6c0g - Revision history

OCA at 14:25, 13 March 2024

2024-03-13T14:25:32Z

←Older revision		Revision as of 14:25, 13 March 2024
Line 1:		Line 1:

	==Lysinoalanine synthase, DurN, from duramycin biosynthesis==		==Lysinoalanine synthase, DurN, from duramycin biosynthesis==
-	<StructureSection load='6c0g' size='340' side='right' caption='[[6c0g]], [[Resolution\|resolution]] 2.15Å' scene=''>	+	<StructureSection load='6c0g' size='340' side='right'caption='[[6c0g]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6c0g]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"streptomyces_cinnamomeus_forma_cinnamomeus"_(sic)_pridham_et_al._1956 "streptomyces cinnamomeus forma cinnamomeus" (sic) pridham et al. 1956~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C0G OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6C0G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6c0g]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_cinnamoneus Streptomyces cinnamoneus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C0G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6C0G FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=K:POTASSIUM+ION'>K</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]] 2.145Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>durN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~53446~~ "~~Streptomyces cinnamomeus forma cinnamomeus~~" ~~(sic) Pridham et al. 1956])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</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=6c0g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c0g OCA], [~~http~~://pdbe.org/6c0g PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6c0g RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6c0g PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6c0g 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=6c0g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c0g OCA], [https://pdbe.org/6c0g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6c0g RCSB], [https://www.ebi.ac.uk/pdbsum/6c0g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6c0g ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/A0A3F2YLX1_STRCJ A0A3F2YLX1_STRCJ]
-	Duramycin is a heavily post-translationally modified peptide that binds phosphatidylethanolamine. It has been investigated as an antibiotic, an inhibitor of viral entry, a therapeutic for cystic fibrosis, and a tumor and vasculature imaging agent. Duramycin contains a beta-hydroxylated Asp (Hya) and four macrocycles, including an essential lysinoalanine (Lal) cross-link. The mechanism of Lal formation is not known. Here we show that Lal is installed stereospecifically by DurN via addition of Lys19 to a dehydroalanine. The structure of DurN reveals an unusual dimer with a new fold. Surprisingly, in the structure of duramycin bound to DurN, no residues of the enzyme are near the Lal cross-link. Instead, Hya15 of the substrate makes interactions with Lal, suggesting it acts as a base to deprotonate Lys19 during catalysis. Biochemical data suggest that DurN preorganizes the reactive conformation of the substrate, such that the Hya15 of the substrate can serve as the catalytic base for Lal formation.	+
-		+
-	~~Substrate-assisted enzymatic formation of lysinoalanine in duramycin.,An L, Cogan DP, Navo CD, Jimenez-Oses G, Nair SK, van der Donk WA Nat Chem Biol. 2018 Oct;14(10)~~:~~928-933. doi: 10.1038~~/~~s41589-018-0122-4. Epub 2018, Sep 3. PMID:30177849<ref>PMID:30177849<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6c0g" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Cogan, D P~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Nair, S K~~]]	+	[[Category: Streptomyces cinnamoneus]]
-	[[Category: ~~Biosynthetic protein~~]]	+	[[Category: Cogan DP]]
-	[[Category: ~~Lysinoalanine synthase]]~~	+	[[Category: Nair SK]]
-	~~[[Category: Michael addition~~]]	+

OCA at 20:16, 19 September 2018

2018-09-19T20:16:40Z

←Older revision		Revision as of 20:16, 19 September 2018
Line 3:		Line 3:
	<StructureSection load='6c0g' size='340' side='right' caption='[[6c0g]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='6c0g' size='340' side='right' caption='[[6c0g]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6c0g]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C0G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6C0G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6c0g]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"streptomyces_cinnamomeus_forma_cinnamomeus"_(sic)_pridham_et_al._1956 "streptomyces cinnamomeus forma cinnamomeus" (sic) pridham et al. 1956]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C0G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6C0G FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">durN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53446 "Streptomyces cinnamomeus forma cinnamomeus" (sic) Pridham et al. 1956])</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=6c0g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c0g OCA], [http://pdbe.org/6c0g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6c0g RCSB], [http://www.ebi.ac.uk/pdbsum/6c0g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6c0g 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=6c0g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c0g OCA], [http://pdbe.org/6c0g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6c0g RCSB], [http://www.ebi.ac.uk/pdbsum/6c0g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6c0g ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Duramycin is a heavily post-translationally modified peptide that binds phosphatidylethanolamine. It has been investigated as an antibiotic, an inhibitor of viral entry, a therapeutic for cystic fibrosis, and a tumor and vasculature imaging agent. Duramycin contains a beta-hydroxylated Asp (Hya) and four macrocycles, including an essential lysinoalanine (Lal) cross-link. The mechanism of Lal formation is not known. Here we show that Lal is installed stereospecifically by DurN via addition of Lys19 to a dehydroalanine. The structure of DurN reveals an unusual dimer with a new fold. Surprisingly, in the structure of duramycin bound to DurN, no residues of the enzyme are near the Lal cross-link. Instead, Hya15 of the substrate makes interactions with Lal, suggesting it acts as a base to deprotonate Lys19 during catalysis. Biochemical data suggest that DurN preorganizes the reactive conformation of the substrate, such that the Hya15 of the substrate can serve as the catalytic base for Lal formation.
		+
		+	Substrate-assisted enzymatic formation of lysinoalanine in duramycin.,An L, Cogan DP, Navo CD, Jimenez-Oses G, Nair SK, van der Donk WA Nat Chem Biol. 2018 Oct;14(10):928-933. doi: 10.1038/s41589-018-0122-4. Epub 2018, Sep 3. PMID:30177849<ref>PMID:30177849</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6c0g" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 10:05, 5 September 2018

2018-09-05T10:05:08Z

←Older revision		Revision as of 10:05, 5 September 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6c0g is ~~ON HOLD until Paper Publication~~	+	==Lysinoalanine synthase, DurN, from duramycin biosynthesis==
-		+	<StructureSection load='6c0g' size='340' side='right' caption='[[6c0g]], [[Resolution\|resolution]] 2.15Å' scene=''>
-	~~Authors~~: ~~Cogan~~, D.P., ~~Nair~~, S.K.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6c0g]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C0G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6C0G FirstGlance]. <br>
-	~~Description~~: ~~Lysinoalanine synthase~~, ~~DurN, from duramycin biosynthesis~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</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=6c0g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c0g OCA], [http://pdbe.org/6c0g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6c0g RCSB], [http://www.ebi.ac.uk/pdbsum/6c0g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6c0g ProSAT]</span></td></tr>
-	[[Category: Nair, S.K]]	+	</table>
-	[[Category: ~~Cogan, D.P~~]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Cogan, D P]]
		+	[[Category: Nair, S K]]
		+	[[Category: Biosynthetic protein]]
		+	[[Category: Lysinoalanine synthase]]
		+	[[Category: Michael addition]]

OCA at 03:58, 25 April 2018

2018-04-25T03:58:20Z

←Older revision		Revision as of 03:58, 25 April 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6c0g is ON HOLD	+	The entry 6c0g is ON HOLD until Paper Publication

	Authors: Cogan, D.P., Nair, S.K.		Authors: Cogan, D.P., Nair, S.K.

OCA: Protected "6c0g" [edit=sysop:move=sysop]

2018-01-10T07:12:00Z

Protected "6c0g" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:12, 10 January 2018

OCA: New page: '''Unreleased structure''' The entry 6c0g is ON HOLD Authors: Cogan, D.P., Nair, S.K. Description: Lysinoalanine synthase, DurN, from duramycin biosynthesis [[Category: Unreleased Stru...

2018-01-10T07:11:59Z

New page: '''Unreleased structure''' The entry 6c0g is ON HOLD Authors: Cogan, D.P., Nair, S.K. Description: Lysinoalanine synthase, DurN, from duramycin biosynthesis [[Category: Unreleased Stru...

New page

'''Unreleased structure'''

The entry 6c0g is ON HOLD

Authors: Cogan, D.P., Nair, S.K.

Description: Lysinoalanine synthase, DurN, from duramycin biosynthesis
[[Category: Unreleased Structures]]
[[Category: Nair, S.K]]
[[Category: Cogan, D.P]]