5mrn - Revision history

OCA at 17:47, 8 November 2023

2023-11-08T17:47:26Z

←Older revision		Revision as of 17:47, 8 November 2023
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	<StructureSection load='5mrn' size='340' side='right'caption='[[5mrn]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5mrn' size='340' side='right'caption='[[5mrn]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5mrn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MRN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5MRN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5mrn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MRN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MRN FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>~~, ~~<scene name='pdbligand=K:POTASSIUM+ION'>K</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]] 2Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[1w77\|1w77]], [[2yc5\|2yc5]], [[4nak\|4nak]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></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_4-phosphate_cytidylyltransferase 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.60 2.7.7.60] </~~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=5mrn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mrn OCA], [https://pdbe.org/5mrn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5mrn RCSB], [https://www.ebi.ac.uk/pdbsum/5mrn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5mrn 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=5mrn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mrn OCA], [~~http~~://pdbe.org/5mrn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5mrn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5mrn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5mrn ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ISPD_ARATH ISPD_ARATH]] Enzyme of the plastid non-mevalonate pathway for isoprenoid biosynthesis that catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate (MEP). Is essential for chloroplast development and required for pigments and gibberellins biosynthesis.<ref>PMID:10841550</ref> <ref>PMID:12029484</ref> <ref>PMID:18236010</ref>	+	[https://www.uniprot.org/uniprot/ISPD_ARATH ISPD_ARATH] Enzyme of the plastid non-mevalonate pathway for isoprenoid biosynthesis that catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate (MEP). Is essential for chloroplast development and required for pigments and gibberellins biosynthesis.<ref>PMID:10841550</ref> <ref>PMID:12029484</ref> <ref>PMID:18236010</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase~~]]	+	[[Category: Arabidopsis thaliana]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bacher, A]]	+	[[Category: Bacher A]]
-	[[Category: Diederich, F]]	+	[[Category: Diederich F]]
-	[[Category: Fischer, M]]	+	[[Category: Fischer M]]
-	[[Category: Frank, A]]	+	[[Category: Frank A]]
-	[[Category: Groll, M]]	+	[[Category: Groll M]]
-	[[Category: Illarionov, B]]	+	[[Category: Illarionov B]]
-	[[Category: Kunfermann, A]]	+	[[Category: Kunfermann A]]
-	[[Category: Schwab, A]]	+	[[Category: Schwab A]]
-	[[Category: Seet, M]]	+	[[Category: Seet M]]
-	[[Category: Witschel, M]]	+	[[Category: Witschel M]]
-	~~[[Category: Anti-infective]]~~	+
-	~~[[Category: Drug discovery]]~~	+
-	~~[[Category: Herbicide]]~~	+
-	~~[[Category: Mutant]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 07:27, 19 August 2020

2020-08-19T07:27:06Z

←Older revision		Revision as of 07:27, 19 August 2020
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	==Arabidopsis thaliana IspD Glu258Ala Mutant==		==Arabidopsis thaliana IspD Glu258Ala Mutant==
-	<StructureSection load='5mrn' size='340' side='right' caption='[[5mrn]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='5mrn' size='340' side='right'caption='[[5mrn]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5mrn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MRN OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5MRN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5mrn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MRN OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5MRN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1w77\|1w77]], [[2yc5\|2yc5]], [[4nak\|4nak]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1w77\|1w77]], [[2yc5\|2yc5]], [[4nak\|4nak]]</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_4-phosphate_cytidylyltransferase 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.60 2.7.7.60] </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_4-phosphate_cytidylyltransferase 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.60 2.7.7.60] </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=5mrn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mrn OCA], [http://pdbe.org/5mrn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mrn RCSB], [http://www.ebi.ac.uk/pdbsum/5mrn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mrn 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=5mrn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mrn OCA], [http://pdbe.org/5mrn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mrn RCSB], [http://www.ebi.ac.uk/pdbsum/5mrn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mrn ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5mrn" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5mrn" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[MEP cytidylyltransferase 3D structures\|MEP cytidylyltransferase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 25:		Line 28:
	</StructureSection>		</StructureSection>
	[[Category: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase]]		[[Category: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase]]
		+	[[Category: Large Structures]]
	[[Category: Bacher, A]]		[[Category: Bacher, A]]
	[[Category: Diederich, F]]		[[Category: Diederich, F]]

OCA at 16:07, 20 October 2017

2017-10-20T16:07:28Z

←Older revision		Revision as of 16:07, 20 October 2017
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5mrn" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5mrn" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[MEP cytidylyltransferase\|MEP cytidylyltransferase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 03:59, 30 August 2017

2017-08-30T03:59:45Z

←Older revision		Revision as of 03:59, 30 August 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5mrn is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Arabidopsis thaliana IspD Glu258Ala Mutant==
		+	<StructureSection load='5mrn' size='340' side='right' caption='[[5mrn]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5mrn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MRN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MRN FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1w77\|1w77]], [[2yc5\|2yc5]], [[4nak\|4nak]]</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_4-phosphate_cytidylyltransferase 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.60 2.7.7.60] </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=5mrn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mrn OCA], [http://pdbe.org/5mrn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mrn RCSB], [http://www.ebi.ac.uk/pdbsum/5mrn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mrn ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ISPD_ARATH ISPD_ARATH]] Enzyme of the plastid non-mevalonate pathway for isoprenoid biosynthesis that catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate (MEP). Is essential for chloroplast development and required for pigments and gibberellins biosynthesis.<ref>PMID:10841550</ref> <ref>PMID:12029484</ref> <ref>PMID:18236010</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Enzymes of the nonmevalonate pathway of isoprenoid biosynthesis are attractive targets for the development of herbicides and drugs against infectious diseases. While this pathway is essential for many pathogens and plants, mammals do not depend on it for the synthesis of isoprenoids. IspD, the third enzyme of the nonmevalonate pathway, is unique in that it has an allosteric regulatory site. We elucidated the binding mode of phenylisoxazoles, a new class of allosteric inhibitors. Allosteric inhibition is effected by large conformational changes of a loop region proximal to the active site. We investigated the different roles of residues in this loop by mutation studies and identified repulsive interactions with Asp291 and Asp292 to be responsible for inhibition. Crystallographic data and the response of mutant enzymes to three different classes of allosteric inhibitors provide an in-depth understanding of the allosteric mechanism. The obtained mutant enzymes show selective resistance to allosteric inhibitors and provide conceptually valuable information for future engineering of herbicide-resistant crops. We found that the isoprenoid precursors IPP and DMAPP are natural inhibitors of Arabidopsis thaliana IspD; however, they do not seem to bind to the allosteric site.

-	~~Authors:~~ Schwab, A., Illarionov, B., Frank, A., Kunfermann, A., Seet, M., Bacher, A., Witschel~~, M.~~, Fischer, M., Groll, M., Diederich, F.	+	Mechanism of Allosteric Inhibition of the Enzyme IspD by Three Different Classes of Ligands.,Schwab A, Illarionov B, Frank A, Kunfermann A, Seet M, Bacher A, Witschel MC, Fischer M, Groll M, Diederich F ACS Chem Biol. 2017 Aug 18;12(8):2132-2138. doi: 10.1021/acschembio.7b00004. Epub, 2017 Jul 7. PMID:28686408<ref>PMID:28686408</ref>

-	~~Description: Arabidopsis thaliana IspD Glu258Ala Mutant~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Schwab, A]]~~	+	<div class="pdbe-citations 5mrn" style="background-color:#fffaf0;"></div>
-	~~[[Category: Frank, A]]~~	+
-	[[~~Category: Kunfermann, A~~]]	+	==See Also==
-	[[Category: ~~Fischer, M~~]]	+	*[[MEP cytidylyltransferase\|MEP cytidylyltransferase]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase]]
	[[Category: Bacher, A]]		[[Category: Bacher, A]]
-	[[Category: Seet, M]]
	[[Category: Diederich, F]]		[[Category: Diederich, F]]
		+	[[Category: Fischer, M]]
		+	[[Category: Frank, A]]
	[[Category: Groll, M]]		[[Category: Groll, M]]
	[[Category: Illarionov, B]]		[[Category: Illarionov, B]]
		+	[[Category: Kunfermann, A]]
		+	[[Category: Schwab, A]]
		+	[[Category: Seet, M]]
	[[Category: Witschel, M]]		[[Category: Witschel, M]]
		+	[[Category: Anti-infective]]
		+	[[Category: Drug discovery]]
		+	[[Category: Herbicide]]
		+	[[Category: Mutant]]
		+	[[Category: Transferase]]

OCA at 11:35, 9 March 2017

2017-03-09T11:35:07Z

←Older revision		Revision as of 11:35, 9 March 2017
Line 7:		Line 7:
	Description: Arabidopsis thaliana IspD Glu258Ala Mutant		Description: Arabidopsis thaliana IspD Glu258Ala Mutant
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Kunfermann, A]]
-	[[Category: Fischer, M]]
-	[[Category: Seet, M]]
-	[[Category: Illarionov, B]]
-	[[Category: Witschel, M]]
	[[Category: Schwab, A]]		[[Category: Schwab, A]]
	[[Category: Frank, A]]		[[Category: Frank, A]]
		+	[[Category: Kunfermann, A]]
		+	[[Category: Fischer, M]]
	[[Category: Bacher, A]]		[[Category: Bacher, A]]
		+	[[Category: Seet, M]]
	[[Category: Diederich, F]]		[[Category: Diederich, F]]
	[[Category: Groll, M]]		[[Category: Groll, M]]
		+	[[Category: Illarionov, B]]
		+	[[Category: Witschel, M]]

OCA at 13:07, 18 January 2017

2017-01-18T13:07:38Z

←Older revision		Revision as of 13:07, 18 January 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5mrn is ON HOLD	+	The entry 5mrn is ON HOLD until Paper Publication

	Authors: Schwab, A., Illarionov, B., Frank, A., Kunfermann, A., Seet, M., Bacher, A., Witschel, M., Fischer, M., Groll, M., Diederich, F.		Authors: Schwab, A., Illarionov, B., Frank, A., Kunfermann, A., Seet, M., Bacher, A., Witschel, M., Fischer, M., Groll, M., Diederich, F.

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

2017-01-04T14:19:29Z

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

←Older revision

Revision as of 14:19, 4 January 2017

OCA: New page: '''Unreleased structure''' The entry 5mrn is ON HOLD Authors: Schwab, A., Illarionov, B., Frank, A., Kunfermann, A., Seet, M., Bacher, A., Witschel, M., Fischer, M., Groll, M., Diederic...

2017-01-04T14:19:28Z

New page: '''Unreleased structure''' The entry 5mrn is ON HOLD Authors: Schwab, A., Illarionov, B., Frank, A., Kunfermann, A., Seet, M., Bacher, A., Witschel, M., Fischer, M., Groll, M., Diederic...

New page

'''Unreleased structure'''

The entry 5mrn is ON HOLD

Authors: Schwab, A., Illarionov, B., Frank, A., Kunfermann, A., Seet, M., Bacher, A., Witschel, M., Fischer, M., Groll, M., Diederich, F.

Description: Arabidopsis thaliana IspD Glu258Ala Mutant
[[Category: Unreleased Structures]]
[[Category: Kunfermann, A]]
[[Category: Fischer, M]]
[[Category: Seet, M]]
[[Category: Illarionov, B]]
[[Category: Witschel, M]]
[[Category: Schwab, A]]
[[Category: Frank, A]]
[[Category: Bacher, A]]
[[Category: Diederich, F]]
[[Category: Groll, M]]