1t0a - Revision history

OCA at 06:22, 23 August 2023

OCA — Wed, 23 Aug 2023 06:22:51 GMT

←Older revision		Revision as of 06:22, 23 August 2023
Line 3:		Line 3:
	<StructureSection load='1t0a' size='340' side='right'caption='[[1t0a]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1t0a' size='340' side='right'caption='[[1t0a]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1t0a]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Sheon Sheon~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T0A OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1T0A FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1t0a]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Shewanella_oneidensis_MR-1 Shewanella oneidensis MR-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T0A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1T0A FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>~~, ~~<scene name='pdbligand=FPP:FARNESYL+DIPHOSPHATE'>FPP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=FPP:FARNESYL+DIPHOSPHATE'>FPP</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td><~~td class~~=~~"sblockDat">IspF ([http~~:~~//www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=211586 SHEON])</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=1t0a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t0a OCA], [https://pdbe.org/1t0a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1t0a RCSB], [https://www.ebi.ac.uk/pdbsum/1t0a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1t0a ProSAT]</span></td></tr>
-	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>[http://en.wikipedia.org/wiki/2-C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.6.1.12 4.6.1.12] </~~span~~></td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1t0a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t0a OCA], [~~http~~://pdbe.org/1t0a PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1t0a RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1t0a PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1t0a ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ISPF_SHEON ISPF_SHEON]] Involved in the biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), two major building blocks of isoprenoid compounds. Catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-CPP) with a corresponding release of cytidine 5-monophosphate (CMP) (By similarity).[HAMAP-Rule:MF_00107]	+	[https://www.uniprot.org/uniprot/ISPF_SHEON ISPF_SHEON] Involved in the biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), two major building blocks of isoprenoid compounds. Catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-CPP) with a corresponding release of cytidine 5-monophosphate (CMP) (By similarity).[HAMAP-Rule:MF_00107]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Sheon~~]]	+	[[Category: Shewanella oneidensis MR-1]]
-	[[Category: Bussiere~~, D E~~]]	+	[[Category: Bussiere DE]]
-	[[Category: Kennedy~~, M A~~]]	+	[[Category: Kennedy MA]]
-	[[Category: Marsing~~, G C~~]]	+	[[Category: Marsing GC]]
-	[[Category: Ni, S]]	+	[[Category: Ni S]]
-	[[Category: Robinson, H]]	+	[[Category: Robinson H]]
-	~~[[Category: Homotrimer]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Mixed alpha beta]]~~	+
-	~~[[Category: Synthase~~]]	+

OCA at 11:38, 24 December 2020

OCA — Thu, 24 Dec 2020 11:38:02 GMT

←Older revision		Revision as of 11:38, 24 December 2020
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	==Crystal Structure of 2C-Methyl-D-Erythritol-2,4-cyclodiphosphate Synthase from Shewanella Oneidensis==		==Crystal Structure of 2C-Methyl-D-Erythritol-2,4-cyclodiphosphate Synthase from Shewanella Oneidensis==
-	<StructureSection load='1t0a' size='340' side='right' caption='[[1t0a]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='1t0a' size='340' side='right'caption='[[1t0a]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1t0a]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Sheon Sheon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T0A OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1T0A FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1t0a]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Sheon Sheon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T0A OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1T0A FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=FPP:FARNESYL+DIPHOSPHATE'>FPP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=FPP:FARNESYL+DIPHOSPHATE'>FPP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IspF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=211586 SHEON])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IspF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=211586 SHEON])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.6.1.12 4.6.1.12] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.6.1.12 4.6.1.12] </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=1t0a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t0a OCA], [http://pdbe.org/1t0a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t0a RCSB], [http://www.ebi.ac.uk/pdbsum/1t0a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1t0a ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1t0a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t0a OCA], [http://pdbe.org/1t0a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t0a RCSB], [http://www.ebi.ac.uk/pdbsum/1t0a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1t0a ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 33:		Line 33:

	==See Also==		==See Also==
-	*[[MECDP synthase\|MECDP synthase]]	+	*[[MECDP synthase 3D structures\|MECDP synthase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 39:		Line 39:
	</StructureSection>		</StructureSection>
	[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]		[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]
		+	[[Category: Large Structures]]
	[[Category: Sheon]]		[[Category: Sheon]]
	[[Category: Bussiere, D E]]		[[Category: Bussiere, D E]]

OCA at 07:39, 14 March 2018

OCA — Wed, 14 Mar 2018 07:39:11 GMT

←Older revision		Revision as of 07:39, 14 March 2018
Line 1:		Line 1:
		+
	==Crystal Structure of 2C-Methyl-D-Erythritol-2,4-cyclodiphosphate Synthase from Shewanella Oneidensis==		==Crystal Structure of 2C-Methyl-D-Erythritol-2,4-cyclodiphosphate Synthase from Shewanella Oneidensis==
	<StructureSection load='1t0a' size='340' side='right' caption='[[1t0a]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1t0a' size='340' side='right' caption='[[1t0a]], [[Resolution\|resolution]] 1.60Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IspF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=211586 SHEON])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IspF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=211586 SHEON])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.6.1.12 4.6.1.12] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.6.1.12 4.6.1.12] </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=1t0a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t0a OCA], [http://pdbe.org/1t0a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t0a RCSB], [http://www.ebi.ac.uk/pdbsum/1t0a 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=1t0a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t0a OCA], [http://pdbe.org/1t0a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t0a RCSB], [http://www.ebi.ac.uk/pdbsum/1t0a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1t0a ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/t0/1t0a_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/t0/1t0a_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 16:46, 9 February 2016

OCA — Tue, 09 Feb 2016 16:46:38 GMT

←Older revision		Revision as of 16:46, 9 February 2016
Line 19:		Line 19:
	<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=1t0a ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 00:12, 11 September 2015

OCA — Fri, 11 Sep 2015 00:12:26 GMT

←Older revision		Revision as of 00:12, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1t0a' size='340' side='right' caption='[[1t0a]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1t0a' size='340' side='right' caption='[[1t0a]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1t0a]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Shewanella_oneidensis Shewanella oneidensis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T0A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T0A FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1t0a]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Sheon Sheon]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T0A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T0A FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=FPP:FARNESYL+DIPHOSPHATE'>FPP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=FPP:FARNESYL+DIPHOSPHATE'>FPP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IspF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~70863 Shewanella oneidensis~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IspF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=211586 SHEON])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.6.1.12 4.6.1.12] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.6.1.12 4.6.1.12] </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=1t0a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t0a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1t0a RCSB], [http://www.ebi.ac.uk/pdbsum/1t0a 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=1t0a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t0a OCA], [http://pdbe.org/1t0a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1t0a RCSB], [http://www.ebi.ac.uk/pdbsum/1t0a 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 1t0a" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 37:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]		[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]
-	[[Category: ~~Shewanella oneidensis~~]]	+	[[Category: Sheon]]
	[[Category: Bussiere, D E]]		[[Category: Bussiere, D E]]
	[[Category: Kennedy, M A]]		[[Category: Kennedy, M A]]

OCA at 08:09, 25 December 2014

OCA — Thu, 25 Dec 2014 08:09:56 GMT

←Older revision		Revision as of 08:09, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1t0a]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Shewanella_oneidensis Shewanella oneidensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T0A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T0A FirstGlance]. <br>		<table><tr><td colspan='2'>[[1t0a]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Shewanella_oneidensis Shewanella oneidensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T0A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T0A FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=FPP:FARNESYL+DIPHOSPHATE'>FPP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=FPP:FARNESYL+DIPHOSPHATE'>FPP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IspF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70863 Shewanella oneidensis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IspF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70863 Shewanella oneidensis])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.6.1.12 4.6.1.12] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.6.1.12 4.6.1.12] </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=1t0a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t0a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1t0a RCSB], [http://www.ebi.ac.uk/pdbsum/1t0a 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=1t0a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t0a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1t0a RCSB], [http://www.ebi.ac.uk/pdbsum/1t0a PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ISPF_SHEON ISPF_SHEON]] Involved in the biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), two major building blocks of isoprenoid compounds. Catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate (CDP-ME2P) to 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-CPP) with a corresponding release of cytidine 5-monophosphate (CMP) (By similarity).[HAMAP-Rule:MF_00107]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 38:
	[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]		[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]
	[[Category: Shewanella oneidensis]]		[[Category: Shewanella oneidensis]]
-	[[Category: Bussiere, D E.]]	+	[[Category: Bussiere, D E]]
-	[[Category: Kennedy, M A.]]	+	[[Category: Kennedy, M A]]
-	[[Category: Marsing, G C.]]	+	[[Category: Marsing, G C]]
-	[[Category: Ni, S.]]	+	[[Category: Ni, S]]
-	[[Category: Robinson, H.]]	+	[[Category: Robinson, H]]
	[[Category: Homotrimer]]		[[Category: Homotrimer]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Mixed alpha beta]]		[[Category: Mixed alpha beta]]
	[[Category: Synthase]]		[[Category: Synthase]]

OCA at 15:01, 29 September 2014

OCA — Mon, 29 Sep 2014 15:01:51 GMT

←Older revision		Revision as of 15:01, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1t0a.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure of 2C-Methyl-D-Erythritol-2,4-cyclodiphosphate Synthase from Shewanella Oneidensis==
		+	<StructureSection load='1t0a' size='340' side='right' caption='[[1t0a]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1t0a]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Shewanella_oneidensis Shewanella oneidensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T0A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1T0A FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=FPP:FARNESYL+DIPHOSPHATE'>FPP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IspF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70863 Shewanella oneidensis])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-C-methyl-D-erythritol_2,4-cyclodiphosphate_synthase 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.6.1.12 4.6.1.12] </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=1t0a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1t0a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1t0a RCSB], [http://www.ebi.ac.uk/pdbsum/1t0a 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/t0/1t0a_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 ==
		+	Isopentenyl pyrophosphate (IPP) is a universal building block for the ubiquitous isoprenoids that are essential to all organisms. The enzymes of the non-mevalonate pathway for IPP synthesis, which is unique to many pathogenic bacteria, have recently been explored as targets for antibiotic development. Several crystal structures of 2C-methyl-D-erythritol-2,4-cyclophosphate (MECDP) synthase, the fifth of seven enzymes involved in the non-mevalonate pathway for synthesis of IPP, have been reported; however, the composition of metal ions in the active site and the presence of a hydrophobic cavity along the non-crystallographic threefold symmetry axis has varied between the reported structures. Here, the structure of MEDCP from Shewanella oneidensis MR1 (SO3437) was determined to 1.6 A resolution in the absence of substrate. The presence of a zinc ion in the active-site cleft, tetrahedrally coordinated by two histidine side chains, an aspartic acid side chain and an ambiguous fourth ligand, was confirmed by zinc anomalous diffraction. Based on analysis of anomalous diffraction data and typical metal-to-ligand bond lengths, it was concluded that an octahedral sodium ion was 3.94 A from the zinc ion. A hydrophobic cavity was observed along the threefold non-crystallographic symmetry axis, filled by a well defined non-protein electron density that could be modeled as farnesyl pyrophosphate (FPP), a downstream product of IPP, suggesting a possible feedback mechanism for enzyme regulation. The high-resolution data clarified the FPP-binding mode compared with previously reported structures. Multiple sequence alignment indicated that the residues critical to the formation of the hydrophobic cavity and for coordinating the pyrophosphate group of FPP are present in the majority of MEDCP synthase enzymes, supporting the idea of a specialized biological function related to FPP binding in a subfamily of MEDCP synthase homologs.

-	~~{{STRUCTURE_1t0a\| PDB=1t0a \| SCENE= }}~~	+	Structure of 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase from Shewanella oneidensis at 1.6 A: identification of farnesyl pyrophosphate trapped in a hydrophobic cavity.,Ni S, Robinson H, Marsing GC, Bussiere DE, Kennedy MA Acta Crystallogr D Biol Crystallogr. 2004 Nov;60(Pt 11):1949-57. Epub 2004, Oct 20. PMID:15502301<ref>PMID:15502301</ref>

-	~~===Crystal Structure of 2C-Methyl-D-Erythritol-2~~,~~4-cyclodiphosphate Synthase from Shewanella Oneidensis===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15502301}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1t0a]] is~~ a ~~3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Shewanella_oneidensis Shewanella oneidensis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1T0A OCA].~~	+

	==See Also==		==See Also==
	*[[MECDP synthase\|MECDP synthase]]		*[[MECDP synthase\|MECDP synthase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:015502301<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]		[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]
	[[Category: Shewanella oneidensis]]		[[Category: Shewanella oneidensis]]

OCA: Protected "1t0a" [edit=sysop:move=sysop]

OCA — Sat, 05 Jan 2013 12:37:03 GMT

Protected "1t0a" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:37, 5 January 2013

OCA at 12:36, 5 January 2013

OCA — Sat, 05 Jan 2013 12:36:57 GMT

←Older revision		Revision as of 12:36, 5 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1t0a.png\|left\|200px]]		[[Image:1t0a.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1t0a", 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.
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	{{STRUCTURE_1t0a\| PDB=1t0a \| SCENE= }}		{{STRUCTURE_1t0a\| PDB=1t0a \| SCENE= }}

	===Crystal Structure of 2C-Methyl-D-Erythritol-2,4-cyclodiphosphate Synthase from Shewanella Oneidensis===		===Crystal Structure of 2C-Methyl-D-Erythritol-2,4-cyclodiphosphate Synthase from Shewanella Oneidensis===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15502301}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15502301 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_15502301}}		{{ABSTRACT_PUBMED_15502301}}

	==About this Structure==		==About this Structure==
-	~~1T0A~~ is a 3 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/~~Bacteria Bacteria~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T0A OCA].	+	[[1t0a]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Shewanella_oneidensis Shewanella oneidensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T0A OCA].
		+
		+	==See Also==
		+	*[[MECDP synthase\|MECDP synthase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15502301~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015502301</ref><references group="xtra"/>
	[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]		[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]
-	[[Category: ~~Bacteria~~]]	+	[[Category: Shewanella oneidensis]]
	[[Category: Bussiere, D E.]]		[[Category: Bussiere, D E.]]
	[[Category: Kennedy, M A.]]		[[Category: Kennedy, M A.]]
Line 32:		Line 23:
	[[Category: Robinson, H.]]		[[Category: Robinson, H.]]
	[[Category: Homotrimer]]		[[Category: Homotrimer]]
		+	[[Category: Lyase]]
	[[Category: Mixed alpha beta]]		[[Category: Mixed alpha beta]]
	[[Category: Synthase]]		[[Category: Synthase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 11:17:25 2009''

OCA at 09:17, 17 February 2009

OCA — Tue, 17 Feb 2009 09:17:26 GMT

←Older revision		Revision as of 09:17, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1T0A is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Bacteria Bacteria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T0A OCA].	+	1T0A is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Bacteria Bacteria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1T0A OCA].

	==Reference==		==Reference==
-	Structure of 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase from Shewanella oneidensis at 1.6 A: identification of farnesyl pyrophosphate trapped in a hydrophobic cavity., Ni S, Robinson H, Marsing GC, Bussiere DE, Kennedy MA, Acta Crystallogr D Biol Crystallogr. 2004 Nov;60(Pt 11):1949-57. Epub 2004, Oct 20. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/15502301 15502301]~~	+	<ref group="xtra">PMID:15502301</ref><references group="xtra"/>
	[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]		[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]
	[[Category: Bacteria]]		[[Category: Bacteria]]
-	[[Category: Single protein]]
	[[Category: Bussiere, D E.]]		[[Category: Bussiere, D E.]]
	[[Category: Kennedy, M A.]]		[[Category: Kennedy, M A.]]
Line 36:		Line 35:
	[[Category: Synthase]]		[[Category: Synthase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 15~~:21:~~02 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 11:17:25 2009''