2jd0 - Revision history

OCA at 14:43, 13 December 2023

2023-12-13T14:43:37Z

←Older revision		Revision as of 14:43, 13 December 2023
Line 3:		Line 3:
	<StructureSection load='2jd0' size='340' side='right'caption='[[2jd0]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='2jd0' size='340' side='right'caption='[[2jd0]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2jd0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Myctu Myctu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JD0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JD0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2jd0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JD0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JD0 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=NDP:NADPH+DIHYDRO~~-~~NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.3Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[2c82\|2c82]], [[2jcv\|2jcv]], [[2jcx\|2jcx]], [[2jcy\|2jcy]], [[2jcz\|2jcz]], [[2jd1\|2jd1]], [[2jd2\|2jd2]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>[https://en.wikipedia.org/wiki/1-deoxy-D-xylulose-5-phosphate_reductoisomerase 1-deoxy-D-xylulose-5-phosphate reductoisomerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.267 1.1.1.267] </~~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=2jd0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jd0 OCA], [https://pdbe.org/2jd0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jd0 RCSB], [https://www.ebi.ac.uk/pdbsum/2jd0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jd0 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=2jd0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jd0 OCA], [https://pdbe.org/2jd0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jd0 RCSB], [https://www.ebi.ac.uk/pdbsum/2jd0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jd0 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DXR_MYCTU DXR_MYCTU] Catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP) (By similarity).
	== 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==
-	*[[DXP reductoisomerase\|DXP reductoisomerase]]	+	*[[DXP reductoisomerase 3D Structures\|DXP reductoisomerase 3D Structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: 1-deoxy-D-xylulose-5-phosphate reductoisomerase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Myctu~~]]	+	[[Category: Mycobacterium tuberculosis H37Rv]]
-	[[Category: Henriksson~~, L M~~]]	+	[[Category: Henriksson LM]]
-	[[Category: Jones~~, T A~~]]	+	[[Category: Jones TA]]
-	[[Category: Mowbray~~, S L~~]]	+	[[Category: Mowbray SL]]
-	[[Category: Unge, T]]	+	[[Category: Unge T]]
-	~~[[Category: 1-deoxy-d-xylulose 5-phosphate reductoisomerase]]~~	+
-	~~[[Category: Doxp/mep pathway]]~~	+
-	~~[[Category: Isoprene biosynthesis]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Nadp]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Rv2870c~~]]	+

OCA at 08:07, 19 January 2022

2022-01-19T08:07:25Z

←Older revision		Revision as of 08:07, 19 January 2022
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	<StructureSection load='2jd0' size='340' side='right'caption='[[2jd0]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='2jd0' size='340' side='right'caption='[[2jd0]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2jd0]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Myctu Myctu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JD0 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2JD0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2jd0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Myctu Myctu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JD0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JD0 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2c82\|2c82]], [[2jcv\|2jcv]], [[2jcx\|2jcx]], [[2jcy\|2jcy]], [[2jcz\|2jcz]], [[2jd1\|2jd1]], [[2jd2\|2jd2]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2c82\|2c82]], [[2jcv\|2jcv]], [[2jcx\|2jcx]], [[2jcy\|2jcy]], [[2jcz\|2jcz]], [[2jd1\|2jd1]], [[2jd2\|2jd2]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/1-deoxy-D-xylulose-5-phosphate_reductoisomerase 1-deoxy-D-xylulose-5-phosphate reductoisomerase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.267 1.1.1.267] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/1-deoxy-D-xylulose-5-phosphate_reductoisomerase 1-deoxy-D-xylulose-5-phosphate reductoisomerase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.267 1.1.1.267] </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=2jd0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jd0 OCA], [~~http~~://pdbe.org/2jd0 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2jd0 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2jd0 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2jd0 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=2jd0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jd0 OCA], [https://pdbe.org/2jd0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jd0 RCSB], [https://www.ebi.ac.uk/pdbsum/2jd0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jd0 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 07:47, 15 April 2020

2020-04-15T07:47:37Z

←Older revision		Revision as of 07:47, 15 April 2020
Line 1:		Line 1:

	==X-ray structure of mutant 1-deoxy-D-xylulose 5-phosphate reductoisomerase, DXR, Rv2870c, from Mycobacterium tuberculosis, in complex with NADPH==		==X-ray structure of mutant 1-deoxy-D-xylulose 5-phosphate reductoisomerase, DXR, Rv2870c, from Mycobacterium tuberculosis, in complex with NADPH==
-	<StructureSection load='2jd0' size='340' side='right' caption='[[2jd0]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='2jd0' size='340' side='right'caption='[[2jd0]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2jd0]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Myctu Myctu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JD0 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2JD0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2jd0]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Myctu Myctu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JD0 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2JD0 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2c82\|2c82]], [[2jcv\|2jcv]], [[2jcx\|2jcx]], [[2jcy\|2jcy]], [[2jcz\|2jcz]], [[2jd1\|2jd1]], [[2jd2\|2jd2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2c82\|2c82]], [[2jcv\|2jcv]], [[2jcx\|2jcx]], [[2jcy\|2jcy]], [[2jcz\|2jcz]], [[2jd1\|2jd1]], [[2jd2\|2jd2]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1-deoxy-D-xylulose-5-phosphate_reductoisomerase 1-deoxy-D-xylulose-5-phosphate reductoisomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.267 1.1.1.267] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1-deoxy-D-xylulose-5-phosphate_reductoisomerase 1-deoxy-D-xylulose-5-phosphate reductoisomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.267 1.1.1.267] </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=2jd0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jd0 OCA], [http://pdbe.org/2jd0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2jd0 RCSB], [http://www.ebi.ac.uk/pdbsum/2jd0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2jd0 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=2jd0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jd0 OCA], [http://pdbe.org/2jd0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2jd0 RCSB], [http://www.ebi.ac.uk/pdbsum/2jd0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2jd0 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	</StructureSection>		</StructureSection>
	[[Category: 1-deoxy-D-xylulose-5-phosphate reductoisomerase]]		[[Category: 1-deoxy-D-xylulose-5-phosphate reductoisomerase]]
		+	[[Category: Large Structures]]
	[[Category: Myctu]]		[[Category: Myctu]]
	[[Category: Henriksson, L M]]		[[Category: Henriksson, L M]]

OCA at 07:15, 11 July 2018

2018-07-11T07:15:40Z

←Older revision		Revision as of 07:15, 11 July 2018
Line 1:		Line 1:
-	==X-~~RAY STRUCTURE OF MUTANT~~ 1-~~DEOXY~~-D-~~XYLULOSE~~ 5-~~PHOSPHATE REDUCTOISOMERASE~~, DXR, ~~RV2870C~~, ~~FROM MYCOBACTERIUM TUBERCULOSIS~~, ~~IN COMPLEX WITH~~ NADPH==	+
		+	==X-ray structure of mutant 1-deoxy-D-xylulose 5-phosphate reductoisomerase, DXR, Rv2870c, from Mycobacterium tuberculosis, in complex with NADPH==
	<StructureSection load='2jd0' size='340' side='right' caption='[[2jd0]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='2jd0' size='340' side='right' caption='[[2jd0]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2c82\|2c82]], [[2jcv\|2jcv]], [[2jcx\|2jcx]], [[2jcy\|2jcy]], [[2jcz\|2jcz]], [[2jd1\|2jd1]], [[2jd2\|2jd2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2c82\|2c82]], [[2jcv\|2jcv]], [[2jcx\|2jcx]], [[2jcy\|2jcy]], [[2jcz\|2jcz]], [[2jd1\|2jd1]], [[2jd2\|2jd2]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1-deoxy-D-xylulose-5-phosphate_reductoisomerase 1-deoxy-D-xylulose-5-phosphate reductoisomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.267 1.1.1.267] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1-deoxy-D-xylulose-5-phosphate_reductoisomerase 1-deoxy-D-xylulose-5-phosphate reductoisomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.267 1.1.1.267] </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=2jd0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jd0 OCA], [http://pdbe.org/2jd0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2jd0 RCSB], [http://www.ebi.ac.uk/pdbsum/2jd0 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=2jd0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jd0 OCA], [http://pdbe.org/2jd0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2jd0 RCSB], [http://www.ebi.ac.uk/pdbsum/2jd0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2jd0 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 12:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jd/2jd0_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jd/2jd0_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2jd0 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 01:53, 12 September 2015

2015-09-12T01:53:20Z

←Older revision		Revision as of 01:53, 12 September 2015
Line 2:		Line 2:
	<StructureSection load='2jd0' size='340' side='right' caption='[[2jd0]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='2jd0' size='340' side='right' caption='[[2jd0]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2jd0]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Mycobacterium_tuberculosis Mycobacterium tuberculosis~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JD0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JD0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2jd0]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Myctu Myctu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JD0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JD0 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2c82\|2c82]], [[2jcv\|2jcv]], [[2jcx\|2jcx]], [[2jcy\|2jcy]], [[2jcz\|2jcz]], [[2jd1\|2jd1]], [[2jd2\|2jd2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2c82\|2c82]], [[2jcv\|2jcv]], [[2jcx\|2jcx]], [[2jcy\|2jcy]], [[2jcz\|2jcz]], [[2jd1\|2jd1]], [[2jd2\|2jd2]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1-deoxy-D-xylulose-5-phosphate_reductoisomerase 1-deoxy-D-xylulose-5-phosphate reductoisomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.267 1.1.1.267] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1-deoxy-D-xylulose-5-phosphate_reductoisomerase 1-deoxy-D-xylulose-5-phosphate reductoisomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.267 1.1.1.267] </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=2jd0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jd0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2jd0 RCSB], [http://www.ebi.ac.uk/pdbsum/2jd0 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=2jd0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jd0 OCA], [http://pdbe.org/2jd0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2jd0 RCSB], [http://www.ebi.ac.uk/pdbsum/2jd0 PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 26:		Line 26:
	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 2jd0" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DXP reductoisomerase\|DXP reductoisomerase]]
	== References ==		== References ==
	<references/>		<references/>
Line 31:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: 1-deoxy-D-xylulose-5-phosphate reductoisomerase]]		[[Category: 1-deoxy-D-xylulose-5-phosphate reductoisomerase]]
-	[[Category: ~~Mycobacterium tuberculosis~~]]	+	[[Category: Myctu]]
	[[Category: Henriksson, L M]]		[[Category: Henriksson, L M]]
	[[Category: Jones, T A]]		[[Category: Jones, T A]]

OCA at 17:06, 19 January 2015

2015-01-19T17:06:37Z

←Older revision		Revision as of 17:06, 19 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2jd0]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JD0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JD0 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2jd0]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JD0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JD0 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2c82\|2c82]], [[2jcv\|2jcv]], [[2jcx\|2jcx]], [[2jcy\|2jcy]], [[2jcz\|2jcz]], [[2jd1\|2jd1]], [[2jd2\|2jd2]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2c82\|2c82]], [[2jcv\|2jcv]], [[2jcx\|2jcx]], [[2jcy\|2jcy]], [[2jcz\|2jcz]], [[2jd1\|2jd1]], [[2jd2\|2jd2]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1-deoxy-D-xylulose-5-phosphate_reductoisomerase 1-deoxy-D-xylulose-5-phosphate reductoisomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.267 1.1.1.267] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1-deoxy-D-xylulose-5-phosphate_reductoisomerase 1-deoxy-D-xylulose-5-phosphate reductoisomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.267 1.1.1.267] </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=2jd0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jd0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2jd0 RCSB], [http://www.ebi.ac.uk/pdbsum/2jd0 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=2jd0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jd0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2jd0 RCSB], [http://www.ebi.ac.uk/pdbsum/2jd0 PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 32:
	[[Category: 1-deoxy-D-xylulose-5-phosphate reductoisomerase]]		[[Category: 1-deoxy-D-xylulose-5-phosphate reductoisomerase]]
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
-	[[Category: Henriksson, L M.]]	+	[[Category: Henriksson, L M]]
-	[[Category: Jones, T A.]]	+	[[Category: Jones, T A]]
-	[[Category: Mowbray, S L.]]	+	[[Category: Mowbray, S L]]
-	[[Category: Unge, T.]]	+	[[Category: Unge, T]]
	[[Category: 1-deoxy-d-xylulose 5-phosphate reductoisomerase]]		[[Category: 1-deoxy-d-xylulose 5-phosphate reductoisomerase]]
	[[Category: Doxp/mep pathway]]		[[Category: Doxp/mep pathway]]

OCA at 10:13, 30 September 2014

2014-09-30T10:13:35Z

←Older revision		Revision as of 10:13, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2jd0.~~png~~\|~~left~~\|200px]]	+	==X-RAY STRUCTURE OF MUTANT 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE, DXR, RV2870C, FROM MYCOBACTERIUM TUBERCULOSIS, IN COMPLEX WITH NADPH==
		+	<StructureSection load='2jd0' size='340' side='right' caption='[[2jd0]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2jd0]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JD0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JD0 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2c82\|2c82]], [[2jcv\|2jcv]], [[2jcx\|2jcx]], [[2jcy\|2jcy]], [[2jcz\|2jcz]], [[2jd1\|2jd1]], [[2jd2\|2jd2]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/1-deoxy-D-xylulose-5-phosphate_reductoisomerase 1-deoxy-D-xylulose-5-phosphate reductoisomerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.267 1.1.1.267] </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=2jd0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jd0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2jd0 RCSB], [http://www.ebi.ac.uk/pdbsum/2jd0 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/jd/2jd0_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 ==
		+	Isopentenyl diphosphate is the precursor of various isoprenoids that are essential to all living organisms. It is produced by the mevalonate pathway in humans but by an alternate route in plants, protozoa, and many bacteria. 1-deoxy-D-xylulose-5-phosphate reductoisomerase catalyzes the second step of this non-mevalonate pathway, which involves an NADPH-dependent rearrangement and reduction of 1-deoxy-D-xylulose 5-phosphate to form 2-C-methyl-D-erythritol 4-phosphate. The use of different pathways, combined with the reported essentiality of the enzyme makes the reductoisomerase a highly promising target for drug design. Here we present several high resolution structures of the Mycobacterium tuberculosis 1-deoxy-D-xylulose-5-phosphate reductoisomerase, representing both wild type and mutant enzyme in various complexes with Mn(2+), NADPH, and the known inhibitor fosmidomycin. The asymmetric unit corresponds to the biological homodimer. Although crystal contacts stabilize an open active site in the B molecule, the A molecule displays a closed conformation, with some differences depending on the ligands bound. An inhibition study with fosmidomycin resulted in an estimated IC(50) value of 80 nm. The double mutant enzyme (D151N/E222Q) has lost its ability to bind the metal and, thereby, also its activity. Our structural information complemented with molecular dynamics simulations and free energy calculations provides the framework for the design of new inhibitors and gives new insights into the reaction mechanism. The conformation of fosmidomycin bound to the metal ion is different from that reported in a previously published structure and indicates that a rearrangement of the intermediate is not required during catalysis.

-	~~{{STRUCTURE_2jd0\| PDB=2jd0 \| SCENE= }}~~	+	Structures of Mycobacterium tuberculosis 1-deoxy-D-xylulose-5-phosphate reductoisomerase provide new insights into catalysis.,Henriksson LM, Unge T, Carlsson J, Aqvist J, Mowbray SL, Jones TA J Biol Chem. 2007 Jul 6;282(27):19905-16. Epub 2007 May 9. PMID:17491006<ref>PMID:17491006</ref>

-	~~===X-RAY STRUCTURE OF MUTANT 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE~~, ~~DXR, RV2870C, FROM MYCOBACTERIUM TUBERCULOSIS, IN COMPLEX WITH NADPH===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17491006}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2jd0]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2JD0 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017491006<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: 1-deoxy-D-xylulose-5-phosphate reductoisomerase]]		[[Category: 1-deoxy-D-xylulose-5-phosphate reductoisomerase]]
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]

OCA: Protected "2jd0" [edit=sysop:move=sysop]

2013-01-07T14:41:51Z

Protected "2jd0" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:41, 7 January 2013

OCA at 14:41, 7 January 2013

2013-01-07T14:41:46Z

←Older revision		Revision as of 14:41, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2jd0.png\|left\|200px]]		[[Image:2jd0.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2jd0", 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_2jd0\| PDB=2jd0 \| SCENE= }}		{{STRUCTURE_2jd0\| PDB=2jd0 \| SCENE= }}

	===X-RAY STRUCTURE OF MUTANT 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE, DXR, RV2870C, FROM MYCOBACTERIUM TUBERCULOSIS, IN COMPLEX WITH NADPH===		===X-RAY STRUCTURE OF MUTANT 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE, DXR, RV2870C, FROM MYCOBACTERIUM TUBERCULOSIS, IN COMPLEX WITH NADPH===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17491006}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17491006 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17491006}}		{{ABSTRACT_PUBMED_17491006}}

	==About this Structure==		==About this Structure==
-	~~2JD0~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JD0 OCA].	+	[[2jd0]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JD0 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17491006~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017491006</ref><references group="xtra"/>
	[[Category: 1-deoxy-D-xylulose-5-phosphate reductoisomerase]]		[[Category: 1-deoxy-D-xylulose-5-phosphate reductoisomerase]]
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
Line 37:		Line 25:
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Rv2870c]]		[[Category: Rv2870c]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 09:33:11 2009''

OCA at 07:33, 18 February 2009

2009-02-18T07:33:13Z

←Older revision		Revision as of 07:33, 18 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2JD0 is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JD0 OCA].	+	2JD0 is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JD0 OCA].

	==Reference==		==Reference==
-	Structures of Mycobacterium tuberculosis 1-deoxy-D-xylulose-5-phosphate reductoisomerase provide new insights into catalysis., Henriksson LM, Unge T, Carlsson J, Aqvist J, Mowbray SL, Jones TA, J Biol Chem. 2007 Jul 6;282(27):19905-16. Epub 2007 May 9. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17491006 17491006]~~	+	<ref group="xtra">PMID:17491006</ref><references group="xtra"/>
	[[Category: 1-deoxy-D-xylulose-5-phosphate reductoisomerase]]		[[Category: 1-deoxy-D-xylulose-5-phosphate reductoisomerase]]
	[[Category: Mycobacterium tuberculosis]]		[[Category: Mycobacterium tuberculosis]]
-	[[Category: Single protein]]
	[[Category: Henriksson, L M.]]		[[Category: Henriksson, L M.]]
	[[Category: Jones, T A.]]		[[Category: Jones, T A.]]
Line 39:		Line 38:
	[[Category: Rv2870c]]		[[Category: Rv2870c]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 15~~:49:~~43 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 09:33:11 2009''