5wa3 - Revision history

OCA at 14:09, 4 October 2023

OCA — Wed, 04 Oct 2023 14:09:26 GMT

←Older revision		Revision as of 14:09, 4 October 2023
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	==Pyridine synthase, TbtD, from thiomuracin biosynthesis==		==Pyridine synthase, TbtD, from thiomuracin biosynthesis==
-	<StructureSection load='5wa3' size='340' side='right' caption='[[5wa3]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='5wa3' size='340' side='right'caption='[[5wa3]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5wa3]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Thebd Thebd~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WA3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5WA3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5wa3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermobispora_bispora_DSM_43833 Thermobispora bispora DSM 43833]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WA3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5WA3 FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~Tbis_0552 (~~[~~http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=469371 THEBD])~~</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]] 2.8Å</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=5wa3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wa3 OCA], [~~http~~://pdbe.org/5wa3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5wa3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5wa3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5wa3 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=5wa3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wa3 OCA], [https://pdbe.org/5wa3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5wa3 RCSB], [https://www.ebi.ac.uk/pdbsum/5wa3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5wa3 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/D6Y504_THEBD D6Y504_THEBD]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Thebd~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Cogan, D P~~]]	+	[[Category: Thermobispora bispora DSM 43833]]
-	[[Category: ~~Nair, S K~~]]	+	[[Category: Cogan DP]]
-	[[Category: ~~Biosynthetic protein]]~~	+	[[Category: Nair SK]]
-	~~[[Category: Diels-alder]]~~	+
-	~~[[Category: Pyridine synthase]]~~	+
-	~~[[Category: Thiomuracin]]~~	+
-	~~[[Category: Thiopeptide~~]]	+

OCA at 07:50, 6 December 2017

OCA — Wed, 06 Dec 2017 07:50:35 GMT

←Older revision		Revision as of 07:50, 6 December 2017
Line 3:		Line 3:
	<StructureSection load='5wa3' size='340' side='right' caption='[[5wa3]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='5wa3' size='340' side='right' caption='[[5wa3]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5wa3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WA3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WA3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5wa3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thebd Thebd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WA3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WA3 FirstGlance]. <br>
-	</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=5wa3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wa3 OCA], [http://pdbe.org/5wa3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wa3 RCSB], [http://www.ebi.ac.uk/pdbsum/5wa3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wa3 ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Tbis_0552 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=469371 THEBD])</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=5wa3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wa3 OCA], [http://pdbe.org/5wa3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wa3 RCSB], [http://www.ebi.ac.uk/pdbsum/5wa3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wa3 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The [4+2] cycloaddition reaction is an enabling transformation in modern synthetic organic chemistry, but there are only limited examples of dedicated natural enzymes that can catalyze this transformation. Thiopeptides (or more formally thiazolyl peptides) are a class of thiazole-containing, highly modified, macrocyclic secondary metabolites made from ribosomally synthesized precursor peptides. The characteristic feature of these natural products is a six-membered nitrogenous heterocycle that is assembled via a formal [4+2] cycloaddition between two dehydroalanine (Dha) residues. This heteroannulation is entirely contingent on enzyme activity, although the mechanism of the requisite pyridine/dehydropiperidine synthase remains to be elucidated. The unusual aza-cylic product is distinct from the more common carbocyclic products of synthetic and biosynthetic [4+2] cycloaddition reactions. To elucidate the mechanism of cycloaddition, we have determined atomic resolution structures of the pyridine synthases involved in the biosynthesis of the thiopeptides thiomuracin (TbtD) and GE2270A (PbtD), in complex with substrates and product analogs. Structure-guided biochemical, mutational, computational, and binding studies elucidate active-site features that explain how orthologs can generate rigid macrocyclic scaffolds of different sizes. Notably, the pyridine synthases show structural similarity to the elimination domain of lanthipeptide dehydratases, wherein insertions of secondary structural elements result in the formation of a distinct active site that catalyzes different chemistry. Comparative analysis identifies other catalysts that contain a shared core protein fold but whose active sites are located in entirely different regions, illustrating a principle predicted from efforts in de novo protein design.
		+
		+	Structural insights into enzymatic [4+2] aza-cycloaddition in thiopeptide antibiotic biosynthesis.,Cogan DP, Hudson GA, Zhang Z, Pogorelov TV, van der Donk WA, Mitchell DA, Nair SK Proc Natl Acad Sci U S A. 2017 Nov 20. pii: 1716035114. doi:, 10.1073/pnas.1716035114. PMID:29158402<ref>PMID:29158402</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5wa3" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Thebd]]
	[[Category: Cogan, D P]]		[[Category: Cogan, D P]]
	[[Category: Nair, S K]]		[[Category: Nair, S K]]

OCA at 07:44, 22 November 2017

OCA — Wed, 22 Nov 2017 07:44:18 GMT

←Older revision		Revision as of 07:44, 22 November 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5wa3 ~~is ON HOLD until Paper Publication~~	+	==Pyridine synthase, TbtD, from thiomuracin biosynthesis==
-		+	<StructureSection load='5wa3' size='340' side='right' caption='[[5wa3]], [[Resolution\|resolution]] 2.80Å' scene=''>
-	~~Authors~~: ~~Cogan~~, D.P., ~~Nair~~, S.K.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5wa3]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5WA3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5WA3 FirstGlance]. <br>
-	~~Description~~: ~~Pyridine synthase~~, ~~TbtD, from thiomuracin biosynthesis~~	+	</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=5wa3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5wa3 OCA], [http://pdbe.org/5wa3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5wa3 RCSB], [http://www.ebi.ac.uk/pdbsum/5wa3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5wa3 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
-	[[Category: Nair, S.K]]	+	__TOC__
-	[[Category: ~~Cogan, D.P~~]]	+	</StructureSection>
		+	[[Category: Cogan, D P]]
		+	[[Category: Nair, S K]]
		+	[[Category: Biosynthetic protein]]
		+	[[Category: Diels-alder]]
		+	[[Category: Pyridine synthase]]
		+	[[Category: Thiomuracin]]
		+	[[Category: Thiopeptide]]

OCA at 05:32, 25 October 2017

OCA — Wed, 25 Oct 2017 05:32:14 GMT

←Older revision		Revision as of 05:32, 25 October 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5wa3 is ON HOLD	+	The entry 5wa3 is ON HOLD until Paper Publication

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

OCA: Protected "5wa3" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 14:36:47 GMT

Protected "5wa3" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:36, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5wa3 is ON HOLD Authors: Cogan, D.P., Nair, S.K. Description: Pyridine synthase, TbtD, from thiomuracin biosynthesis [[Category: Unreleased Structu...

OCA — Wed, 27 Sep 2017 14:36:46 GMT

New page: '''Unreleased structure''' The entry 5wa3 is ON HOLD Authors: Cogan, D.P., Nair, S.K. Description: Pyridine synthase, TbtD, from thiomuracin biosynthesis [[Category: Unreleased Structu...

New page

'''Unreleased structure'''

The entry 5wa3 is ON HOLD

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

Description: Pyridine synthase, TbtD, from thiomuracin biosynthesis
[[Category: Unreleased Structures]]
[[Category: Nair, S.K]]
[[Category: Cogan, D.P]]