OCA at 13:14, 24 January 2024

OCA — Wed, 24 Jan 2024 13:14:48 GMT

←Older revision		Revision as of 13:14, 24 January 2024
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	==Structure of truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Deinococcus radiodurans==		==Structure of truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Deinococcus radiodurans==
-	<StructureSection load='6xxg' size='340' side='right'caption='[[6xxg]]' scene=''>	+	<StructureSection load='6xxg' size='340' side='right'caption='[[6xxg]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XXG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6XXG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6xxg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans_R1 Deinococcus radiodurans R1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XXG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6XXG FirstGlance]. <br>
-	</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=6xxg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xxg OCA], [~~http~~://pdbe.org/6xxg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6xxg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6xxg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6xxg ProSAT]</span></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]] 2.099Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TPP:THIAMINE+DIPHOSPHATE'>TPP</scene></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=6xxg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xxg OCA], [https://pdbe.org/6xxg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6xxg RCSB], [https://www.ebi.ac.uk/pdbsum/6xxg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6xxg ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DXS_DEIRA DXS_DEIRA] Catalyzes the acyloin condensation reaction between C atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D-xylulose-5-phosphate (DXP) (By similarity).[HAMAP-Rule:MF_00315]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In this report, we describe a truncated Deinococcus radiodurans 1-deoxy-D-xylulose-5-phosphate synthase (DXS) protein that retains enzymatic activity, while slowing protein degradation and showing improved crystallization properties. With modern drug-design approaches relying heavily on the elucidation of atomic interactions of potential new drugs with their targets, the need for co-crystal structures with the compounds of interest is high. DXS itself is a promising drug target, as it catalyzes the first reaction in the 2-C-methyl-D-erythritol 4-phosphate (MEP)-pathway for the biosynthesis of the universal precursors of terpenes, which are essential secondary metabolites. In contrast to many bacteria and pathogens, which employ the MEP pathway, mammals use the distinct mevalonate-pathway for the biosynthesis of these precursors, which makes all enzymes of the MEP-pathway potential new targets for the development of anti-infectives. However, crystallization of DXS has proven to be challenging: while the first X-ray structures from Escherichia coli and D. radiodurans were solved in 2004, since then only two additions have been made in 2019 that were obtained under anoxic conditions. The presented site of truncation can potentially also be transferred to other homologues, opening up the possibility for the determination of crystal structures from pathogenic species, which until now could not be crystallized. This manuscript also provides a further example that truncation of a variable region of a protein can lead to improved structural data.
		+
		+	Identification of a 1-deoxy-D-xylulose-5-phosphate synthase (DXS) mutant with improved crystallographic properties.,Gierse RM, Reddem ER, Alhayek A, Baitinger D, Hamid Z, Jakobi H, Laber B, Lange G, Hirsch AKH, Groves MR Biochem Biophys Res Commun. 2021 Jan 5;539:42-47. doi:, 10.1016/j.bbrc.2020.12.069. PMID:33421767<ref>PMID:33421767</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6xxg" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Deinococcus radiodurans R1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Gierse RM]]		[[Category: Gierse RM]]
	[[Category: Grooves MR]]		[[Category: Grooves MR]]
	[[Category: Reddem E]]		[[Category: Reddem E]]

OCA at 08:11, 20 January 2021

OCA — Wed, 20 Jan 2021 08:11:51 GMT

←Older revision		Revision as of 08:11, 20 January 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 6xxg is ~~ON HOLD until Paper Publication~~	+	==Structure of truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Deinococcus radiodurans==
-		+	<StructureSection load='6xxg' size='340' side='right'caption='[[6xxg]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6XXG OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6XXG FirstGlance]. <br>
-	~~Description~~:	+	</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=6xxg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6xxg OCA], [http://pdbe.org/6xxg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6xxg RCSB], [http://www.ebi.ac.uk/pdbsum/6xxg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6xxg ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Gierse RM]]
		+	[[Category: Grooves MR]]
		+	[[Category: Reddem E]]

OCA at 08:15, 26 February 2020

OCA — Wed, 26 Feb 2020 08:15:34 GMT

←Older revision		Revision as of 08:15, 26 February 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6xxg is ON HOLD	+	The entry 6xxg is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6xxg" [edit=sysop:move=sysop]

OCA — Wed, 05 Feb 2020 06:28:01 GMT

Protected "6xxg" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:28, 5 February 2020

OCA: New page: '''Unreleased structure''' The entry 6xxg is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 05 Feb 2020 06:28:00 GMT

New page: '''Unreleased structure''' The entry 6xxg is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6xxg is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

6xxg - Revision history

OCA at 13:14, 24 January 2024

OCA at 08:11, 20 January 2021

OCA at 08:15, 26 February 2020

OCA: Protected "6xxg" [edit=sysop:move=sysop]

OCA: New page: '''Unreleased structure''' The entry 6xxg is ON HOLD Authors: Description: Category: Unreleased Structures