3g1h - Revision history

OCA at 06:56, 6 September 2023

OCA — Wed, 06 Sep 2023 06:56:04 GMT

←Older revision		Revision as of 06:56, 6 September 2023
Line 3:		Line 3:
	<StructureSection load='3g1h' size='340' side='right'caption='[[3g1h]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='3g1h' size='340' side='right'caption='[[3g1h]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3g1h]] is a 13 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=3G1H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3G1H FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3g1h]] is a 13 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=3G1H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3G1H FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=H2U:5~~,~~6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</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]] 2.3Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[3g18\|3g18]], [[3g1a\|3g1a]], [[3g1d\|3g1d]], [[3g1f\|3g1f]], [[3g1s\|3g1s]], [[3g1v\|3g1v]], [[3g1x\|3g1x]], [[3g1y\|3g1y]], [[3g22\|3g22]], [[3g24\|3g24]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</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=3g1h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g1h OCA], [https://pdbe.org/3g1h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3g1h RCSB], [https://www.ebi.ac.uk/pdbsum/3g1h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3g1h 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=3g1h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g1h OCA], [https://pdbe.org/3g1h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3g1h RCSB], [https://www.ebi.ac.uk/pdbsum/3g1h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3g1h 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: Chan KK]]
-	[[Category: Chan~~, K K~~]]	+	[[Category: Fedorov AA]]
-	[[Category: Fedorov~~, A A~~]]	+	[[Category: Fedorov EV]]
-	[[Category: Fedorov~~, E V~~]]	+	[[Category: Gerlt JA]]
-	[[Category: Gerlt~~, J A]]~~	+
-	~~[[Category: Decarboxylase]]~~	+
-	~~[[Category: H2-ump]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Orotidine 5'-monophosphate decarboxylase]]~~	+
-	~~[[Category: Pyrimidine biosynthesis~~]]	+

OCA at 20:00, 20 October 2021

OCA — Wed, 20 Oct 2021 20:00:54 GMT

←Older revision		Revision as of 20:00, 20 October 2021
Line 1:		Line 1:

	==Crystal structure of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with 5,6-dihydrouridine 5'-monophosphate==		==Crystal structure of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with 5,6-dihydrouridine 5'-monophosphate==
-	<StructureSection load='3g1h' size='340' side='right' caption='[[3g1h]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='3g1h' size='340' side='right'caption='[[3g1h]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3g1h]] is a 13 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=3G1H OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3G1H FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3g1h]] is a 13 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=3G1H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3G1H FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3g18\|3g18]], [[3g1a\|3g1a]], [[3g1d\|3g1d]], [[3g1f\|3g1f]], [[3g1s\|3g1s]], [[3g1v\|3g1v]], [[3g1x\|3g1x]], [[3g1y\|3g1y]], [[3g22\|3g22]], [[3g24\|3g24]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3g18\|3g18]], [[3g1a\|3g1a]], [[3g1d\|3g1d]], [[3g1f\|3g1f]], [[3g1s\|3g1s]], [[3g1v\|3g1v]], [[3g1x\|3g1x]], [[3g1y\|3g1y]], [[3g22\|3g22]], [[3g24\|3g24]]</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=3g1h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g1h OCA], [~~http~~://pdbe.org/3g1h PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3g1h RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3g1h PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3g1h 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=3g1h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g1h OCA], [https://pdbe.org/3g1h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3g1h RCSB], [https://www.ebi.ac.uk/pdbsum/3g1h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3g1h 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 33:		Line 33:

	==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/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Metth]]		[[Category: Metth]]
	[[Category: Orotidine-5'-phosphate decarboxylase]]		[[Category: Orotidine-5'-phosphate decarboxylase]]

OCA at 07:55, 5 December 2018

OCA — Wed, 05 Dec 2018 07:55:29 GMT

←Older revision		Revision as of 07:55, 5 December 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/g1/3g1h_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g1/3g1h_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 31:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 3g1h" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3g1h" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Uridine 5'-monophosphate synthase\|Uridine 5'-monophosphate synthase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:50, 5 August 2016

OCA — Fri, 05 Aug 2016 08:50:22 GMT

←Older revision		Revision as of 08:50, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with 5,6-dihydrouridine 5'-monophosphate==		==Crystal structure of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with 5,6-dihydrouridine 5'-monophosphate==
	<StructureSection load='3g1h' size='340' side='right' caption='[[3g1h]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='3g1h' size='340' side='right' caption='[[3g1h]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3g1h]] is a 13 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=3G1H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G1H FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3g1h]] is a 13 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=3G1H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G1H FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3g18\|3g18]], [[3g1a\|3g1a]], [[3g1d\|3g1d]], [[3g1f\|3g1f]], [[3g1s\|3g1s]], [[3g1v\|3g1v]], [[3g1x\|3g1x]], [[3g1y\|3g1y]], [[3g22\|3g22]], [[3g24\|3g24]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3g18\|3g18]], [[3g1a\|3g1a]], [[3g1d\|3g1d]], [[3g1f\|3g1f]], [[3g1s\|3g1s]], [[3g1v\|3g1v]], [[3g1x\|3g1x]], [[3g1y\|3g1y]], [[3g22\|3g22]], [[3g24\|3g24]]</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=3g1h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g1h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g1h RCSB], [http://www.ebi.ac.uk/pdbsum/3g1h 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=3g1h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g1h OCA], [http://pdbe.org/3g1h PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3g1h RCSB], [http://www.ebi.ac.uk/pdbsum/3g1h PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3g1h 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=3g1h 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 3g1h" 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 17:25, 25 December 2014

OCA — Thu, 25 Dec 2014 17:25:30 GMT

←Older revision		Revision as of 17:25, 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=3g1h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g1h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g1h RCSB], [http://www.ebi.ac.uk/pdbsum/3g1h 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=3g1h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g1h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g1h RCSB], [http://www.ebi.ac.uk/pdbsum/3g1h 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 10:14, 3 December 2014

OCA — Wed, 03 Dec 2014 10:14:59 GMT

←Older revision		Revision as of 10:14, 3 December 2014
Line 1:		Line 1:
-	[[~~Image:~~3g1h.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with 5,6-dihydrouridine 5'-monophosphate==
		+	<StructureSection load='3g1h' size='340' side='right' caption='[[3g1h]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3g1h]] is a 13 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=3G1H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3G1H FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3g18\|3g18]], [[3g1a\|3g1a]], [[3g1d\|3g1d]], [[3g1f\|3g1f]], [[3g1s\|3g1s]], [[3g1v\|3g1v]], [[3g1x\|3g1x]], [[3g1y\|3g1y]], [[3g22\|3g22]], [[3g24\|3g24]]</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=3g1h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3g1h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3g1h RCSB], [http://www.ebi.ac.uk/pdbsum/3g1h 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/g1/3g1h_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 reaction catalyzed by orotidine 5'-monophosphate decarboxylase (OMPDC) involves a stabilized anionic intermediate, although the structural basis for the rate acceleration (k(cat)/k(non), 7.1 x 10(16)) and proficiency [(k(cat)/K(M))/k(non), 4.8 x 10(22) M(-1)] is uncertain. That the OMPDCs from Methanothermobacter thermautotrophicus (MtOMPDC) and Saccharomyces cerevisiae (ScOMPDC) catalyze the exchange of H6 of the UMP product with solvent deuterium allows an estimate of a lower limit on the rate acceleration associated with stabilization of the intermediate and its flanking transition states (>or=10(10)). The origin of the "missing" contribution, <or=10(7) ( approximately 10(17) total - >or=10(10)), is of interest. Based on structures of liganded complexes, unfavorable electrostatic interactions between the substrate carboxylate group and a proximal Asp (Asp 70 in MtOMPDC and Asp 91 in ScOMPDC) have been proposed to contribute to the catalytic efficiency [Wu, N., Mo, Y., Gao, J., and Pai, E. F. (2000) Proc. Natl. Acad. Sci. U.S.A. 97, 2017-2022]. We investigated that hypothesis by structural and functional characterization of the D70N and D70G mutants of MtOMPDC and the D91N mutant of ScOMPDC. The substitutions for Asp 70 in MtOMPDC significantly decrease the value of k(cat) for decarboxylation of FOMP (a more reactive substrate analogue) but have little effect on the value of k(ex) for exchange of H6 of FUMP with solvent deuterium; the structures of wild-type MtOMPDC and its mutants are superimposable when complexed with 6-azaUMP. In contrast, the D91N mutant of ScOMPDC does not catalyze exchange of H6 of FUMP; the structures of wild-type ScOMPDC and its D91N mutant are not superimposable when complexed with 6-azaUMP, with differences in both the conformation of the active site loop and the orientation of the ligand vis a vis the active site residues. We propose that the differential effects of substitutions for Asp 70 of MtOMPDC on decarboxylation and exchange provide additional evidence for a carbanionic intermediate as well as the involvement of Asp 70 in substrate destabilization.

-	~~{{STRUCTURE_3g1h\| PDB=3g1h \| SCENE= }}~~	+	Mechanism of the orotidine 5'-monophosphate decarboxylase-catalyzed reaction: evidence for substrate destabilization.,Chan KK, Wood BM, Fedorov AA, Fedorov EV, Imker HJ, Amyes TL, Richard JP, Almo SC, Gerlt JA Biochemistry. 2009 Jun 23;48(24):5518-31. PMID:19435314<ref>PMID:19435314</ref>

-	~~===Crystal structure of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with 5~~,~~6-dihydrouridine 5'-monophosphate===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19435314}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[3g1h]] is~~ a ~~13 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=3G1H OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:019435314<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[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: Chan, K K.]]	+	[[Category: Chan, K K]]
-	[[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: Decarboxylase]]		[[Category: Decarboxylase]]
	[[Category: H2-ump]]		[[Category: H2-ump]]

OCA: Protected "3g1h" [edit=sysop:move=sysop]

OCA — Wed, 20 Feb 2013 14:31:28 GMT

Protected "3g1h" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:31, 20 February 2013

OCA at 14:31, 20 February 2013

OCA — Wed, 20 Feb 2013 14:31:23 GMT

←Older revision		Revision as of 14:31, 20 February 2013
Line 1:		Line 1:
-	~~{{Seed}}~~	+	[[Image:3g1h.png\|left\|200px]]
-	[[Image:3g1h.~~jpg~~\|left\|200px]]	+

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3g1h", creates the "Structure Box" on the page.
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-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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-	-->
	{{STRUCTURE_3g1h\| PDB=3g1h \| SCENE= }}		{{STRUCTURE_3g1h\| PDB=3g1h \| SCENE= }}

	===Crystal structure of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with 5,6-dihydrouridine 5'-monophosphate===		===Crystal structure of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with 5,6-dihydrouridine 5'-monophosphate===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19435314}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19435314 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19435314}}		{{ABSTRACT_PUBMED_19435314}}

	==About this Structure==		==About this Structure==
-	~~3G1H~~ is a 13 ~~chains~~ structure ~~of 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=3G1H OCA].	+	[[3g1h]] is a 13 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=3G1H OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19435314~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019435314</ref><references group="xtra"/>
	[[Category: Methanothermobacter thermautotrophicus str. delta h]]		[[Category: Methanothermobacter thermautotrophicus str. delta h]]
	[[Category: Orotidine-5'-phosphate decarboxylase]]		[[Category: Orotidine-5'-phosphate decarboxylase]]
Line 31:		Line 19:
	[[Category: Fedorov, E V.]]		[[Category: Fedorov, E V.]]
	[[Category: Gerlt, J A.]]		[[Category: Gerlt, J A.]]
-	[[Category: Crystal structure]]
	[[Category: Decarboxylase]]		[[Category: Decarboxylase]]
	[[Category: H2-ump]]		[[Category: H2-ump]]
Line 37:		Line 24:
	[[Category: Orotidine 5'-monophosphate decarboxylase]]		[[Category: Orotidine 5'-monophosphate decarboxylase]]
	[[Category: Pyrimidine biosynthesis]]		[[Category: Pyrimidine biosynthesis]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jun 25 09:17:55 2009''

OCA at 06:17, 25 June 2009

OCA — Thu, 25 Jun 2009 06:17:57 GMT

←Older revision		Revision as of 06:17, 25 June 2009
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3g1h.jpg\|left\|200px]]

-	The ~~entry 3g1h~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3g1h", 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_3g1h\| PDB=3g1h \| SCENE= }}

-	~~Authors: Fedorov~~, ~~A.A., Fedorov, E.V., Chan, K.K., Gerlt, J.A., Almo, S.C.~~	+	===Crystal structure of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with 5,6-dihydrouridine 5'-monophosphate===

-	Description: Crystal structure of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with 5,6-dihydrouridine 5'-monophosphate

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Mar 4 14~~:43:05 2009''	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_19435314}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 19435314 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_19435314}}
		+
		+	==About this Structure==
		+	3G1H is a 13 chains structure of 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=3G1H OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:19435314</ref><references group="xtra"/>
		+	[[Category: Methanothermobacter thermautotrophicus str. delta h]]
		+	[[Category: Orotidine-5'-phosphate decarboxylase]]
		+	[[Category: Almo, S C.]]
		+	[[Category: Chan, K K.]]
		+	[[Category: Fedorov, A A.]]
		+	[[Category: Fedorov, E V.]]
		+	[[Category: Gerlt, J A.]]
		+	[[Category: Crystal structure]]
		+	[[Category: Decarboxylase]]
		+	[[Category: H2-ump]]
		+	[[Category: Lyase]]
		+	[[Category: Orotidine 5'-monophosphate decarboxylase]]
		+	[[Category: Pyrimidine biosynthesis]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jun 25 09:17:55 2009''

OCA at 12:43, 4 March 2009

OCA — Wed, 04 Mar 2009 12:43:06 GMT

←Older revision		Revision as of 12:43, 4 March 2009
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3g1h is ON HOLD	+	The entry 3g1h is ON HOLD until Paper Publication

	Authors: Fedorov, A.A., Fedorov, E.V., Chan, K.K., Gerlt, J.A., Almo, S.C.		Authors: Fedorov, A.A., Fedorov, E.V., Chan, K.K., Gerlt, J.A., Almo, S.C.
Line 7:		Line 7:
	Description: Crystal structure of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with 5,6-dihydrouridine 5'-monophosphate		Description: Crystal structure of orotidine 5'-monophosphate decarboxylase from Methanobacterium thermoautotrophicum complexed with 5,6-dihydrouridine 5'-monophosphate

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Feb 18 08~~:54:12 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 4 14:43:05 2009''