1eix - Revision history

OCA at 07:03, 7 February 2024

OCA — Wed, 07 Feb 2024 07:03:24 GMT

←Older revision		Revision as of 07:03, 7 February 2024
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	<StructureSection load='1eix' size='340' side='right'caption='[[1eix]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1eix' size='340' side='right'caption='[[1eix]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1eix]] is a 4 chain structure with sequence from [https://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=1EIX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EIX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1eix]] is a 4 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=1EIX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EIX FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=BMQ:1~~-(5~~-PHOSPHO-BETA-D-RIBOFURANOSYL)BARBITURIC+ACID'>BMQ</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]] 2.5Å</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMQ:1-(5-PHOSPHO-BETA-D-RIBOFURANOSYL)BARBITURIC+ACID'>BMQ</scene></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=1eix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eix OCA], [https://pdbe.org/1eix PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1eix RCSB], [https://www.ebi.ac.uk/pdbsum/1eix PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1eix 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=1eix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eix OCA], [https://pdbe.org/1eix PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1eix RCSB], [https://www.ebi.ac.uk/pdbsum/1eix PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1eix ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PYRF_ECOLI PYRF_ECOLI]] Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP).[HAMAP-Rule:MF_01200_B]	+	[https://www.uniprot.org/uniprot/PYRF_ECOLI PYRF_ECOLI] Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP).[HAMAP-Rule:MF_01200_B]
	== 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=1eix 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=1eix ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Orotidine 5'-monophosphate decarboxylase (ODCase) catalyzes the decarboxylation of orotidine 5'-monophosphate, the last step in the de novo synthesis of uridine 5'-monophosphate. ODCase is a very proficient enzyme [Radzicka, A., and Wolfenden, R. (1995) Science 267, 90-93], enhancing the reaction rate by a factor of 10(17). This proficiency has been enigmatic, since it is achieved without metal ions or cofactors. Here we present a 2.5 A resolution structure of ODCase complexed with the inhibitor 1-(5'-phospho-beta-D-ribofuranosyl)barbituric acid. It shows a closely packed dimer composed of two alpha/beta-barrels with two shared active sites. The orientation of the orotate moiety of the substrate is unambiguously deduced from the structure, and previously proposed catalytic mechanisms involving protonation of O2 or O4 can be ruled out. The proximity of the OMP carboxylate group with Asp71 appears to be instrumental for the decarboxylation of OMP, either through charge repulsion or through the formation of a very short O.H.O hydrogen bond between the two carboxylate groups.
-
-	Structural basis for the catalytic mechanism of a proficient enzyme: orotidine 5'-monophosphate decarboxylase.,Harris P, Navarro Poulsen JC, Jensen KF, Larsen S Biochemistry. 2000 Apr 18;39(15):4217-24. PMID:10757968<ref>PMID:10757968</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1eix" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Orotidine-5'-phosphate decarboxylase]]~~	+	[[Category: Harris P]]
-	[[Category: Harris, P]]	+	[[Category: Jensen KF]]
-	[[Category: Jensen~~, K F~~]]	+	[[Category: Larsen S]]
-	[[Category: Larsen, S]]	+	[[Category: Poulsen JCN]]
-	[[Category: Poulsen~~, J C.N]]~~	+
-	~~[[Category: Alpha-beta-barrel]]~~	+
-	~~[[Category: Homodimer]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Protein-inhibitor complex~~]]	+

OCA at 09:50, 15 September 2021

OCA — Wed, 15 Sep 2021 09:50:40 GMT

←Older revision		Revision as of 09:50, 15 September 2021
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	<StructureSection load='1eix' size='340' side='right'caption='[[1eix]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1eix' size='340' side='right'caption='[[1eix]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1eix]] is a 4 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=1EIX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1EIX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1eix]] is a 4 chain structure with sequence from [https://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=1EIX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EIX FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMQ:1-(5-PHOSPHO-BETA-D-RIBOFURANOSYL)BARBITURIC+ACID'>BMQ</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMQ:1-(5-PHOSPHO-BETA-D-RIBOFURANOSYL)BARBITURIC+ACID'>BMQ</scene></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=1eix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eix OCA], [~~http~~://pdbe.org/1eix PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1eix RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1eix PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1eix 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=1eix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eix OCA], [https://pdbe.org/1eix PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1eix RCSB], [https://www.ebi.ac.uk/pdbsum/1eix PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1eix ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PYRF_ECOLI PYRF_ECOLI]] Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP).[HAMAP-Rule:MF_01200_B]	+	[[https://www.uniprot.org/uniprot/PYRF_ECOLI PYRF_ECOLI]] Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP).[HAMAP-Rule:MF_01200_B]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 19:19, 11 December 2019

OCA — Wed, 11 Dec 2019 19:19:58 GMT

←Older revision		Revision as of 19:19, 11 December 2019
Line 1:		Line 1:

	==STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM E. COLI, CO-CRYSTALLISED WITH THE INHIBITOR BMP==		==STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM E. COLI, CO-CRYSTALLISED WITH THE INHIBITOR BMP==
-	<StructureSection load='1eix' size='340' side='right' caption='[[1eix]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='1eix' size='340' side='right'caption='[[1eix]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1eix]] is a 4 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=1EIX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EIX FirstGlance]. <br>		<table><tr><td colspan='2'>[[1eix]] is a 4 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=1EIX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EIX FirstGlance]. <br>
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Orotidine-5'-phosphate decarboxylase]]		[[Category: Orotidine-5'-phosphate decarboxylase]]
	[[Category: Harris, P]]		[[Category: Harris, P]]

OCA at 07:18, 20 December 2017

OCA — Wed, 20 Dec 2017 07:18:17 GMT

←Older revision		Revision as of 07:18, 20 December 2017
Line 1:		Line 1:
		+
	==STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM E. COLI, CO-CRYSTALLISED WITH THE INHIBITOR BMP==		==STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM E. COLI, CO-CRYSTALLISED WITH THE INHIBITOR BMP==
	<StructureSection load='1eix' size='340' side='right' caption='[[1eix]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1eix' size='340' side='right' caption='[[1eix]], [[Resolution\|resolution]] 2.50Å' scene=''>
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMQ:1-(5-PHOSPHO-BETA-D-RIBOFURANOSYL)BARBITURIC+ACID'>BMQ</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMQ:1-(5-PHOSPHO-BETA-D-RIBOFURANOSYL)BARBITURIC+ACID'>BMQ</scene></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=1eix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eix OCA], [http://pdbe.org/1eix PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1eix RCSB], [http://www.ebi.ac.uk/pdbsum/1eix 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=1eix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eix OCA], [http://pdbe.org/1eix PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1eix RCSB], [http://www.ebi.ac.uk/pdbsum/1eix PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1eix ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ei/1eix_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ei/1eix_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 02:32, 8 February 2016

OCA — Mon, 08 Feb 2016 02:32:21 GMT

←Older revision		Revision as of 02:32, 8 February 2016
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1eix ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:02, 10 September 2015

OCA — Thu, 10 Sep 2015 07:02:10 GMT

←Older revision		Revision as of 07:02, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1eix' size='340' side='right' caption='[[1eix]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='1eix' size='340' side='right' caption='[[1eix]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1eix]] is a 4 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=1EIX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EIX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1eix]] is a 4 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=1EIX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EIX FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMQ:1-(5-PHOSPHO-BETA-D-RIBOFURANOSYL)BARBITURIC+ACID'>BMQ</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMQ:1-(5-PHOSPHO-BETA-D-RIBOFURANOSYL)BARBITURIC+ACID'>BMQ</scene></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=1eix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eix OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1eix RCSB], [http://www.ebi.ac.uk/pdbsum/1eix 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=1eix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eix OCA], [http://pdbe.org/1eix PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1eix RCSB], [http://www.ebi.ac.uk/pdbsum/1eix PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		Line 27:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1eix" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Orotidine-5'-phosphate decarboxylase]]		[[Category: Orotidine-5'-phosphate decarboxylase]]
	[[Category: Harris, P]]		[[Category: Harris, P]]

OCA at 19:55, 24 December 2014

OCA — Wed, 24 Dec 2014 19:55:18 GMT

←Older revision		Revision as of 19:55, 24 December 2014
Line 7:		Line 7:
	<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=1eix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eix OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1eix RCSB], [http://www.ebi.ac.uk/pdbsum/1eix 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=1eix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eix OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1eix RCSB], [http://www.ebi.ac.uk/pdbsum/1eix PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PYRF_ECOLI PYRF_ECOLI]] Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP).[HAMAP-Rule:MF_01200_B]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 22:00, 22 December 2014

OCA — Mon, 22 Dec 2014 22:00:32 GMT

←Older revision		Revision as of 22:00, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1eix]] is a 4 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=1EIX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EIX FirstGlance]. <br>		<table><tr><td colspan='2'>[[1eix]] is a 4 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=1EIX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EIX FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMQ:1-(5-PHOSPHO-BETA-D-RIBOFURANOSYL)BARBITURIC+ACID'>BMQ</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMQ:1-(5-PHOSPHO-BETA-D-RIBOFURANOSYL)BARBITURIC+ACID'>BMQ</scene></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=1eix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eix OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1eix RCSB], [http://www.ebi.ac.uk/pdbsum/1eix 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=1eix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eix OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1eix RCSB], [http://www.ebi.ac.uk/pdbsum/1eix 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 31:		Line 31:
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Orotidine-5'-phosphate decarboxylase]]		[[Category: Orotidine-5'-phosphate decarboxylase]]
-	[[Category: Harris, P.]]	+	[[Category: Harris, P]]
-	[[Category: Jensen, K F.]]	+	[[Category: Jensen, K F]]
-	[[Category: Larsen, S.]]	+	[[Category: Larsen, S]]
-	[[Category: Poulsen, J C.N.]]	+	[[Category: Poulsen, J C.N]]
	[[Category: Alpha-beta-barrel]]		[[Category: Alpha-beta-barrel]]
	[[Category: Homodimer]]		[[Category: Homodimer]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Protein-inhibitor complex]]		[[Category: Protein-inhibitor complex]]

OCA at 11:27, 24 September 2014

OCA — Wed, 24 Sep 2014 11:27:56 GMT

←Older revision		Revision as of 11:27, 24 September 2014
Line 1:		Line 1:
-	[[~~Image~~:1eix.~~png\|left~~\|200px]]	+	==STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM E. COLI, CO-CRYSTALLISED WITH THE INHIBITOR BMP==
		+	<StructureSection load='1eix' size='340' side='right' caption='[[1eix]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1eix]] is a 4 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=1EIX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EIX FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMQ:1-(5-PHOSPHO-BETA-D-RIBOFURANOSYL)BARBITURIC+ACID'>BMQ</scene><br>
		+	<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=1eix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eix OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1eix RCSB], [http://www.ebi.ac.uk/pdbsum/1eix 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/ei/1eix_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'-monophosphate decarboxylase (ODCase) catalyzes the decarboxylation of orotidine 5'-monophosphate, the last step in the de novo synthesis of uridine 5'-monophosphate. ODCase is a very proficient enzyme [Radzicka, A., and Wolfenden, R. (1995) Science 267, 90-93], enhancing the reaction rate by a factor of 10(17). This proficiency has been enigmatic, since it is achieved without metal ions or cofactors. Here we present a 2.5 A resolution structure of ODCase complexed with the inhibitor 1-(5'-phospho-beta-D-ribofuranosyl)barbituric acid. It shows a closely packed dimer composed of two alpha/beta-barrels with two shared active sites. The orientation of the orotate moiety of the substrate is unambiguously deduced from the structure, and previously proposed catalytic mechanisms involving protonation of O2 or O4 can be ruled out. The proximity of the OMP carboxylate group with Asp71 appears to be instrumental for the decarboxylation of OMP, either through charge repulsion or through the formation of a very short O.H.O hydrogen bond between the two carboxylate groups.

-	~~{{STRUCTURE_1eix\| PDB=1eix \| SCENE= }}~~	+	Structural basis for the catalytic mechanism of a proficient enzyme: orotidine 5'-monophosphate decarboxylase.,Harris P, Navarro Poulsen JC, Jensen KF, Larsen S Biochemistry. 2000 Apr 18;39(15):4217-24. PMID:10757968<ref>PMID:10757968</ref>

-	~~===STRUCTURE OF OROTIDINE 5'-MONOPHOSPHATE DECARBOXYLASE FROM E. COLI~~, ~~CO-CRYSTALLISED WITH THE INHIBITOR BMP===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~==About this Structure==~~	+	<references/>
-	~~[[1eix]] is~~ a ~~4 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=1EIX OCA].~~	+	__TOC__
-		+	</StructureSection>
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:010757968<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Orotidine-5'-phosphate decarboxylase]]		[[Category: Orotidine-5'-phosphate decarboxylase]]

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

OCA — Thu, 08 Nov 2012 14:39:35 GMT

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

←Older revision

Revision as of 14:39, 8 November 2012