6mmz - Revision history

OCA at 06:34, 11 October 2023

2023-10-11T06:34:32Z

←Older revision		Revision as of 06:34, 11 October 2023
Line 3:		Line 3:
	<StructureSection load='6mmz' size='340' side='right'caption='[[6mmz]], [[Resolution\|resolution]] 3.30Å' scene=''>		<StructureSection load='6mmz' size='340' side='right'caption='[[6mmz]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6mmz]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Uncultivated_bacterium Uncultivated~~ bacterium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MMZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MMZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6mmz]] is a 6 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=6MMZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MMZ FirstGlance]. <br>
-	</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=SO4:SULFATE+ION'>SO4</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]] 3.3Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</scene><~~/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=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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;~~'>~~[[5ht0\|5ht0]]~~</~~div~~><~~/td></tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>[https://en.wikipedia.org/wiki/Aminoglycoside_N(3')-acetyltransferase Aminoglycoside N(3')-acetyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.81 2.3.1.81] </~~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=6mmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mmz OCA], [https://pdbe.org/6mmz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6mmz RCSB], [https://www.ebi.ac.uk/pdbsum/6mmz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6mmz 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=6mmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mmz OCA], [https://pdbe.org/6mmz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6mmz RCSB], [https://www.ebi.ac.uk/pdbsum/6mmz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6mmz ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A059X981_9BACT A0A059X981_9BACT]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Uncultivated~~ bacterium]]	+	[[Category: Uncultured bacterium]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Joachimiak A]]
-	[[Category: Joachimiak, A]]	+	[[Category: Satchell KJ]]
-	[[Category: Satchell~~, K J~~]]	+	[[Category: Savchenko A]]
-	[[Category: Savchenko, A]]	+	[[Category: Skarina T]]
-	[[Category: Skarina, T]]	+	[[Category: Stogios PJ]]
-	[[Category: Stogios~~, P J~~]]	+	[[Category: Xu Z]]
-	[[Category: Xu, Z]]	+	[[Category: Yim V]]
-	[[Category: Yim, V]]	+
-	~~[[Category: Acetyltransferase]]~~	+
-	~~[[Category: Aminoglycoside]]~~	+
-	~~[[Category: Antibiotic resistance]]~~	+
-	~~[[Category: Antibiotic_nat family]]~~	+
-	~~[[Category: Coenzyme some]]~~	+
-	~~[[Category: Csgid]]~~	+
-	~~[[Category: Metagenome]]~~	+
-	~~[[Category: National institute of allergy and infectious disease]]~~	+
-	~~[[Category: Niaid]]~~	+
-	~~[[Category: Soil]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 10:29, 6 April 2022

2022-04-06T10:29:07Z

←Older revision		Revision as of 10:29, 6 April 2022
Line 3:		Line 3:
	<StructureSection load='6mmz' size='340' side='right'caption='[[6mmz]], [[Resolution\|resolution]] 3.30Å' scene=''>		<StructureSection load='6mmz' size='340' side='right'caption='[[6mmz]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6mmz]] is a 6 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=6MMZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6MMZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6mmz]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Uncultivated_bacterium Uncultivated bacterium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MMZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MMZ 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=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</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=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ht0\|5ht0]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[5ht0\|5ht0]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Aminoglycoside_N(3')-acetyltransferase Aminoglycoside N(3')-acetyltransferase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.81 2.3.1.81] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Aminoglycoside_N(3')-acetyltransferase Aminoglycoside N(3')-acetyltransferase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.81 2.3.1.81] </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=6mmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mmz OCA], [~~http~~://pdbe.org/6mmz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6mmz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6mmz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6mmz 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=6mmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mmz OCA], [https://pdbe.org/6mmz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6mmz RCSB], [https://www.ebi.ac.uk/pdbsum/6mmz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6mmz ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The environmental microbiome harbors a vast repertoire of antibiotic resistance genes (ARGs) which can serve as evolutionary predecessors for ARGs found in pathogenic bacteria, or can be directly mobilized to pathogens in the presence of selection pressures. Thus, ARGs from benign environmental bacteria are an important resource for understanding clinically relevant resistance. Here, we conduct a comprehensive functional analysis of the Antibiotic_NAT family of aminoglycoside acetyltransferases. We determined a pan-family antibiogram of 21 Antibiotic_NAT enzymes, including 8 derived from clinical isolates and 13 from environmental metagenomic samples. We find that environment-derived representatives confer high-level, broad-spectrum resistance, including against the atypical aminoglycoside apramycin, and that a metagenome-derived gene likely is ancestral to an aac(3) gene found in clinical isolates. Through crystallographic analysis, we rationalize the molecular basis for diversification of substrate specificity across the family. This work provides critical data on the molecular mechanism underpinning resistance to established and emergent aminoglycoside antibiotics and broadens our understanding of ARGs in the environment.
		+
		+	Structural and molecular rationale for the diversification of resistance mediated by the Antibiotic_NAT family.,Stogios PJ, Bordeleau E, Xu Z, Skarina T, Evdokimova E, Chou S, Diorio-Toth L, D'Souza AW, Patel S, Dantas G, Wright GD, Savchenko A Commun Biol. 2022 Mar 25;5(1):263. doi: 10.1038/s42003-022-03219-w. PMID:35338238<ref>PMID:35338238</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6mmz" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:00, 18 December 2019

2019-12-18T11:00:04Z

←Older revision		Revision as of 11:00, 18 December 2019
Line 1:		Line 1:

	==Crystal structure of meta-AAC0038, an environmental aminoglycoside resistance enzyme, H29A mutant apoenzyme==		==Crystal structure of meta-AAC0038, an environmental aminoglycoside resistance enzyme, H29A mutant apoenzyme==
-	<StructureSection load='6mmz' size='340' side='right' caption='[[6mmz]], [[Resolution\|resolution]] 3.30Å' scene=''>	+	<StructureSection load='6mmz' size='340' side='right'caption='[[6mmz]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6mmz]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MMZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MMZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6mmz]] is a 6 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=6MMZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MMZ 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=SO4:SULFATE+ION'>SO4</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=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
Line 12:		Line 12:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Uncultivated bacterium]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Joachimiak, A]]		[[Category: Joachimiak, A]]

OCA at 06:06, 24 October 2018

2018-10-24T06:06:21Z

←Older revision		Revision as of 06:06, 24 October 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6mmz ~~is ON HOLD~~	+	==Crystal structure of meta-AAC0038, an environmental aminoglycoside resistance enzyme, H29A mutant apoenzyme==
-		+	<StructureSection load='6mmz' size='340' side='right' caption='[[6mmz]], [[Resolution\|resolution]] 3.30Å' scene=''>
-	~~Authors~~: ~~Stogios, P~~.J., ~~Skarina, T~~., ~~Xu, Z~~., ~~Yim, V~~., ~~Savchenko, A~~., ~~Joachimiak, A~~., ~~Satchell, K~~.J., ~~Center for Structural Genomics of Infectious Diseases (CSGID)~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6mmz]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MMZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MMZ FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of meta-AAC0038~~, ~~an environmental aminoglycoside resistance enzyme, H29A mutant apoenzyme~~	+	</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=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5ht0\|5ht0]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aminoglycoside_N(3')-acetyltransferase Aminoglycoside N(3')-acetyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.81 2.3.1.81] </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=6mmz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mmz OCA], [http://pdbe.org/6mmz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mmz RCSB], [http://www.ebi.ac.uk/pdbsum/6mmz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mmz ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Structural genomic]]
		+	[[Category: Joachimiak, A]]
		+	[[Category: Satchell, K J]]
	[[Category: Savchenko, A]]		[[Category: Savchenko, A]]
-	[[Category: Yim, V]]
-	[[Category: Stogios, P.J]]
	[[Category: Skarina, T]]		[[Category: Skarina, T]]
-	[[Category: ~~Joachimiak~~, ~~A]]~~	+	[[Category: Stogios, P J]]
-	~~[[Category: Satchell, K.~~J]]	+
	[[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: Antibiotic_nat family]]
		+	[[Category: Coenzyme some]]
		+	[[Category: Csgid]]
		+	[[Category: Metagenome]]
		+	[[Category: National institute of allergy and infectious disease]]
		+	[[Category: Niaid]]
		+	[[Category: Soil]]
		+	[[Category: Transferase]]

OCA: Protected "6mmz" [edit=sysop:move=sysop]

2018-10-10T06:33:10Z

Protected "6mmz" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:33, 10 October 2018

OCA: New page: '''Unreleased structure''' The entry 6mmz is ON HOLD Authors: Stogios, P.J., Skarina, T., Xu, Z., Yim, V., Savchenko, A., Joachimiak, A., Satchell, K.J., Center for Structural Genomics ...

2018-10-10T06:33:08Z

New page: '''Unreleased structure''' The entry 6mmz is ON HOLD Authors: Stogios, P.J., Skarina, T., Xu, Z., Yim, V., Savchenko, A., Joachimiak, A., Satchell, K.J., Center for Structural Genomics ...

New page

'''Unreleased structure'''

The entry 6mmz is ON HOLD

Authors: Stogios, P.J., Skarina, T., Xu, Z., Yim, V., Savchenko, A., Joachimiak, A., Satchell, K.J., Center for Structural Genomics of Infectious Diseases (CSGID)

Description: Crystal structure of meta-AAC0038, an environmental aminoglycoside resistance enzyme, H29A mutant apoenzyme
[[Category: Unreleased Structures]]
[[Category: Savchenko, A]]
[[Category: Yim, V]]
[[Category: Stogios, P.J]]
[[Category: Skarina, T]]
[[Category: Joachimiak, A]]
[[Category: Satchell, K.J]]
[[Category: Xu, Z]]
[[Category: Center For Structural Genomics Of Infectious Diseases (Csgid)]]