1u40 - Revision history

OCA at 06:37, 23 August 2023

OCA — Wed, 23 Aug 2023 06:37:50 GMT

←Older revision		Revision as of 06:37, 23 August 2023
Line 3:		Line 3:
	<StructureSection load='1u40' size='340' side='right'caption='[[1u40]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1u40' size='340' side='right'caption='[[1u40]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1u40]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U40 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1U40 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1u40]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U40 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1U40 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CDM:4~~-~~DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL'>CDM</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]] 2.8Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[1u3p\|1u3p]], [[1u3l\|1u3l]], [[1jy8\|1jy8]], [[1u43\|1u43]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CDM:4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL'>CDM</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=~~562~~ "~~Bacillus coli~~" ~~Migula 1895])</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=1u40 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u40 OCA], [https://pdbe.org/1u40 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1u40 RCSB], [https://www.ebi.ac.uk/pdbsum/1u40 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1u40 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=1u40 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u40 OCA], [~~http~~://pdbe.org/1u40 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1u40 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1u40 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1u40 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ISPF_ECOLI ISPF_ECOLI]] 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). Also converts 4-diphosphocytidyl-2-C-methyl-D-erythritol into 2-C-methyl-D-erythritol 3,4-cyclophosphate and CMP.<ref>PMID:10694574</ref> <ref>PMID:22839733</ref>	+	[https://www.uniprot.org/uniprot/ISPF_ECOLI ISPF_ECOLI] 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). Also converts 4-diphosphocytidyl-2-C-methyl-D-erythritol into 2-C-methyl-D-erythritol 3,4-cyclophosphate and CMP.<ref>PMID:10694574</ref> <ref>PMID:22839733</ref>
	== 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: ~~Bacillus~~ coli ~~migula 1895]]~~	+	[[Category: Escherichia coli]]
-	~~[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bacher, A]]	+	[[Category: Bacher A]]
-	[[Category: Eisenreich, W]]	+	[[Category: Eisenreich W]]
-	[[Category: Gerhardt, S]]	+	[[Category: Gerhardt S]]
-	[[Category: Hecht, S]]	+	[[Category: Hecht S]]
-	[[Category: Kaiser, J]]	+	[[Category: Kaiser J]]
-	[[Category: Rohdich, F]]	+	[[Category: Rohdich F]]
-	[[Category: Steinbacher, S]]	+	[[Category: Steinbacher S]]
-	[[Category: Wungsintaweekul, J]]	+	[[Category: Wungsintaweekul J]]
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Mep pathway]]~~	+
-	~~[[Category: Terpene biosynthesis~~]]	+

OCA at 07:20, 30 December 2020

OCA — Wed, 30 Dec 2020 07:20:32 GMT

←Older revision		Revision as of 07:20, 30 December 2020
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	==IspF with 4-diphosphocytidyl-2C-methyl-D-erythritol==		==IspF with 4-diphosphocytidyl-2C-methyl-D-erythritol==
-	<StructureSection load='1u40' size='340' side='right' caption='[[1u40]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='1u40' size='340' side='right'caption='[[1u40]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1u40]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U40 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1U40 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1u40]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U40 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1U40 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CDM:4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL'>CDM</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=CDM:4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL'>CDM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1u3p\|1u3p]], [[1u3l\|1u3l]], [[1jy8\|1jy8]], [[1u43\|1u43]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1u3p\|1u3p]], [[1u3l\|1u3l]], [[1jy8\|1jy8]], [[1u43\|1u43]]</div></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=562 "Bacillus coli" Migula 1895])</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=562 "Bacillus coli" Migula 1895])</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=1u40 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u40 OCA], [http://pdbe.org/1u40 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1u40 RCSB], [http://www.ebi.ac.uk/pdbsum/1u40 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1u40 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=1u40 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u40 OCA], [http://pdbe.org/1u40 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1u40 RCSB], [http://www.ebi.ac.uk/pdbsum/1u40 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1u40 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 40:		Line 40:
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
	[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]		[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]
		+	[[Category: Large Structures]]
	[[Category: Bacher, A]]		[[Category: Bacher, A]]
	[[Category: Eisenreich, W]]		[[Category: Eisenreich, W]]

OCA at 08:22, 21 March 2018

OCA — Wed, 21 Mar 2018 08:22:48 GMT

←Older revision		Revision as of 08:22, 21 March 2018
Line 1:		Line 1:
		+
	==IspF with 4-diphosphocytidyl-2C-methyl-D-erythritol==		==IspF with 4-diphosphocytidyl-2C-methyl-D-erythritol==
	<StructureSection load='1u40' size='340' side='right' caption='[[1u40]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1u40' size='340' side='right' caption='[[1u40]], [[Resolution\|resolution]] 2.80Å' 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=562 "Bacillus coli" Migula 1895])</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=562 "Bacillus coli" Migula 1895])</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=1u40 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u40 OCA], [http://pdbe.org/1u40 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1u40 RCSB], [http://www.ebi.ac.uk/pdbsum/1u40 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=1u40 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u40 OCA], [http://pdbe.org/1u40 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1u40 RCSB], [http://www.ebi.ac.uk/pdbsum/1u40 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1u40 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/u4/1u40_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/u4/1u40_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>
	</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=1u40 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 09:39, 11 September 2015

OCA — Fri, 11 Sep 2015 09:39:57 GMT

←Older revision		Revision as of 09:39, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1u40' size='340' side='right' caption='[[1u40]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1u40' size='340' side='right' caption='[[1u40]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1u40]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U40 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U40 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1u40]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U40 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U40 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CDM:4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL'>CDM</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=CDM:4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL'>CDM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1u3p\|1u3p]], [[1u3l\|1u3l]], [[1jy8\|1jy8]], [[1u43\|1u43]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1u3p\|1u3p]], [[1u3l\|1u3l]], [[1jy8\|1jy8]], [[1u43\|1u43]]</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=562 ~~Escherichia~~ coli])</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=562 "Bacillus coli" Migula 1895])</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=1u40 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u40 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1u40 RCSB], [http://www.ebi.ac.uk/pdbsum/1u40 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=1u40 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u40 OCA], [http://pdbe.org/1u40 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1u40 RCSB], [http://www.ebi.ac.uk/pdbsum/1u40 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 1u40" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
	[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]		[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]
-	[[Category: Escherichia coli]]
	[[Category: Bacher, A]]		[[Category: Bacher, A]]
	[[Category: Eisenreich, W]]		[[Category: Eisenreich, W]]

OCA at 14:37, 25 December 2014

OCA — Thu, 25 Dec 2014 14:37:51 GMT

←Older revision		Revision as of 14:37, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1u40]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U40 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U40 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1u40]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U40 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U40 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CDM:4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL'>CDM</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=CDM:4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL'>CDM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1u3p\|1u3p]], [[1u3l\|1u3l]], [[1jy8\|1jy8]], [[1u43\|1u43]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1u3p\|1u3p]], [[1u3l\|1u3l]], [[1jy8\|1jy8]], [[1u43\|1u43]]</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=562 Escherichia coli])</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=562 Escherichia coli])</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=1u40 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u40 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1u40 RCSB], [http://www.ebi.ac.uk/pdbsum/1u40 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=1u40 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u40 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1u40 RCSB], [http://www.ebi.ac.uk/pdbsum/1u40 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ISPF_ECOLI ISPF_ECOLI]] 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). Also converts 4-diphosphocytidyl-2-C-methyl-D-erythritol into 2-C-methyl-D-erythritol 3,4-cyclophosphate and CMP.<ref>PMID:10694574</ref> <ref>PMID:22839733</ref>
	== 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: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Bacher, A.]]	+	[[Category: Bacher, A]]
-	[[Category: Eisenreich, W.]]	+	[[Category: Eisenreich, W]]
-	[[Category: Gerhardt, S.]]	+	[[Category: Gerhardt, S]]
-	[[Category: Hecht, S.]]	+	[[Category: Hecht, S]]
-	[[Category: Kaiser, J.]]	+	[[Category: Kaiser, J]]
-	[[Category: Rohdich, F.]]	+	[[Category: Rohdich, F]]
-	[[Category: Steinbacher, S.]]	+	[[Category: Steinbacher, S]]
-	[[Category: Wungsintaweekul, J.]]	+	[[Category: Wungsintaweekul, J]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Mep pathway]]		[[Category: Mep pathway]]
	[[Category: Terpene biosynthesis]]		[[Category: Terpene biosynthesis]]

OCA at 21:43, 29 September 2014

OCA — Mon, 29 Sep 2014 21:43:01 GMT

←Older revision		Revision as of 21:43, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1u40.~~png~~\|~~left~~\|200px]]	+	==IspF with 4-diphosphocytidyl-2C-methyl-D-erythritol==
		+	<StructureSection load='1u40' size='340' side='right' caption='[[1u40]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1u40]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U40 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1U40 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CDM:4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL'>CDM</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1u3p\|1u3p]], [[1u3l\|1u3l]], [[1jy8\|1jy8]], [[1u43\|1u43]]</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=562 Escherichia coli])</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=1u40 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1u40 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1u40 RCSB], [http://www.ebi.ac.uk/pdbsum/1u40 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/u4/1u40_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 ==
		+	Isoprenoids are biosynthesized from isopentenyl diphosphate and the isomeric dimethylallyl diphosphate via the mevalonate pathway or a mevalonate-independent pathway that was identified during the last decade. The non-mevalonate pathway is present in many bacteria, some algae and in certain protozoa such as the malaria parasite Plasmodium falciparum and in the plastids of higher plants, but not in mammals and archaea. Therefore, these enzymes have been recognised as promising drug targets. We report the crystal structure of Escherichia coli 2C- methyl-d-erythritol-2,4-cyclodiphosphate synthase (IspF), which converts 4-diphosphocytidyl-2C-methyl-d-erythritol 2-phosphate into 2C-methyl-d-erythritol 2,4-cyclodiphosphate and CMP in a Mg-dependent reaction. The protein forms homotrimers that tightly bind one zinc ion per subunit at the active site, which helps to position the substrate for direct attack of the 2-phosphate group on the beta-phosphate.

-	~~{{STRUCTURE_1u40\| PDB=1u40 \| SCENE= }}~~	+	Structure of 2C-methyl-d-erythritol-2,4-cyclodiphosphate synthase involved in mevalonate-independent biosynthesis of isoprenoids.,Steinbacher S, Kaiser J, Wungsintaweekul J, Hecht S, Eisenreich W, Gerhardt S, Bacher A, Rohdich F J Mol Biol. 2002 Feb 8;316(1):79-88. PMID:11829504<ref>PMID:11829504</ref>

-	~~===IspF with 4-diphosphocytidyl-2C-methyl-D-erythritol===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_11829504}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1u40]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli Escherichia coli]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1U40 OCA].~~	+

	==See Also==		==See Also==
	*[[MECDP synthase\|MECDP synthase]]		*[[MECDP synthase\|MECDP synthase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:011829504<~~/~~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: Escherichia coli]]		[[Category: Escherichia coli]]

OCA: Protected "1u40" [edit=sysop:move=sysop]

OCA — Sat, 05 Jan 2013 13:08:38 GMT

Protected "1u40" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:08, 5 January 2013

OCA at 13:08, 5 January 2013

OCA — Sat, 05 Jan 2013 13:08:36 GMT

←Older revision		Revision as of 13:08, 5 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1u40.png\|left\|200px]]		[[Image:1u40.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1u40", 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_1u40\| PDB=1u40 \| SCENE= }}		{{STRUCTURE_1u40\| PDB=1u40 \| SCENE= }}

	===IspF with 4-diphosphocytidyl-2C-methyl-D-erythritol===		===IspF with 4-diphosphocytidyl-2C-methyl-D-erythritol===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_11829504}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 11829504 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_11829504}}		{{ABSTRACT_PUBMED_11829504}}

	==About this Structure==		==About this Structure==
-	~~1U40~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U40 OCA].	+	[[1u40]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U40 OCA].
		+
		+	==See Also==
		+	*[[MECDP synthase\|MECDP synthase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~11829504~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:011829504</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: Escherichia coli]]		[[Category: Escherichia coli]]
Line 37:		Line 28:
	[[Category: Mep pathway]]		[[Category: Mep pathway]]
	[[Category: Terpene biosynthesis]]		[[Category: Terpene biosynthesis]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 18:53:52 2009''

OCA at 16:53, 17 February 2009

OCA — Tue, 17 Feb 2009 16:53:54 GMT

←Older revision		Revision as of 16:53, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1U40 is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U40 OCA].	+	1U40 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1U40 OCA].

	==Reference==		==Reference==
-	Structure of 2C-methyl-d-erythritol-2,4-cyclodiphosphate synthase involved in mevalonate-independent biosynthesis of isoprenoids., Steinbacher S, Kaiser J, Wungsintaweekul J, Hecht S, Eisenreich W, Gerhardt S, Bacher A, Rohdich F, J Mol Biol. 2002 Feb 8;316(1):79-88. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/11829504 11829504]~~	+	<ref group="xtra">PMID:11829504</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: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Single protein]]
	[[Category: Bacher, A.]]		[[Category: Bacher, A.]]
	[[Category: Eisenreich, W.]]		[[Category: Eisenreich, W.]]
Line 39:		Line 38:
	[[Category: Terpene biosynthesis]]		[[Category: Terpene biosynthesis]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue ~~Jul 29 02~~:57:~~56 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 18:53:52 2009''

OCA at 23:58, 28 July 2008

OCA — Mon, 28 Jul 2008 23:58:06 GMT

←Older revision		Revision as of 23:58, 28 July 2008
Line 1:		Line 1:
-	[[Image:1u40.~~gif~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:1u40.png\|left\|200px]]

	<!--		<!--
Line 9:		Line 10:
	{{STRUCTURE_1u40\| PDB=1u40 \| SCENE= }}		{{STRUCTURE_1u40\| PDB=1u40 \| SCENE= }}

-	~~'''~~IspF with 4-diphosphocytidyl-2C-methyl-D-erythritol~~'''~~	+	===IspF with 4-diphosphocytidyl-2C-methyl-D-erythritol===


-	~~==Overview==~~	+	<!--
-	Isoprenoids are biosynthesized from isopentenyl diphosphate and the isomeric dimethylallyl diphosphate via the mevalonate pathway or a mevalonate-independent pathway that was identified during the last decade. The ~~non-mevalonate pathway is present in many bacteria~~, ~~some algae and in certain protozoa such as~~ the ~~malaria parasite Plasmodium falciparum and in~~ the ~~plastids of higher plants, but not in mammals and archaea. Therefore, these enzymes have been recognised~~ as ~~promising drug targets~~. ~~We report the crystal structure of Escherichia coli 2C- methyl-d-erythritol-2,4-cyclodiphosphate synthase (IspF~~), ~~which converts 4-diphosphocytidyl-2C-methyl-d-erythritol 2-phosphate into 2C-methyl-d-erythritol 2,4-cyclodiphosphate and CMP in a Mg-dependent reaction~~. ~~The protein forms homotrimers that tightly bind one zinc ion per subunit at the active site, which helps to position the substrate for direct attack of the 2~~-~~phosphate group on the beta~~-~~phosphate.~~	+	The line below this paragraph, {{ABSTRACT_PUBMED_11829504}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 11829504 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_11829504}}

	==About this Structure==		==About this Structure==
Line 34:		Line 38:
	[[Category: Mep pathway]]		[[Category: Mep pathway]]
	[[Category: Terpene biosynthesis]]		[[Category: Terpene biosynthesis]]
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sat May 3 10~~:44:13 2008''	+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 02:57:56 2008''