx RCSB], [https://www.ebi.ac.uk/pdbsum/1dqx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dqx ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/PYRF_YEAST PYRF_YEAST]
	== 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=1dqx 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=1dqx ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Orotidine 5'-phosphate decarboxylase produces the largest rate enhancement that has been reported for any enzyme. The crystal structure of the recombinant Saccharomyces cerevisiae enzyme has been determined in the absence and presence of the proposed transition state analog 6-hydroxyuridine 5'-phosphate, at a resolution of 2.1 A and 2.4 A, respectively. Orotidine 5'-phosphate decarboxylase folds as a TIM-barrel with the ligand binding site near the open end of the barrel. The binding of 6-hydroxyuridine 5'-phosphate is accompanied by protein loop movements that envelop the ligand almost completely, forming numerous favorable interactions with the phosphoryl group, the ribofuranosyl group, and the pyrimidine ring. Lysine-93 appears to be anchored in such a way as to optimize electrostatic interactions with developing negative charge at C-6 of the pyrimidine ring, and to donate the proton that replaces the carboxylate group at C-6 of the product. In addition, H-bonds from the active site to O-2 and O-4 help to delocalize negative charge in the transition state. Interactions between the enzyme and the phosphoribosyl group anchor the pyrimidine within the active site, helping to explain the phosphoribosyl group's remarkably large contribution to catalysis despite its distance from the site of decarboxylation.
-
-	Anatomy of a proficient enzyme: the structure of orotidine 5'-monophosphate decarboxylase in the presence and absence of a potential transition state analog.,Miller BG, Hassell AM, Wolfenden R, Milburn MV, Short SA Proc Natl Acad Sci U S A. 2000 Feb 29;97(5):2011-6. PMID:10681417<ref>PMID:10681417</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1dqx" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Uridine 5'-monophosphate synthase 3D structures\|Uridine 5'-monophosphate synthase 3D structures]]		*[[Uridine 5'-monophosphate synthase 3D structures\|Uridine 5'-monophosphate synthase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 18824]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Orotidine-5'-phosphate decarboxylase~~]]	+	[[Category: Saccharomyces cerevisiae]]
-	[[Category: Hassell~~, A M~~]]	+	[[Category: Hassell AM]]
-	[[Category: Milburn~~, M V~~]]	+	[[Category: Milburn MV]]
-	[[Category: Miller~~, B G~~]]	+	[[Category: Miller BG]]
-	[[Category: Short~~, S A~~]]	+	[[Category: Short SA]]
-	[[Category: Wolfenden, R]]	+	[[Category: Wolfenden R]]
-	~~[[Category: 6-hydroxyuridine 5'-phosphate]]~~	+
-	~~[[Category: Bmp]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Omp]]~~	+
-	~~[[Category: Orotidine 5'phosphate decarboxylase]]~~	+
-	~~[[Category: Tim barrel]]~~	+
-	~~[[Category: Ump]]~~	+
-	~~[[Category: Uridine 5'phosphate~~]]	+

OCA at 13:11, 13 October 2021

OCA — Wed, 13 Oct 2021 13:11:18 GMT

←Older revision		Revision as of 13:11, 13 October 2021
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	<StructureSection load='1dqx' size='340' side='right'caption='[[1dqx]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1dqx' size='340' side='right'caption='[[1dqx]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1dqx]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DQX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1DQX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1dqx]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DQX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DQX FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMP:6-HYDROXYURIDINE-5-PHOSPHATE'>BMP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMP:6-HYDROXYURIDINE-5-PHOSPHATE'>BMP</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dqw\|1dqw]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1dqw\|1dqw]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Orotidine-5'-phosphate_decarboxylase Orotidine-5'-phosphate decarboxylase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.23 4.1.1.23] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Orotidine-5'-phosphate_decarboxylase Orotidine-5'-phosphate decarboxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.23 4.1.1.23] </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=1dqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dqx OCA], [~~http~~://pdbe.org/1dqx PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1dqx RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1dqx PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1dqx ProSAT]</span></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=1dqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dqx OCA], [https://pdbe.org/1dqx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dqx RCSB], [https://www.ebi.ac.uk/pdbsum/1dqx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dqx ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 30:		Line 30:

	==See Also==		==See Also==
-	*[[Uridine 5'-monophosphate synthase\|Uridine 5'-monophosphate synthase]]	+	*[[Uridine 5'-monophosphate synthase 3D structures\|Uridine 5'-monophosphate synthase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:30, 8 January 2020

OCA — Wed, 08 Jan 2020 10:30:35 GMT

←Older revision		Revision as of 10:30, 8 January 2020
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	==CRYSTAL STRUCTURE OF OROTIDINE 5'-PHOSPHATE DECARBOXYLASE COMPLEXED TO 6-HYDROXYURIDINE 5'-PHOSPHATE (BMP)==		==CRYSTAL STRUCTURE OF OROTIDINE 5'-PHOSPHATE DECARBOXYLASE COMPLEXED TO 6-HYDROXYURIDINE 5'-PHOSPHATE (BMP)==
-	<StructureSection load='1dqx' size='340' side='right' caption='[[1dqx]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='1dqx' size='340' side='right'caption='[[1dqx]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1dqx]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DQX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DQX FirstGlance]. <br>		<table><tr><td colspan='2'>[[1dqx]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DQX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DQX FirstGlance]. <br>
Line 36:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 18824]]		[[Category: Atcc 18824]]
		+	[[Category: Large Structures]]
	[[Category: Orotidine-5'-phosphate decarboxylase]]		[[Category: Orotidine-5'-phosphate decarboxylase]]
	[[Category: Hassell, A M]]		[[Category: Hassell, A M]]

OCA at 06:09, 4 April 2018

OCA — Wed, 04 Apr 2018 06:09:12 GMT

←Older revision		Revision as of 06:09, 4 April 2018
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	</div>		</div>
	<div class="pdbe-citations 1dqx" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1dqx" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Uridine 5'-monophosphate synthase\|Uridine 5'-monophosphate synthase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:50, 13 December 2017

OCA — Wed, 13 Dec 2017 07:50:33 GMT

←Older revision		Revision as of 07:50, 13 December 2017
Line 1:		Line 1:
		+
	==CRYSTAL STRUCTURE OF OROTIDINE 5'-PHOSPHATE DECARBOXYLASE COMPLEXED TO 6-HYDROXYURIDINE 5'-PHOSPHATE (BMP)==		==CRYSTAL STRUCTURE OF OROTIDINE 5'-PHOSPHATE DECARBOXYLASE COMPLEXED TO 6-HYDROXYURIDINE 5'-PHOSPHATE (BMP)==
	<StructureSection load='1dqx' size='340' side='right' caption='[[1dqx]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1dqx' size='340' side='right' caption='[[1dqx]], [[Resolution\|resolution]] 2.40Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dqw\|1dqw]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dqw\|1dqw]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Orotidine-5'-phosphate_decarboxylase Orotidine-5'-phosphate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.23 4.1.1.23] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Orotidine-5'-phosphate_decarboxylase Orotidine-5'-phosphate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.23 4.1.1.23] </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=1dqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dqx OCA], [http://pdbe.org/1dqx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dqx RCSB], [http://www.ebi.ac.uk/pdbsum/1dqx 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=1dqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dqx OCA], [http://pdbe.org/1dqx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dqx RCSB], [http://www.ebi.ac.uk/pdbsum/1dqx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1dqx ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dq/1dqx_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dq/1dqx_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>
Line 27:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 1dqx" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1dqx" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Uridine 5'-monophosphate synthase\|Uridine 5'-monophosphate synthase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 15:17, 7 February 2016

OCA — Sun, 07 Feb 2016 15:17:07 GMT

←Older revision		Revision as of 15:17, 7 February 2016
Line 16:		Line 16:
	<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=1dqx ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 02:43, 10 September 2015

OCA — Thu, 10 Sep 2015 02:43:23 GMT

←Older revision		Revision as of 02:43, 10 September 2015
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	<StructureSection load='1dqx' size='340' side='right' caption='[[1dqx]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1dqx' size='340' side='right' caption='[[1dqx]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1dqx]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Saccharomyces_cerevisiae Saccharomyces cerevisiae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DQX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DQX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1dqx]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DQX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DQX FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMP:6-HYDROXYURIDINE-5-PHOSPHATE'>BMP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMP:6-HYDROXYURIDINE-5-PHOSPHATE'>BMP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dqw\|1dqw]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dqw\|1dqw]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Orotidine-5'-phosphate_decarboxylase Orotidine-5'-phosphate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.23 4.1.1.23] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Orotidine-5'-phosphate_decarboxylase Orotidine-5'-phosphate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.23 4.1.1.23] </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=1dqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dqx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dqx RCSB], [http://www.ebi.ac.uk/pdbsum/1dqx 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=1dqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dqx OCA], [http://pdbe.org/1dqx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dqx RCSB], [http://www.ebi.ac.uk/pdbsum/1dqx PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	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 1dqx" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 33:		Line 34:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 18824]]
	[[Category: Orotidine-5'-phosphate decarboxylase]]		[[Category: Orotidine-5'-phosphate decarboxylase]]
-	[[Category: Saccharomyces cerevisiae]]
	[[Category: Hassell, A M]]		[[Category: Hassell, A M]]
	[[Category: Milburn, M V]]		[[Category: Milburn, M V]]

OCA at 23:46, 22 December 2014

OCA — Mon, 22 Dec 2014 23:46:50 GMT

←Older revision		Revision as of 23:46, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1dqx]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DQX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DQX FirstGlance]. <br>		<table><tr><td colspan='2'>[[1dqx]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DQX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DQX FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMP:6-HYDROXYURIDINE-5-PHOSPHATE'>BMP</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMP:6-HYDROXYURIDINE-5-PHOSPHATE'>BMP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dqw\|1dqw]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dqw\|1dqw]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Orotidine-5'-phosphate_decarboxylase Orotidine-5'-phosphate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.23 4.1.1.23] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Orotidine-5'-phosphate_decarboxylase Orotidine-5'-phosphate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.23 4.1.1.23] </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=1dqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dqx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dqx RCSB], [http://www.ebi.ac.uk/pdbsum/1dqx 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=1dqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dqx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dqx RCSB], [http://www.ebi.ac.uk/pdbsum/1dqx PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 35:
	[[Category: Orotidine-5'-phosphate decarboxylase]]		[[Category: Orotidine-5'-phosphate decarboxylase]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
-	[[Category: Hassell, A M.]]	+	[[Category: Hassell, A M]]
-	[[Category: Milburn, M V.]]	+	[[Category: Milburn, M V]]
-	[[Category: Miller, B G.]]	+	[[Category: Miller, B G]]
-	[[Category: Short, S A.]]	+	[[Category: Short, S A]]
-	[[Category: Wolfenden, R.]]	+	[[Category: Wolfenden, R]]
	[[Category: 6-hydroxyuridine 5'-phosphate]]		[[Category: 6-hydroxyuridine 5'-phosphate]]
	[[Category: Bmp]]		[[Category: Bmp]]

OCA at 10:39, 10 September 2014

OCA — Wed, 10 Sep 2014 10:39:39 GMT

←Older revision		Revision as of 10:39, 10 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1dqx.~~png~~\|~~left~~\|200px]]	+	==CRYSTAL STRUCTURE OF OROTIDINE 5'-PHOSPHATE DECARBOXYLASE COMPLEXED TO 6-HYDROXYURIDINE 5'-PHOSPHATE (BMP)==
		+	<StructureSection load='1dqx' size='340' side='right' caption='[[1dqx]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1dqx]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DQX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DQX FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMP:6-HYDROXYURIDINE-5-PHOSPHATE'>BMP</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dqw\|1dqw]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Orotidine-5'-phosphate_decarboxylase Orotidine-5'-phosphate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.23 4.1.1.23] </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=1dqx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dqx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dqx RCSB], [http://www.ebi.ac.uk/pdbsum/1dqx 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/dq/1dqx_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 ==
		+	Orotidine 5'-phosphate decarboxylase produces the largest rate enhancement that has been reported for any enzyme. The crystal structure of the recombinant Saccharomyces cerevisiae enzyme has been determined in the absence and presence of the proposed transition state analog 6-hydroxyuridine 5'-phosphate, at a resolution of 2.1 A and 2.4 A, respectively. Orotidine 5'-phosphate decarboxylase folds as a TIM-barrel with the ligand binding site near the open end of the barrel. The binding of 6-hydroxyuridine 5'-phosphate is accompanied by protein loop movements that envelop the ligand almost completely, forming numerous favorable interactions with the phosphoryl group, the ribofuranosyl group, and the pyrimidine ring. Lysine-93 appears to be anchored in such a way as to optimize electrostatic interactions with developing negative charge at C-6 of the pyrimidine ring, and to donate the proton that replaces the carboxylate group at C-6 of the product. In addition, H-bonds from the active site to O-2 and O-4 help to delocalize negative charge in the transition state. Interactions between the enzyme and the phosphoribosyl group anchor the pyrimidine within the active site, helping to explain the phosphoribosyl group's remarkably large contribution to catalysis despite its distance from the site of decarboxylation.

-	~~{{STRUCTURE_1dqx\| PDB=1dqx \| SCENE= }}~~	+	Anatomy of a proficient enzyme: the structure of orotidine 5'-monophosphate decarboxylase in the presence and absence of a potential transition state analog.,Miller BG, Hassell AM, Wolfenden R, Milburn MV, Short SA Proc Natl Acad Sci U S A. 2000 Feb 29;97(5):2011-6. PMID:10681417<ref>PMID:10681417</ref>

-	~~===CRYSTAL STRUCTURE OF OROTIDINE 5'-PHOSPHATE DECARBOXYLASE COMPLEXED TO 6-HYDROXYURIDINE 5'-PHOSPHATE (BMP)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_10681417}}~~	+	==See Also==
-		+	*[[Uridine 5'-monophosphate synthase\|Uridine 5'-monophosphate synthase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~1dqx~~]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DQX OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:010681417<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Orotidine-5'-phosphate decarboxylase]]		[[Category: Orotidine-5'-phosphate decarboxylase]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]

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

OCA — Wed, 31 Oct 2012 09:50:30 GMT

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

←Older revision

Revision as of 09:50, 31 October 2012