3wk1 - Revision history

OCA at 13:13, 8 November 2023

2023-11-08T13:13:30Z

←Older revision		Revision as of 13:13, 8 November 2023
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	<StructureSection load='3wk1' size='340' side='right'caption='[[3wk1]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='3wk1' size='340' side='right'caption='[[3wk1]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3wk1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"methanobacterium_thermoautotrophicus"_(sic)_zeikus_and_wolfe_1972 "methanobacterium thermoautotrophicus" (sic) zeikus and wolfe 1972~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WK1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WK1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3wk1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WK1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WK1 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>~~, ~~<scene name='pdbligand=O7E:6-(ETHOXYCARBONYL)URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>O7E</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]] 1.6Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[3wjw\|3wjw]], [[3wjx\|3wjx]], [[3wjy\|3wjy]], [[3wkz\|3wkz]], [[3wk0\|3wk0]], [[3wk2\|3wk2]], [[3wk3\|3wk3]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=O7E:6-(ETHOXYCARBONYL)URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>O7E</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>pyrF, MTH_129 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~145262~~ "~~Methanobacterium thermoautotrophicus~~" ~~(sic) Zeikus and Wolfe 1972])</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=3wk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wk1 OCA], [https://pdbe.org/3wk1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wk1 RCSB], [https://www.ebi.ac.uk/pdbsum/3wk1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wk1 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=3wk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wk1 OCA], [https://pdbe.org/3wk1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wk1 RCSB], [https://www.ebi.ac.uk/pdbsum/3wk1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wk1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PYRF_METTH PYRF_METTH]] Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP).[HAMAP-Rule:MF_01200_A]	+	[https://www.uniprot.org/uniprot/PYRF_METTH PYRF_METTH] Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP).[HAMAP-Rule:MF_01200_A]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Orotidine-5'-phosphate decarboxylase~~]]	+	[[Category: Methanothermobacter thermautotrophicus]]
-	[[Category: Fujihashi, M]]	+	[[Category: Fujihashi M]]
-	[[Category: Miki, K]]	+	[[Category: Miki K]]
-	[[Category: Pai~~, E F]]~~	+	[[Category: Pai EF]]
-	~~[[Category: Decarboxylase]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Protein-ligand complex]]~~	+
-	~~[[Category: Pyrimidine biosynthesis]]~~	+
-	~~[[Category: Tim barrel~~]]	+

OCA at 05:39, 3 August 2022

2022-08-03T05:39:33Z

←Older revision		Revision as of 05:39, 3 August 2022
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	==Wild-type orotidine 5'-monophosphate decarboxylase from M. thermoautotrophicus complexed with orotidine 5'-monophosphate ethyl ester==		==Wild-type orotidine 5'-monophosphate decarboxylase from M. thermoautotrophicus complexed with orotidine 5'-monophosphate ethyl ester==
-	<StructureSection load='3wk1' size='340' side='right' caption='[[3wk1]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='3wk1' size='340' side='right'caption='[[3wk1]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3wk1]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"methanobacterium_thermoautotrophicus"_(sic)_zeikus_and_wolfe_1972 "methanobacterium thermoautotrophicus" (sic) zeikus and wolfe 1972]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WK1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3WK1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3wk1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"methanobacterium_thermoautotrophicus"_(sic)_zeikus_and_wolfe_1972 "methanobacterium thermoautotrophicus" (sic) zeikus and wolfe 1972]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WK1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WK1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=O7E:6-(ETHOXYCARBONYL)URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>O7E</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=O7E:6-(ETHOXYCARBONYL)URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>O7E</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wjw\|3wjw]], [[3wjx\|3wjx]], [[3wjy\|3wjy]], [[3wkz\|3wkz]], [[3wk0\|3wk0]], [[3wk2\|3wk2]], [[3wk3\|3wk3]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3wjw\|3wjw]], [[3wjx\|3wjx]], [[3wjy\|3wjy]], [[3wkz\|3wkz]], [[3wk0\|3wk0]], [[3wk2\|3wk2]], [[3wk3\|3wk3]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pyrF, MTH_129 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=145262 "Methanobacterium thermoautotrophicus" (sic) Zeikus and Wolfe 1972])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pyrF, MTH_129 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=145262 "Methanobacterium thermoautotrophicus" (sic) Zeikus and Wolfe 1972])</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=3wk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wk1 OCA], [~~http~~://pdbe.org/3wk1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3wk1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3wk1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3wk1 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=3wk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wk1 OCA], [https://pdbe.org/3wk1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wk1 RCSB], [https://www.ebi.ac.uk/pdbsum/3wk1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wk1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PYRF_METTH PYRF_METTH]] Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP).[HAMAP-Rule:MF_01200_A]	+	[[https://www.uniprot.org/uniprot/PYRF_METTH PYRF_METTH]] Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP).[HAMAP-Rule:MF_01200_A]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 3wk1" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3wk1" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Uridine 5'-monophosphate synthase 3D structures\|Uridine 5'-monophosphate synthase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Orotidine-5'-phosphate decarboxylase]]		[[Category: Orotidine-5'-phosphate decarboxylase]]
	[[Category: Fujihashi, M]]		[[Category: Fujihashi, M]]

OCA at 07:54, 5 August 2016

2016-08-05T07:54:28Z

←Older revision		Revision as of 07:54, 5 August 2016
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		+
	==Wild-type orotidine 5'-monophosphate decarboxylase from M. thermoautotrophicus complexed with orotidine 5'-monophosphate ethyl ester==		==Wild-type orotidine 5'-monophosphate decarboxylase from M. thermoautotrophicus complexed with orotidine 5'-monophosphate ethyl ester==
	<StructureSection load='3wk1' size='340' side='right' caption='[[3wk1]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='3wk1' size='340' side='right' caption='[[3wk1]], [[Resolution\|resolution]] 1.60Å' scene=''>
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	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pyrF, MTH_129 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=145262 "Methanobacterium thermoautotrophicus" (sic) Zeikus and Wolfe 1972])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pyrF, MTH_129 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=145262 "Methanobacterium thermoautotrophicus" (sic) Zeikus and Wolfe 1972])</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=3wk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wk1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wk1 RCSB], [http://www.ebi.ac.uk/pdbsum/3wk1 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=3wk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wk1 OCA], [http://pdbe.org/3wk1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wk1 RCSB], [http://www.ebi.ac.uk/pdbsum/3wk1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wk1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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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 3wk1" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 00:28, 25 December 2014

2014-12-25T00:28:25Z

←Older revision		Revision as of 00:28, 25 December 2014
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	<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=3wk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wk1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wk1 RCSB], [http://www.ebi.ac.uk/pdbsum/3wk1 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=3wk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wk1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wk1 RCSB], [http://www.ebi.ac.uk/pdbsum/3wk1 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PYRF_METTH PYRF_METTH]] Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP).[HAMAP-Rule:MF_01200_A]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 16:09, 21 December 2014

2014-12-21T16:09:30Z

←Older revision		Revision as of 16:09, 21 December 2014
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-	~~{{STRUCTURE_3wk1\| PDB=3wk1 \| SCENE= }}~~	+	==Wild-type orotidine 5'-monophosphate decarboxylase from M. thermoautotrophicus complexed with orotidine 5'-monophosphate ethyl ester==
-	===Wild-type orotidine 5'-monophosphate decarboxylase from M. thermoautotrophicus complexed with orotidine 5'-monophosphate ethyl ester===	+	<StructureSection load='3wk1' size='340' side='right' caption='[[3wk1]], [[Resolution\|resolution]] 1.60Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24151964}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3wk1]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"methanobacterium_thermoautotrophicus"_(sic)_zeikus_and_wolfe_1972 "methanobacterium thermoautotrophicus" (sic) zeikus and wolfe 1972]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WK1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WK1 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=O7E:6-(ETHOXYCARBONYL)URIDINE+5-(DIHYDROGEN+PHOSPHATE)'>O7E</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wjw\|3wjw]], [[3wjx\|3wjx]], [[3wjy\|3wjy]], [[3wkz\|3wkz]], [[3wk0\|3wk0]], [[3wk2\|3wk2]], [[3wk3\|3wk3]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pyrF, MTH_129 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=145262 "Methanobacterium thermoautotrophicus" (sic) Zeikus and Wolfe 1972])</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=3wk1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wk1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wk1 RCSB], [http://www.ebi.ac.uk/pdbsum/3wk1 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Orotidine 5'-monophosphate decarboxylase (ODCase) accelerates the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP) by 17 orders of magnitude. Eight new crystal structures with ligand analogues combined with computational analyses of the enzyme's short-lived intermediates and the intrinsic electronic energies to distort the substrate and other ligands improve our understanding of the still controversially discussed reaction mechanism. In their respective complexes, 6-methyl-UMP displays significant distortion of its methyl substituent bond, 6-amino-UMP shows the competition between the K72 and C6 substituents for a position close to D70, and the methyl and ethyl esters of OMP both induce rotation of the carboxylate group substituent out of the plane of the pyrimidine ring. Molecular dynamics and quantum mechanics/molecular mechanics computations of the enzyme-substrate complex also show the bond between the carboxylate group and the pyrimidine ring to be distorted, with the distortion contributing a 10-15% decrease of the DeltaDeltaG() value. These results are consistent with ODCase using both substrate distortion and transition-state stabilization, primarily exerted by K72, in its catalysis of the OMP decarboxylation reaction.

-	~~==Function==~~	+	Substrate distortion contributes to the catalysis of orotidine 5'-monophosphate decarboxylase.,Fujihashi M, Ishida T, Kuroda S, Kotra LP, Pai EF, Miki K J Am Chem Soc. 2013 Nov 20;135(46):17432-43. doi: 10.1021/ja408197k. Epub 2013, Nov 11. PMID:24151964<ref>PMID:24151964</ref>
-	~~[[http://www.uniprot.org/uniprot/PYRF_METTH PYRF_METTH]] Catalyzes~~ the ~~decarboxylation~~ of orotidine 5'-monophosphate (~~OMP~~) ~~to uridine 5'~~-~~monophosphate (UMP)~~.~~[HAMAP-Rule~~:~~MF_01200_A]~~	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3wk1]] is~~ a ~~1 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=3WK1 OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:024151964</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Orotidine-5'-phosphate decarboxylase]]		[[Category: Orotidine-5'-phosphate decarboxylase]]
-	[[Category: Fujihashi, M.]]	+	[[Category: Fujihashi, M]]
-	[[Category: Miki, K.]]	+	[[Category: Miki, K]]
-	[[Category: Pai, E F.]]	+	[[Category: Pai, E F]]
	[[Category: Decarboxylase]]		[[Category: Decarboxylase]]
	[[Category: Lyase]]		[[Category: Lyase]]

OCA at 07:18, 4 December 2013

2013-12-04T07:18:01Z

←Older revision		Revision as of 07:18, 4 December 2013
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-	''~~'Unreleased structure'''~~	+	{{STRUCTURE_3wk1\| PDB=3wk1 \| SCENE= }}
		+	===Wild-type orotidine 5'-monophosphate decarboxylase from M. thermoautotrophicus complexed with orotidine 5'-monophosphate ethyl ester===
		+	{{ABSTRACT_PUBMED_24151964}}

-	~~The entry 3wk1 is ON HOLD until Paper Publication~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/PYRF_METTH PYRF_METTH]] Catalyzes the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP).[HAMAP-Rule:MF_01200_A]

-	~~Authors~~: ~~Fujihashi, M~~.~~, Pai, E~~.F.~~, Miki, K~~.	+	==About this Structure==
		+	[[3wk1]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WK1 OCA].

-	~~Description~~: ~~Wild~~-~~type orotidine~~ 5'-~~monophosphate~~ decarboxylase ~~from~~ M. ~~thermoautotrophicus complexed with orotidine 5'~~-~~monophosphate ethyl ester~~	+	==Reference==
		+	<ref group="xtra">PMID:024151964</ref><references group="xtra"/><references/>
		+	[[Category: Orotidine-5'-phosphate decarboxylase]]
		+	[[Category: Fujihashi, M.]]
		+	[[Category: Miki, K.]]
		+	[[Category: Pai, E F.]]
		+	[[Category: Decarboxylase]]
		+	[[Category: Lyase]]
		+	[[Category: Protein-ligand complex]]
		+	[[Category: Pyrimidine biosynthesis]]
		+	[[Category: Tim barrel]]

OCA at 12:32, 20 November 2013

2013-11-20T12:32:24Z

←Older revision		Revision as of 12:32, 20 November 2013
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3wk1 is ON HOLD	+	The entry 3wk1 is ON HOLD until Paper Publication

	Authors: Fujihashi, M., Pai, E.F., Miki, K.		Authors: Fujihashi, M., Pai, E.F., Miki, K.

	Description: Wild-type orotidine 5'-monophosphate decarboxylase from M. thermoautotrophicus complexed with orotidine 5'-monophosphate ethyl ester		Description: Wild-type orotidine 5'-monophosphate decarboxylase from M. thermoautotrophicus complexed with orotidine 5'-monophosphate ethyl ester

OCA: Protected "3wk1" [edit=sysop:move=sysop]

2013-10-23T05:34:18Z

Protected "3wk1" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:34, 23 October 2013

OCA: New page: '''Unreleased structure''' The entry 3wk1 is ON HOLD Authors: Fujihashi, M., Pai, E.F., Miki, K. Description: Wild-type orotidine 5'-monophosphate decarboxylase from M. thermoautotroph...

2013-10-23T05:34:17Z

New page: '''Unreleased structure''' The entry 3wk1 is ON HOLD Authors: Fujihashi, M., Pai, E.F., Miki, K. Description: Wild-type orotidine 5'-monophosphate decarboxylase from M. thermoautotroph...

New page

'''Unreleased structure'''

The entry 3wk1 is ON HOLD

Authors: Fujihashi, M., Pai, E.F., Miki, K.

Description: Wild-type orotidine 5'-monophosphate decarboxylase from M. thermoautotrophicus complexed with orotidine 5'-monophosphate ethyl ester