OCA at 16:11, 18 October 2023

2023-10-18T16:11:12Z

←Older revision		Revision as of 16:11, 18 October 2023
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-	====	+	==Chryseobacterium gregarium RiPP-associated ATP-grasp ligase in complex with ADP, and a leader and core peptide==
-	<StructureSection load='7mgv' size='340' side='right'caption='[[7mgv]]' scene=''>	+	<StructureSection load='7mgv' size='340' side='right'caption='[[7mgv]], [[Resolution\|resolution]] 2.44Å' 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= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7mgv]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Chryseobacterium_gregarium_DSM_19109 Chryseobacterium gregarium DSM 19109]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7MGV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7MGV 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=7mgv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mgv OCA], [https://pdbe.org/7mgv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mgv RCSB], [https://www.ebi.ac.uk/pdbsum/7mgv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mgv ProSAT]</span></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]] 2.44Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=7mgv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mgv OCA], [https://pdbe.org/7mgv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mgv RCSB], [https://www.ebi.ac.uk/pdbsum/7mgv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mgv ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Among the ribosomally synthesized and post-translationally modified peptide (RiPP) natural products, "graspetides" (formerly known as microviridins) contain macrocyclic esters and amides that are formed by ATP-grasp ligase tailoring enzymes using the side chains of Asp/Glu as acceptors and Thr/Ser/Lys as donors. Graspetides exhibit diverse patterns of macrocylization and connectivities exemplified by microviridins, that have a caged tricyclic core, and thuringin and plesiocin that feature a "hairpin topology" with cross-strand omega-ester bonds. Here, we characterize chryseoviridin, a new type of multicore RiPP encoded by Chryseobacterium gregarium DS19109 (Phylum Bacteroidetes) and solve a 2.44 A resolution crystal structure of a quaternary complex consisting of the ATP-grasp ligase CdnC bound to ADP, a conserved leader peptide and a peptide substrate. HRMS/MS analyses show that chryseoviridin contains four consecutive five- or six-residue macrocycles ending with a microviridin-like core. The crystal structure captures respective subunits of the CdnC homodimer in the apo or substrate-bound state revealing a large conformational change in the B-domain upon substrate binding. A docked model of ATP places the gamma-phosphate group within 2.8 A of the Asp acceptor residue. The orientation of the bound substrate is consistent with a model in which macrocyclization occurs in the N- to C-terminal direction for core peptides containing multiple Thr/Ser-to-Asp macrocycles. Using systematically varied sequences, we validate this model and identify two- or three-amino acid templating elements that flank the macrolactone and are required for enzyme activity in vitro. This work reveals the structural basis for omega-ester bond formation in RiPP biosynthesis.
		+
		+	Structural Basis for a Dual Function ATP Grasp Ligase That Installs Single and Bicyclic omega-Ester Macrocycles in a New Multicore RiPP Natural Product.,Zhao G, Kosek D, Liu HB, Ohlemacher SI, Blackburne B, Nikolskaya A, Makarova KS, Sun J, Barry Iii CE, Koonin EV, Dyda F, Bewley CA J Am Chem Soc. 2021 Jun 2;143(21):8056-8068. doi: 10.1021/jacs.1c02316. Epub 2021 , May 24. PMID:34028251<ref>PMID:34028251</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7mgv" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Chryseobacterium gregarium DSM 19109]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Bewley CA]]
		+	[[Category: Dyda F]]
		+	[[Category: Kosek D]]
		+	[[Category: Zhao G]]

OCA at 07:33, 25 June 2021

2021-06-25T07:33:10Z

←Older revision		Revision as of 07:33, 25 June 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7mgv ~~is ON HOLD~~	+	====
-		+	<StructureSection load='7mgv' size='340' side='right'caption='[[7mgv]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= 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=7mgv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7mgv OCA], [https://pdbe.org/7mgv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7mgv RCSB], [https://www.ebi.ac.uk/pdbsum/7mgv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7mgv ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

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

2021-04-21T06:24:15Z

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

←Older revision

Revision as of 06:24, 21 April 2021

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

2021-04-21T06:24:13Z

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

New page

'''Unreleased structure'''

The entry 7mgv is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

7mgv - Revision history

OCA at 16:11, 18 October 2023

OCA at 07:33, 25 June 2021

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

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