6ecb - Revision history

OCA at 06:23, 11 October 2023

2023-10-11T06:23:11Z

← Older revision		Revision as of 06:23, 11 October 2023
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	<StructureSection load='6ecb' size='340' side='right'caption='[[6ecb]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='6ecb' size='340' side='right'caption='[[6ecb]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6ecb]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Streptomyces_tsusimaensis Streptomyces tsusimaensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ECB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6ECB FirstGlance]. <br>		<table><tr><td colspan='2'>[[6ecb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_tsusimaensis Streptomyces tsusimaensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ECB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ECB FirstGlance]. <br>
	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[6ecc\|6ecc]], [[6ecd\|6ecd]], [[6ece\|6ece]], [[6ecf\|6ecf]]</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]] 1.7Å</td></tr>
	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">vlm2 ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5~~&~~id=285482 Streptomyces tsusimaensis])~~</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=6ecb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ecb OCA], [https://pdbe.org/6ecb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ecb RCSB], [https://www.ebi.ac.uk/pdbsum/6ecb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ecb 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=6ecb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ecb OCA], [~~http~~://pdbe.org/6ecb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ecb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ecb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ecb ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/Q1PSF3_9ACTN Q1PSF3_9ACTN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Streptomyces tsusimaensis]]		[[Category: Streptomyces tsusimaensis]]
	[[Category: Alonzo~~, D A~~]]		[[Category: Alonzo DA]]
	[[Category: Schmeing~~, T M]]~~		[[Category: Schmeing TM]]
	~~[[Category: Depsipeptide]]~~
	~~[[Category: Hydrolase]]~~
	~~[[Category: Non-ribosomal peptide synthetase]]~~
	~~[[Category: Nonribosomal peptide synthetase]]~~
	~~[[Category: Nrp]]~~
	~~[[Category: Thioesterase]]~~
	~~[[Category: Thioesterase domain]]~~
	~~[[Category: Valinomycin~~]]

OCA at 08:58, 8 January 2020

2020-01-08T08:58:02Z

← Older revision		Revision as of 08:58, 8 January 2020
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	==Vlm2 thioesterase domain wild type structure 1==		==Vlm2 thioesterase domain wild type structure 1==
	<StructureSection load='6ecb' size='340' side='right' caption='[[6ecb]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='6ecb' size='340' side='right'caption='[[6ecb]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6ecb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_tsusimaensis Streptomyces tsusimaensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ECB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ECB FirstGlance]. <br>		<table><tr><td colspan='2'>[[6ecb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_tsusimaensis Streptomyces tsusimaensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ECB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ECB FirstGlance]. <br>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Streptomyces tsusimaensis]]		[[Category: Streptomyces tsusimaensis]]
	[[Category: Alonzo, D A]]		[[Category: Alonzo, D A]]

OCA at 08:38, 26 December 2018

2018-12-26T08:38:40Z

← Older revision		Revision as of 08:38, 26 December 2018
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	<StructureSection load='6ecb' size='340' side='right' caption='[[6ecb]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='6ecb' size='340' side='right' caption='[[6ecb]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6ecb]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ECB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ECB FirstGlance]. <br>		<table><tr><td colspan='2'>[[6ecb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_tsusimaensis Streptomyces tsusimaensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ECB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ECB FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6ecc\|6ecc]], [[6ecd\|6ecd]], [[6ece\|6ece]], [[6ecf\|6ecf]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6ecc\|6ecc]], [[6ecd\|6ecd]], [[6ece\|6ece]], [[6ecf\|6ecf]]</td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">vlm2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=285482 Streptomyces tsusimaensis])</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=6ecb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ecb OCA], [http://pdbe.org/6ecb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ecb RCSB], [http://www.ebi.ac.uk/pdbsum/6ecb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ecb 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=6ecb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ecb OCA], [http://pdbe.org/6ecb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ecb RCSB], [http://www.ebi.ac.uk/pdbsum/6ecb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ecb ProSAT]</span></td></tr>
	</table>		</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Many enzymes catalyse reactions that proceed through covalent acyl-enzyme (ester or thioester) intermediates(1). These enzymes include serine hydrolases(2,3) (encoded by one per cent of human genes, and including serine proteases and thioesterases), cysteine proteases (including caspases), and many components of the ubiquitination machinery(4,5). Their important acyl-enzyme intermediates are unstable, commonly having half-lives of minutes to hours(6). In some cases, acyl-enzyme complexes can be stabilized using substrate analogues or active-site mutations but, although these approaches can provide valuable insight(7-10), they often result in complexes that are substantially non-native. Here we develop a strategy for incorporating 2,3-diaminopropionic acid (DAP) into recombinant proteins, via expansion of the genetic code(11). We show that replacing catalytic cysteine or serine residues of enzymes with DAP permits their first-step reaction with native substrates, allowing the efficient capture of acyl-enzyme complexes that are linked through a stable amide bond. For one of these enzymes, the thioesterase domain of valinomycin synthetase(12), we elucidate the biosynthetic pathway by which it progressively oligomerizes tetradepsipeptidyl substrates to a dodecadepsipeptidyl intermediate, which it then cyclizes to produce valinomycin. By trapping the first and last acyl-thioesterase intermediates in the catalytic cycle as DAP conjugates, we provide structural insight into how conformational changes in thioesterase domains of such nonribosomal peptide synthetases control the oligomerization and cyclization of linear substrates. The encoding of DAP will facilitate the characterization of diverse acyl-enzyme complexes, and may be extended to capturing the native substrates of transiently acylated proteins of unknown function.

			Trapping biosynthetic acyl-enzyme intermediates with encoded 2,3-diaminopropionic acid.,Huguenin-Dezot N, Alonzo DA, Heberlig GW, Mahesh M, Nguyen DP, Dornan MH, Boddy CN, Schmeing TM, Chin JW Nature. 2018 Dec 12. pii: 10.1038/s41586-018-0781-z. doi:, 10.1038/s41586-018-0781-z. PMID:30542153<ref>PMID:30542153</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 6ecb" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Streptomyces tsusimaensis]]
	[[Category: Alonzo, D A]]		[[Category: Alonzo, D A]]
	[[Category: Schmeing, T M]]		[[Category: Schmeing, T M]]

OCA at 06:45, 12 December 2018

2018-12-12T06:45:16Z

← Older revision		Revision as of 06:45, 12 December 2018
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	~~'''Unreleased structure'''~~

	~~The entry~~ 6ecb is ~~ON HOLD until Paper Publication~~		==Vlm2 thioesterase domain wild type structure 1==
			<StructureSection load='6ecb' size='340' side='right' caption='[[6ecb]], [[Resolution\|resolution]] 1.70Å' scene=''>
	~~Authors~~:		== Structural highlights ==
			<table><tr><td colspan='2'>[[6ecb]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ECB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ECB FirstGlance]. <br>
	~~Description~~:		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6ecc\|6ecc]], [[6ecd\|6ecd]], [[6ece\|6ece]], [[6ecf\|6ecf]]</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=6ecb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ecb OCA], [http://pdbe.org/6ecb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ecb RCSB], [http://www.ebi.ac.uk/pdbsum/6ecb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ecb ProSAT]</span></td></tr>
			</table>
			__TOC__
			</StructureSection>
			[[Category: Alonzo, D A]]
			[[Category: Schmeing, T M]]
			[[Category: Depsipeptide]]
			[[Category: Hydrolase]]
			[[Category: Non-ribosomal peptide synthetase]]
			[[Category: Nonribosomal peptide synthetase]]
			[[Category: Nrp]]
			[[Category: Thioesterase]]
			[[Category: Thioesterase domain]]
			[[Category: Valinomycin]]

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

2018-08-15T14:52:35Z

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

← Older revision	Revision as of 14:52, 15 August 2018
(No difference)

OCA: New page: '''Unreleased structure''' The entry 6ecb is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

2018-08-15T14:52:34Z

New page: '''Unreleased structure''' The entry 6ecb is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6ecb is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]