8dcl - Revision history

OCA at 17:26, 18 October 2023

2023-10-18T17:26:59Z

←Older revision		Revision as of 17:26, 18 October 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[8dcl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Campylobacter_jejuni Campylobacter jejuni]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8DCL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8DCL FirstGlance]. <br>		<table><tr><td colspan='2'>[[8dcl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Campylobacter_jejuni Campylobacter jejuni]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8DCL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8DCL FirstGlance]. <br>
-	</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>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.55Å</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>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=8dcl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8dcl OCA], [https://pdbe.org/8dcl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8dcl RCSB], [https://www.ebi.ac.uk/pdbsum/8dcl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8dcl 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=8dcl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8dcl OCA], [https://pdbe.org/8dcl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8dcl RCSB], [https://www.ebi.ac.uk/pdbsum/8dcl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8dcl ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/Q6EF58_CAMJU Q6EF58_CAMJU]] Catalyzes the epimerization of the C3' and C5'positions of dTDP-6-deoxy-D-xylo-4-hexulose, forming dTDP-6-deoxy-L-lyxo-4-hexulose.[ARBA:ARBA00001997]	+	[https://www.uniprot.org/uniprot/Q6EF58_CAMJU Q6EF58_CAMJU] Catalyzes the epimerization of the C3' and C5'positions of dTDP-6-deoxy-D-xylo-4-hexulose, forming dTDP-6-deoxy-L-lyxo-4-hexulose.[ARBA:ARBA00001997]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 06:32, 28 September 2022

2022-09-28T06:32:00Z

←Older revision		Revision as of 06:32, 28 September 2022
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-	==~~crystal~~ structure of the GDP-D-~~GLYCERO~~-4-~~KETO~~-D-~~LYXO~~-~~HEPTOSE~~-3-~~EPIMERASE~~ from campylobacter jejuni, serotype HS:23/36==	+	==Crystal structure of the GDP-D-glycero-4-keto-D-lyxo-heptose-3-epimerase from campylobacter jejuni, serotype HS:23/36==
-	<StructureSection load='8dcl' size='340' side='right'caption='[[8dcl]]' scene=''>	+	<StructureSection load='8dcl' size='340' side='right'caption='[[8dcl]], [[Resolution\|resolution]] 1.55Å' 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=8DCL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8DCL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[8dcl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Campylobacter_jejuni Campylobacter jejuni]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8DCL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8DCL FirstGlance]. <br>
-	</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=8dcl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8dcl OCA], [https://pdbe.org/8dcl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8dcl RCSB], [https://www.ebi.ac.uk/pdbsum/8dcl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8dcl ProSAT]</span></td></tr>	+	</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>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=8dcl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8dcl OCA], [https://pdbe.org/8dcl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8dcl RCSB], [https://www.ebi.ac.uk/pdbsum/8dcl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8dcl ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/Q6EF58_CAMJU Q6EF58_CAMJU]] Catalyzes the epimerization of the C3' and C5'positions of dTDP-6-deoxy-D-xylo-4-hexulose, forming dTDP-6-deoxy-L-lyxo-4-hexulose.[ARBA:ARBA00001997]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Campylobacter jejuni is a human pathogen and one of the leading causes of food poisoning in Europe and the United States. The outside of the bacterium is coated with a capsular polysaccharide that assists in the evasion of the host immune system. Many of the serotyped strains of C. jejuni contain a 6-deoxy-heptose moiety that is biosynthesized from GDP-d-glycero-d-manno-heptose by the successive actions of a 4,6-dehydratase, a C3/C5-epimerase, and a C4-reductase. We identified 18 different C3/C5-epimerases that could be clustered together into three groups at a sequence identity of >89%. Four of the enzymes from the largest cluster (from serotypes HS:3, HS:10, HS:23/36, and HS:41) were shown to only catalyze the epimerization at C3. Three enzymes from the second largest cluster (HS:2, HS:15, and HS:42) were shown to catalyze the epimerization at C3 and C5. Enzymes from the third cluster were not characterized. The three-dimensional structures of the epimerases from serotypes HS:3, HS:23/36, HS:15, and HS:41 were determined to resolutions of 1.5-1.9 A. The overall subunit architecture places these enzymes into the diverse "cupin" superfamily. Within X-ray coordinate error, the immediate regions surrounding the active sites are identical, suggesting that factors extending farther out may influence product outcome. The X-ray crystal structures are consistent with His-67 and Tyr-134 acting as general acid/base catalysts for the epimerization of C3 and/or C5. Two amino acid changes (A76V/C136L) were enough to convert the C3-epimerase from serotype HS:3 to one that could now catalyze the epimerization at both C3 and C5.
		+
		+	C3- and C3/C5-Epimerases Required for the Biosynthesis of the Capsular Polysaccharides from Campylobacter jejuni.,Ghosh MK, Xiang DF, Thoden JB, Holden HM, Raushel FM Biochemistry. 2022 Sep 20;61(18):2036-2048. doi: 10.1021/acs.biochem.2c00364., Epub 2022 Sep 12. PMID:36093987<ref>PMID:36093987</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 8dcl" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Campylobacter jejuni]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Thoden, JB,~~ Ghosh, MK~~, Xiang, DF, Raushel, FM,~~ Holden, HM]]	+	[[Category: Ghosh MK]]
		+	[[Category: Holden HM]]
		+	[[Category: Raushel FM]]
		+	[[Category: Thoden JB]]
		+	[[Category: Xiang DF]]

OCA at 07:29, 29 June 2022

2022-06-29T07:29:46Z

←Older revision		Revision as of 07:29, 29 June 2022
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-	'''Unreleased structure'''

-	~~The entry 8dcl is ON HOLD~~	+	==crystal structure of the GDP-D-GLYCERO-4-KETO-D-LYXO-HEPTOSE-3-EPIMERASE from campylobacter jejuni, serotype HS:23/36==
-		+	<StructureSection load='8dcl' size='340' side='right'caption='[[8dcl]]' scene=''>
-	~~Authors: Thoden, J.B., Ghosh, M.K., Xiang, D.F., Raushel, F.M., Holden, H.M.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8DCL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8DCL FirstGlance]. <br>
-	~~Description:~~ crystal structure of the GDP-D-GLYCERO-4-KETO-D-LYXO-HEPTOSE-3-EPIMERASE from campylobacter jejuni, serotype HS:23/36	+	</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=8dcl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8dcl OCA], [https://pdbe.org/8dcl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8dcl RCSB], [https://www.ebi.ac.uk/pdbsum/8dcl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8dcl ProSAT]</span></td></tr>
-	[[~~Category: Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Thoden, J~~.B]]	+	__TOC__
-	[[~~Category~~: ~~Ghosh~~, M.K]]	+	</StructureSection>
-	[~~[Category~~: ~~Xiang~~, D.F]]	+	[[Category: Large Structures]]
-	[[Category: ~~Holden, H.M~~]]	+	[[Category: Thoden, JB, Ghosh, MK, Xiang, DF, Raushel, FM, Holden, HM]]
-	[[Category: Raushel, ~~F.M~~]]	+

OCA: Protected "8dcl" [edit=sysop:move=sysop]

2022-06-22T07:31:16Z

Protected "8dcl" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:31, 22 June 2022

OCA: New page: '''Unreleased structure''' The entry 8dcl is ON HOLD Authors: Thoden, J.B., Ghosh, M.K., Xiang, D.F., Raushel, F.M., Holden, H.M. Description: crystal structure of the GDP-D-GLYCERO-4-...

2022-06-22T07:31:15Z

New page: '''Unreleased structure''' The entry 8dcl is ON HOLD Authors: Thoden, J.B., Ghosh, M.K., Xiang, D.F., Raushel, F.M., Holden, H.M. Description: crystal structure of the GDP-D-GLYCERO-4-...

New page

'''Unreleased structure'''

The entry 8dcl is ON HOLD

Authors: Thoden, J.B., Ghosh, M.K., Xiang, D.F., Raushel, F.M., Holden, H.M.

Description: crystal structure of the GDP-D-GLYCERO-4-KETO-D-LYXO-HEPTOSE-3-EPIMERASE from campylobacter jejuni, serotype HS:23/36
[[Category: Unreleased Structures]]
[[Category: Thoden, J.B]]
[[Category: Ghosh, M.K]]
[[Category: Xiang, D.F]]
[[Category: Holden, H.M]]
[[Category: Raushel, F.M]]