5tpu - Revision history

OCA at 13:07, 4 October 2023

OCA — Wed, 04 Oct 2023 13:07:18 GMT

←Older revision		Revision as of 13:07, 4 October 2023
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	<StructureSection load='5tpu' size='340' side='right'caption='[[5tpu]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5tpu' size='340' side='right'caption='[[5tpu]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5tpu]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"campylobacter_fetus_subsp._jejuni"_smibert_1974 "campylobacter fetus subsp.~~ jejuni~~" smibert 1974~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TPU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5TPU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5tpu]] is a 4 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=5TPU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5TPU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=TYD:THYMIDINE-5-DIPHOSPHATE'>TYD</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]] 2Å</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=5tpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tpu OCA], [~~http~~://pdbe.org/5tpu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5tpu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5tpu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5tpu ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=TYD:THYMIDINE-5-DIPHOSPHATE'>TYD</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=5tpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tpu OCA], [https://pdbe.org/5tpu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5tpu RCSB], [https://www.ebi.ac.uk/pdbsum/5tpu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5tpu ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9ALS4_CAMJU Q9ALS4_CAMJU]
	<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: Campylobacter ~~fetus subsp.~~ jejuni ~~smibert 1974~~]]	+	[[Category: Campylobacter jejuni]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cunningham~~, A M~~]]	+	[[Category: Cunningham AM]]
-	[[Category: Gilbert, M]]	+	[[Category: Gilbert M]]
-	[[Category: Goneau, M F]]	+	[[Category: Goneau M-F]]
-	[[Category: Holden~~, H M~~]]	+	[[Category: Holden HM]]
-	[[Category: Li~~, J Z~~]]	+	[[Category: Li JZ]]
-	[[Category: Riegert~~, A S~~]]	+	[[Category: Riegert AS]]
-	[[Category: Schoenhofen~~, I C~~]]	+	[[Category: Schoenhofen IC]]
-	[[Category: Thoden~~, J B~~]]	+	[[Category: Thoden JB]]
-	[[Category: Vinogradov, E]]	+	[[Category: Vinogradov E]]
-	~~[[Category: Deoxy-sugar]]~~	+
-	~~[[Category: Isomerase]]~~	+
-	~~[[Category: Ketoisomerase]]~~	+
-	~~[[Category: Quinovose~~]]	+

OCA at 09:04, 1 January 2020

OCA — Wed, 01 Jan 2020 09:04:25 GMT

←Older revision		Revision as of 09:04, 1 January 2020
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	==x-ray structure of the WlaRB TDP-quinovose 3,4-ketoisomerase from campylobacter jejuni==		==x-ray structure of the WlaRB TDP-quinovose 3,4-ketoisomerase from campylobacter jejuni==
-	<StructureSection load='5tpu' size='340' side='right' caption='[[5tpu]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='5tpu' size='340' side='right'caption='[[5tpu]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5tpu]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"campylobacter_fetus_subsp._jejuni"_smibert_1974 "campylobacter fetus subsp. jejuni" smibert 1974]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TPU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TPU FirstGlance]. <br>		<table><tr><td colspan='2'>[[5tpu]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"campylobacter_fetus_subsp._jejuni"_smibert_1974 "campylobacter fetus subsp. jejuni" smibert 1974]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TPU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TPU FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: Campylobacter fetus subsp. jejuni smibert 1974]]		[[Category: Campylobacter fetus subsp. jejuni smibert 1974]]
		+	[[Category: Large Structures]]
	[[Category: Cunningham, A M]]		[[Category: Cunningham, A M]]
	[[Category: Gilbert, M]]		[[Category: Gilbert, M]]

OCA at 14:26, 6 November 2017

OCA — Mon, 06 Nov 2017 14:26:19 GMT

←Older revision		Revision as of 14:26, 6 November 2017
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	<StructureSection load='5tpu' size='340' side='right' caption='[[5tpu]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5tpu' size='340' side='right' caption='[[5tpu]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5tpu]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TPU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TPU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5tpu]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"campylobacter_fetus_subsp._jejuni"_smibert_1974 "campylobacter fetus subsp. jejuni" smibert 1974]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TPU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TPU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=TYD:THYMIDINE-5-DIPHOSPHATE'>TYD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=TYD:THYMIDINE-5-DIPHOSPHATE'>TYD</scene></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=5tpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tpu OCA], [http://pdbe.org/5tpu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tpu RCSB], [http://www.ebi.ac.uk/pdbsum/5tpu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tpu 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=5tpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tpu OCA], [http://pdbe.org/5tpu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tpu RCSB], [http://www.ebi.ac.uk/pdbsum/5tpu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tpu ProSAT]</span></td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Campylobacter fetus subsp. jejuni smibert 1974]]
	[[Category: Cunningham, A M]]		[[Category: Cunningham, A M]]
	[[Category: Gilbert, M]]		[[Category: Gilbert, M]]

OCA at 17:57, 1 February 2017

OCA — Wed, 01 Feb 2017 17:57:14 GMT

←Older revision		Revision as of 17:57, 1 February 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5tpu is ~~ON HOLD until Paper~~ Publication	+	==x-ray structure of the WlaRB TDP-quinovose 3,4-ketoisomerase from campylobacter jejuni==
		+	<StructureSection load='5tpu' size='340' side='right' caption='[[5tpu]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5tpu]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5TPU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5TPU FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=TYD:THYMIDINE-5-DIPHOSPHATE'>TYD</scene></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=5tpu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5tpu OCA], [http://pdbe.org/5tpu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5tpu RCSB], [http://www.ebi.ac.uk/pdbsum/5tpu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5tpu ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The Gram-negative bacterium Campylobacter jejuni 81116 (Penner serotype HS:6) has a class E lipooligosaccharide (LOS) biosynthesis locus containing 19 genes, which encode for 11 putative glycosyltransferases, 1 lipid A acyltransferase and 7 enzymes thought to be involved in the biosynthesis of dideoxyhexosamine (ddHexN) moieties. Although the LOS outer core structure of C. jejuni 81116 is still unknown, recent mass spectrometry analyses suggest that it contains acetylated forms of two ddHexN residues. For this investigation, five of the genes encoding enzymes reportedly involved in the biosyntheses of these sugar residues were examined, rmlA, rmlB, wlaRA, wlaRB and wlaRG Specifically, these genes were cloned and expressed in Escherichia coli, and the corresponding enzymes were purified and tested for biochemical activity. Here we present data demonstrating that RmlA functions as a glucose-1-phosphate thymidylyltransferase and that RmlB is a thymidine diphosphate (dTDP)-glucose 4,6-dehydratase. We also show, through nuclear magnetic resonance spectroscopy and mass spectrometry analyses, that WlaRG, when utilized in coupled assays with either WlaRA or WlaRB and dTDP-4-keto-6-deoxyglucose, results in the production of either dTDP-3-amino-3,6-dideoxy-d-galactose (dTDP-Fuc3N) or dTDP-3-amino-3,6-dideoxy-d-glucose (dTDP-Qui3N), respectively. In addition, the X-ray crystallographic structures of the 3,4-ketoisomerases, WlaRA and WlaRB, were determined to 2.14 and 2.0 A resolutions, respectively. Taken together, the data reported herein demonstrate that C. jejuni 81116 utilizes five enzymes to synthesize dTDP-Fuc3N or dTDP-Qui3N and that WlaRG, an aminotransferase, can function on sugars with differing stereochemistry about their C-4' carbons. Importantly, the data reveal that C. jejuni 81116 has the ability to synthesize two isomeric ddHexN forms.

-	~~Authors: Holden, H.M., Thoden, J.B~~., Li~~, J.Z.~~, Riegert~~, A.S.~~, Goneau~~, M.-F.~~, Cunningham~~, A.M.~~, Vinogradov, E., Schoenhofen, ~~I.C.~~, ~~Gilbert~~, M.	+	Characterization of the dTDP-Fuc3N and dTDP-Qui3N biosynthetic pathways in Campylobacter jejuni 81116dagger.,Li ZZ, Riegert AS, Goneau MF, Cunningham AM, Vinogradov E, Li J, Schoenhofen IC, Thoden JB, Holden HM, Gilbert M Glycobiology. 2017 Jan 16. pii: cww136. doi: 10.1093/glycob/cww136. PMID:28096310<ref>PMID:28096310</ref>

-	~~Description: x-ray structure~~ of the ~~WlaRB TDP~~-~~quinovose 3,4~~-~~ketoisomerase from campylobacter jejuni~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	~~[[Category: Schoenhofen, I.C]]~~	+	<div class="pdbe-citations 5tpu" style="background-color:#fffaf0;"></div>
-	~~[[Category: Riegert, A.S]]~~	+	== References ==
-	~~[[Category: Vinogradov, E]]~~	+	<references/>
-	~~[[Category: Thoden, J.B]]~~	+	__TOC__
-	[[Category: Li, ~~J.Z]]~~	+	</StructureSection>
-	~~[[Category: Holden, H.~~M]]	+	[[Category: Cunningham, A M]]
-	~~[[Category: Goneau, M.-F~~]]	+
	[[Category: Gilbert, M]]		[[Category: Gilbert, M]]
-	[[Category: ~~Cunningham~~, A.M]]	+	[[Category: Goneau, M F]]
		+	[[Category: Holden, H M]]
		+	[[Category: Li, J Z]]
		+	[[Category: Riegert, A S]]
		+	[[Category: Schoenhofen, I C]]
		+	[[Category: Thoden, J B]]
		+	[[Category: Vinogradov, E]]
		+	[[Category: Deoxy-sugar]]
		+	[[Category: Isomerase]]
		+	[[Category: Ketoisomerase]]
		+	[[Category: Quinovose]]

OCA at 17:44, 9 December 2016

OCA — Fri, 09 Dec 2016 17:44:05 GMT

←Older revision		Revision as of 17:44, 9 December 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5tpu is ON HOLD	+	The entry 5tpu is ON HOLD until Paper Publication

	Authors: Holden, H.M., Thoden, J.B., Li, J.Z., Riegert, A.S., Goneau, M.-F., Cunningham, A.M., Vinogradov, E., Schoenhofen, I.C., Gilbert, M.		Authors: Holden, H.M., Thoden, J.B., Li, J.Z., Riegert, A.S., Goneau, M.-F., Cunningham, A.M., Vinogradov, E., Schoenhofen, I.C., Gilbert, M.

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

OCA — Wed, 02 Nov 2016 17:00:49 GMT

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

←Older revision

Revision as of 17:00, 2 November 2016

OCA: New page: '''Unreleased structure''' The entry 5tpu is ON HOLD Authors: Holden, H.M., Thoden, J.B., Li, J.Z., Riegert, A.S., Goneau, M.-F., Cunningham, A.M., Vinogradov, E., Schoenhofen, I.C., Gi...

OCA — Wed, 02 Nov 2016 17:00:47 GMT

New page: '''Unreleased structure''' The entry 5tpu is ON HOLD Authors: Holden, H.M., Thoden, J.B., Li, J.Z., Riegert, A.S., Goneau, M.-F., Cunningham, A.M., Vinogradov, E., Schoenhofen, I.C., Gi...

New page

'''Unreleased structure'''

The entry 5tpu is ON HOLD

Authors: Holden, H.M., Thoden, J.B., Li, J.Z., Riegert, A.S., Goneau, M.-F., Cunningham, A.M., Vinogradov, E., Schoenhofen, I.C., Gilbert, M.

Description: x-ray structure of the WlaRB TDP-quinovose 3,4-ketoisomerase from campylobacter jejuni
[[Category: Unreleased Structures]]
[[Category: Schoenhofen, I.C]]
[[Category: Riegert, A.S]]
[[Category: Vinogradov, E]]
[[Category: Thoden, J.B]]
[[Category: Li, J.Z]]
[[Category: Holden, H.M]]
[[Category: Goneau, M.-F]]
[[Category: Gilbert, M]]
[[Category: Cunningham, A.M]]