3ern - Revision history

OCA at 15:22, 1 November 2023

OCA — Wed, 01 Nov 2023 15:22:59 GMT

←Older revision		Revision as of 15:22, 1 November 2023
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	<StructureSection load='3ern' size='340' side='right'caption='[[3ern]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3ern' size='340' side='right'caption='[[3ern]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ern]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ERN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ERN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ern]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ERN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ERN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CAR:CYTOSINE+ARABINOSE-5-PHOSPHATE'>CAR</scene>, <scene name='pdbligand=GPP:GERANYL+DIPHOSPHATE'>GPP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.1Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ispF ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CAR:CYTOSINE+ARABINOSE-5-PHOSPHATE'>CAR</scene>, <scene name='pdbligand=GPP:GERANYL+DIPHOSPHATE'>GPP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://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 [https://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'>[https://proteopedia.org/fgij/fg.htm?mol=3ern FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ern OCA], [https://pdbe.org/3ern PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ern RCSB], [https://www.ebi.ac.uk/pdbsum/3ern PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ern ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ern FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ern OCA], [https://pdbe.org/3ern PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ern RCSB], [https://www.ebi.ac.uk/pdbsum/3ern PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ern ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[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>	+	[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: 2-~~C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]~~	+	[[Category: Escherichia coli K-12]]
-	~~[[Category: Ecoli~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hunter~~, W N~~]]	+	[[Category: Hunter WN]]
-	[[Category: Kemp~~, L A~~]]	+	[[Category: Kemp LA]]
-	[[Category: Ramsden~~, N L]]~~	+	[[Category: Ramsden NL]]
-	~~[[Category: Isoprene biosynthesis]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Magnesium]]~~	+
-	~~[[Category: Manganese]]~~	+
-	~~[[Category: Mecdp-synthase]]~~	+
-	~~[[Category: Metal-binding~~]]	+

OCA at 09:14, 23 February 2022

OCA — Wed, 23 Feb 2022 09:14:28 GMT

←Older revision		Revision as of 09:14, 23 February 2022
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	==Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase complexed with AraCMP==		==Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase complexed with AraCMP==
-	<StructureSection load='3ern' size='340' side='right' caption='[[3ern]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='3ern' size='340' side='right'caption='[[3ern]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ern]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ERN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3ERN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ern]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ERN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ERN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAR:CYTOSINE+ARABINOSE-5-PHOSPHATE'>CAR</scene>, <scene name='pdbligand=GPP:GERANYL+DIPHOSPHATE'>GPP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=CAR:CYTOSINE+ARABINOSE-5-PHOSPHATE'>CAR</scene>, <scene name='pdbligand=GPP:GERANYL+DIPHOSPHATE'>GPP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=83333 ECOLI])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ispF ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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'>[https://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 [https://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=3ern FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ern OCA], [~~http~~://pdbe.org/3ern PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3ern RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3ern PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3ern ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ern FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ern OCA], [https://pdbe.org/3ern PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ern RCSB], [https://www.ebi.ac.uk/pdbsum/3ern PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ern 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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	==See Also==		==See Also==
-	*[[MECDP synthase\|MECDP synthase]]	+	*[[MECDP synthase 3D structures\|MECDP synthase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 39:		Line 39:
	[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]		[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]
	[[Category: Ecoli]]		[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: Hunter, W N]]		[[Category: Hunter, W N]]
	[[Category: Kemp, L A]]		[[Category: Kemp, L A]]

OCA at 21:23, 2 December 2018

OCA — Sun, 02 Dec 2018 21:23:10 GMT

←Older revision		Revision as of 21:23, 2 December 2018
Line 1:		Line 1:
		+
	==Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase complexed with AraCMP==		==Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase complexed with AraCMP==
	<StructureSection load='3ern' size='340' side='right' caption='[[3ern]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3ern' size='340' side='right' caption='[[3ern]], [[Resolution\|resolution]] 2.10Å' scene=''>
Line 6:		Line 7:
	<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=83333 ECOLI])</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=83333 ECOLI])</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=3ern FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ern OCA], [http://pdbe.org/3ern PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ern RCSB], [http://www.ebi.ac.uk/pdbsum/3ern 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=3ern FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ern OCA], [http://pdbe.org/3ern PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ern RCSB], [http://www.ebi.ac.uk/pdbsum/3ern PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ern ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/er/3ern_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/er/3ern_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 08:11, 7 February 2016

OCA — Sun, 07 Feb 2016 08:11:07 GMT

←Older revision		Revision as of 08:11, 7 February 2016
Line 2:		Line 2:
	<StructureSection load='3ern' size='340' side='right' caption='[[3ern]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3ern' size='340' side='right' caption='[[3ern]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ern]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli_k-12 Escherichia coli k-12~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ERN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ERN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ern]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ERN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ERN FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAR:CYTOSINE+ARABINOSE-5-PHOSPHATE'>CAR</scene>, <scene name='pdbligand=GPP:GERANYL+DIPHOSPHATE'>GPP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=CAR:CYTOSINE+ARABINOSE-5-PHOSPHATE'>CAR</scene>, <scene name='pdbligand=GPP:GERANYL+DIPHOSPHATE'>GPP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=83333 ~~Escherichia coli K-12~~])</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=83333 ECOLI])</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=3ern FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ern OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ern RCSB], [http://www.ebi.ac.uk/pdbsum/3ern 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=3ern FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ern OCA], [http://pdbe.org/3ern PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ern RCSB], [http://www.ebi.ac.uk/pdbsum/3ern PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 18:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3ern ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 3ern" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]		[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]
-	[[Category: ~~Escherichia coli k-12~~]]	+	[[Category: Ecoli]]
	[[Category: Hunter, W N]]		[[Category: Hunter, W N]]
	[[Category: Kemp, L A]]		[[Category: Kemp, L A]]

OCA at 13:34, 24 December 2014

OCA — Wed, 24 Dec 2014 13:34:50 GMT

←Older revision		Revision as of 13:34, 24 December 2014
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	<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=3ern FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ern OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ern RCSB], [http://www.ebi.ac.uk/pdbsum/3ern 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=3ern FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ern OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ern RCSB], [http://www.ebi.ac.uk/pdbsum/3ern 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]]

OCA at 08:36, 26 November 2014

OCA — Wed, 26 Nov 2014 08:36:42 GMT

←Older revision		Revision as of 08:36, 26 November 2014
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-	[[~~Image:~~3ern.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase complexed with AraCMP==
		+	<StructureSection load='3ern' size='340' side='right' caption='[[3ern]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3ern]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ERN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ERN FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAR:CYTOSINE+ARABINOSE-5-PHOSPHATE'>CAR</scene>, <scene name='pdbligand=GPP:GERANYL+DIPHOSPHATE'>GPP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=83333 Escherichia coli K-12])</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=3ern FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ern OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ern RCSB], [http://www.ebi.ac.uk/pdbsum/3ern 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/er/3ern_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The nonmevalonate route to isoprenoid biosynthesis is essential in Gram-negative bacteria and apicomplexan parasites. The enzymes of this pathway are absent from mammals, contributing to their appeal as chemotherapeutic targets. One enzyme, 2C-methyl-d-erythritol-2,4-cyclodiphosphate synthase (IspF), has been validated as a target by genetic approaches in bacteria. Virtual screening against Escherichia coli IspF (EcIspF) was performed by combining a hierarchical filtering methodology with molecular docking. Docked compounds were inspected and 10 selected for experimental validation. A surface plasmon resonance assay was developed and two weak ligands identified. Crystal structures of EcIspF complexes were determined to support rational ligand development. Cytosine analogues and Zn(2+)-binding moieties were characterized. One of the putative Zn(2+)-binding compounds gave the lowest measured K(D) to date (1.92 +/- 0.18 muM). These data provide a framework for the development of IspF inhibitors to generate lead compounds of therapeutic potential against microbial pathogens.

-	~~{{STRUCTURE_3ern\| PDB=3ern \| SCENE= }}~~	+	A structure-based approach to ligand discovery for 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase: a target for antimicrobial therapy.,Ramsden NL, Buetow L, Dawson A, Kemp LA, Ulaganathan V, Brenk R, Klebe G, Hunter WN J Med Chem. 2009 Apr 23;52(8):2531-42. PMID:19320487<ref>PMID:19320487</ref>

-	~~===Crystal structure of 2C-methyl-D-erythritol 2~~,~~4-clycodiphosphate synthase complexed with AraCMP===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19320487}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3ern]] is~~ a ~~6 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=3ERN OCA].~~	+

	==See Also==		==See Also==
	*[[MECDP synthase\|MECDP synthase]]		*[[MECDP synthase\|MECDP synthase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:019320487<~~/~~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 k-12]]		[[Category: Escherichia coli k-12]]
-	[[Category: Hunter, W N.]]	+	[[Category: Hunter, W N]]
-	[[Category: Kemp, L A.]]	+	[[Category: Kemp, L A]]
-	[[Category: Ramsden, N L.]]	+	[[Category: Ramsden, N L]]
	[[Category: Isoprene biosynthesis]]		[[Category: Isoprene biosynthesis]]
	[[Category: Lyase]]		[[Category: Lyase]]

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

OCA — Wed, 06 Feb 2013 13:19:44 GMT

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

←Older revision

Revision as of 13:19, 6 February 2013

OCA at 13:19, 6 February 2013

OCA — Wed, 06 Feb 2013 13:19:42 GMT

←Older revision		Revision as of 13:19, 6 February 2013
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-	{{Seed}}
	[[Image:3ern.png\|left\|200px]]		[[Image:3ern.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3ern", 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_3ern\| PDB=3ern \| SCENE= }}		{{STRUCTURE_3ern\| PDB=3ern \| SCENE= }}

	===Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase complexed with AraCMP===		===Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase complexed with AraCMP===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19320487}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19320487 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_19320487}}		{{ABSTRACT_PUBMED_19320487}}

	==About this Structure==		==About this Structure==
-	~~3ERN~~ is a 6 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ERN OCA].	+	[[3ern]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ERN OCA].
		+
		+	==See Also==
		+	*[[MECDP synthase\|MECDP synthase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19320487~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019320487</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 k-12]]		[[Category: Escherichia coli k-12]]
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	[[Category: Mecdp-synthase]]		[[Category: Mecdp-synthase]]
	[[Category: Metal-binding]]		[[Category: Metal-binding]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Sep 21 19:23:53 2009''

OCA at 16:23, 21 September 2009

OCA — Mon, 21 Sep 2009 16:23:55 GMT

←Older revision		Revision as of 16:23, 21 September 2009
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	===Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase complexed with AraCMP===		===Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase complexed with AraCMP===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_19320487}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 19320487 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_19320487}}

	==About this Structure==		==About this Structure==
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	[[Category: Metal-binding]]		[[Category: Metal-binding]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Sep 21 16:46:48 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Sep 21 19:23:53 2009''

OCA at 13:46, 21 September 2009

OCA — Mon, 21 Sep 2009 13:46:49 GMT

←Older revision		Revision as of 13:46, 21 September 2009
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-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3ern.png\|left\|200px]]

-	The ~~entry 3ern~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3ern", 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_3ern\| PDB=3ern \| SCENE= }}

-	~~Authors: Hunter~~, ~~W.N., Ramsden, N.L., Buetow, L., Dawson, A., Kemp, L.A., Ulaganathan, V., Brenk, R., Klebe, G.~~	+	===Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase complexed with AraCMP===

-	Description: Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase complexed with AraCMP

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Oct 29 10~~:28:~~44 2008~~''	+	==About this Structure==
		+	3ERN is a 6 chains structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli_k-12 Escherichia coli k-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ERN OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:19320487</ref><references group="xtra"/>
		+	[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]
		+	[[Category: Escherichia coli k-12]]
		+	[[Category: Hunter, W N.]]
		+	[[Category: Kemp, L A.]]
		+	[[Category: Ramsden, N L.]]
		+	[[Category: Isoprene biosynthesis]]
		+	[[Category: Lyase]]
		+	[[Category: Magnesium]]
		+	[[Category: Manganese]]
		+	[[Category: Mecdp-synthase]]
		+	[[Category: Metal-binding]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Sep 21 16:46:48 2009''