1km1 - Revision history

OCA at 07:25, 14 February 2024

OCA — Wed, 14 Feb 2024 07:25:59 GMT

←Older revision		Revision as of 07:25, 14 February 2024
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	<StructureSection load='1km1' size='340' side='right'caption='[[1km1]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1km1' size='340' side='right'caption='[[1km1]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1km1]] is a 2 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=1KM1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KM1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1km1]] is a 2 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=1KM1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KM1 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=UP6:~~6~~-AZA+URIDINE+5-MONOPHOSPHATE'>UP6</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;'>[[1kly\|1kly]], [[1klz\|1klz]], [[1km0\|1km0]], [[1km2\|1km2]], [[1km3\|1km3]], [[1km4\|1km4]], [[1km5\|1km5]], [[1km6\|1km6]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=UP6:6-AZA+URIDINE+5-MONOPHOSPHATE'>UP6</scene></td></tr>
-	~~<tr~~ id~~='activity'><td class~~="~~sblockLbl~~"><~~b>Activity:</b></td><td class~~=~~"sblockDat"><span class~~=~~'plainlinks'>[https~~:~~//en.wikipedia.org/wiki/Orotidine~~-5'-~~phosphate_decarboxylase Orotidine-5~~'~~-phosphate decarboxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.23 4.1.1.23]~~ </~~span~~></td></tr>	+
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1km1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1km1 OCA], [https://pdbe.org/1km1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1km1 RCSB], [https://www.ebi.ac.uk/pdbsum/1km1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1km1 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=1km1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1km1 OCA], [https://pdbe.org/1km1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1km1 RCSB], [https://www.ebi.ac.uk/pdbsum/1km1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1km1 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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	</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=1km1 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=1km1 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The crystal structures of orotidine 5'-monophosphate decarboxylases from four different sources have been published recently. However, the detailed mechanism of catalysis of the most proficient enzyme known to date remains elusive. As the ligand-protein interactions at the orotate binding site are crucial to the understanding of this enzyme, we mutated several of the residues surrounding the aromatic part of the substrate, individually and in combination. The ensuing effects on enzyme structure and stability were characterized by X-ray crystallography of inhibitor, product, or substrate complexes and by chemical denaturation with guanidine hydrochloride, respectively. The results are consistent with the residues K42D70K72D75B being charged and forming an 'alternate charge network' around the reactive part of the substrate. In addition to exerting charge-charge repulsion on the orotate carboxylate, Asp70 also makes a crucial contribution to enzyme stability. Consequently, orotidine 5'-monophosphate decarboxylases seem to require the presence of a negative charge at this position for catalysis as well as for correct and stable folding.
-
-	Mapping the active site-ligand interactions of orotidine 5'-monophosphate decarboxylase by crystallography.,Wu N, Gillon W, Pai EF Biochemistry. 2002 Mar 26;41(12):4002-11. PMID:11900543<ref>PMID:11900543</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1km1" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Uridine 5'-monophosphate synthase 3D structures\|Uridine 5'-monophosphate synthase 3D structures]]		*[[Uridine 5'-monophosphate synthase 3D structures\|Uridine 5'-monophosphate synthase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Orotidine-5'-phosphate decarboxylase~~]]	+	[[Category: Methanothermobacter thermautotrophicus]]
-	[[Category: Gillon, W]]	+	[[Category: Gillon W]]
-	[[Category: Pai~~, E F~~]]	+	[[Category: Pai EF]]
-	[[Category: Wu, N]]	+	[[Category: Wu N]]
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Tim barrel~~]]	+

OCA at 06:33, 18 August 2021

OCA — Wed, 18 Aug 2021 06:33:10 GMT

←Older revision		Revision as of 06:33, 18 August 2021
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	<StructureSection load='1km1' size='340' side='right'caption='[[1km1]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1km1' size='340' side='right'caption='[[1km1]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1km1]] is a 2 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=1KM1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1KM1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1km1]] is a 2 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=1KM1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KM1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=UP6:6-AZA+URIDINE+5-MONOPHOSPHATE'>UP6</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=UP6:6-AZA+URIDINE+5-MONOPHOSPHATE'>UP6</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kly\|1kly]], [[1klz\|1klz]], [[1km0\|1km0]], [[1km2\|1km2]], [[1km3\|1km3]], [[1km4\|1km4]], [[1km5\|1km5]], [[1km6\|1km6]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1kly\|1kly]], [[1klz\|1klz]], [[1km0\|1km0]], [[1km2\|1km2]], [[1km3\|1km3]], [[1km4\|1km4]], [[1km5\|1km5]], [[1km6\|1km6]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Orotidine-5'-phosphate_decarboxylase Orotidine-5'-phosphate decarboxylase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.23 4.1.1.23] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Orotidine-5'-phosphate_decarboxylase Orotidine-5'-phosphate decarboxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.23 4.1.1.23] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1km1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1km1 OCA], [~~http~~://pdbe.org/1km1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1km1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1km1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1km1 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=1km1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1km1 OCA], [https://pdbe.org/1km1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1km1 RCSB], [https://www.ebi.ac.uk/pdbsum/1km1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1km1 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 32:		Line 32:

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

OCA at 09:07, 6 November 2019

OCA — Wed, 06 Nov 2019 09:07:37 GMT

←Older revision		Revision as of 09:07, 6 November 2019
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	==Orotidine monophosphate decarboxylase mutant S127A crystal structure==		==Orotidine monophosphate decarboxylase mutant S127A crystal structure==
-	<StructureSection load='1km1' size='340' side='right' caption='[[1km1]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='1km1' size='340' side='right'caption='[[1km1]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1km1]] is a 2 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=1KM1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KM1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1km1]] is a 2 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=1KM1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KM1 FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 1km1" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1km1" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Uridine 5'-monophosphate synthase\|Uridine 5'-monophosphate synthase]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Orotidine-5'-phosphate decarboxylase]]		[[Category: Orotidine-5'-phosphate decarboxylase]]
	[[Category: Gillon, W]]		[[Category: Gillon, W]]

OCA at 21:17, 24 January 2018

OCA — Wed, 24 Jan 2018 21:17:51 GMT

←Older revision		Revision as of 21:17, 24 January 2018
Line 1:		Line 1:
		+
	==Orotidine monophosphate decarboxylase mutant S127A crystal structure==		==Orotidine monophosphate decarboxylase mutant S127A crystal structure==
	<StructureSection load='1km1' size='340' side='right' caption='[[1km1]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1km1' size='340' side='right' caption='[[1km1]], [[Resolution\|resolution]] 1.60Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kly\|1kly]], [[1klz\|1klz]], [[1km0\|1km0]], [[1km2\|1km2]], [[1km3\|1km3]], [[1km4\|1km4]], [[1km5\|1km5]], [[1km6\|1km6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kly\|1kly]], [[1klz\|1klz]], [[1km0\|1km0]], [[1km2\|1km2]], [[1km3\|1km3]], [[1km4\|1km4]], [[1km5\|1km5]], [[1km6\|1km6]]</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=1km1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1km1 OCA], [http://pdbe.org/1km1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1km1 RCSB], [http://www.ebi.ac.uk/pdbsum/1km1 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=1km1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1km1 OCA], [http://pdbe.org/1km1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1km1 RCSB], [http://www.ebi.ac.uk/pdbsum/1km1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1km1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/km/1km1_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/km/1km1_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 04:01, 9 February 2016

OCA — Tue, 09 Feb 2016 04:01:04 GMT

←Older revision		Revision as of 04:01, 9 February 2016
Line 18:		Line 18:
	<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=1km1 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 18:25, 10 September 2015

OCA — Thu, 10 Sep 2015 18:25:38 GMT

←Older revision		Revision as of 18:25, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1km1' size='340' side='right' caption='[[1km1]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1km1' size='340' side='right' caption='[[1km1]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1km1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KM1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KM1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1km1]] is a 2 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=1KM1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KM1 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=UP6:6-AZA+URIDINE+5-MONOPHOSPHATE'>UP6</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=UP6:6-AZA+URIDINE+5-MONOPHOSPHATE'>UP6</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kly\|1kly]], [[1klz\|1klz]], [[1km0\|1km0]], [[1km2\|1km2]], [[1km3\|1km3]], [[1km4\|1km4]], [[1km5\|1km5]], [[1km6\|1km6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kly\|1kly]], [[1klz\|1klz]], [[1km0\|1km0]], [[1km2\|1km2]], [[1km3\|1km3]], [[1km4\|1km4]], [[1km5\|1km5]], [[1km6\|1km6]]</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=1km1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1km1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1km1 RCSB], [http://www.ebi.ac.uk/pdbsum/1km1 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=1km1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1km1 OCA], [http://pdbe.org/1km1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1km1 RCSB], [http://www.ebi.ac.uk/pdbsum/1km1 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 1km1" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Methanothermobacter thermautotrophicus]]
	[[Category: Orotidine-5'-phosphate decarboxylase]]		[[Category: Orotidine-5'-phosphate decarboxylase]]
	[[Category: Gillon, W]]		[[Category: Gillon, W]]

OCA at 04:17, 25 December 2014

OCA — Thu, 25 Dec 2014 04:17:12 GMT

←Older revision		Revision as of 04:17, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1km1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KM1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KM1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1km1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KM1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KM1 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=UP6:6-AZA+URIDINE+5-MONOPHOSPHATE'>UP6</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=UP6:6-AZA+URIDINE+5-MONOPHOSPHATE'>UP6</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kly\|1kly]], [[1klz\|1klz]], [[1km0\|1km0]], [[1km2\|1km2]], [[1km3\|1km3]], [[1km4\|1km4]], [[1km5\|1km5]], [[1km6\|1km6]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kly\|1kly]], [[1klz\|1klz]], [[1km0\|1km0]], [[1km2\|1km2]], [[1km3\|1km3]], [[1km4\|1km4]], [[1km5\|1km5]], [[1km6\|1km6]]</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=1km1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1km1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1km1 RCSB], [http://www.ebi.ac.uk/pdbsum/1km1 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=1km1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1km1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1km1 RCSB], [http://www.ebi.ac.uk/pdbsum/1km1 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]]
Line 32:		Line 34:
	[[Category: Methanothermobacter thermautotrophicus]]		[[Category: Methanothermobacter thermautotrophicus]]
	[[Category: Orotidine-5'-phosphate decarboxylase]]		[[Category: Orotidine-5'-phosphate decarboxylase]]
-	[[Category: Gillon, W.]]	+	[[Category: Gillon, W]]
-	[[Category: Pai, E F.]]	+	[[Category: Pai, E F]]
-	[[Category: Wu, N.]]	+	[[Category: Wu, N]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Tim barrel]]		[[Category: Tim barrel]]

OCA at 10:53, 28 September 2014

OCA — Sun, 28 Sep 2014 10:53:59 GMT

←Older revision		Revision as of 10:53, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1km1.~~png~~\|~~left~~\|200px]]	+	==Orotidine monophosphate decarboxylase mutant S127A crystal structure==
		+	<StructureSection load='1km1' size='340' side='right' caption='[[1km1]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1km1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KM1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KM1 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=UP6:6-AZA+URIDINE+5-MONOPHOSPHATE'>UP6</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1kly\|1kly]], [[1klz\|1klz]], [[1km0\|1km0]], [[1km2\|1km2]], [[1km3\|1km3]], [[1km4\|1km4]], [[1km5\|1km5]], [[1km6\|1km6]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Orotidine-5'-phosphate_decarboxylase Orotidine-5'-phosphate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.23 4.1.1.23] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1km1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1km1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1km1 RCSB], [http://www.ebi.ac.uk/pdbsum/1km1 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/km/1km1_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 crystal structures of orotidine 5'-monophosphate decarboxylases from four different sources have been published recently. However, the detailed mechanism of catalysis of the most proficient enzyme known to date remains elusive. As the ligand-protein interactions at the orotate binding site are crucial to the understanding of this enzyme, we mutated several of the residues surrounding the aromatic part of the substrate, individually and in combination. The ensuing effects on enzyme structure and stability were characterized by X-ray crystallography of inhibitor, product, or substrate complexes and by chemical denaturation with guanidine hydrochloride, respectively. The results are consistent with the residues K42D70K72D75B being charged and forming an 'alternate charge network' around the reactive part of the substrate. In addition to exerting charge-charge repulsion on the orotate carboxylate, Asp70 also makes a crucial contribution to enzyme stability. Consequently, orotidine 5'-monophosphate decarboxylases seem to require the presence of a negative charge at this position for catalysis as well as for correct and stable folding.

-	~~{{STRUCTURE_1km1\| PDB=1km1 \| SCENE= }}~~	+	Mapping the active site-ligand interactions of orotidine 5'-monophosphate decarboxylase by crystallography.,Wu N, Gillon W, Pai EF Biochemistry. 2002 Mar 26;41(12):4002-11. PMID:11900543<ref>PMID:11900543</ref>

-	~~===Orotidine monophosphate decarboxylase mutant S127A crystal structure===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_11900543}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1km1]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1KM1 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:011900543<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Methanothermobacter thermautotrophicus]]		[[Category: Methanothermobacter thermautotrophicus]]
	[[Category: Orotidine-5'-phosphate decarboxylase]]		[[Category: Orotidine-5'-phosphate decarboxylase]]

OCA: Protected "1km1" [edit=sysop:move=sysop]

OCA — Wed, 05 Dec 2012 20:41:26 GMT

Protected "1km1" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:41, 5 December 2012

OCA at 20:41, 5 December 2012

OCA — Wed, 05 Dec 2012 20:41:24 GMT

←Older revision		Revision as of 20:41, 5 December 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1km1.png\|left\|200px]]		[[Image:1km1.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1km1", 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_1km1\| PDB=1km1 \| SCENE= }}		{{STRUCTURE_1km1\| PDB=1km1 \| SCENE= }}

	===Orotidine monophosphate decarboxylase mutant S127A crystal structure===		===Orotidine monophosphate decarboxylase mutant S127A crystal structure===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_11900543}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 11900543 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_11900543}}		{{ABSTRACT_PUBMED_11900543}}

	==About this Structure==		==About this Structure==
-	~~1KM1~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KM1 OCA].	+	[[1km1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Methanothermobacter_thermautotrophicus Methanothermobacter thermautotrophicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KM1 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~11900543~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:011900543</ref><references group="xtra"/>
	[[Category: Methanothermobacter thermautotrophicus]]		[[Category: Methanothermobacter thermautotrophicus]]
	[[Category: Orotidine-5'-phosphate decarboxylase]]		[[Category: Orotidine-5'-phosphate decarboxylase]]
Line 29:		Line 17:
	[[Category: Pai, E F.]]		[[Category: Pai, E F.]]
	[[Category: Wu, N.]]		[[Category: Wu, N.]]
		+	[[Category: Lyase]]
	[[Category: Tim barrel]]		[[Category: Tim barrel]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 06:18:30 2009''