6c0y: Difference between revisions

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 ==Lysinoalanine synthase, DurN, from duramycin biosynthesis bound to duramycin==
-<StructureSection load='6c0y' size='340' side='right' caption='[[6c0y]], [[Resolution|resolution]] 1.66&Aring;' scene=''>
+<StructureSection load='6c0y' size='340' side='right'caption='[[6c0y]], [[Resolution|resolution]] 1.66&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6c0y]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Streptomyces_cinnamoneus Streptomyces cinnamoneus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C0Y OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6C0Y FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6c0y]] is a 16 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=6C0Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6C0Y 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]] 1.66&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=BH2:(3R)-3-HYDROXY-L-ASPARTIC+ACID'>BH2</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=DBB:D-ALPHA-AMINOBUTYRIC+ACID'>DBB</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BH2:(3R)-3-HYDROXY-L-ASPARTIC+ACID'>BH2</scene>, <scene name='pdbligand=DAL:D-ALANINE'>DAL</scene>, <scene name='pdbligand=DBB:D-ALPHA-AMINOBUTYRIC+ACID'>DBB</scene>, <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=6c0y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c0y OCA], [http://pdbe.org/6c0y PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6c0y RCSB], [http://www.ebi.ac.uk/pdbsum/6c0y PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6c0y 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=6c0y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c0y OCA], [https://pdbe.org/6c0y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6c0y RCSB], [https://www.ebi.ac.uk/pdbsum/6c0y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6c0y ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/A0A3F2YLX1_STRCJ A0A3F2YLX1_STRCJ]
+<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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 6c0y" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Streptomyces cinnamoneus]]
-[[Category: Cogan, D P]]
+[[Category: Cogan DP]]
-[[Category: Nair, S K]]
+[[Category: Nair SK]]
-[[Category: Biosynthetic protein]]
-[[Category: Lysinoalanine synthase]]
-[[Category: Michael addition]]