5bju - Revision history

OCA at 12:17, 6 March 2024

OCA — Wed, 06 Mar 2024 12:17:19 GMT

←Older revision		Revision as of 12:17, 6 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5bju]] 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=5BJU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BJU FirstGlance]. <br>		<table><tr><td colspan='2'>[[5bju]] 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=5BJU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BJU 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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</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='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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</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=5bju FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bju OCA], [https://pdbe.org/5bju PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bju RCSB], [https://www.ebi.ac.uk/pdbsum/5bju PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bju 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=5bju FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bju OCA], [https://pdbe.org/5bju PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bju RCSB], [https://www.ebi.ac.uk/pdbsum/5bju PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bju ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/O86159_CAMJU O86159_CAMJU]		[https://www.uniprot.org/uniprot/O86159_CAMJU O86159_CAMJU]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Within recent years it has become apparent that protein glycosylation is not limited to eukaryotes. Indeed, in Campylobacter jejuni, a Gram-negative bacterium, more than 60 of its proteins are known to be glycosylated. One of the sugars found in such glycosylated proteins is 2,4-diacetamido-2,4,6-trideoxy-alpha-d-glucopyranose, hereafter referred to as QuiNAc4NAc. The pathway for its biosynthesis, initiating with UDP-GlcNAc, requires three enzymes referred to as PglF, PglE, and PlgD. The focus of this investigation is on PglF, an NAD+-dependent sugar 4,6-dehydratase known to belong to the short chain dehydrogenase/reductase (SDR) superfamily. Specifically, PglF catalyzes the first step in the pathway, namely, the dehydration of UDP-GlcNAc to UDP-2-acetamido-2,6-dideoxy-alpha-d-xylo-hexos-4-ulose. Most members of the SDR superfamily contain a characteristic signature sequence of YXXXK where the conserved tyrosine functions as a catalytic acid or a base. Strikingly, in PglF, this residue is a methionine. Here we describe a detailed structural and functional investigation of PglF from C. jejuni. For this investigation five X-ray structures were determined to resolutions of 2.0 A or better. In addition, kinetic analyses of the wild-type and site-directed variants were performed. On the basis of the data reported herein, a new catalytic mechanism for a SDR superfamily member is proposed that does not require the typically conserved tyrosine residue.
-
-	Structural and Biochemical Investigation of PglF from Campylobacter jejuni Reveals a New Mechanism for a Member of the Short Chain Dehydrogenase/Reductase Superfamily.,Riegert AS, Thoden JB, Schoenhofen IC, Watson DC, Young NM, Tipton PA, Holden HM Biochemistry. 2017 Nov 3. doi: 10.1021/acs.biochem.7b00910. PMID:29053280<ref>PMID:29053280</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5bju" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 06:42, 31 May 2023

OCA — Wed, 31 May 2023 06:42:14 GMT

←Older revision		Revision as of 06:42, 31 May 2023
Line 3:		Line 3:
	<StructureSection load='5bju' size='340' side='right'caption='[[5bju]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5bju' size='340' side='right'caption='[[5bju]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5bju]] is a 2 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=5BJU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5BJU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5bju]] 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=5BJU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5BJU 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>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene>~~</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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">wlaL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=197 "Campylobacter fetus subsp. jejuni" Smibert 1974])</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=5bju FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bju OCA], [https://pdbe.org/5bju PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5bju RCSB], [https://www.ebi.ac.uk/pdbsum/5bju PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5bju 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=5bju FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bju OCA], [~~http~~://pdbe.org/5bju PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5bju RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5bju PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5bju ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/O86159_CAMJU O86159_CAMJU]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Campylobacter ~~fetus subsp.~~ jejuni ~~smibert 1974~~]]	+	[[Category: Campylobacter jejuni]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Holden~~, H M~~]]	+	[[Category: Holden HM]]
-	[[Category: Riegert~~, A S~~]]	+	[[Category: Riegert AS]]
-	[[Category: Thoden~~, J B]]~~	+	[[Category: Thoden JB]]
-	~~[[Category: 6-dehydratase]]~~	+
-	~~[[Category: Campylobacter]]~~	+
-	~~[[Category: Deoxysugar]]~~	+
-	~~[[Category: Membrane protein~~]]	+

OCA at 08:51, 1 January 2020

OCA — Wed, 01 Jan 2020 08:51:13 GMT

←Older revision		Revision as of 08:51, 1 January 2020
Line 1:		Line 1:

	==X-ray structure of the PglF dehydratase from Campylobacter jejuni in complex with UDP and NAD(H)==		==X-ray structure of the PglF dehydratase from Campylobacter jejuni in complex with UDP and NAD(H)==
-	<StructureSection load='5bju' size='340' side='right' caption='[[5bju]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='5bju' size='340' side='right'caption='[[5bju]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5bju]] is a 2 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=5BJU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BJU FirstGlance]. <br>		<table><tr><td colspan='2'>[[5bju]] is a 2 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=5BJU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BJU FirstGlance]. <br>
Line 22:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Campylobacter fetus subsp. jejuni smibert 1974]]		[[Category: Campylobacter fetus subsp. jejuni smibert 1974]]
		+	[[Category: Large Structures]]
	[[Category: Holden, H M]]		[[Category: Holden, H M]]
	[[Category: Riegert, A S]]		[[Category: Riegert, A S]]

OCA at 07:22, 29 November 2017

OCA — Wed, 29 Nov 2017 07:22:01 GMT

←Older revision		Revision as of 07:22, 29 November 2017
Line 3:		Line 3:
	<StructureSection load='5bju' size='340' side='right' caption='[[5bju]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5bju' size='340' side='right' caption='[[5bju]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5bju]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BJU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BJU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5bju]] is a 2 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=5BJU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BJU 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>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</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>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">wlaL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=197 "Campylobacter fetus subsp. jejuni" Smibert 1974])</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=5bju FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bju OCA], [http://pdbe.org/5bju PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bju RCSB], [http://www.ebi.ac.uk/pdbsum/5bju PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5bju 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=5bju FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bju OCA], [http://pdbe.org/5bju PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bju RCSB], [http://www.ebi.ac.uk/pdbsum/5bju PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5bju ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Campylobacter fetus subsp. jejuni smibert 1974]]
	[[Category: Holden, H M]]		[[Category: Holden, H M]]
	[[Category: Riegert, A S]]		[[Category: Riegert, A S]]

OCA at 07:32, 8 November 2017

OCA — Wed, 08 Nov 2017 07:32:12 GMT

←Older revision		Revision as of 07:32, 8 November 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5bju is ~~ON HOLD until Paper~~ Publication	+	==X-ray structure of the PglF dehydratase from Campylobacter jejuni in complex with UDP and NAD(H)==
		+	<StructureSection load='5bju' size='340' side='right' caption='[[5bju]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5bju]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BJU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BJU 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>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</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=5bju FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bju OCA], [http://pdbe.org/5bju PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bju RCSB], [http://www.ebi.ac.uk/pdbsum/5bju PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5bju ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Within recent years it has become apparent that protein glycosylation is not limited to eukaryotes. Indeed, in Campylobacter jejuni, a Gram-negative bacterium, more than 60 of its proteins are known to be glycosylated. One of the sugars found in such glycosylated proteins is 2,4-diacetamido-2,4,6-trideoxy-alpha-d-glucopyranose, hereafter referred to as QuiNAc4NAc. The pathway for its biosynthesis, initiating with UDP-GlcNAc, requires three enzymes referred to as PglF, PglE, and PlgD. The focus of this investigation is on PglF, an NAD+-dependent sugar 4,6-dehydratase known to belong to the short chain dehydrogenase/reductase (SDR) superfamily. Specifically, PglF catalyzes the first step in the pathway, namely, the dehydration of UDP-GlcNAc to UDP-2-acetamido-2,6-dideoxy-alpha-d-xylo-hexos-4-ulose. Most members of the SDR superfamily contain a characteristic signature sequence of YXXXK where the conserved tyrosine functions as a catalytic acid or a base. Strikingly, in PglF, this residue is a methionine. Here we describe a detailed structural and functional investigation of PglF from C. jejuni. For this investigation five X-ray structures were determined to resolutions of 2.0 A or better. In addition, kinetic analyses of the wild-type and site-directed variants were performed. On the basis of the data reported herein, a new catalytic mechanism for a SDR superfamily member is proposed that does not require the typically conserved tyrosine residue.

-	~~Authors: Riegert, A.S~~., Thoden, ~~J.B.~~, ~~Holden~~, H.M.	+	Structural and Biochemical Investigation of PglF from Campylobacter jejuni Reveals a New Mechanism for a Member of the Short Chain Dehydrogenase/Reductase Superfamily.,Riegert AS, Thoden JB, Schoenhofen IC, Watson DC, Young NM, Tipton PA, Holden HM Biochemistry. 2017 Nov 3. doi: 10.1021/acs.biochem.7b00910. PMID:29053280<ref>PMID:29053280</ref>

-	~~Description: X-ray structure~~ of the ~~PglF dehydratase from Campylobacter jejuni in complex with UDP and NAD(H)~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Riegert, A.S]]	+	<div class="pdbe-citations 5bju" style="background-color:#fffaf0;"></div>
-	[[Category: Thoden, J.B]]	+	== References ==
-	[[Category: ~~Holden, H.M~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Holden, H M]]
		+	[[Category: Riegert, A S]]
		+	[[Category: Thoden, J B]]
		+	[[Category: 6-dehydratase]]
		+	[[Category: Campylobacter]]
		+	[[Category: Deoxysugar]]
		+	[[Category: Membrane protein]]

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

OCA — Wed, 27 Sep 2017 10:36:45 GMT

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

←Older revision

Revision as of 10:36, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5bju is ON HOLD until Paper Publication Authors: Riegert, A.S., Thoden, J.B., Holden, H.M. Description: X-ray structure of the PglF dehydratase fro...

OCA — Wed, 27 Sep 2017 10:36:43 GMT

New page: '''Unreleased structure''' The entry 5bju is ON HOLD until Paper Publication Authors: Riegert, A.S., Thoden, J.B., Holden, H.M. Description: X-ray structure of the PglF dehydratase fro...

New page

'''Unreleased structure'''

The entry 5bju is ON HOLD until Paper Publication

Authors: Riegert, A.S., Thoden, J.B., Holden, H.M.

Description: X-ray structure of the PglF dehydratase from Campylobacter jejuni in complex with UDP and NAD(H)
[[Category: Unreleased Structures]]
[[Category: Riegert, A.S]]
[[Category: Thoden, J.B]]
[[Category: Holden, H.M]]