7js6: Difference between revisions

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~~'''Unreleased structure'''~~

~~The entry~~ 7js6 is ~~ON HOLD~~

==Solution NMR structure of des-citrulassin F==

== Structural highlights ==

<table><tr><td colspan='2'>Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JS6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7JS6 FirstGlance]. <br>

</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR, 20 models</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=7js6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7js6 OCA], [https://pdbe.org/7js6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7js6 RCSB], [https://www.ebi.ac.uk/pdbsum/7js6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7js6 ProSAT]</span></td></tr>

</table>

== Publication Abstract from PubMed ==

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a family of natural products defined by a genetically encoded precursor peptide that is processed by associated biosynthetic enzymes to form the mature product. Lasso peptides are a class of RiPP defined by an isopeptide linkage between the N-terminal amine and an internal Asp/Glu residue with the C-terminal sequence threaded through the macrocycle. This unique lariat topology, which typically provides considerable stability toward heat and proteases, has stimulated interest in lasso peptides as potential therapeutics. Post-translational modifications beyond the class-defining, threaded macrolactam have been reported, including one example of Arg deimination to yield citrulline (Cit). Although a Cit-containing lasso peptide (i.e., citrulassin) was serendipitously discovered during a genome-guided campaign, the gene(s) responsible for Arg deimination has remained unknown. Herein, we describe the use of reactivity-based screening to discriminate bacterial strains that produce Arg- versus Cit-bearing citrulassins, yielding 13 new lasso peptide variants. Partial phylogenetic profiling identified a distally encoded peptidyl arginine deiminase (PAD) gene ubiquitous to the Cit-containing variants. Absence of this gene correlated strongly with lasso peptide variants only containing Arg (i.e., des-citrulassin). Heterologous expression of the PAD gene in a des-citrulassin producer resulted in the production of the deiminated analog, confirming PAD involvement in Arg deimination. The PADs were then bioinformatically surveyed to provide a deeper understanding of their taxonomic distribution and genomic contexts and to facilitate future studies that will evaluate any additional biochemical roles for the superfamily.

~~Authors:~~ Harris, L.A.~~, Mitchell, D~~.A.

Reactivity-Based Screening for Citrulline-Containing Natural Products Reveals a Family of Bacterial Peptidyl Arginine Deiminases.,Harris LA, Saint-Vincent PMB, Guo X, Hudson GA, DiCaprio AJ, Zhu L, Mitchell DA ACS Chem Biol. 2020 Nov 29. doi: 10.1021/acschembio.0c00685. PMID:33249828<ref>PMID:33249828</ref>

~~Description~~: ~~Solution NMR structure of citrulassin F~~

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

[[Category: ~~Unreleased~~ Structures]]

</div>

[[Category: Harris~~, L.A~~]]

[[Category: Mitchell~~, D.A~~]]

== References ==

__TOC__

</StructureSection>

[[Category: Large Structures]]

[[Category: Harris LA]]

[[Category: Mitchell DA]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 7js6 is ON HOLD
+==Solution NMR structure of des-citrulassin F==
+<StructureSection load='7js6' size='340' side='right'caption='[[7js6]]' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JS6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7JS6 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR, 20 models</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=7js6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7js6 OCA], [https://pdbe.org/7js6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7js6 RCSB], [https://www.ebi.ac.uk/pdbsum/7js6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7js6 ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a family of natural products defined by a genetically encoded precursor peptide that is processed by associated biosynthetic enzymes to form the mature product. Lasso peptides are a class of RiPP defined by an isopeptide linkage between the N-terminal amine and an internal Asp/Glu residue with the C-terminal sequence threaded through the macrocycle. This unique lariat topology, which typically provides considerable stability toward heat and proteases, has stimulated interest in lasso peptides as potential therapeutics. Post-translational modifications beyond the class-defining, threaded macrolactam have been reported, including one example of Arg deimination to yield citrulline (Cit). Although a Cit-containing lasso peptide (i.e., citrulassin) was serendipitously discovered during a genome-guided campaign, the gene(s) responsible for Arg deimination has remained unknown. Herein, we describe the use of reactivity-based screening to discriminate bacterial strains that produce Arg- versus Cit-bearing citrulassins, yielding 13 new lasso peptide variants. Partial phylogenetic profiling identified a distally encoded peptidyl arginine deiminase (PAD) gene ubiquitous to the Cit-containing variants. Absence of this gene correlated strongly with lasso peptide variants only containing Arg (i.e., des-citrulassin). Heterologous expression of the PAD gene in a des-citrulassin producer resulted in the production of the deiminated analog, confirming PAD involvement in Arg deimination. The PADs were then bioinformatically surveyed to provide a deeper understanding of their taxonomic distribution and genomic contexts and to facilitate future studies that will evaluate any additional biochemical roles for the superfamily.
-Authors: Harris, L.A., Mitchell, D.A.
+Reactivity-Based Screening for Citrulline-Containing Natural Products Reveals a Family of Bacterial Peptidyl Arginine Deiminases.,Harris LA, Saint-Vincent PMB, Guo X, Hudson GA, DiCaprio AJ, Zhu L, Mitchell DA ACS Chem Biol. 2020 Nov 29. doi: 10.1021/acschembio.0c00685. PMID:33249828<ref>PMID:33249828</ref>
-Description: Solution NMR structure of citrulassin F
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Harris, L.A]]
+<div class="pdbe-citations 7js6" style="background-color:#fffaf0;"></div>
-[[Category: Mitchell, D.A]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Harris LA]]
+[[Category: Mitchell DA]]