1iv4 - Revision history

OCA at 23:37, 27 December 2023

2023-12-27T23:37:26Z

←Older revision		Revision as of 23:37, 27 December 2023
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	<StructureSection load='1iv4' size='340' side='right'caption='[[1iv4]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='1iv4' size='340' side='right'caption='[[1iv4]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1iv4]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IV4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IV4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1iv4]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IV4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IV4 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=C5P:CYTIDINE~~-~~5-MONOPHOSPHATE'>C5P</scene>~~, ~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.55Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[1iv1\|1iv1]], [[1iv2\|1iv2]], [[1iv3\|1iv3]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C5P:CYTIDINE-5-MONOPHOSPHATE'>C5P</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=1iv4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iv4 OCA], [https://pdbe.org/1iv4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1iv4 RCSB], [https://www.ebi.ac.uk/pdbsum/1iv4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1iv4 ProSAT], [https://www.topsan.org/Proteins/RSGI/1iv4 TOPSAN]</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=1iv4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iv4 OCA], [https://pdbe.org/1iv4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1iv4 RCSB], [https://www.ebi.ac.uk/pdbsum/1iv4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1iv4 ProSAT], [https://www.topsan.org/Proteins/RSGI/1iv4 TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/ISPF_THET8 ISPF_THET8]] 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).<ref>PMID:12499535</ref>	+	[https://www.uniprot.org/uniprot/ISPF_THET8 ISPF_THET8] 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).<ref>PMID:12499535</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: Flavobacterium thermophilum yoshida and oshima 1971]]
-	[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kishida, H]]	+	[[Category: Thermus thermophilus]]
-	[[Category: Kuzuyama, T]]	+	[[Category: Kishida H]]
-	[[Category: Park, S Y]]	+	[[Category: Kuzuyama T]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Park S-Y]]
-	[[Category: Sirouzu, M]]	+	[[Category: Sirouzu M]]
-	[[Category: Tame~~, J R.H~~]]	+	[[Category: Tame JRH]]
-	[[Category: Terada, T]]	+	[[Category: Terada T]]
-	[[Category: Unzai, S]]	+	[[Category: Unzai S]]
-	[[Category: Wada, T]]	+	[[Category: Wada T]]
-	[[Category: Yokoyama, S]]	+	[[Category: Yokoyama S]]
-	~~[[Category: Isoprenoid]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Non-mevalonate]]~~	+
-	~~[[Category: Rsgi]]~~	+
-	~~[[Category: Synthase~~]]	+

OCA at 07:14, 14 April 2021

2021-04-14T07:14:15Z

←Older revision		Revision as of 07:14, 14 April 2021
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	<StructureSection load='1iv4' size='340' side='right'caption='[[1iv4]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='1iv4' size='340' side='right'caption='[[1iv4]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1iv4]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IV4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1IV4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1iv4]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IV4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IV4 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C5P:CYTIDINE-5-MONOPHOSPHATE'>C5P</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C5P:CYTIDINE-5-MONOPHOSPHATE'>C5P</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iv1\|1iv1]], [[1iv2\|1iv2]], [[1iv3\|1iv3]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1iv1\|1iv1]], [[1iv2\|1iv2]], [[1iv3\|1iv3]]</div></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=1iv4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iv4 OCA], [~~http~~://pdbe.org/1iv4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1iv4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1iv4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1iv4 ProSAT], [~~http~~://www.topsan.org/Proteins/RSGI/1iv4 TOPSAN]</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=1iv4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iv4 OCA], [https://pdbe.org/1iv4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1iv4 RCSB], [https://www.ebi.ac.uk/pdbsum/1iv4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1iv4 ProSAT], [https://www.topsan.org/Proteins/RSGI/1iv4 TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/ISPF_THET8 ISPF_THET8]] 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).<ref>PMID:12499535</ref>	+	[[https://www.uniprot.org/uniprot/ISPF_THET8 ISPF_THET8]] 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).<ref>PMID:12499535</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/>

OCA at 07:03, 10 July 2019

2019-07-10T07:03:11Z

←Older revision		Revision as of 07:03, 10 July 2019
Line 1:		Line 1:

	==Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase (bound form Substrate)==		==Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase (bound form Substrate)==
-	<StructureSection load='1iv4' size='340' side='right' caption='[[1iv4]], [[Resolution\|resolution]] 1.55Å' scene=''>	+	<StructureSection load='1iv4' size='340' side='right'caption='[[1iv4]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1iv4]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IV4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IV4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1iv4]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IV4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IV4 FirstGlance]. <br>
Line 15:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iv/1iv4_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iv/1iv4_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>
Line 39:		Line 39:
	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]		[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]		[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]
		+	[[Category: Large Structures]]
	[[Category: Kishida, H]]		[[Category: Kishida, H]]
	[[Category: Kuzuyama, T]]		[[Category: Kuzuyama, T]]

OCA at 09:54, 4 October 2017

2017-10-04T09:54:33Z

←Older revision		Revision as of 09:54, 4 October 2017
Line 1:		Line 1:
		+
	==Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase (bound form Substrate)==		==Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase (bound form Substrate)==
	<StructureSection load='1iv4' size='340' side='right' caption='[[1iv4]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='1iv4' size='340' side='right' caption='[[1iv4]], [[Resolution\|resolution]] 1.55Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iv1\|1iv1]], [[1iv2\|1iv2]], [[1iv3\|1iv3]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iv1\|1iv1]], [[1iv2\|1iv2]], [[1iv3\|1iv3]]</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=1iv4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iv4 OCA], [http://pdbe.org/1iv4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1iv4 RCSB], [http://www.ebi.ac.uk/pdbsum/1iv4 PDBsum], [http://www.topsan.org/Proteins/RSGI/1iv4 TOPSAN]</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=1iv4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iv4 OCA], [http://pdbe.org/1iv4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1iv4 RCSB], [http://www.ebi.ac.uk/pdbsum/1iv4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1iv4 ProSAT], [http://www.topsan.org/Proteins/RSGI/1iv4 TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		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=1iv4 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 13:43, 11 September 2015

2015-09-11T13:43:03Z

←Older revision		Revision as of 13:43, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1iv4' size='340' side='right' caption='[[1iv4]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='1iv4' size='340' side='right' caption='[[1iv4]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1iv4]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thermus_thermophilus Thermus thermophilus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IV4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IV4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1iv4]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IV4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IV4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C5P:CYTIDINE-5-MONOPHOSPHATE'>C5P</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C5P:CYTIDINE-5-MONOPHOSPHATE'>C5P</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iv1\|1iv1]], [[1iv2\|1iv2]], [[1iv3\|1iv3]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iv1\|1iv1]], [[1iv2\|1iv2]], [[1iv3\|1iv3]]</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=1iv4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iv4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1iv4 RCSB], [http://www.ebi.ac.uk/pdbsum/1iv4 PDBsum], [http://www.topsan.org/Proteins/RSGI/1iv4 TOPSAN]</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=1iv4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iv4 OCA], [http://pdbe.org/1iv4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1iv4 RCSB], [http://www.ebi.ac.uk/pdbsum/1iv4 PDBsum], [http://www.topsan.org/Proteins/RSGI/1iv4 TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1iv4" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]		[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]
-	[[Category: Thermus thermophilus]]
	[[Category: Kishida, H]]		[[Category: Kishida, H]]
	[[Category: Kuzuyama, T]]		[[Category: Kuzuyama, T]]

OCA at 17:13, 25 December 2014

2014-12-25T17:13:51Z

←Older revision		Revision as of 17:13, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1iv4]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IV4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IV4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1iv4]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IV4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IV4 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C5P:CYTIDINE-5-MONOPHOSPHATE'>C5P</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C5P:CYTIDINE-5-MONOPHOSPHATE'>C5P</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iv1\|1iv1]], [[1iv2\|1iv2]], [[1iv3\|1iv3]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iv1\|1iv1]], [[1iv2\|1iv2]], [[1iv3\|1iv3]]</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=1iv4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iv4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1iv4 RCSB], [http://www.ebi.ac.uk/pdbsum/1iv4 PDBsum], [http://www.topsan.org/Proteins/RSGI/1iv4 TOPSAN]</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=1iv4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iv4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1iv4 RCSB], [http://www.ebi.ac.uk/pdbsum/1iv4 PDBsum], [http://www.topsan.org/Proteins/RSGI/1iv4 TOPSAN]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ISPF_THET8 ISPF_THET8]] 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).<ref>PMID:12499535</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]		[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
-	[[Category: Kishida, H.]]	+	[[Category: Kishida, H]]
-	[[Category: Kuzuyama, T.]]	+	[[Category: Kuzuyama, T]]
-	[[Category: Park, S Y.]]	+	[[Category: Park, S Y]]
-	[[Category: ~~RSGI, RIKEN~~ Structural ~~Genomics/Proteomics Initiative.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Sirouzu, M.]]	+	[[Category: Sirouzu, M]]
-	[[Category: Tame, J R.H.]]	+	[[Category: Tame, J R.H]]
-	[[Category: Terada, T.]]	+	[[Category: Terada, T]]
-	[[Category: Unzai, S.]]	+	[[Category: Unzai, S]]
-	[[Category: Wada, T.]]	+	[[Category: Wada, T]]
-	[[Category: Yokoyama, S.]]	+	[[Category: Yokoyama, S]]
	[[Category: Isoprenoid]]		[[Category: Isoprenoid]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Non-mevalonate]]		[[Category: Non-mevalonate]]
-	[[Category: Riken structural genomics/proteomics initiative]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
-	[[Category: Structural genomic]]
	[[Category: Synthase]]		[[Category: Synthase]]

OCA at 11:51, 28 September 2014

2014-09-28T11:51:43Z

←Older revision		Revision as of 11:51, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1iv4.~~png~~\|~~left~~\|200px]]	+	==Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase (bound form Substrate)==
		+	<StructureSection load='1iv4' size='340' side='right' caption='[[1iv4]], [[Resolution\|resolution]] 1.55Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1iv4]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IV4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1IV4 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C5P:CYTIDINE-5-MONOPHOSPHATE'>C5P</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iv1\|1iv1]], [[1iv2\|1iv2]], [[1iv3\|1iv3]]</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=1iv4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iv4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1iv4 RCSB], [http://www.ebi.ac.uk/pdbsum/1iv4 PDBsum], [http://www.topsan.org/Proteins/RSGI/1iv4 TOPSAN]</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/iv/1iv4_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 ==
		+	Precursors for isoprenoid synthesis are essential in all organisms. These compounds are synthesized by one of two known routes: the well characterized mevalonate pathway or a recently discovered non-mevalonate route which is used in many bacteria and human pathogens. Since the second pathway is both vital and unlike any found in humans, enzymes catalysing reactions along this synthetic route are possible drug targets. The structure of one such enzyme from the thermophilic bacterium Thermus thermophilus has been solved to high resolution in the presence of substrate and with a substrate analogue. Enzyme co-crystallized with substrate shows only one product, cytosine monophosphate (CMP), in the active site. At the high resolution of the refinement (1.6 A) the positions and coordination of the magnesium ions in the active site are clearly seen.

-	~~{{STRUCTURE_1iv4\| PDB=1iv4 \| SCENE= }}~~	+	Structure and catalytic mechanism of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MECDP) synthase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis.,Kishida H, Wada T, Unzai S, Kuzuyama T, Takagi M, Terada T, Shirouzu M, Yokoyama S, Tame JR, Park SY Acta Crystallogr D Biol Crystallogr. 2003 Jan;59(Pt 1):23-31. Epub 2002, Dec 19. PMID:12499535<ref>PMID:12499535</ref>

-	~~===Structure of 2C-Methyl-D-erythritol-2~~,~~4-cyclodiphosphate Synthase (bound form Substrate)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_12499535}}~~	+	==See Also==
-		+	*[[MECDP synthase\|MECDP synthase]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~1iv4~~]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IV4 OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:012499535<~~/~~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: Thermus thermophilus]]		[[Category: Thermus thermophilus]]

OCA: Protected "1iv4" [edit=sysop:move=sysop]

2012-11-28T15:10:18Z

Protected "1iv4" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:10, 28 November 2012

OCA at 15:10, 28 November 2012

2012-11-28T15:10:13Z

←Older revision		Revision as of 15:10, 28 November 2012
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-	{{Seed}}
	[[Image:1iv4.png\|left\|200px]]		[[Image:1iv4.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1iv4", 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_1iv4\| PDB=1iv4 \| SCENE= }}		{{STRUCTURE_1iv4\| PDB=1iv4 \| SCENE= }}

	===Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase (bound form Substrate)===		===Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase (bound form Substrate)===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12499535}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12499535 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_12499535}}		{{ABSTRACT_PUBMED_12499535}}

	==About this Structure==		==About this Structure==
-	~~1IV4~~ is a 6 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IV4 OCA].	+	[[1iv4]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IV4 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12499535~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012499535</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: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
Line 37:		Line 25:
	[[Category: Yokoyama, S.]]		[[Category: Yokoyama, S.]]
	[[Category: Isoprenoid]]		[[Category: Isoprenoid]]
		+	[[Category: Lyase]]
	[[Category: Non-mevalonate]]		[[Category: Non-mevalonate]]
	[[Category: Riken structural genomics/proteomics initiative]]		[[Category: Riken structural genomics/proteomics initiative]]
Line 42:		Line 31:
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Synthase]]		[[Category: Synthase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 23:53:23 2009''

OCA at 21:53, 17 February 2009

2009-02-17T21:53:25Z

←Older revision		Revision as of 21:53, 17 February 2009
Line 23:		Line 23:

	==Reference==		==Reference==
-	Structure and catalytic mechanism of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MECDP) synthase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis., Kishida H, Wada T, Unzai S, Kuzuyama T, Takagi M, Terada T, Shirouzu M, Yokoyama S, Tame JR, Park SY, Acta Crystallogr D Biol Crystallogr. 2003 Jan;59(Pt 1):23-31. Epub 2002, Dec 19. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/12499535 12499535]~~	+	<ref group="xtra">PMID:12499535</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: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
Line 43:		Line 43:
	[[Category: Synthase]]		[[Category: Synthase]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Nov 16 15~~:05:~~54 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 23:53:23 2009''