2e6y - Revision history

OCA at 11:08, 11 September 2015

OCA — Fri, 11 Sep 2015 11:08:24 GMT

←Older revision		Revision as of 11:08, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2e6y' size='340' side='right' caption='[[2e6y]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='2e6y' size='340' side='right' caption='[[2e6y]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2e6y]] 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=2E6Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E6Y FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2e6y]] 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=2E6Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E6Y FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=U5P:URIDINE-5-MONOPHOSPHATE'>U5P</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=U5P:URIDINE-5-MONOPHOSPHATE'>U5P</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dv7\|1dv7]], [[1dvj\|1dvj]], [[1kly\|1kly]], [[1klz\|1klz]], [[1km0\|1km0]], [[1km1\|1km1]], [[1km2\|1km2]], [[1km3\|1km3]], [[1km4\|1km4]], [[1km5\|1km5]], [[1km6\|1km6]], [[1lol\|1lol]], [[1loq\|1loq]], [[1lor\|1lor]], [[1los\|1los]], [[1lp6\|1lp6]], [[1x1z\|1x1z]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dv7\|1dv7]], [[1dvj\|1dvj]], [[1kly\|1kly]], [[1klz\|1klz]], [[1km0\|1km0]], [[1km1\|1km1]], [[1km2\|1km2]], [[1km3\|1km3]], [[1km4\|1km4]], [[1km5\|1km5]], [[1km6\|1km6]], [[1lol\|1lol]], [[1loq\|1loq]], [[1lor\|1lor]], [[1los\|1los]], [[1lp6\|1lp6]], [[1x1z\|1x1z]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pyrF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=145262 ~~Methanothermobacter thermautotrophicus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pyrF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=145262 "Methanobacterium thermoautotrophicus" (sic) Zeikus and Wolfe 1972])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Orotidine-5'-phosphate_decarboxylase Orotidine-5'-phosphate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.23 4.1.1.23] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Orotidine-5'-phosphate_decarboxylase Orotidine-5'-phosphate decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.23 4.1.1.23] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2e6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e6y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2e6y RCSB], [http://www.ebi.ac.uk/pdbsum/2e6y 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=2e6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e6y OCA], [http://pdbe.org/2e6y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2e6y RCSB], [http://www.ebi.ac.uk/pdbsum/2e6y PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 29:		Line 29:
	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 2e6y" 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: Bello, A M]]		[[Category: Bello, A M]]

OCA at 15:38, 25 December 2014

OCA — Thu, 25 Dec 2014 15:38:06 GMT

←Older revision		Revision as of 15:38, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2e6y]] 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=2E6Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E6Y FirstGlance]. <br>		<table><tr><td colspan='2'>[[2e6y]] 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=2E6Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E6Y FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=U5P:URIDINE-5-MONOPHOSPHATE'>U5P</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=U5P:URIDINE-5-MONOPHOSPHATE'>U5P</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dv7\|1dv7]], [[1dvj\|1dvj]], [[1kly\|1kly]], [[1klz\|1klz]], [[1km0\|1km0]], [[1km1\|1km1]], [[1km2\|1km2]], [[1km3\|1km3]], [[1km4\|1km4]], [[1km5\|1km5]], [[1km6\|1km6]], [[1lol\|1lol]], [[1loq\|1loq]], [[1lor\|1lor]], [[1los\|1los]], [[1lp6\|1lp6]], [[1x1z\|1x1z]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dv7\|1dv7]], [[1dvj\|1dvj]], [[1kly\|1kly]], [[1klz\|1klz]], [[1km0\|1km0]], [[1km1\|1km1]], [[1km2\|1km2]], [[1km3\|1km3]], [[1km4\|1km4]], [[1km5\|1km5]], [[1km6\|1km6]], [[1lol\|1lol]], [[1loq\|1loq]], [[1lor\|1lor]], [[1los\|1los]], [[1lp6\|1lp6]], [[1x1z\|1x1z]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pyrF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=145262 Methanothermobacter thermautotrophicus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pyrF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=145262 Methanothermobacter thermautotrophicus])</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=2e6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e6y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2e6y RCSB], [http://www.ebi.ac.uk/pdbsum/2e6y 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=2e6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e6y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2e6y RCSB], [http://www.ebi.ac.uk/pdbsum/2e6y 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 33:		Line 35:
	[[Category: Methanothermobacter thermautotrophicus]]		[[Category: Methanothermobacter thermautotrophicus]]
	[[Category: Orotidine-5'-phosphate decarboxylase]]		[[Category: Orotidine-5'-phosphate decarboxylase]]
-	[[Category: Bello, A M.]]	+	[[Category: Bello, A M]]
-	[[Category: Fujihashi, M.]]	+	[[Category: Fujihashi, M]]
-	[[Category: Kotra, L P.]]	+	[[Category: Kotra, L P]]
-	[[Category: Pai, E F.]]	+	[[Category: Pai, E F]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Tim-barrel]]		[[Category: Tim-barrel]]

OCA at 00:39, 30 September 2014

OCA — Tue, 30 Sep 2014 00:39:34 GMT

←Older revision		Revision as of 00:39, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2e6y.~~png~~\|~~left~~\|200px]]	+	==Covalent complex of orotidine 5'-monophosphate decarboxylase (ODCase) with 6-Iodo-UMP==
		+	<StructureSection load='2e6y' size='340' side='right' caption='[[2e6y]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2e6y]] 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=2E6Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2E6Y FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=U5P:URIDINE-5-MONOPHOSPHATE'>U5P</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dv7\|1dv7]], [[1dvj\|1dvj]], [[1kly\|1kly]], [[1klz\|1klz]], [[1km0\|1km0]], [[1km1\|1km1]], [[1km2\|1km2]], [[1km3\|1km3]], [[1km4\|1km4]], [[1km5\|1km5]], [[1km6\|1km6]], [[1lol\|1lol]], [[1loq\|1loq]], [[1lor\|1lor]], [[1los\|1los]], [[1lp6\|1lp6]], [[1x1z\|1x1z]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pyrF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=145262 Methanothermobacter thermautotrophicus])</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=2e6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e6y OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2e6y RCSB], [http://www.ebi.ac.uk/pdbsum/2e6y 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/e6/2e6y_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Orotidine 5'-monophosphate decarboxylase (ODCase) has evolved to catalyze the decarboxylation of orotidine 5'-monophosphate without any covalent intermediates. Active site residues in ODCase are involved in an extensive hydrogen-bonding network. We discovered that 6-iodouridine 5'-monophosphate (6-iodo-UMP) irreversibly inhibits the catalytic activities of ODCases from Methanobacterium thermoautotrophicum and Plasmodium falciparum. Mass spectral analysis of the enzyme-inhibitor complex confirms covalent attachment of the inhibitor to ODCase accompanied by the loss of two protons and the iodo moiety. The X-ray crystal structure (1.6 A resolution) of the complex of the inhibitor and ODCase clearly shows the covalent bond formation with the active site Lys-72 [corrected] residue. 6-Iodo-UMP inhibits ODCase in a time- and concentration-dependent fashion. 6-Iodouridine, the nucleoside form of 6-iodo-UMP, exhibited potent antiplasmodial activity, with IC50s of 4.4 +/- 1.3 microM and 6.2 +/- 0.7 microM against P. falciparum ItG and 3D7 isolates, respectively. 6-Iodouridine 5'-monophosphate is a novel covalent inhibitor of ODCase, and its nucleoside analogue paves the way to a new class of inhibitors against malaria.

-	~~{{STRUCTURE_2e6y\| PDB=2e6y \| SCENE= }}~~	+	A potent, covalent inhibitor of orotidine 5'-monophosphate decarboxylase with antimalarial activity.,Bello AM, Poduch E, Fujihashi M, Amani M, Li Y, Crandall I, Hui R, Lee PI, Kain KC, Pai EF, Kotra LP J Med Chem. 2007 Mar 8;50(5):915-21. Epub 2007 Feb 10. PMID:17290979<ref>PMID:17290979</ref>

-	~~===Covalent complex~~ of ~~orotidine 5'-monophosphate decarboxylase (ODCase) with 6-Iodo-UMP===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17290979}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2e6y]] 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=2E6Y OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017290979<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Methanothermobacter thermautotrophicus]]		[[Category: Methanothermobacter thermautotrophicus]]
	[[Category: Orotidine-5'-phosphate decarboxylase]]		[[Category: Orotidine-5'-phosphate decarboxylase]]

OCA: Protected "2e6y" [edit=sysop:move=sysop]

OCA — Sun, 06 Jan 2013 10:01:13 GMT

Protected "2e6y" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:01, 6 January 2013

OCA at 10:01, 6 January 2013

OCA — Sun, 06 Jan 2013 10:01:11 GMT

←Older revision		Revision as of 10:01, 6 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2e6y.png\|left\|200px]]		[[Image:2e6y.png\|left\|200px]]

-	<!--
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	{{STRUCTURE_2e6y\| PDB=2e6y \| SCENE= }}		{{STRUCTURE_2e6y\| PDB=2e6y \| SCENE= }}

	===Covalent complex of orotidine 5'-monophosphate decarboxylase (ODCase) with 6-Iodo-UMP===		===Covalent complex of orotidine 5'-monophosphate decarboxylase (ODCase) with 6-Iodo-UMP===

-
-	<!--
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	{{ABSTRACT_PUBMED_17290979}}		{{ABSTRACT_PUBMED_17290979}}

	==About this Structure==		==About this Structure==
-	~~2E6Y~~ 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=2E6Y OCA].	+	[[2e6y]] 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=2E6Y OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17290979~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017290979</ref><references group="xtra"/>
	[[Category: Methanothermobacter thermautotrophicus]]		[[Category: Methanothermobacter thermautotrophicus]]
	[[Category: Orotidine-5'-phosphate decarboxylase]]		[[Category: Orotidine-5'-phosphate decarboxylase]]
Line 30:		Line 18:
	[[Category: Kotra, L P.]]		[[Category: Kotra, L P.]]
	[[Category: Pai, E F.]]		[[Category: Pai, E F.]]
		+	[[Category: Lyase]]
	[[Category: Tim-barrel]]		[[Category: Tim-barrel]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 20:39:01 2009''

OCA at 18:39, 17 February 2009

OCA — Tue, 17 Feb 2009 18:39:02 GMT

←Older revision		Revision as of 18:39, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2E6Y is a ~~[[Single protein]]~~ structure of ~~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=2E6Y OCA].	+	2E6Y 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=2E6Y OCA].

	==Reference==		==Reference==
-	A potent, covalent inhibitor of orotidine 5'-monophosphate decarboxylase with antimalarial activity., Bello AM, Poduch E, Fujihashi M, Amani M, Li Y, Crandall I, Hui R, Lee PI, Kain KC, Pai EF, Kotra LP, J Med Chem. 2007 Mar 8;50(5):915-21. Epub 2007 Feb 10. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17290979 17290979]~~	+	<ref group="xtra">PMID:17290979</ref><references group="xtra"/>
	[[Category: Methanothermobacter thermautotrophicus]]		[[Category: Methanothermobacter thermautotrophicus]]
	[[Category: Orotidine-5'-phosphate decarboxylase]]		[[Category: Orotidine-5'-phosphate decarboxylase]]
-	[[Category: Single protein]]
	[[Category: Bello, A M.]]		[[Category: Bello, A M.]]
	[[Category: Fujihashi, M.]]		[[Category: Fujihashi, M.]]
Line 33:		Line 32:
	[[Category: Tim-barrel]]		[[Category: Tim-barrel]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 29 04~~:33:~~59 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 20:39:01 2009''

OCA at 01:34, 29 July 2008

OCA — Tue, 29 Jul 2008 01:34:01 GMT

←Older revision		Revision as of 01:34, 29 July 2008
Line 1:		Line 1:
-	[[Image:2e6y.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:2e6y.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_2e6y\| PDB=2e6y \| SCENE= }}		{{STRUCTURE_2e6y\| PDB=2e6y \| SCENE= }}

-	~~'''~~Covalent complex of orotidine 5'-monophosphate decarboxylase (ODCase) with 6-Iodo-UMP~~'''~~	+	===Covalent complex of orotidine 5'-monophosphate decarboxylase (ODCase) with 6-Iodo-UMP===


-	~~==Overview==~~	+	<!--
-	~~Orotidine 5'~~-~~monophosphate decarboxylase (ODCase) has evolved to catalyze the decarboxylation of orotidine 5'~~-monophosphate without any covalent intermediates. Active site residues in ODCase are involved in an extensive hydrogen-bonding network. We discovered that 6-iodouridine 5'-monophosphate (6-iodo-UMP) irreversibly inhibits the catalytic activities of ODCases from Methanobacterium thermoautotrophicum and Plasmodium falciparum. Mass spectral analysis of the enzyme-inhibitor complex confirms covalent attachment of the ~~inhibitor~~ to ~~ODCase accompanied by~~ the ~~loss of two protons and the iodo moiety. The X-ray crystal structure~~ (1.6 A resolution) of the complex of the inhibitor and ODCase clearly shows the covalent bond formation with the active site Lys-72 [corrected] residue. 6-Iodo-UMP inhibits ODCase in a time- and concentration-dependent fashion. 6-Iodouridine, the nucleoside form of 6-iodo-UMP, exhibited potent antiplasmodial activity, with IC50s of 4.4 +/~~- 1.3 microM and 6.2 +~~/~~- 0~~.~~7 microM against P~~. ~~falciparum ItG and 3D7 isolates~~, ~~respectively~~. 6-~~Iodouridine 5'~~-~~monophosphate is a novel covalent inhibitor of ODCase, and its nucleoside analogue paves the way to a new class of inhibitors against malaria.~~	+	The line below this paragraph, {{ABSTRACT_PUBMED_17290979}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 17290979 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_17290979}}

	==About this Structure==		==About this Structure==
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	[[Category: Pai, E F.]]		[[Category: Pai, E F.]]
	[[Category: Tim-barrel]]		[[Category: Tim-barrel]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 02~~:02:42 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 04:33:59 2008''

OCA at 23:02, 3 May 2008

OCA — Sat, 03 May 2008 23:02:43 GMT

←Older revision		Revision as of 23:02, 3 May 2008
Line 1:		Line 1:
	[[Image:2e6y.gif\|left\|200px]]		[[Image:2e6y.gif\|left\|200px]]

-	~~{{Structure~~	+	<!--
-	~~\|PDB= 2e6y \|SIZE=350\|CAPTION=~~ <~~scene name='initialview01'>2e6y</scene>, resolution 1.60Å~~	+	The line below this paragraph, containing "STRUCTURE_2e6y", creates the "Structure Box" on the page.
-	~~\|SITE=~~	+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	~~\|LIGAND= <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=U5P:URIDINE~~-~~5'~~-~~MONOPHOSPHATE'>U5P</scene>~~	+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	~~\|ACTIVITY= <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>~~	+	or leave the SCENE parameter empty for the default display.
-	~~\|GENE= pyrF~~ (~~[http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=145262 Methanothermobacter thermautotrophicus]~~)	+	-->
-	~~\|DOMAIN=~~	+	{{STRUCTURE_2e6y\| PDB=2e6y \| SCENE= }}
-	~~\|RELATEDENTRY=[[1dv7\|1dv7]]~~, [[1dvj\|1dvj]], [[1kly\|1kly]], [[1klz\|1klz]], [[1km0\|1km0]], [[1km1\|1km1]], [[1km2\|1km2]], [[1km3\|1km3]], [[1km4\|1km4]], [[1km5\|1km5]], [[1km6\|1km6]], [[1lol\|1lol]], [[1loq\|1loq]], [[1lor\|1lor]], [[1los\|1los]], [[1lp6\|1lp6]], [[1x1z\|1x1z]]	+
-	~~\|RESOURCES=<span class='plainlinks'>[http://oca~~.~~weizmann.ac.il/oca~~-~~docs/fgij/fg.htm?mol=2e6y FirstGlance], [http://oca.weizmann.ac.il/oca~~-~~bin/ocaids?id~~=2e6y ~~OCA], [http://www.ebi.ac.uk/pdbsum/2e6y PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId~~=~~2e6y RCSB]</span>~~	+
-	}}	+

	'''Covalent complex of orotidine 5'-monophosphate decarboxylase (ODCase) with 6-Iodo-UMP'''		'''Covalent complex of orotidine 5'-monophosphate decarboxylase (ODCase) with 6-Iodo-UMP'''
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	[[Category: Kotra, L P.]]		[[Category: Kotra, L P.]]
	[[Category: Pai, E F.]]		[[Category: Pai, E F.]]
-	[[Category: ~~tim~~-barrel]]	+	[[Category: Tim-barrel]]
-		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 02:02:42 2008''
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Mar 31~~ 02:44:36 2008''	+

OCA at 23:44, 30 March 2008

OCA — Sun, 30 Mar 2008 23:44:37 GMT

←Older revision		Revision as of 23:44, 30 March 2008
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	\|PDB= 2e6y \|SIZE=350\|CAPTION= <scene name='initialview01'>2e6y</scene>, resolution 1.60Å		\|PDB= 2e6y \|SIZE=350\|CAPTION= <scene name='initialview01'>2e6y</scene>, resolution 1.60Å
	\|SITE=		\|SITE=
-	\|LIGAND= <scene name='pdbligand=~~U5P~~:~~URIDINE-5'-MONOPHOSPHATE~~'>~~U5P~~</scene> ~~and~~ <scene name='pdbligand=~~GOL~~:~~GLYCEROL~~'>~~GOL~~</scene>	+	\|LIGAND= <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=U5P:URIDINE-5'-MONOPHOSPHATE'>U5P</scene>
-	\|ACTIVITY= [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]	+	\|ACTIVITY= <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>
	\|GENE= pyrF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=145262 Methanothermobacter thermautotrophicus])		\|GENE= pyrF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=145262 Methanothermobacter thermautotrophicus])
		+	\|DOMAIN=
		+	\|RELATEDENTRY=[[1dv7\|1dv7]], [[1dvj\|1dvj]], [[1kly\|1kly]], [[1klz\|1klz]], [[1km0\|1km0]], [[1km1\|1km1]], [[1km2\|1km2]], [[1km3\|1km3]], [[1km4\|1km4]], [[1km5\|1km5]], [[1km6\|1km6]], [[1lol\|1lol]], [[1loq\|1loq]], [[1lor\|1lor]], [[1los\|1los]], [[1lp6\|1lp6]], [[1x1z\|1x1z]]
		+	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2e6y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e6y OCA], [http://www.ebi.ac.uk/pdbsum/2e6y PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2e6y RCSB]</span>
	}}		}}

Line 27:		Line 30:
	[[Category: Kotra, L P.]]		[[Category: Kotra, L P.]]
	[[Category: Pai, E F.]]		[[Category: Pai, E F.]]
-	[[Category: GOL]]
-	[[Category: U5P]]
	[[Category: tim-barrel]]		[[Category: tim-barrel]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun~~ Mar ~~23 14~~:59:30 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:44:36 2008''

OCA at 12:59, 23 March 2008

OCA — Sun, 23 Mar 2008 12:59:30 GMT

←Older revision		Revision as of 12:59, 23 March 2008
Line 4:		Line 4:
	\|PDB= 2e6y \|SIZE=350\|CAPTION= <scene name='initialview01'>2e6y</scene>, resolution 1.60Å		\|PDB= 2e6y \|SIZE=350\|CAPTION= <scene name='initialview01'>2e6y</scene>, resolution 1.60Å
	\|SITE=		\|SITE=
-	\|LIGAND= <scene name='pdbligand=U5P:URIDINE-5'-MONOPHOSPHATE'>U5P</scene> and <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>	+	\|LIGAND= <scene name='pdbligand=U5P:URIDINE-5'-MONOPHOSPHATE'>U5P</scene> and <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>
	\|ACTIVITY= [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]		\|ACTIVITY= [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]
	\|GENE= pyrF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=145262 Methanothermobacter thermautotrophicus])		\|GENE= pyrF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=145262 Methanothermobacter thermautotrophicus])
Line 31:		Line 31:
	[[Category: tim-barrel]]		[[Category: tim-barrel]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu~~ Mar ~~20 16~~:36:06 2008''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 23 14:59:30 2008''