7txs - Revision history

OCA at 17:09, 18 October 2023

OCA — Wed, 18 Oct 2023 17:09:09 GMT

←Older revision		Revision as of 17:09, 18 October 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7txs]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Acinetobacter_baumannii Acinetobacter baumannii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7TXS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TXS FirstGlance]. <br>		<table><tr><td colspan='2'>[[7txs]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Acinetobacter_baumannii Acinetobacter baumannii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7TXS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TXS FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NH9:[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methyl+(3R)-4-({3-[(2-{[(1S)-1-{[(2R,3S,4S,5R,6R)-4,5-dihydroxy-6-{[(R)-hydroxy{[(R)-hydroxy{[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)oxolan-2-yl]methoxy}phosphoryl]oxy}phosphoryl]oxy}-2-methyloxan-3-yl]amino}ethyl]sulfanyl}ethyl)amino]-3-oxopropyl}amino)-3-hydroxy-2,2-dimethyl-4-oxobutyl+dihydrogen+diphosphate+(non-preferred+name)'>NH9</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]] 1.25Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NH9:[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methyl+(3R)-4-({3-[(2-{[(1S)-1-{[(2R,3S,4S,5R,6R)-4,5-dihydroxy-6-{[(R)-hydroxy{[(R)-hydroxy{[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)oxolan-2-yl]methoxy}phosphoryl]oxy}phosphoryl]oxy}-2-methyloxan-3-yl]amino}ethyl]sulfanyl}ethyl)amino]-3-oxopropyl}amino)-3-hydroxy-2,2-dimethyl-4-oxobutyl+dihydrogen+diphosphate+(non-preferred+name)'>NH9</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=7txs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7txs OCA], [https://pdbe.org/7txs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7txs RCSB], [https://www.ebi.ac.uk/pdbsum/7txs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7txs 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=7txs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7txs OCA], [https://pdbe.org/7txs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7txs RCSB], [https://www.ebi.ac.uk/pdbsum/7txs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7txs ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/A0A334FGR6_ACIBA A0A334FGR6_ACIBA]]	+	[https://www.uniprot.org/uniprot/A0A334FGR6_ACIBA A0A334FGR6_ACIBA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 05:31, 8 September 2022

OCA — Thu, 08 Sep 2022 05:31:03 GMT

←Older revision		Revision as of 05:31, 8 September 2022
Line 3:		Line 3:
	<StructureSection load='7txs' size='340' side='right'caption='[[7txs]], [[Resolution\|resolution]] 1.25Å' scene=''>		<StructureSection load='7txs' size='340' side='right'caption='[[7txs]], [[Resolution\|resolution]] 1.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7txs]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7TXS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TXS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7txs]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Acinetobacter_baumannii Acinetobacter baumannii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7TXS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TXS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NH9:[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methyl+(3R)-4-({3-[(2-{[(1S)-1-{[(2R,3S,4S,5R,6R)-4,5-dihydroxy-6-{[(R)-hydroxy{[(R)-hydroxy{[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)oxolan-2-yl]methoxy}phosphoryl]oxy}phosphoryl]oxy}-2-methyloxan-3-yl]amino}ethyl]sulfanyl}ethyl)amino]-3-oxopropyl}amino)-3-hydroxy-2,2-dimethyl-4-oxobutyl+dihydrogen+diphosphate+(non-preferred+name)'>NH9</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NH9:[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methyl+(3R)-4-({3-[(2-{[(1S)-1-{[(2R,3S,4S,5R,6R)-4,5-dihydroxy-6-{[(R)-hydroxy{[(R)-hydroxy{[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)oxolan-2-yl]methoxy}phosphoryl]oxy}phosphoryl]oxy}-2-methyloxan-3-yl]amino}ethyl]sulfanyl}ethyl)amino]-3-oxopropyl}amino)-3-hydroxy-2,2-dimethyl-4-oxobutyl+dihydrogen+diphosphate+(non-preferred+name)'>NH9</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7txp\|7txp]], [[7txq\|7txq]]</div></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=7txs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7txs OCA], [https://pdbe.org/7txs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7txs RCSB], [https://www.ebi.ac.uk/pdbsum/7txs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7txs 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=7txs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7txs OCA], [https://pdbe.org/7txs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7txs RCSB], [https://www.ebi.ac.uk/pdbsum/7txs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7txs ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/A0A334FGR6_ACIBA A0A334FGR6_ACIBA]]
	<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: Large Structures]]
-	[[Category: Herkert, N R]]
-	[[Category: Holden, H M]]
-	[[Category: Thoden, J B]]
-	[[Category: 4-amino-4]]
-	[[Category: 6-dideoxy-d-glucose]]
	[[Category: Acinetobacter baumannii]]		[[Category: Acinetobacter baumannii]]
-	[[Category: ~~Beta helix~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~N-acetyltransferase~~]]	+	[[Category: Herkert NR]]
-	[[Category: ~~Transferase~~]]	+	[[Category: Holden HM]]
		+	[[Category: Thoden JB]]

OCA at 11:18, 30 March 2022

OCA — Wed, 30 Mar 2022 11:18:23 GMT

←Older revision		Revision as of 11:18, 30 March 2022
Line 1:		Line 1:

	==X-ray structure of the VioB N-aetyltransferase from Acinetobacter baumannii in the presence of a reaction intermediate==		==X-ray structure of the VioB N-aetyltransferase from Acinetobacter baumannii in the presence of a reaction intermediate==
-	<StructureSection load='7txs' size='340' side='right'caption='[[7txs]]' scene=''>	+	<StructureSection load='7txs' size='340' side='right'caption='[[7txs]], [[Resolution\|resolution]] 1.25Å' 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=7TXS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TXS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7txs]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7TXS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TXS 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=7txs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7txs OCA], [https://pdbe.org/7txs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7txs RCSB], [https://www.ebi.ac.uk/pdbsum/7txs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7txs 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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NH9:[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methyl+(3R)-4-({3-[(2-{[(1S)-1-{[(2R,3S,4S,5R,6R)-4,5-dihydroxy-6-{[(R)-hydroxy{[(R)-hydroxy{[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)oxolan-2-yl]methoxy}phosphoryl]oxy}phosphoryl]oxy}-2-methyloxan-3-yl]amino}ethyl]sulfanyl}ethyl)amino]-3-oxopropyl}amino)-3-hydroxy-2,2-dimethyl-4-oxobutyl+dihydrogen+diphosphate+(non-preferred+name)'>NH9</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[7txp\|7txp]], [[7txq\|7txq]]</div></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=7txs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7txs OCA], [https://pdbe.org/7txs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7txs RCSB], [https://www.ebi.ac.uk/pdbsum/7txs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7txs ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Acinetobacter baumannii is a Gram-negative bacterium commonly found in soil and water that can cause human infections of the blood, lungs, and urinary tract. Of particular concern is its prevalence in healthcare settings where it can survive on surfaces and shared equipment for extended periods of time. The capsular polysaccharide surrounding the organism is known to be the major contributor to virulence. The structure of the K57 capsular polysaccharide produced by A. baumannii isolate BAL_212 from Vietnam was recently shown to contain the rare sugar 4-acetamido-4,6-dideoxy-d-glucose. Three enzymes are required for its biosynthesis, one of which is encoded by the gene H6W49_RS17300 and referred to as VioB, a putative N-acetyltransferase. Here we describe a combined structural and functional analysis of VioB. Kinetic analyses show that the enzyme does, indeed, function on dTDP-4-amino-4,6-dideoxy-d-glucose with a catalytic efficiency of 3.9 x 10(4) M(-1) s(-1) (+/- 6000), albeit at a reduced value compared to similar enzymes. Three high-resolution X-ray structures of various enzyme/ligand complexes were determined to resolutions of 1.65 A or better. One of these models represents an intermediate analogue of the tetrahedral transition state. Differences between the VioB structure and those determined for the N-acetyltransferases from Campylobacter jejuni (PglD), Caulobacter crescentus (PerB), and Psychrobacter cryohalolentis (Pcryo_0637) are highlighted. Taken together this investigation sheds new insight into the Type I sugar N-acetyltransferases. This article is protected by copyright. All rights reserved.
		+
		+	Structure and Function of an N-acetyltransferase from the Human Pathogen Acinetobacter baumannii Isolate BAL_212.,Herkert NR, Thoden JB, Holden HM Proteins. 2022 Mar 11. doi: 10.1002/prot.26334. PMID:35277885<ref>PMID:35277885</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7txs" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Herkert NR]]	+	[[Category: Herkert, N R]]
-	[[Category: Holden HM]]	+	[[Category: Holden, H M]]
-	[[Category: Thoden JB]]	+	[[Category: Thoden, J B]]
		+	[[Category: 4-amino-4]]
		+	[[Category: 6-dideoxy-d-glucose]]
		+	[[Category: Acinetobacter baumannii]]
		+	[[Category: Beta helix]]
		+	[[Category: N-acetyltransferase]]
		+	[[Category: Transferase]]

OCA at 06:08, 9 March 2022

OCA — Wed, 09 Mar 2022 06:08:11 GMT

←Older revision		Revision as of 06:08, 9 March 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 7txs is ON HOLD~~	+	==X-ray structure of the VioB N-aetyltransferase from Acinetobacter baumannii in the presence of a reaction intermediate==
-		+	<StructureSection load='7txs' size='340' side='right'caption='[[7txs]]' scene=''>
-	~~Authors: Herkert, N.R., Thoden, J.B., 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=7TXS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7TXS FirstGlance]. <br>
-	~~Description:~~ X-ray structure of the VioB N-aetyltransferase from Acinetobacter baumannii in the presence of a reaction intermediate	+	</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=7txs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7txs OCA], [https://pdbe.org/7txs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7txs RCSB], [https://www.ebi.ac.uk/pdbsum/7txs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7txs ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Thoden, J.B~~]]	+	__TOC__
-	[[Category: Holden~~, H.M~~]]	+	</StructureSection>
-	[[Category: ~~Herkert, N.R~~]]	+	[[Category: Large Structures]]
		+	[[Category: Herkert NR]]
		+	[[Category: Holden HM]]
		+	[[Category: Thoden JB]]

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

OCA — Wed, 16 Feb 2022 09:13:42 GMT

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

←Older revision

Revision as of 09:13, 16 February 2022

OCA: New page: '''Unreleased structure''' The entry 7txs is ON HOLD Authors: Herkert, N.R., Thoden, J.B., Holden, H.M. Description: X-ray structure of the VioB N-aetyltransferase from Acinetobacter b...

OCA — Wed, 16 Feb 2022 09:13:41 GMT

New page: '''Unreleased structure''' The entry 7txs is ON HOLD Authors: Herkert, N.R., Thoden, J.B., Holden, H.M. Description: X-ray structure of the VioB N-aetyltransferase from Acinetobacter b...

New page

'''Unreleased structure'''

The entry 7txs is ON HOLD

Authors: Herkert, N.R., Thoden, J.B., Holden, H.M.

Description: X-ray structure of the VioB N-aetyltransferase from Acinetobacter baumannii in the presence of a reaction intermediate
[[Category: Unreleased Structures]]
[[Category: Thoden, J.B]]
[[Category: Holden, H.M]]
[[Category: Herkert, N.R]]