6cav - Revision history

OCA at 15:00, 4 October 2023

2023-10-04T15:00:06Z

←Older revision		Revision as of 15:00, 4 October 2023
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	<StructureSection load='6cav' size='340' side='right'caption='[[6cav]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='6cav' size='340' side='right'caption='[[6cav]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6cav]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus~~ aureus~~" (rosenbach 1884) zopf 1885~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CAV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6CAV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6cav]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Staphylococcus_aureus Staphylococcus aureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CAV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6CAV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=84D:Dibekacin'>84D</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.6Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aacA-aphD, R015, VRA0030 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=84D:Dibekacin'>84D</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=6cav FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cav OCA], [~~http~~://pdbe.org/6cav PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6cav RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6cav PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6cav 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=6cav FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cav OCA], [https://pdbe.org/6cav PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6cav RCSB], [https://www.ebi.ac.uk/pdbsum/6cav PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6cav ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/AACA_STAAU AACA_STAAU]] Resistance to gentamicin, tobramycin, and kanamycin. Tobramycin and kanamycin resistance is due to the ACC activity, specified by N-terminal region, and the gentamicin resistance is due to the APH activity encoded by the C-terminal region of the protein.	+	[https://www.uniprot.org/uniprot/AACA_STAAU AACA_STAAU] Resistance to gentamicin, tobramycin, and kanamycin. Tobramycin and kanamycin resistance is due to the ACC activity, specified by N-terminal region, and the gentamicin resistance is due to the APH activity encoded by the C-terminal region of the protein.
	<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: ~~Berghuis, A M~~]]	+	[[Category: Staphylococcus aureus]]
-	[[Category: ~~Caldwell, S J~~]]	+	[[Category: Berghuis AM]]
-	[[Category: ~~Aminoglycoside]]~~	+	[[Category: Caldwell SJ]]
-	~~[[Category: Antibiotic]]~~	+
-	~~[[Category: Kinase]]~~	+
-	~~[[Category: Resistance]]~~	+
-	~~[[Category: Transferase]]~~	+
-	~~[[Category: Transferase-antibiotic complex~~]]	+

OCA at 08:41, 8 January 2020

2020-01-08T08:41:31Z

←Older revision		Revision as of 08:41, 8 January 2020
Line 1:		Line 1:

	==Aminoglycoside Phosphotransferase (2'')-Ia in complex with GMPPNP, Magnesium, and Dibekacin==		==Aminoglycoside Phosphotransferase (2'')-Ia in complex with GMPPNP, Magnesium, and Dibekacin==
-	<StructureSection load='6cav' size='340' side='right' caption='[[6cav]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='6cav' size='340' side='right'caption='[[6cav]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6cav]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CAV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CAV FirstGlance]. <br>		<table><tr><td colspan='2'>[[6cav]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CAV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CAV FirstGlance]. <br>
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Berghuis, A M]]		[[Category: Berghuis, A M]]
	[[Category: Caldwell, S J]]		[[Category: Caldwell, S J]]

OCA at 08:32, 2 May 2018

2018-05-02T08:32:34Z

←Older revision		Revision as of 08:32, 2 May 2018
Line 3:		Line 3:
	<StructureSection load='6cav' size='340' side='right' caption='[[6cav]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='6cav' size='340' side='right' caption='[[6cav]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6cav]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CAV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CAV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6cav]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_aureus"_(rosenbach_1884)_zopf_1885 "micrococcus aureus" (rosenbach 1884) zopf 1885]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CAV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CAV FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=84D:Dibekacin'>84D</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=84D:Dibekacin'>84D</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aacA-aphD, R015, VRA0030 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1280 "Micrococcus aureus" (Rosenbach 1884) Zopf 1885])</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=6cav FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cav OCA], [http://pdbe.org/6cav PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cav RCSB], [http://www.ebi.ac.uk/pdbsum/6cav PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cav 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=6cav FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cav OCA], [http://pdbe.org/6cav PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cav RCSB], [http://www.ebi.ac.uk/pdbsum/6cav PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cav ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/AACA_STAAU AACA_STAAU]] Resistance to gentamicin, tobramycin, and kanamycin. Tobramycin and kanamycin resistance is due to the ACC activity, specified by N-terminal region, and the gentamicin resistance is due to the APH activity encoded by the C-terminal region of the protein.		[[http://www.uniprot.org/uniprot/AACA_STAAU AACA_STAAU]] Resistance to gentamicin, tobramycin, and kanamycin. Tobramycin and kanamycin resistance is due to the ACC activity, specified by N-terminal region, and the gentamicin resistance is due to the APH activity encoded by the C-terminal region of the protein.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	APH(2")-Ia aminoglycoside resistance enzyme forms the C-terminal domain of the bifunctional AAC(6')-Ie/APH(2")-Ia enzyme and confers high-level resistance to natural 4,6-disubstituted aminoglycosides. In addition, reports have suggested that the enzyme can phosphorylate 4,5-disubstituted compounds and aminoglycosides with substitutions at the N1-position. Previously determined structures of the enzyme with aminoglycosides bound have not indicated how these non-canonical substrates could bind and be modified by the enzyme. We carried out crystallographic studies to directly observe the interaction of these compounds with the aminoglycoside-binding site and probe the means by which these non-canonical substrates interact with the enzyme. We find that APH(2")-Ia maintains a preferred mode of binding aminoglycosides using the conserved neamine rings when possible, with flexibility that allows it to accommodate additional rings. However, if this binding mode is made impossible because of additional substitutions to the standard 4,5- or 4,6-disubstituted aminoglycoside architecture as in lividomycin A or the N1-substituted aminoglycosides, it is still possible for these aminoglycosides to bind to the antibiotic-binding site, using alternate binding modes, explaining the low rates of non-canonical phosphorylation activities seen in enzyme assays. Furthermore, structural studies of a clinically-observed arbekacin-resistant mutant of APH(2")-Ia reveals an altered aminoglycoside binding site that can stabilize an alternative binding mode for N1-substituted aminoglycosides. This mutation could alter and expand the aminoglycoside resistance spectrum of the wildtype enzyme in response to newly developed aminoglycosides.
		+
		+	Plasticity of aminoglycoside binding to antibiotic kinase APH(2")-Ia.,Caldwell SJ, Berghuis AM Antimicrob Agents Chemother. 2018 Apr 16. pii: AAC.00202-18. doi:, 10.1128/AAC.00202-18. PMID:29661878<ref>PMID:29661878</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6cav" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 13:52, 11 April 2018

2018-04-11T13:52:06Z

←Older revision		Revision as of 13:52, 11 April 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6cav is ON HOLD until Paper Publication~~	+	==Aminoglycoside Phosphotransferase (2'')-Ia in complex with GMPPNP, Magnesium, and Dibekacin==
-		+	<StructureSection load='6cav' size='340' side='right' caption='[[6cav]], [[Resolution\|resolution]] 2.60Å' scene=''>
-	~~Authors: Caldwell, S.J., Berghuis, A.M.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6cav]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CAV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CAV FirstGlance]. <br>
-	~~Description:~~ Aminoglycoside Phosphotransferase (2'')-Ia in complex with GMPPNP, Magnesium, and Dibekacin	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=84D:Dibekacin'>84D</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GNP:PHOSPHOAMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<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=6cav FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cav OCA], [http://pdbe.org/6cav PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cav RCSB], [http://www.ebi.ac.uk/pdbsum/6cav PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cav ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Caldwell~~, S.J]]	+	</table>
-	[[Category: Berghuis, A.M]]	+	== Function ==
		+	[[http://www.uniprot.org/uniprot/AACA_STAAU AACA_STAAU]] Resistance to gentamicin, tobramycin, and kanamycin. Tobramycin and kanamycin resistance is due to the ACC activity, specified by N-terminal region, and the gentamicin resistance is due to the APH activity encoded by the C-terminal region of the protein.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Berghuis, A M]]
		+	[[Category: Caldwell, S J]]
		+	[[Category: Aminoglycoside]]
		+	[[Category: Antibiotic]]
		+	[[Category: Kinase]]
		+	[[Category: Resistance]]
		+	[[Category: Transferase]]
		+	[[Category: Transferase-antibiotic complex]]

OCA at 04:36, 4 April 2018

2018-04-04T04:36:50Z

←Older revision		Revision as of 04:36, 4 April 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6cav is ON HOLD	+	The entry 6cav is ON HOLD until Paper Publication

	Authors: Caldwell, S.J., Berghuis, A.M.		Authors: Caldwell, S.J., Berghuis, A.M.

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

2018-02-07T05:13:51Z

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

←Older revision

Revision as of 05:13, 7 February 2018

OCA: New page: '''Unreleased structure''' The entry 6cav is ON HOLD Authors: Caldwell, S.J., Berghuis, A.M. Description: Aminoglycoside Phosphotransferase (2'')-Ia in complex with GMPPNP, Magnesium, ...

2018-02-07T05:13:49Z

New page: '''Unreleased structure''' The entry 6cav is ON HOLD Authors: Caldwell, S.J., Berghuis, A.M. Description: Aminoglycoside Phosphotransferase (2'')-Ia in complex with GMPPNP, Magnesium, ...

New page

'''Unreleased structure'''

The entry 6cav is ON HOLD

Authors: Caldwell, S.J., Berghuis, A.M.

Description: Aminoglycoside Phosphotransferase (2'')-Ia in complex with GMPPNP, Magnesium, and Dibekacin
[[Category: Unreleased Structures]]
[[Category: Caldwell, S.J]]
[[Category: Berghuis, A.M]]