5kry - Revision history

OCA at 10:52, 27 September 2023

2023-09-27T10:52:47Z

←Older revision		Revision as of 10:52, 27 September 2023
Line 3:		Line 3:
	<StructureSection load='5kry' size='340' side='right'caption='[[5kry]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='5kry' size='340' side='right'caption='[[5kry]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kry]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Vibvu Vibvu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KRY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5KRY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kry]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_vulnificus_CMCP6 Vibrio vulnificus CMCP6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KRY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KRY FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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">[[5kqo\|5kqo]]~~, [[~~5krv~~\|~~5krv]], [[5krr\|5krr]], [[5ks1\|5ks1~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>dxr, VV1_1866 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id~~=216895 VIBVU])</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=5kry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kry OCA], [https://pdbe.org/5kry PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kry RCSB], [https://www.ebi.ac.uk/pdbsum/5kry PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kry 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/~~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=5kry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kry OCA], [~~http~~://pdbe.org/5kry PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5kry RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5kry PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5kry ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DXR_VIBVU DXR_VIBVU]] Catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP).	+	[https://www.uniprot.org/uniprot/DXR_VIBVU DXR_VIBVU] Catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 21:

	==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: ~~Vibvu~~]]	+	[[Category: Vibrio vulnificus CMCP6]]
-	[[Category: Abdulsalam~~, R W~~]]	+	[[Category: Abdulsalam RW]]
-	[[Category: Chruszcz, M]]	+	[[Category: Chruszcz M]]
-	[[Category: Ussin, N]]	+	[[Category: Ussin N]]
-	~~[[Category: Dxr 1-deoxy-d-xylulose 5-phosphate reductoisomerase]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 06:00, 12 June 2019

2019-06-12T06:00:42Z

←Older revision		Revision as of 06:00, 12 June 2019
Line 1:		Line 1:

	==1-deoxy-D-xylulose 5-phosphate reductoisomerase from Vibrio vulnificus==		==1-deoxy-D-xylulose 5-phosphate reductoisomerase from Vibrio vulnificus==
-	<StructureSection load='5kry' size='340' side='right' caption='[[5kry]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='5kry' size='340' side='right'caption='[[5kry]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kry]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KRY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KRY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kry]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Vibvu Vibvu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KRY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KRY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5kqo\|5kqo]], [[5krv\|5krv]], [[5krr\|5krr]], [[5ks1\|5ks1]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5kqo\|5kqo]], [[5krv\|5krv]], [[5krr\|5krr]], [[5ks1\|5ks1]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dxr, VV1_1866 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=216895 VIBVU])</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=5kry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kry OCA], [http://pdbe.org/5kry PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kry RCSB], [http://www.ebi.ac.uk/pdbsum/5kry PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kry 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=5kry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kry OCA], [http://pdbe.org/5kry PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kry RCSB], [http://www.ebi.ac.uk/pdbsum/5kry PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kry ProSAT]</span></td></tr>
Line 11:		Line 12:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/DXR_VIBVU DXR_VIBVU]] Catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP).		[[http://www.uniprot.org/uniprot/DXR_VIBVU DXR_VIBVU]] Catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Vibrio vulnificus, a gram-negative bacterium, is the leading cause of seafood-borne illnesses and mortality in the United States. Previous studies have identified metabolites 2-C-methylerythritol 4-phosphate (MEP) as being essential for V. vulnificus growth and function. It was shown that 1-deoxy-D-xylulose-5-phosphate reductoisomerase (Dxr) is a critical enzyme in the viability of V. vulnificus, and many other bacteria, as it catalyzes the rearrangement of 1-deoxy-D-xylulose-5-phosphate (Dxp) to 2-C-methylerythritol 4-phosphate (MEP) within the MEP pathway, found in plants and bacteria. The MEP pathway produces the isoprenoids, isopentenyl diphosphate and dimethylallyl pyrophosphate. In this study, we produced and structurally characterized V. vulnificus Dxr. The enzyme forms a dimeric assembly and contains a metal ion in the active site. Protein produced in Escherichia coli co-purifies with Mg(2+) ions, however the Mg(2+) cations may be substituted with Mn(2+), as both of these metals may be utilized by Dxrs. These findings will provide a basis for the design of Dxr inhibitors that may find application as antimicrobial compounds.
		+
		+	Structural characterization of 1-deoxy-D-xylulose 5-phosphate Reductoisomerase from Vibrio vulnificus.,Ussin NK, Bagnell AM, Offermann LR, Abdulsalam R, Perdue ML, Magee P, Chruszcz M Biochim Biophys Acta Proteins Proteom. 2018 Dec;1866(12):1209-1215. doi:, 10.1016/j.bbapap.2018.09.008. Epub 2018 Sep 29. PMID:30278288<ref>PMID:30278288</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5kry" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DXP reductoisomerase\|DXP reductoisomerase]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: 1-deoxy-D-xylulose-5-phosphate reductoisomerase]]		[[Category: 1-deoxy-D-xylulose-5-phosphate reductoisomerase]]
		+	[[Category: Large Structures]]
		+	[[Category: Vibvu]]
	[[Category: Abdulsalam, R W]]		[[Category: Abdulsalam, R W]]
	[[Category: Chruszcz, M]]		[[Category: Chruszcz, M]]

OCA at 10:11, 10 September 2017

2017-09-10T10:11:24Z

←Older revision		Revision as of 10:11, 10 September 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5kry is ~~ON HOLD until Jul 07 2018~~	+	==1-deoxy-D-xylulose 5-phosphate reductoisomerase from Vibrio vulnificus==
-		+	<StructureSection load='5kry' size='340' side='right' caption='[[5kry]], [[Resolution\|resolution]] 2.30Å' scene=''>
-	~~Authors~~: ~~Ussin~~, N., ~~Abdulsalam~~, R.W., ~~Chruszcz~~, M.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5kry]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KRY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KRY FirstGlance]. <br>
-	~~Description~~: 1-deoxy-D-xylulose 5-phosphate reductoisomerase ~~from Vibrio vulnificus~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5kqo\|5kqo]], [[5krv\|5krv]], [[5krr\|5krr]], [[5ks1\|5ks1]]</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=5kry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kry OCA], [http://pdbe.org/5kry PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kry RCSB], [http://www.ebi.ac.uk/pdbsum/5kry PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kry ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DXR_VIBVU DXR_VIBVU]] Catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP).
		+	__TOC__
		+	</StructureSection>
		+	[[Category: 1-deoxy-D-xylulose-5-phosphate reductoisomerase]]
		+	[[Category: Abdulsalam, R W]]
		+	[[Category: Chruszcz, M]]
	[[Category: Ussin, N]]		[[Category: Ussin, N]]
-	[[Category: ~~Abdulsalam, R.W~~]]	+	[[Category: Dxr 1-deoxy-d-xylulose 5-phosphate reductoisomerase]]
-	[[Category: ~~Chruszcz, M~~]]	+	[[Category: Oxidoreductase]]

OCA at 01:59, 4 August 2016

2016-08-04T01:59:29Z

←Older revision		Revision as of 01:59, 4 August 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5kry is ON HOLD	+	The entry 5kry is ON HOLD until Jul 07 2018

	Authors: Ussin, N., Abdulsalam, R.W., Chruszcz, M.		Authors: Ussin, N., Abdulsalam, R.W., Chruszcz, M.

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

2016-07-14T09:39:35Z

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

←Older revision

Revision as of 09:39, 14 July 2016

OCA: New page: '''Unreleased structure''' The entry 5kry is ON HOLD Authors: Ussin, N., Abdulsalam, R.W., Chruszcz, M. Description: 1-deoxy-D-xylulose 5-phosphate reductoisomerase from Vibrio vulnifi...

2016-07-14T09:39:33Z

New page: '''Unreleased structure''' The entry 5kry is ON HOLD Authors: Ussin, N., Abdulsalam, R.W., Chruszcz, M. Description: 1-deoxy-D-xylulose 5-phosphate reductoisomerase from Vibrio vulnifi...

New page

'''Unreleased structure'''

The entry 5kry is ON HOLD

Authors: Ussin, N., Abdulsalam, R.W., Chruszcz, M.

Description: 1-deoxy-D-xylulose 5-phosphate reductoisomerase from Vibrio vulnificus
[[Category: Unreleased Structures]]
[[Category: Ussin, N]]
[[Category: Abdulsalam, R.W]]
[[Category: Chruszcz, M]]