7kdy - Revision history

OCA at 07:17, 3 April 2024

OCA — Wed, 03 Apr 2024 07:17:30 GMT

←Older revision		Revision as of 07:17, 3 April 2024
Line 3:		Line 3:
	<StructureSection load='7kdy' size='340' side='right'caption='[[7kdy]], [[Resolution\|resolution]] 1.94Å' scene=''>		<StructureSection load='7kdy' size='340' side='right'caption='[[7kdy]], [[Resolution\|resolution]] 1.94Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7kdy]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KDY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KDY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7kdy]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_tokunonensis Streptomyces tokunonensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KDY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KDY FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5AD:5-DEOXYADENOSINE'>5AD</scene>, <scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MET:METHIONINE'>MET</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=WCD:(2R,3R,5R)-3-{[2-({N-[(2R)-2,4-dihydroxy-3,3-dimethylbutanoyl]-beta-alanyl}amino)ethyl]sulfanyl}-7-oxo-1-azabicyclo[3.2.0]heptane-2-carboxylic+acid'>WCD</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]] 1.939Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5AD:5-DEOXYADENOSINE'>5AD</scene>, <scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MET:METHIONINE'>MET</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=WCD:(2R,3R,5R)-3-{[2-({N-[(2R)-2,4-dihydroxy-3,3-dimethylbutanoyl]-beta-alanyl}amino)ethyl]sulfanyl}-7-oxo-1-azabicyclo[3.2.0]heptane-2-carboxylic+acid'>WCD</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=7kdy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kdy OCA], [https://pdbe.org/7kdy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kdy RCSB], [https://www.ebi.ac.uk/pdbsum/7kdy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kdy 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=7kdy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kdy OCA], [https://pdbe.org/7kdy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kdy RCSB], [https://www.ebi.ac.uk/pdbsum/7kdy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kdy ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/A0A6B9HEI0_9ACTN A0A6B9HEI0_9ACTN]
-	Carbapenems are antibiotics of last resort in the clinic. Owing to their potency and broad-spectrum activity, they are an important part of the antibiotic arsenal. The vital role of carbapenems is exemplified by the approval acquired by Merck from the US Food and Drug Administration (FDA) for the use of an imipenem combination therapy to treat the increased levels of hospital-acquired and ventilator-associated bacterial pneumonia that have occurred during the COVID-19 pandemic(1). The C6 hydroxyethyl side chain distinguishes the clinically used carbapenems from the other classes of beta-lactam antibiotics and is responsible for their low susceptibility to inactivation by occluding water from the beta-lactamase active site(2). The construction of the C6 hydroxyethyl side chain is mediated by cobalamin- or B12-dependent radical S-adenosylmethionine (SAM) enzymes(3). These radical SAM methylases (RSMTs) assemble the alkyl backbone by sequential methylation reactions, and thereby underlie the therapeutic usefulness of clinically used carbapenems. Here we present X-ray crystal structures of TokK, a B12-dependent RSMT that catalyses three-sequential methylations during the biosynthesis of asparenomycin A. These structures, which contain the two metallocofactors of the enzyme and were determined in the presence and absence of a carbapenam substrate, provide a visualization of a B12-dependent RSMT that uses the radical mechanism that is shared by most of these enzymes. The structures provide insight into the stereochemistry of initial C6 methylation and suggest that substrate positioning governs the rate of each methylation event.	+
-		+
-	~~Structure of a B12-dependent radical SAM enzyme in carbapenem biosynthesis.,Knox HL, Sinner EK, Townsend CA, Boal AK, Booker SJ Nature. 2022 Feb;602(7896)~~:~~343-348. doi: 10.1038~~/~~s41586-021-04392-4. Epub 2022, Feb 2. PMID:35110734<ref>PMID:35110734<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 7kdy" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Boal, A K~~]]	+	[[Category: Streptomyces tokunonensis]]
-	[[Category: ~~Booker, S J~~]]	+	[[Category: Boal AK]]
-	[[Category: ~~Knox, H L~~]]	+	[[Category: Booker SJ]]
-	[[Category: ~~B12]]~~	+	[[Category: Knox HL]]
-	~~[[Category: Beta-lactam antibiotic synthesis]]~~	+
-	~~[[Category: Cobalamin]]~~	+
-	~~[[Category: Fes cluster]]~~	+
-	~~[[Category: Methyltransferase]]~~	+
-	~~[[Category: Radical sam]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 11:01, 16 February 2022

OCA — Wed, 16 Feb 2022 11:01:48 GMT

←Older revision		Revision as of 11:01, 16 February 2022
Line 7:		Line 7:
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7kdy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kdy OCA], [https://pdbe.org/7kdy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kdy RCSB], [https://www.ebi.ac.uk/pdbsum/7kdy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kdy 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=7kdy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kdy OCA], [https://pdbe.org/7kdy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kdy RCSB], [https://www.ebi.ac.uk/pdbsum/7kdy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kdy ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Carbapenems are antibiotics of last resort in the clinic. Owing to their potency and broad-spectrum activity, they are an important part of the antibiotic arsenal. The vital role of carbapenems is exemplified by the approval acquired by Merck from the US Food and Drug Administration (FDA) for the use of an imipenem combination therapy to treat the increased levels of hospital-acquired and ventilator-associated bacterial pneumonia that have occurred during the COVID-19 pandemic(1). The C6 hydroxyethyl side chain distinguishes the clinically used carbapenems from the other classes of beta-lactam antibiotics and is responsible for their low susceptibility to inactivation by occluding water from the beta-lactamase active site(2). The construction of the C6 hydroxyethyl side chain is mediated by cobalamin- or B12-dependent radical S-adenosylmethionine (SAM) enzymes(3). These radical SAM methylases (RSMTs) assemble the alkyl backbone by sequential methylation reactions, and thereby underlie the therapeutic usefulness of clinically used carbapenems. Here we present X-ray crystal structures of TokK, a B12-dependent RSMT that catalyses three-sequential methylations during the biosynthesis of asparenomycin A. These structures, which contain the two metallocofactors of the enzyme and were determined in the presence and absence of a carbapenam substrate, provide a visualization of a B12-dependent RSMT that uses the radical mechanism that is shared by most of these enzymes. The structures provide insight into the stereochemistry of initial C6 methylation and suggest that substrate positioning governs the rate of each methylation event.
		+
		+	Structure of a B12-dependent radical SAM enzyme in carbapenem biosynthesis.,Knox HL, Sinner EK, Townsend CA, Boal AK, Booker SJ Nature. 2022 Feb;602(7896):343-348. doi: 10.1038/s41586-021-04392-4. Epub 2022, Feb 2. PMID:35110734<ref>PMID:35110734</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7kdy" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:10, 2 February 2022

OCA — Wed, 02 Feb 2022 07:10:56 GMT

←Older revision		Revision as of 07:10, 2 February 2022
Line 1:		Line 1:

	==Crystal structure of Streptomyces tokunonesis TokK with hydroxycobalamin, 5'-deoxyadenosine, methionine, and (2R)-pantetheinylated carbapenam==		==Crystal structure of Streptomyces tokunonesis TokK with hydroxycobalamin, 5'-deoxyadenosine, methionine, and (2R)-pantetheinylated carbapenam==
-	<StructureSection load='7kdy' size='340' side='right'caption='[[7kdy]]' scene=''>	+	<StructureSection load='7kdy' size='340' side='right'caption='[[7kdy]], [[Resolution\|resolution]] 1.94Å' 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=7KDY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KDY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7kdy]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KDY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KDY 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=7kdy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kdy OCA], [https://pdbe.org/7kdy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kdy RCSB], [https://www.ebi.ac.uk/pdbsum/7kdy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kdy 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=5AD:5-DEOXYADENOSINE'>5AD</scene>, <scene name='pdbligand=B12:COBALAMIN'>B12</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MET:METHIONINE'>MET</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=WCD:(2R,3R,5R)-3-{[2-({N-[(2R)-2,4-dihydroxy-3,3-dimethylbutanoyl]-beta-alanyl}amino)ethyl]sulfanyl}-7-oxo-1-azabicyclo[3.2.0]heptane-2-carboxylic+acid'>WCD</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=7kdy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kdy OCA], [https://pdbe.org/7kdy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kdy RCSB], [https://www.ebi.ac.uk/pdbsum/7kdy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kdy ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Boal AK]]	+	[[Category: Boal, A K]]
-	[[Category: Booker SJ]]	+	[[Category: Booker, S J]]
-	[[Category: Knox HL]]	+	[[Category: Knox, H L]]
		+	[[Category: B12]]
		+	[[Category: Beta-lactam antibiotic synthesis]]
		+	[[Category: Cobalamin]]
		+	[[Category: Fes cluster]]
		+	[[Category: Methyltransferase]]
		+	[[Category: Radical sam]]
		+	[[Category: Transferase]]

OCA at 09:56, 12 January 2022

OCA — Wed, 12 Jan 2022 09:56:37 GMT

←Older revision		Revision as of 09:56, 12 January 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7kdy is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of Streptomyces tokunonesis TokK with hydroxycobalamin, 5'-deoxyadenosine, methionine, and (2R)-pantetheinylated carbapenam==
-		+	<StructureSection load='7kdy' size='340' side='right'caption='[[7kdy]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KDY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KDY FirstGlance]. <br>
-	~~Description~~:	+	</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=7kdy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kdy OCA], [https://pdbe.org/7kdy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kdy RCSB], [https://www.ebi.ac.uk/pdbsum/7kdy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kdy ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Boal AK]]
		+	[[Category: Booker SJ]]
		+	[[Category: Knox HL]]

OCA at 05:29, 25 November 2020

OCA — Wed, 25 Nov 2020 05:29:04 GMT

←Older revision		Revision as of 05:29, 25 November 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7kdy is ON HOLD	+	The entry 7kdy is ON HOLD until Paper Publication

	Authors:		Authors:

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

OCA — Wed, 21 Oct 2020 06:51:21 GMT

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

←Older revision

Revision as of 06:51, 21 October 2020

OCA: New page: '''Unreleased structure''' The entry 7kdy is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 21 Oct 2020 06:51:20 GMT

New page: '''Unreleased structure''' The entry 7kdy is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7kdy is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]