6bxm: Difference between revisions
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New page: '''Unreleased structure''' The entry 6bxm is ON HOLD Authors: Fenwick, M.K., Torelli, A.T., Zhang, Y., Dong, M., Kathiresan, V., Carantoa, J.D., Dzikovski, B., Lancaster, K.M., Freed, J... |
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==Crystal structure of Candidatus Methanoperedens nitroreducens Dph2 with 4Fe-4S cluster and SAM/cleaved SAM== | |||
<StructureSection load='6bxm' size='340' side='right'caption='[[6bxm]], [[Resolution|resolution]] 2.25Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6bxm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Candidatus_Methanoperedens_nitroreducens Candidatus Methanoperedens nitroreducens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BXM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6BXM FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.252Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ABA:ALPHA-AMINOBUTYRIC+ACID'>ABA</scene>, <scene name='pdbligand=MTA:5-DEOXY-5-METHYLTHIOADENOSINE'>MTA</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</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=6bxm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bxm OCA], [https://pdbe.org/6bxm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6bxm RCSB], [https://www.ebi.ac.uk/pdbsum/6bxm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6bxm ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/A0A062UZ78_9EURY A0A062UZ78_9EURY] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Diphthamide biosynthesis involves a carbon-carbon bond-forming reaction catalyzed by a radical S-adenosylmethionine (SAM) enzyme that cleaves a carbon-sulfur (C-S) bond in SAM to generate a 3-amino-3-carboxypropyl (ACP) radical. Using rapid freezing, we have captured an organometallic intermediate with an iron-carbon (Fe-C) bond between ACP and the enzyme's [4Fe-4S] cluster. In the presence of the substrate protein, elongation factor 2, this intermediate converts to an organic radical, formed by addition of the ACP radical to a histidine side chain. Crystal structures of archaeal diphthamide biosynthetic radical SAM enzymes reveal that the carbon of the SAM C-S bond being cleaved is positioned near the unique cluster Fe, able to react with the cluster. Our results explain how selective C-S bond cleavage is achieved in this radical SAM enzyme. | |||
Organometallic and radical intermediates reveal mechanism of diphthamide biosynthesis.,Dong M, Kathiresan V, Fenwick MK, Torelli AT, Zhang Y, Caranto JD, Dzikovski B, Sharma A, Lancaster KM, Freed JH, Ealick SE, Hoffman BM, Lin H Science. 2018 Mar 16;359(6381):1247-1250. doi: 10.1126/science.aao6595. PMID:29590073<ref>PMID:29590073</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 6bxm" style="background-color:#fffaf0;"></div> | ||
[[Category: Carantoa | == References == | ||
[[Category: Dong | <references/> | ||
[[Category: | __TOC__ | ||
[[Category: | </StructureSection> | ||
[[Category: | [[Category: Candidatus Methanoperedens nitroreducens]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Carantoa JD]] | ||
[[Category: | [[Category: Dong M]] | ||
[[Category: | [[Category: Dzikovski B]] | ||
[[Category: | [[Category: Ealick SE]] | ||
[[Category: | [[Category: Fenwick MK]] | ||
[[Category: Freed JH]] | |||
[[Category: Hoffman BM]] | |||
[[Category: Kathiresan V]] | |||
[[Category: Lancaster KM]] | |||
[[Category: Lin H]] | |||
[[Category: Torelli AT]] | |||
[[Category: Zhang Y]] | |||
Latest revision as of 13:03, 13 August 2026
Crystal structure of Candidatus Methanoperedens nitroreducens Dph2 with 4Fe-4S cluster and SAM/cleaved SAM
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