6vo8 - Revision history

OCA at 08:15, 11 October 2023

OCA — Wed, 11 Oct 2023 08:15:58 GMT

←Older revision		Revision as of 08:15, 11 October 2023
Line 3:		Line 3:
	<StructureSection load='6vo8' size='340' side='right'caption='[[6vo8]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='6vo8' size='340' side='right'caption='[[6vo8]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6vo8]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Camje Camje~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VO8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6VO8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6vo8]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Campylobacter_jejuni_subsp._jejuni_NCTC_11168_=_ATCC_700819 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VO8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6VO8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GZ0:[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+[(2~{R},3~{S},4~{S},5~{S},6~{S})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]+hydrogen+phosphate'>GZ0</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</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]] 2.4Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6vo6\|6vo6]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GZ0:[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+[(2~{R},3~{S},4~{S},5~{S},6~{S})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]+hydrogen+phosphate'>GZ0</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Cj1427c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=192222 CAMJE])</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=6vo8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vo8 OCA], [https://pdbe.org/6vo8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6vo8 RCSB], [https://www.ebi.ac.uk/pdbsum/6vo8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6vo8 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/UDP-glucose_4-epimerase UDP-glucose 4-epimerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.3.2 5.1.3.2] </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=6vo8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vo8 OCA], [~~http~~://pdbe.org/6vo8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6vo8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6vo8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6vo8 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/GMHD_CAMJE GMHD_CAMJE] NAD-dependent dehydrogenase involved in the biosynthesis of heptose moieties with a hydroxyl group at C6 found on the capsular polysaccharide (CPS) of C.jejuni. Catalyzes the initial oxidation of C4 of the GDP-D-glycero-alpha-D-manno-heptose to form GDP-D-glycero-4-keto-alpha-D-lyxo-heptose in the presence of alpha-ketoglutarate required to recycle the NADH nucleotide.<ref>PMID:32168448</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: ~~Camje~~]]	+	[[Category: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: UDP-glucose 4-epimerase]]~~	+	[[Category: Anderson TK]]
-	[[Category: Anderson~~, T K~~]]	+	[[Category: Holden HM]]
-	[[Category: Holden~~, H M~~]]	+	[[Category: Huddleston JP]]
-	[[Category: Huddleston~~, J P~~]]	+	[[Category: Raushel FM]]
-	[[Category: Raushel~~, F M~~]]	+	[[Category: Spencer KD]]
-	[[Category: Spencer~~, K D~~]]	+	[[Category: Thoden JB]]
-	[[Category: Thoden~~, J B]]~~	+
-	~~[[Category: Capsular polysaccharide]]~~	+
-	~~[[Category: Dehydrogenase]]~~	+
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 06:12, 22 April 2020

OCA — Wed, 22 Apr 2020 06:12:42 GMT

←Older revision		Revision as of 06:12, 22 April 2020
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	<StructureSection load='6vo8' size='340' side='right'caption='[[6vo8]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='6vo8' size='340' side='right'caption='[[6vo8]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6vo8]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VO8 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6VO8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6vo8]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Camje Camje]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VO8 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6VO8 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GZ0:[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+[(2~{R},3~{S},4~{S},5~{S},6~{S})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]+hydrogen+phosphate'>GZ0</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GZ0:[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+[(2~{R},3~{S},4~{S},5~{S},6~{S})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]+hydrogen+phosphate'>GZ0</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6vo6\|6vo6]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6vo6\|6vo6]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Cj1427c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=192222 CAMJE])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-glucose_4-epimerase UDP-glucose 4-epimerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.3.2 5.1.3.2] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-glucose_4-epimerase UDP-glucose 4-epimerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.3.2 5.1.3.2] </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=6vo8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vo8 OCA], [http://pdbe.org/6vo8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vo8 RCSB], [http://www.ebi.ac.uk/pdbsum/6vo8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vo8 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=6vo8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vo8 OCA], [http://pdbe.org/6vo8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vo8 RCSB], [http://www.ebi.ac.uk/pdbsum/6vo8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vo8 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Camje]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: UDP-glucose 4-epimerase]]		[[Category: UDP-glucose 4-epimerase]]

OCA at 10:24, 27 March 2020

OCA — Fri, 27 Mar 2020 10:24:12 GMT

←Older revision		Revision as of 10:24, 27 March 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6vo8 is ~~ON HOLD until Paper~~ Publication	+	==X-ray structure of the Cj1427 in the presence of NADH and GDP-D-glycero-D-mannoheptose, an essential NAD-dependent dehydrogenase from Campylobacter jejuni==
		+	<StructureSection load='6vo8' size='340' side='right'caption='[[6vo8]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6vo8]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6VO8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6VO8 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GZ0:[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]+[(2~{R},3~{S},4~{S},5~{S},6~{S})-6-[(1~{S})-1,2-bis(oxidanyl)ethyl]-3,4,5-tris(oxidanyl)oxan-2-yl]+hydrogen+phosphate'>GZ0</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6vo6\|6vo6]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UDP-glucose_4-epimerase UDP-glucose 4-epimerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.3.2 5.1.3.2] </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=6vo8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6vo8 OCA], [http://pdbe.org/6vo8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6vo8 RCSB], [http://www.ebi.ac.uk/pdbsum/6vo8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6vo8 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Many strains of Campylobacter jejuni display modified heptose residues in their capsular polysaccharides (CPS). The precursor heptose was previously shown to be GDP-d-glycero-alpha-d-manno-heptose, from which a variety of modifications of the sugar moiety have been observed. These modifications include the generation of 6-deoxy derivatives and alterations of the stereochemistry at C3-C6. Previous work has focused on the enzymes responsible for the generation of the 6-deoxy derivatives and those involved in altering the stereochemistry at C3 and C5. However, the generation of the 6-hydroxyl heptose residues remains uncertain due to the lack of a specific enzyme to catalyze the initial oxidation at C4 of GDP-d-glycero-alpha-d-manno-heptose. Here we reexamine the previously reported role of Cj1427, a dehydrogenase found in C. jejuni NTCC 11168 (HS:2). We show that Cj1427 is co-purified with bound NADH, thus hindering catalysis of oxidation reactions. However, addition of a co-substrate, alpha-ketoglutarate, converts the bound NADH to NAD(+). In this form, Cj1427 catalyzes the oxidation of l-2-hydroxyglutarate back to alpha-ketoglutarate. The crystal structure of Cj1427 with bound GDP-d-glycero-alpha-d-manno-heptose shows that the NAD(H) cofactor is ideally positioned to catalyze the oxidation at C4 of the sugar substrate. Additionally, the overall fold of the Cj1427 subunit places it into the well-defined short-chain dehydrogenase/reductase superfamily. The observed quaternary structure of the tetrameric enzyme, however, is highly unusual for members of this superfamily.

-	~~Authors: Spencer~~, ~~K.D~~., Anderson, ~~T.K.~~, Thoden, ~~J.B.~~, ~~Huddleston, J~~.P.~~, Raushel, F~~.M.~~, Holden, H~~.M.	+	Structural Analysis of Cj1427, an Essential NAD-Dependent Dehydrogenase for the Biosynthesis of the Heptose Residues in the Capsular Polysaccharides of Campylobacter jejuni.,Huddleston JP, Anderson TK, Spencer KD, Thoden JB, Raushel FM, Holden HM Biochemistry. 2020 Mar 23. doi: 10.1021/acs.biochem.0c00096. PMID:32168450<ref>PMID:32168450</ref>

-	~~Description: X-ray structure~~ of the ~~Cj1427 in the presence~~ of ~~NADH and GDP~~-D-~~glycero~~-D-~~mannoheptose~~, ~~an essential NAD-dependent dehydrogenase from Campylobacter jejuni~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Huddleston, J.P]]	+	<div class="pdbe-citations 6vo8" style="background-color:#fffaf0;"></div>
-	[[Category: Spencer, K.D]]	+	== References ==
-	[[Category: Thoden, J.B]]	+	<references/>
-	[[Category: ~~Raushel, F.M~~]]	+	__TOC__
-	[[Category: ~~Anderson, T.K~~]]	+	</StructureSection>
-	[[Category: ~~Holden, H.M~~]]	+	[[Category: Large Structures]]
		+	[[Category: UDP-glucose 4-epimerase]]
		+	[[Category: Anderson, T K]]
		+	[[Category: Holden, H M]]
		+	[[Category: Huddleston, J P]]
		+	[[Category: Raushel, F M]]
		+	[[Category: Spencer, K D]]
		+	[[Category: Thoden, J B]]
		+	[[Category: Capsular polysaccharide]]
		+	[[Category: Dehydrogenase]]
		+	[[Category: Isomerase]]
		+	[[Category: Oxidoreductase]]

OCA at 02:41, 13 February 2020

OCA — Thu, 13 Feb 2020 02:41:30 GMT

←Older revision		Revision as of 02:41, 13 February 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6vo8 is ON HOLD	+	The entry 6vo8 is ON HOLD until Paper Publication

	Authors: Spencer, K.D., Anderson, T.K., Thoden, J.B., Huddleston, J.P., Raushel, F.M., Holden, H.M.		Authors: Spencer, K.D., Anderson, T.K., Thoden, J.B., Huddleston, J.P., Raushel, F.M., Holden, H.M.
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	Description: X-ray structure of the Cj1427 in the presence of NADH and GDP-D-glycero-D-mannoheptose, an essential NAD-dependent dehydrogenase from Campylobacter jejuni		Description: X-ray structure of the Cj1427 in the presence of NADH and GDP-D-glycero-D-mannoheptose, an essential NAD-dependent dehydrogenase from Campylobacter jejuni
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Thoden, J.B]]
-	[[Category: Anderson, T.K]]
-	[[Category: Holden, H.M]]
	[[Category: Huddleston, J.P]]		[[Category: Huddleston, J.P]]
	[[Category: Spencer, K.D]]		[[Category: Spencer, K.D]]
		+	[[Category: Thoden, J.B]]
	[[Category: Raushel, F.M]]		[[Category: Raushel, F.M]]
		+	[[Category: Anderson, T.K]]
		+	[[Category: Holden, H.M]]

OCA: Protected "6vo8" [edit=sysop:move=sysop]

OCA — Wed, 05 Feb 2020 06:23:21 GMT

Protected "6vo8" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:23, 5 February 2020

OCA: New page: '''Unreleased structure''' The entry 6vo8 is ON HOLD Authors: Spencer, K.D., Anderson, T.K., Thoden, J.B., Huddleston, J.P., Raushel, F.M., Holden, H.M. Description: X-ray structure of...

OCA — Wed, 05 Feb 2020 06:23:19 GMT

New page: '''Unreleased structure''' The entry 6vo8 is ON HOLD Authors: Spencer, K.D., Anderson, T.K., Thoden, J.B., Huddleston, J.P., Raushel, F.M., Holden, H.M. Description: X-ray structure of...

New page

'''Unreleased structure'''

The entry 6vo8 is ON HOLD

Authors: Spencer, K.D., Anderson, T.K., Thoden, J.B., Huddleston, J.P., Raushel, F.M., Holden, H.M.

Description: X-ray structure of the Cj1427 in the presence of NADH and GDP-D-glycero-D-mannoheptose, an essential NAD-dependent dehydrogenase from Campylobacter jejuni
[[Category: Unreleased Structures]]
[[Category: Thoden, J.B]]
[[Category: Anderson, T.K]]
[[Category: Holden, H.M]]
[[Category: Huddleston, J.P]]
[[Category: Spencer, K.D]]
[[Category: Raushel, F.M]]