3m1z - Revision history

OCA at 08:47, 6 September 2023

OCA — Wed, 06 Sep 2023 08:47:25 GMT

←Older revision		Revision as of 08:47, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='3m1z' size='340' side='right'caption='[[3m1z]], [[Resolution\|resolution]] 1.42Å' scene=''>		<StructureSection load='3m1z' size='340' side='right'caption='[[3m1z]], [[Resolution\|resolution]] 1.42Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3m1z]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Metth Metth~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M1Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3M1Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3m1z]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus_str._Delta_H Methanothermobacter thermautotrophicus str. Delta H]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M1Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3M1Z 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]] 1.42Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[3ltp\|3ltp]], [[3m5z\|3m5z]], [[3m5y\|3m5y]], [[3m5x\|3m5x]], [[3m47\|3m47]], [[3m44\|3m44]], [[3m43\|3m43]], [[3m41\|3m41]]</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='~~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~~=187420 METTH])</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=3m1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m1z OCA], [https://pdbe.org/3m1z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3m1z RCSB], [https://www.ebi.ac.uk/pdbsum/3m1z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3m1z 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=3m1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m1z OCA], [https://pdbe.org/3m1z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3m1z RCSB], [https://www.ebi.ac.uk/pdbsum/3m1z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3m1z 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]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Metth]]~~	+	[[Category: Methanothermobacter thermautotrophicus str. Delta H]]
-	~~[[Category: Orotidine-5'-phosphate decarboxylase~~]]	+	[[Category: Almo SC]]
-	[[Category: Almo~~, S C~~]]	+	[[Category: Fedorov AA]]
-	[[Category: Fedorov~~, A A~~]]	+	[[Category: Fedorov EV]]
-	[[Category: Fedorov~~, E V~~]]	+	[[Category: Gerlt JA]]
-	[[Category: Gerlt~~, J A~~]]	+	[[Category: Wood BM]]
-	[[Category: Wood~~, B M]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Orotidine 5'-monophosphate decarboxylase~~]]	+

OCA at 12:41, 13 October 2021

OCA — Wed, 13 Oct 2021 12:41:32 GMT

←Older revision		Revision as of 12:41, 13 October 2021
Line 1:		Line 1:

	==Crystal structure of the mutant V182A.V201A of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP==		==Crystal structure of the mutant V182A.V201A of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP==
-	<StructureSection load='3m1z' size='340' side='right' caption='[[3m1z]], [[Resolution\|resolution]] 1.42Å' scene=''>	+	<StructureSection load='3m1z' size='340' side='right'caption='[[3m1z]], [[Resolution\|resolution]] 1.42Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3m1z]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Metth Metth]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M1Z OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3M1Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3m1z]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Metth Metth]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M1Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3M1Z 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">[[3ltp\|3ltp]], [[3m5z\|3m5z]], [[3m5y\|3m5y]], [[3m5x\|3m5x]], [[3m47\|3m47]], [[3m44\|3m44]], [[3m43\|3m43]], [[3m41\|3m41]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ltp\|3ltp]], [[3m5z\|3m5z]], [[3m5y\|3m5y]], [[3m5x\|3m5x]], [[3m47\|3m47]], [[3m44\|3m44]], [[3m43\|3m43]], [[3m41\|3m41]]</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=187420 METTH])</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=187420 METTH])</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=3m1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m1z OCA], [~~http~~://pdbe.org/3m1z PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3m1z RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3m1z PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3m1z 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=3m1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m1z OCA], [https://pdbe.org/3m1z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3m1z RCSB], [https://www.ebi.ac.uk/pdbsum/3m1z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3m1z 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]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 3m1z" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3m1z" 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: Metth]]		[[Category: Metth]]
	[[Category: Orotidine-5'-phosphate decarboxylase]]		[[Category: Orotidine-5'-phosphate decarboxylase]]

OCA at 19:25, 24 January 2018

OCA — Wed, 24 Jan 2018 19:25:49 GMT

←Older revision		Revision as of 19:25, 24 January 2018
Line 16:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m1/3m1z_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m1/3m1z_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 41:		Line 41:
	[[Category: Fedorov, E V]]		[[Category: Fedorov, E V]]
	[[Category: Gerlt, J A]]		[[Category: Gerlt, J A]]
-	[[Category: Wood, BM]]	+	[[Category: Wood, B M]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Orotidine 5'-monophosphate decarboxylase]]		[[Category: Orotidine 5'-monophosphate decarboxylase]]

OCA at 19:52, 5 August 2016

OCA — Fri, 05 Aug 2016 19:52:45 GMT

←Older revision		Revision as of 19:52, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of the mutant V182A.V201A of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP==		==Crystal structure of the mutant V182A.V201A of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP==
	<StructureSection load='3m1z' size='340' side='right' caption='[[3m1z]], [[Resolution\|resolution]] 1.42Å' scene=''>		<StructureSection load='3m1z' size='340' side='right' caption='[[3m1z]], [[Resolution\|resolution]] 1.42Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3m1z]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Methanothermobacter_thermautotrophicus_str._delta_h Methanothermobacter thermautotrophicus str. delta h~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M1Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3M1Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3m1z]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Metth Metth]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M1Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3M1Z 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">[[3ltp\|3ltp]], [[3m5z\|3m5z]], [[3m5y\|3m5y]], [[3m5x\|3m5x]], [[3m47\|3m47]], [[3m44\|3m44]], [[3m43\|3m43]], [[3m41\|3m41]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ltp\|3ltp]], [[3m5z\|3m5z]], [[3m5y\|3m5y]], [[3m5x\|3m5x]], [[3m47\|3m47]], [[3m44\|3m44]], [[3m43\|3m43]], [[3m41\|3m41]]</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=187420 ~~Methanothermobacter thermautotrophicus str. Delta H~~])</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=187420 METTH])</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=3m1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m1z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3m1z RCSB], [http://www.ebi.ac.uk/pdbsum/3m1z 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=3m1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m1z OCA], [http://pdbe.org/3m1z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3m1z RCSB], [http://www.ebi.ac.uk/pdbsum/3m1z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3m1z ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	<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=3m1z ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 29:		Line 30:
	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 3m1z" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Methanothermobacter thermautotrophicus str. delta h~~]]	+	[[Category: Metth]]
	[[Category: Orotidine-5'-phosphate decarboxylase]]		[[Category: Orotidine-5'-phosphate decarboxylase]]
	[[Category: Almo, S C]]		[[Category: Almo, S C]]

OCA at 05:22, 25 December 2014

OCA — Thu, 25 Dec 2014 05:22:46 GMT

←Older revision		Revision as of 05:22, 25 December 2014
Line 9:		Line 9:
	<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=3m1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m1z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3m1z RCSB], [http://www.ebi.ac.uk/pdbsum/3m1z 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=3m1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m1z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3m1z RCSB], [http://www.ebi.ac.uk/pdbsum/3m1z 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]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 15:56, 18 December 2014

OCA — Thu, 18 Dec 2014 15:56:39 GMT

←Older revision		Revision as of 15:56, 18 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3m1z\| PDB=3m1z \| SCENE= }}~~	+	==Crystal structure of the mutant V182A.V201A of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP==
-	===Crystal structure of the mutant V182A.V201A of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP===	+	<StructureSection load='3m1z' size='340' side='right' caption='[[3m1z]], [[Resolution\|resolution]] 1.42Å' scene=''>
-	~~{{ABSTRACT_PUBMED_20369850}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3m1z]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus_str._delta_h Methanothermobacter thermautotrophicus str. delta h]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M1Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3M1Z 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>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ltp\|3ltp]], [[3m5z\|3m5z]], [[3m5y\|3m5y]], [[3m5x\|3m5x]], [[3m47\|3m47]], [[3m44\|3m44]], [[3m43\|3m43]], [[3m41\|3m41]]</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=187420 Methanothermobacter thermautotrophicus str. Delta H])</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=3m1z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m1z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3m1z RCSB], [http://www.ebi.ac.uk/pdbsum/3m1z 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/m1/3m1z_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 ==
		+	The structural factors responsible for the extraordinary rate enhancement ( approximately 10(17)) of the reaction catalyzed by orotidine 5'-monophosphate decarboxylase (OMPDC) have not been defined. Catalysis requires a conformational change that closes an active site loop and "clamps" the orotate base proximal to hydrogen-bonded networks that destabilize the substrate and stabilize the intermediate. In the OMPDC from Methanobacter thermoautotrophicus, a "remote" structurally conserved cluster of hydrophobic residues that includes Val 182 in the active site loop is assembled in the closed, catalytically active conformation. Substitution of these residues with Ala decreases k(cat)/K(m) with a minimal effect on k(cat), providing evidence that the cluster stabilizes the closed conformation. The intrinsic binding energies of the 5'-phosphate group of orotidine 5'-monophosphate for the mutant enzymes are similar to that for the wild type, supporting this conclusion.

-	~~==Function==~~	+	Conformational changes in orotidine 5'-monophosphate decarboxylase: "remote" residues that stabilize the active conformation.,Wood BM, Amyes TL, Fedorov AA, Fedorov EV, Shabila A, Almo SC, Richard JP, Gerlt JA Biochemistry. 2010 May 4;49(17):3514-6. PMID:20369850<ref>PMID:20369850</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>
-	~~[[3m1z]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Methanothermobacter_thermautotrophicus_str~~.~~_delta_h Methanothermobacter thermautotrophicus str. delta h]. Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3M1Z OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:020369850</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Methanothermobacter thermautotrophicus str. delta h]]		[[Category: Methanothermobacter thermautotrophicus str. delta h]]
	[[Category: Orotidine-5'-phosphate decarboxylase]]		[[Category: Orotidine-5'-phosphate decarboxylase]]
-	[[Category: Almo, S C.]]	+	[[Category: Almo, S C]]
-	[[Category: Fedorov, A A.]]	+	[[Category: Fedorov, A A]]
-	[[Category: Fedorov, E V.]]	+	[[Category: Fedorov, E V]]
-	[[Category: Gerlt, J A.]]	+	[[Category: Gerlt, J A]]
	[[Category: Wood, BM]]		[[Category: Wood, BM]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Orotidine 5'-monophosphate decarboxylase]]		[[Category: Orotidine 5'-monophosphate decarboxylase]]

OCA: Protected "3m1z" [edit=sysop:move=sysop]

OCA — Wed, 10 Apr 2013 23:18:44 GMT

Protected "3m1z" [edit=sysop:move=sysop]

←Older revision

Revision as of 23:18, 10 April 2013

OCA at 23:18, 10 April 2013

OCA — Wed, 10 Apr 2013 23:18:40 GMT

←Older revision		Revision as of 23:18, 10 April 2013
Line 1:		Line 1:
-	{{Seed}}
-	[[Image:3m1z.jpg\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3m1z", 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_3m1z\| PDB=3m1z \| SCENE= }}		{{STRUCTURE_3m1z\| PDB=3m1z \| SCENE= }}
-
	===Crystal structure of the mutant V182A.V201A of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP===		===Crystal structure of the mutant V182A.V201A of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP===
		+	{{ABSTRACT_PUBMED_20369850}}

-		+	==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]
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_20369850}}, adds the Publication Abstract to the page~~	+
-	~~(as it appears on PubMed at~~ http://www.~~pubmed~~.~~gov~~)~~, where 20369850 is the PubMed ID number~~.	+
-	-->	+
-	~~{{ABSTRACT_PUBMED_20369850}}~~	+

	==About this Structure==		==About this Structure==
-	~~3M1Z~~ is a 2 ~~chains~~ structure with ~~sequences~~ from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus_str._delta_h Methanothermobacter thermautotrophicus str. delta h]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M1Z OCA].	+	[[3m1z]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus_str._delta_h Methanothermobacter thermautotrophicus str. delta h]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M1Z OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20369850~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020369850</ref><references group="xtra"/><references/>
	[[Category: Methanothermobacter thermautotrophicus str. delta h]]		[[Category: Methanothermobacter thermautotrophicus str. delta h]]
	[[Category: Orotidine-5'-phosphate decarboxylase]]		[[Category: Orotidine-5'-phosphate decarboxylase]]
Line 33:		Line 20:
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Orotidine 5'-monophosphate decarboxylase]]		[[Category: Orotidine 5'-monophosphate decarboxylase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 16 08:41:32 2010''

OCA at 04:36, 16 June 2010

OCA — Wed, 16 Jun 2010 04:36:32 GMT

←Older revision		Revision as of 04:36, 16 June 2010
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3m1z.jpg\|left\|200px]]

-	The ~~entry 3m1z~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3m1z", 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_3m1z\| PDB=3m1z \| SCENE= }}

-	~~Authors: Fedorov, A.A., Fedorov, E.V., Wood, BM, Gerlt, J.A., Almo, S.C~~.	+	===Crystal structure of the mutant V182A.V201A of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP===

-	Description: Crystal structure of the mutant V182A.V201A of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Apr 14 09~~:21:21 2010''	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_20369850}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 20369850 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_20369850}}
		+
		+	==About this Structure==
		+	3M1Z is a 2 chains structure with sequences from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus_str._delta_h Methanothermobacter thermautotrophicus str. delta h]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M1Z OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:20369850</ref><references group="xtra"/>
		+	[[Category: Methanothermobacter thermautotrophicus str. delta h]]
		+	[[Category: Orotidine-5'-phosphate decarboxylase]]
		+	[[Category: Almo, S C.]]
		+	[[Category: Fedorov, A A.]]
		+	[[Category: Fedorov, E V.]]
		+	[[Category: Gerlt, J A.]]
		+	[[Category: Wood, BM]]
		+	[[Category: Lyase]]
		+	[[Category: Orotidine 5'-monophosphate decarboxylase]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 16 08:41:32 2010''

OCA at 06:21, 14 April 2010

OCA — Wed, 14 Apr 2010 06:21:22 GMT

←Older revision		Revision as of 06:21, 14 April 2010
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3m1z is ON HOLD	+	The entry 3m1z is ON HOLD until Paper Publication

	Authors: Fedorov, A.A., Fedorov, E.V., Wood, BM, Gerlt, J.A., Almo, S.C.		Authors: Fedorov, A.A., Fedorov, E.V., Wood, BM, Gerlt, J.A., Almo, S.C.
Line 7:		Line 7:
	Description: Crystal structure of the mutant V182A.V201A of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP		Description: Crystal structure of the mutant V182A.V201A of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with inhibitor BMP

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Mar 17~~ 09:12:47 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 14 09:21:21 2010''