5iwy - Revision history

OCA at 10:35, 6 September 2023

OCA — Wed, 06 Sep 2023 10:35:47 GMT

←Older revision		Revision as of 10:35, 6 September 2023
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	==Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Bacillus subtitis complexed with CMP and Mg2+==		==Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Bacillus subtitis complexed with CMP and Mg2+==
-	<StructureSection load='5iwy' size='340' side='right' caption='[[5iwy]], [[Resolution\|resolution]] 1.99Å' scene=''>	+	<StructureSection load='5iwy' size='340' side='right'caption='[[5iwy]], [[Resolution\|resolution]] 1.99Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5iwy]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bacsu Bacsu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IWY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5IWY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5iwy]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IWY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IWY 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='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.99Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Related_structure~~\|~~Related:]]</b></td><td class="sblockDat">[[5iwx\|5iwx~~]]</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='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>ispF, yacN, BSU00910 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~224308 BACSU])</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=5iwy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iwy OCA], [https://pdbe.org/5iwy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5iwy RCSB], [https://www.ebi.ac.uk/pdbsum/5iwy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5iwy 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~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5iwy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iwy OCA], [~~http~~://pdbe.org/5iwy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5iwy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5iwy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5iwy ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ISPF_BACSU ISPF_BACSU]] 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:17458547</ref>	+	[https://www.uniprot.org/uniprot/ISPF_BACSU ISPF_BACSU] 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:17458547</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 5iwy" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5iwy" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[MECDP synthase 3D structures\|MECDP synthase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase~~]]	+	[[Category: Bacillus subtilis subsp. subtilis str. 168]]
-	[[Category: ~~Bacsu~~]]	+	[[Category: Large Structures]]
-	[[Category: Jin, Y]]	+	[[Category: Jin Y]]
-	[[Category: Liu~~, Z C~~]]	+	[[Category: Liu ZC]]
-	[[Category: Wang~~, G G]]~~	+	[[Category: Wang GG]]
-	~~[[Category: Lyase~~]]	+

OCA at 06:55, 15 February 2018

OCA — Thu, 15 Feb 2018 06:55:03 GMT

←Older revision		Revision as of 06:55, 15 February 2018
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	<StructureSection load='5iwy' size='340' side='right' caption='[[5iwy]], [[Resolution\|resolution]] 1.99Å' scene=''>		<StructureSection load='5iwy' size='340' side='right' caption='[[5iwy]], [[Resolution\|resolution]] 1.99Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5iwy]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IWY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IWY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5iwy]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IWY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IWY 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">[[5iwx\|5iwx]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5iwx\|5iwx]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ispF, yacN, BSU00910 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</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=5iwy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iwy OCA], [http://pdbe.org/5iwy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5iwy RCSB], [http://www.ebi.ac.uk/pdbsum/5iwy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5iwy ProSAT]</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=5iwy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iwy OCA], [http://pdbe.org/5iwy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5iwy RCSB], [http://www.ebi.ac.uk/pdbsum/5iwy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5iwy ProSAT]</span></td></tr>
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/ISPF_BACSU ISPF_BACSU]] 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:17458547</ref>		[[http://www.uniprot.org/uniprot/ISPF_BACSU ISPF_BACSU]] 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:17458547</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	2-C-methyl-d-erythritol 2, 4-cyclodiphosphate synthase (IspF) is a key enzyme in the 2-C-Methyl-d-erythritol-4-phosphate (MEP) pathway of isoprenoid biosynthesis. This enzyme catalyzes the 4-diphosphocytidyl-2-C-methyl-d-erythritol 2-phosphate (CDPME2P) to 2-C-methyl-d-erythritol 2, 4-cyclodiphosphate (MEcDP) with concomitant release of cytidine 5'-diphospate (cytosine monophosphate) (CMP). Bacillus subtilis is a potential host cell for the production of isoprenoids, but few studies are performed on the key enzymes of MEP pathway in B. subtilis In this work, the high resolution crystal structures of IspF in native and complex with CMP from B. subtilis have been determinated. Structural comparisons indicate that there is a looser packing of the subunits of IspF in B. subtilis , whereas the solvent accessible surface of its active pockets is smaller than that in Escherichia coli. Meanwhile, the protein-protein associations of 2-C-Methyl-d-erythritol-4-phosphatecytidyltransferase (IspD), 4-diphosphocytidyl-2-C-methyl-d-erythritol kinase (IspE) and IspF from B. subtilis and E. coli , which catalyze three consecutive steps in the MEP pathway, are analyzed by native gel shift and size exclusion chromatography methods. The data here shows that protein complex assembly is not detectable. These results will be useful for isoprenoid biosynthesis by metabolic engineering.
		+
		+	Crystal structure of IspF from Bacillus subtilis and absence of protein complex assembly among IspD/IspE/IspF enzymes in the MEP pathway.,Liu Z, Jin Y, Liu W, Tao Y, Wang G Biosci Rep. 2018 Jan 15. pii: BSR20171370. doi: 10.1042/BSR20171370. PMID:29335298<ref>PMID:29335298</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5iwy" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]		[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]
		+	[[Category: Bacsu]]
	[[Category: Jin, Y]]		[[Category: Jin, Y]]
	[[Category: Liu, Z C]]		[[Category: Liu, Z C]]
	[[Category: Wang, G G]]		[[Category: Wang, G G]]
	[[Category: Lyase]]		[[Category: Lyase]]

OCA at 13:44, 29 March 2017

OCA — Wed, 29 Mar 2017 13:44:49 GMT

←Older revision		Revision as of 13:44, 29 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5iwy is ON HOLD until Mar 23 2018~~	+	==Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Bacillus subtitis complexed with CMP and Mg2+==
-		+	<StructureSection load='5iwy' size='340' side='right' caption='[[5iwy]], [[Resolution\|resolution]] 1.99Å' scene=''>
-	~~Authors: Liu, Z.C., Jin, Y., Wang, G.G.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5iwy]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IWY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IWY FirstGlance]. <br>
-	~~Description:~~ Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Bacillus subtitis complexed with CMP and Mg2+	+	</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>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5iwx\|5iwx]]</td></tr>
-	[[~~Category~~: ~~Wang~~, G.G]]	+	<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>
-	[[~~Category~~: ~~Liu~~, Z.C]]	+	<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=5iwy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5iwy OCA], [http://pdbe.org/5iwy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5iwy RCSB], [http://www.ebi.ac.uk/pdbsum/5iwy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5iwy ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ISPF_BACSU ISPF_BACSU]] 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:17458547</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase]]
	[[Category: Jin, Y]]		[[Category: Jin, Y]]
		+	[[Category: Liu, Z C]]
		+	[[Category: Wang, G G]]
		+	[[Category: Lyase]]

OCA: Protected "5iwy" [edit=sysop:move=sysop]

OCA — Wed, 11 May 2016 01:06:02 GMT

Protected "5iwy" [edit=sysop:move=sysop]

←Older revision

Revision as of 01:06, 11 May 2016

OCA: New page: '''Unreleased structure''' The entry 5iwy is ON HOLD until Mar 23 2018 Authors: Liu, Z.C., Jin, Y., Wang, G.G. Description: Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphos...

OCA — Wed, 11 May 2016 01:06:00 GMT

New page: '''Unreleased structure''' The entry 5iwy is ON HOLD until Mar 23 2018 Authors: Liu, Z.C., Jin, Y., Wang, G.G. Description: Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphos...

New page

'''Unreleased structure'''

The entry 5iwy is ON HOLD until Mar 23 2018

Authors: Liu, Z.C., Jin, Y., Wang, G.G.

Description: Crystal structure of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Bacillus subtitis complexed with CMP and Mg2+
[[Category: Unreleased Structures]]
[[Category: Wang, G.G]]
[[Category: Liu, Z.C]]
[[Category: Jin, Y]]