7bvj - Revision history

OCA at 15:36, 29 November 2023

OCA — Wed, 29 Nov 2023 15:36:43 GMT

←Older revision		Revision as of 15:36, 29 November 2023
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	<StructureSection load='7bvj' size='340' side='right'caption='[[7bvj]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='7bvj' size='340' side='right'caption='[[7bvj]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7bvj]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Acif2 Acif2~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BVJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=7BVJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7bvj]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Acidithiobacillus_ferrooxidans_ATCC_23270 Acidithiobacillus ferrooxidans ATCC 23270]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BVJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BVJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=F8U:(2R,3R)-2,3-bis(oxidanyl)butane-1,4-disulfonic+acid'>F8U</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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]] 2.15Å</td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AFE_1457 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243159 ACIF2])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=F8U:(2R,3R)-2,3-bis(oxidanyl)butane-1,4-disulfonic+acid'>F8U</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></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=7bvj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bvj OCA], [~~http~~://pdbe.org/7bvj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7bvj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7bvj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7bvj 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=7bvj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bvj OCA], [https://pdbe.org/7bvj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bvj RCSB], [https://www.ebi.ac.uk/pdbsum/7bvj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bvj ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/B7JA34_ACIF2 B7JA34_ACIF2]
	<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: ~~Acif2~~]]	+	[[Category: Acidithiobacillus ferrooxidans ATCC 23270]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Wangkanont, K]]	+	[[Category: Wangkanont K]]
-	~~[[Category: Gnna]]~~	+
-	~~[[Category: Lipopolysaccharide]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Udp-glcnac]]~~	+
-	~~[[Category: Udp-n-acetylglucosamine 3-dehydrogenase~~]]	+

OCA at 07:04, 30 December 2020

OCA — Wed, 30 Dec 2020 07:04:12 GMT

←Older revision		Revision as of 07:04, 30 December 2020
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	==UDP-N-acetylglucosamine 3-dehydrogenase GnnA from Acidithiobacillus ferrooxidans (P21)==		==UDP-N-acetylglucosamine 3-dehydrogenase GnnA from Acidithiobacillus ferrooxidans (P21)==
-	<StructureSection load='7bvj' size='340' side='right'caption='[[7bvj]]' scene=''>	+	<StructureSection load='7bvj' size='340' side='right'caption='[[7bvj]], [[Resolution\|resolution]] 2.15Å' 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=7BVJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7BVJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7bvj]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Acif2 Acif2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BVJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7BVJ 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=7bvj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bvj OCA], [http://pdbe.org/7bvj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7bvj RCSB], [http://www.ebi.ac.uk/pdbsum/7bvj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7bvj 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=F8U:(2R,3R)-2,3-bis(oxidanyl)butane-1,4-disulfonic+acid'>F8U</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AFE_1457 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243159 ACIF2])</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=7bvj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bvj OCA], [http://pdbe.org/7bvj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7bvj RCSB], [http://www.ebi.ac.uk/pdbsum/7bvj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7bvj ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Lipopolysaccharide (LPS) is a crucial component in the outer membrane of Gram-negative bacteria that contributes to both pathogenicity as well as immunity against pathogenic bacteria. Typical LPS contains GlcN disaccharide as the core of lipid A. However, some bacteria such as Acidithiobacillus ferrooxidans and Leptospira interrogans contain GlcN3N in lipid A instead. This modification has been shown to dampen the host immune response and increase resistance to antimicrobial peptides. Therefore, investigation of the enzymes responsible for the biosynthesis of GlcN3N has promising applications in the development of vaccines, antibiotics, or usage of the enzymes in chemoenzymatic synthesis of modified LPS. Here, we describe biochemical and structural investigation of GnnA from A. ferrooxidans (AfGnnA) that is responsible for oxidation of UDP-GlcNAc, which subsequently undergoes transamination to produce UDP-GlcNAc3N as a precursor for LPS biosynthesis. AfGnnA is specific for NAD(+) and UDP-GlcNAc. The crystal structures of AfGnnA in combination with molecular dynamics simulation and mutational analysis suggest the substrate recognition mode and the catalytic mechanism. K91 or H164 is a potential catalytic base in the oxidation reaction. The results will not only provide insights into the biosynthesis of unusual LPS but will also lay the foundation for development of more immunogenic vaccines, novel antibiotics, or utilization of GnnA in the synthesis of UDP-sugars or modified LPS.
		+
		+	Biochemical and Structural Investigation of GnnA in the Lipopolysaccharide Biosynthesis Pathway of Acidithiobacillus ferrooxidans.,Manissorn J, Sitthiyotha T, Montalban JRE, Chunsrivirot S, Thongnuek P, Wangkanont K ACS Chem Biol. 2020 Dec 18;15(12):3235-3243. doi: 10.1021/acschembio.0c00791., Epub 2020 Nov 17. PMID:33200610<ref>PMID:33200610</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7bvj" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Acif2]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Wangkanont K]]	+	[[Category: Wangkanont, K]]
		+	[[Category: Gnna]]
		+	[[Category: Lipopolysaccharide]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Udp-glcnac]]
		+	[[Category: Udp-n-acetylglucosamine 3-dehydrogenase]]

OCA at 07:54, 2 December 2020

OCA — Wed, 02 Dec 2020 07:54:14 GMT

←Older revision		Revision as of 07:54, 2 December 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 7bvj ~~is ON HOLD until Paper Publication~~	+	==UDP-N-acetylglucosamine 3-dehydrogenase GnnA from Acidithiobacillus ferrooxidans (P21)==
-		+	<StructureSection load='7bvj' size='340' side='right'caption='[[7bvj]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BVJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7BVJ 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=7bvj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bvj OCA], [http://pdbe.org/7bvj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7bvj RCSB], [http://www.ebi.ac.uk/pdbsum/7bvj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7bvj ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Wangkanont K]]

OCA: Protected "7bvj" [edit=sysop:move=sysop]

OCA — Wed, 22 Apr 2020 04:36:12 GMT

Protected "7bvj" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:36, 22 April 2020

OCA: New page: '''Unreleased structure''' The entry 7bvj is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 22 Apr 2020 04:36:10 GMT

New page: '''Unreleased structure''' The entry 7bvj is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7bvj is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]