6np3 - Revision history

OCA at 06:57, 11 October 2023

OCA — Wed, 11 Oct 2023 06:57:18 GMT

←Older revision		Revision as of 06:57, 11 October 2023
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	<StructureSection load='6np3' size='340' side='right'caption='[[6np3]], [[Resolution\|resolution]] 1.15Å' scene=''>		<StructureSection load='6np3' size='340' side='right'caption='[[6np3]], [[Resolution\|resolution]] 1.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6np3]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"aerobacter_cloacae"_(jordan_1890)_bergey_et_al._1923 "aerobacter~~ cloacae~~" (jordan 1890) bergey et al. 1923~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NP3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6NP3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6np3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterobacter_cloacae Enterobacter cloacae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NP3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6NP3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLL:(2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDROXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL'>LLL</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]] 1.15Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aac 3-VI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=550 "Aerobacter cloacae" (Jordan 1890) Bergey et al. 1923])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LLL:(2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDROXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL'>LLL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=6np3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6np3 OCA], [https://pdbe.org/6np3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6np3 RCSB], [https://www.ebi.ac.uk/pdbsum/6np3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6np3 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=6np3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6np3 OCA], [~~http~~://pdbe.org/6np3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6np3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6np3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6np3 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q47030_ENTCL Q47030_ENTCL]
	<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: Enterobacter cloacae]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Cuneo~~, M J~~]]	+	[[Category: Cuneo MJ]]
-	[[Category: Kumar, P]]	+	[[Category: Kumar P]]
-	~~[[Category: Antibiotic]]~~	+
-	~~[[Category: Antibiotic modifying enzyme]]~~	+
-	~~[[Category: Substrate selectivity]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 08:28, 6 November 2019

OCA — Wed, 06 Nov 2019 08:28:00 GMT

←Older revision		Revision as of 08:28, 6 November 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6np3 is ~~ON HOLD until Paper~~ Publication	+	==AAC-VIa bound to Gentamicin==
		+	<StructureSection load='6np3' size='340' side='right'caption='[[6np3]], [[Resolution\|resolution]] 1.15Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6np3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"aerobacter_cloacae"_(jordan_1890)_bergey_et_al._1923 "aerobacter cloacae" (jordan 1890) bergey et al. 1923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NP3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NP3 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LLL:(2R,3R,4R,5R)-2-((1S,2S,3R,4S,6R)-4,6-DIAMINO-3-((2R,3R,6S)-3-AMINO-6-(AMINOMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-2-HYDROXYCYCLOHEXYLOXY)-5-METHYL-4-(METHYLAMINO)-TETRAHYDRO-2H-PYRAN-3,5-DIOL'>LLL</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">aac 3-VI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=550 "Aerobacter cloacae" (Jordan 1890) Bergey et al. 1923])</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=6np3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6np3 OCA], [http://pdbe.org/6np3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6np3 RCSB], [http://www.ebi.ac.uk/pdbsum/6np3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6np3 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The position, bonding and dynamics of hydrogen atoms in the catalytic centers of proteins are essential for catalysis. The role of short hydrogen bonds in catalysis has remained highly debated and led to establishment of several distinctive geometrical arrangements of hydrogen atoms vis-a-vis the heavier donor and acceptor counterparts, that is, low-barrier, single-well or short canonical hydrogen bonds. Here we demonstrate how the position of a hydrogen atom in the catalytic triad of an aminoglycoside inactivating enzyme leads to a thirty-fold increase in catalytic turnover. A low-barrier hydrogen bond is present in the enzyme active site for the substrates that are turned over the best, whereas a canonical hydrogen bond is found with the least preferred substrate. This is the first comparison of these hydrogen bonds involving an identical catalytic network, while directly demonstrating how active site electrostatics adapt to the electronic nature of substrates to tune catalysis.

-	~~Authors: Kumar~~, P., Cuneo, M.J.	+	Low-Barrier and Canonical Hydrogen Bonds Modulate Activity and Specificity of a Catalytic Triad.,Kumar P, Agarwal PK, Waddell MB, Mittag T, Serpersu EH, Cuneo MJ Angew Chem Int Ed Engl. 2019 Nov 4;58(45):16260-16266. doi:, 10.1002/anie.201908535. Epub 2019 Sep 24. PMID:31515870<ref>PMID:31515870</ref>

-	~~Description: AAC~~-~~VIa bound to Gentamicin~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: Cuneo, M.J]]	+	<div class="pdbe-citations 6np3" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Cuneo, M J]]
	[[Category: Kumar, P]]		[[Category: Kumar, P]]
		+	[[Category: Antibiotic]]
		+	[[Category: Antibiotic modifying enzyme]]
		+	[[Category: Substrate selectivity]]
		+	[[Category: Transferase]]

OCA: Protected "6np3" [edit=sysop:move=sysop]

OCA — Wed, 30 Jan 2019 06:41:57 GMT

Protected "6np3" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:41, 30 January 2019

OCA: New page: '''Unreleased structure''' The entry 6np3 is ON HOLD until Paper Publication Authors: Kumar, P., Cuneo, M.J. Description: AAC-VIa bound to Gentamicin [[Category: Unreleased Structures]...

OCA — Wed, 30 Jan 2019 06:41:55 GMT

New page: '''Unreleased structure''' The entry 6np3 is ON HOLD until Paper Publication Authors: Kumar, P., Cuneo, M.J. Description: AAC-VIa bound to Gentamicin [[Category: Unreleased Structures]...

New page

'''Unreleased structure'''

The entry 6np3 is ON HOLD until Paper Publication

Authors: Kumar, P., Cuneo, M.J.

Description: AAC-VIa bound to Gentamicin
[[Category: Unreleased Structures]]
[[Category: Cuneo, M.J]]
[[Category: Kumar, P]]