5u08 - Revision history

OCA at 13:17, 4 October 2023

OCA — Wed, 04 Oct 2023 13:17:23 GMT

←Older revision		Revision as of 13:17, 4 October 2023
Line 3:		Line 3:
	<StructureSection load='5u08' size='340' side='right'caption='[[5u08]], [[Resolution\|resolution]] 1.52Å' scene=''>		<StructureSection load='5u08' size='340' side='right'caption='[[5u08]], [[Resolution\|resolution]] 1.52Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5u08]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Uncultivated_bacterium Uncultivated~~ bacterium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U08 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5U08 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5u08]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Uncultured_bacterium Uncultured bacterium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U08 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5U08 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SIS:(1S,2S,3R,4S,6R)-4,6-DIAMINO-3-{[(2S,3R)-3-AMINO-6-(AMINOMETHYL)-3,4-DIHYDRO-2H-PYRAN-2-YL]OXY}-2-HYDROXYCYCLOHEXYL+3-DEOXY-4-C-METHYL-3-(METHYLAMINO)-BETA-L-ARABINOPYRANOSIDE'>SIS</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]] 1.52Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hmn\|5hmn]], [[5f46\|5f46]], [[5f48\|5f48]], [[5f47\|5f47]], [[5f49\|5f49]]~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SIS:(1S,2S,3R,4S,6R)-4,6-DIAMINO-3-{[(2S,3R)-3-AMINO-6-(AMINOMETHYL)-3,4-DIHYDRO-2H-PYRAN-2-YL]OXY}-2-HYDROXYCYCLOHEXYL+3-DEOXY-4-C-METHYL-3-(METHYLAMINO)-BETA-L-ARABINOPYRANOSIDE'>SIS</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=5u08 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u08 OCA], [~~http~~://pdbe.org/5u08 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5u08 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5u08 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5u08 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=5u08 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u08 OCA], [https://pdbe.org/5u08 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5u08 RCSB], [https://www.ebi.ac.uk/pdbsum/5u08 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5u08 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A059WZ16_9BACT A0A059WZ16_9BACT]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Uncultivated~~ bacterium]]	+	[[Category: Uncultured bacterium]]
-	[[Category: Anderson~~, W F]]~~	+	[[Category: Anderson WF]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Savchenko A]]
-	[[Category: Savchenko, A]]	+	[[Category: Skarina T]]
-	[[Category: Skarina, T]]	+	[[Category: Stogios PJ]]
-	[[Category: Stogios~~, P J~~]]	+	[[Category: Wawrzak Z]]
-	[[Category: Wawrzak, Z]]	+	[[Category: Xu Z]]
-	[[Category: Xu, Z]]	+	[[Category: Yim V]]
-	[[Category: Yim, V]]	+
-	~~[[Category: Acetyltransferase]]~~	+
-	~~[[Category: Aminoglycoside]]~~	+
-	~~[[Category: Antibiotic resistance]]~~	+
-	~~[[Category: Coenzyme some]]~~	+
-	~~[[Category: Csgid]]~~	+
-	~~[[Category: Gcn5-n-acetyltransferase fold]]~~	+
-	~~[[Category: Gnat fold]]~~	+
-	~~[[Category: Metagenome]]~~	+
-	~~[[Category: Sisomicin]]~~	+
-	~~[[Category: Soil]]~~	+
-	~~[[Category: Transferase-antibiotic complex~~]]	+

OCA at 08:02, 3 April 2019

OCA — Wed, 03 Apr 2019 08:02:48 GMT

←Older revision		Revision as of 08:02, 3 April 2019
Line 1:		Line 1:

-	==Crystal structure of an aminoglycoside acetyltransferase ~~ENV0020~~ from an uncultured soil metagenomic sample in complex with sisomicin==	+	==Crystal structure of an aminoglycoside acetyltransferase meta-AAC0020 from an uncultured soil metagenomic sample in complex with sisomicin==
-	<StructureSection load='5u08' size='340' side='right' caption='[[5u08]], [[Resolution\|resolution]] 1.52Å' scene=''>	+	<StructureSection load='5u08' size='340' side='right'caption='[[5u08]], [[Resolution\|resolution]] 1.52Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5u08]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U08 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5U08 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5u08]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Uncultivated_bacterium Uncultivated bacterium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U08 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5U08 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SIS:(1S,2S,3R,4S,6R)-4,6-DIAMINO-3-{[(2S,3R)-3-AMINO-6-(AMINOMETHYL)-3,4-DIHYDRO-2H-PYRAN-2-YL]OXY}-2-HYDROXYCYCLOHEXYL+3-DEOXY-4-C-METHYL-3-(METHYLAMINO)-BETA-L-ARABINOPYRANOSIDE'>SIS</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SIS:(1S,2S,3R,4S,6R)-4,6-DIAMINO-3-{[(2S,3R)-3-AMINO-6-(AMINOMETHYL)-3,4-DIHYDRO-2H-PYRAN-2-YL]OXY}-2-HYDROXYCYCLOHEXYL+3-DEOXY-4-C-METHYL-3-(METHYLAMINO)-BETA-L-ARABINOPYRANOSIDE'>SIS</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hmn\|5hmn]], [[5f46\|5f46]], [[5f48\|5f48]], [[5f47\|5f47]], [[5f49\|5f49]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hmn\|5hmn]], [[5f46\|5f46]], [[5f48\|5f48]], [[5f47\|5f47]], [[5f49\|5f49]]</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=5u08 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u08 OCA], [http://pdbe.org/5u08 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u08 RCSB], [http://www.ebi.ac.uk/pdbsum/5u08 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u08 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=5u08 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u08 OCA], [http://pdbe.org/5u08 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u08 RCSB], [http://www.ebi.ac.uk/pdbsum/5u08 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u08 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Aminoglycoside N-acetyltransferases (AACs) confer resistance against the clinical use of aminoglycoside antibiotics. The origin of AACs can be traced to environmental microbial species representing a vast reservoir for new and emerging resistance enzymes, which are currently undercharacterized. Here, we performed detailed structural characterization and functional analyses of four metagenomic AAC (meta-AACs) enzymes recently identified in a survey of agricultural and grassland soil microbiomes ( Forsberg et al. Nature 2014 , 509 , 612 ). These enzymes are new members of the Gcn5-Related-N-Acetyltransferase superfamily and confer resistance to the aminoglycosides gentamicin C, sisomicin, and tobramycin. Moreover, the meta-AAC0020 enzyme demonstrated activity comparable with an AAC(3)-I enzyme that serves as a model AAC enzyme identified in a clinical bacterial isolate. The crystal structure of meta-AAC0020 in complex with sisomicin confirmed an unexpected AAC(6') regiospecificity of this enzyme and revealed a drug binding mechanism distinct from previously characterized AAC(6') enzymes. Together, our data highlights the presence of highly active antibiotic-modifying enzymes in the environmental microbiome and reveals unexpected diversity in substrate specificity. These observations of additional AAC enzymes must be considered in the search for novel aminoglycosides less prone to resistance.
		+
		+	Structural and Functional Survey of Environmental Aminoglycoside Acetyltransferases Reveals Functionality of Resistance Enzymes.,Xu Z, Stogios PJ, Quaile AT, Forsberg KJ, Patel S, Skarina T, Houliston S, Arrowsmith C, Dantas G, Savchenko A ACS Infect Dis. 2017 Sep 8;3(9):653-665. doi: 10.1021/acsinfecdis.7b00068. Epub, 2017 Aug 16. PMID:28756664<ref>PMID:28756664</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5u08" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Uncultivated bacterium]]
	[[Category: Anderson, W F]]		[[Category: Anderson, W F]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]

OCA at 09:29, 10 March 2017

OCA — Fri, 10 Mar 2017 09:29:02 GMT

←Older revision		Revision as of 09:29, 10 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5u08 ~~is ON HOLD~~	+	==Crystal structure of an aminoglycoside acetyltransferase ENV0020 from an uncultured soil metagenomic sample in complex with sisomicin==
-		+	<StructureSection load='5u08' size='340' side='right' caption='[[5u08]], [[Resolution\|resolution]] 1.52Å' scene=''>
-	~~Authors~~: ~~Xu, Z~~., ~~Skarina~~, T., ~~Wawrzak~~, Z., ~~Stogios~~, P.J., ~~Yim, V~~., ~~Savchenko, A~~., ~~Anderson~~, W.F., ~~Center for Structural Genomics of Infectious Diseases (CSGID)~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5u08]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5U08 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5U08 FirstGlance]. <br>
-	~~Description: Crystal structure of an aminoglycoside acetyltransferase ENV0020 from an uncultured soil metagenomic sample in complex with sisomicin~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SIS:(1S,2S,3R,4S,6R)-4,6-DIAMINO-3-{[(2S,3R)-3-AMINO-6-(AMINOMETHYL)-3,4-DIHYDRO-2H-PYRAN-2-YL]OXY}-2-HYDROXYCYCLOHEXYL+3-DEOXY-4-C-METHYL-3-(METHYLAMINO)-BETA-L-ARABINOPYRANOSIDE'>SIS</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5hmn\|5hmn]], [[5f46\|5f46]], [[5f48\|5f48]], [[5f47\|5f47]], [[5f49\|5f49]]</td></tr>
-	[[Category: ~~Wawrzak, Z~~]]	+	<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=5u08 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5u08 OCA], [http://pdbe.org/5u08 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5u08 RCSB], [http://www.ebi.ac.uk/pdbsum/5u08 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5u08 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Anderson, W F]]
		+	[[Category: Structural genomic]]
	[[Category: Savchenko, A]]		[[Category: Savchenko, A]]
-	[[Category: Yim, V]]
-	[[Category: Stogios, P.J]]
	[[Category: Skarina, T]]		[[Category: Skarina, T]]
-	[[Category: ~~Anderson~~, ~~W.F~~]]	+	[[Category: Stogios, P J]]
		+	[[Category: Wawrzak, Z]]
	[[Category: Xu, Z]]		[[Category: Xu, Z]]
-	[[Category: ~~Center For Structural Genomics Of Infectious Diseases (~~Csgid)]]	+	[[Category: Yim, V]]
		+	[[Category: Acetyltransferase]]
		+	[[Category: Aminoglycoside]]
		+	[[Category: Antibiotic resistance]]
		+	[[Category: Coenzyme some]]
		+	[[Category: Csgid]]
		+	[[Category: Gcn5-n-acetyltransferase fold]]
		+	[[Category: Gnat fold]]
		+	[[Category: Metagenome]]
		+	[[Category: Sisomicin]]
		+	[[Category: Soil]]
		+	[[Category: Transferase-antibiotic complex]]

OCA: Protected "5u08" [edit=sysop:move=sysop]

OCA — Fri, 09 Dec 2016 18:08:08 GMT

Protected "5u08" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:08, 9 December 2016

OCA: New page: '''Unreleased structure''' The entry 5u08 is ON HOLD Authors: Xu, Z., Skarina, T., Wawrzak, Z., Stogios, P.J., Yim, V., Savchenko, A., Anderson, W.F., Center for Structural Genomics of ...

OCA — Fri, 09 Dec 2016 18:08:06 GMT

New page: '''Unreleased structure''' The entry 5u08 is ON HOLD Authors: Xu, Z., Skarina, T., Wawrzak, Z., Stogios, P.J., Yim, V., Savchenko, A., Anderson, W.F., Center for Structural Genomics of ...

New page

'''Unreleased structure'''

The entry 5u08 is ON HOLD

Authors: Xu, Z., Skarina, T., Wawrzak, Z., Stogios, P.J., Yim, V., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Description: Crystal structure of an aminoglycoside acetyltransferase ENV0020 from an uncultured soil metagenomic sample in complex with sisomicin
[[Category: Unreleased Structures]]
[[Category: Wawrzak, Z]]
[[Category: Savchenko, A]]
[[Category: Yim, V]]
[[Category: Stogios, P.J]]
[[Category: Skarina, T]]
[[Category: Anderson, W.F]]
[[Category: Xu, Z]]
[[Category: Center For Structural Genomics Of Infectious Diseases (Csgid)]]