6pe3

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Current revision (14:33, 6 March 2024) (edit) (undo)
 
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<StructureSection load='6pe3' size='340' side='right'caption='[[6pe3]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
<StructureSection load='6pe3' size='340' side='right'caption='[[6pe3]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6pe3]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PE3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PE3 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6pe3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Methanocaldococcus_jannaschii_DSM_2661 Methanocaldococcus jannaschii DSM 2661]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PE3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PE3 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
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<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=6pe3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pe3 OCA], [http://pdbe.org/6pe3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pe3 RCSB], [http://www.ebi.ac.uk/pdbsum/6pe3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pe3 ProSAT]</span></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6pe3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pe3 OCA], [https://pdbe.org/6pe3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pe3 RCSB], [https://www.ebi.ac.uk/pdbsum/6pe3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pe3 ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/Y1094_METJA Y1094_METJA]
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YcaO enzymes are known to catalyze the ATP-dependent formation of azoline heterocycles, thioamides, and (macro)lactamidines on peptide substrates. These enzymes are found in multiple biosynthetic pathways, including those for several different classes of ribosomally synthesized and post-translationally modified peptides (RiPPs). However, there are major knowledge gaps in the mechanistic and structural underpinnings that govern each of the known YcaO-mediated modifications. Here, we present the first structure of any YcaO enzyme bound to its peptide substrate in the active site, specifically that from Methanocaldococcus jannaschii which is involved in the thioamidation of the alpha-subunit of methyl-coenzyme M reductase (McrA). The structural data are leveraged to identify and test the residues involved in substrate binding and catalysis by site-directed mutagenesis. We also show that thioamide-forming YcaOs can carry out the cyclodehydration of a related peptide substrate, which underscores the mechanistic conservation across the YcaO family and allows for the extrapolation of mechanistic details to azoline-forming YcaOs involved in RiPP biosynthesis. A bioinformatic survey of all YcaOs highlights the diverse sequence space in azoline-forming YcaOs and suggests their early divergence from a common ancestor. The data presented within provide a detailed molecular framework for understanding this family of enzymes, which reconcile several decades of prior data on RiPP cyclodehydratases. These studies also provide the foundational knowledge to impact our mechanistic understanding of additional RiPP biosynthetic classes.
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Mechanistic Basis for Ribosomal Peptide Backbone Modifications.,Dong SH, Liu A, Mahanta N, Mitchell DA, Nair SK ACS Cent Sci. 2019 May 22;5(5):842-851. doi: 10.1021/acscentsci.9b00124. Epub, 2019 Apr 16. PMID:31139720<ref>PMID:31139720</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 6pe3" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Dong, S H]]
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[[Category: Methanocaldococcus jannaschii DSM 2661]]
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[[Category: Nair, S K]]
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[[Category: Dong S-H]]
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[[Category: Atp]]
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[[Category: Nair SK]]
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[[Category: Biosynthetic protein]]
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[[Category: Methanocaldococcus jannaschii]]
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[[Category: Thioamide]]
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[[Category: Ycao]]
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Current revision

Structure of YcaO enzyme from Methanocaldococcus jannaschii in complex with ATP

PDB ID 6pe3

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