6BXL
Crystal structure of Pyrococcus horikoshii Dph2 with 4Fe-4S cluster and SAM
Summary for 6BXL
| Entry DOI | 10.2210/pdb6bxl/pdb |
| Descriptor | 2-(3-amino-3-carboxypropyl)histidine synthase, S-ADENOSYLMETHIONINE, IRON/SULFUR CLUSTER, ... (4 entities in total) |
| Functional Keywords | diphthamide biosynthesis, radical sam enzyme, biosynthetic protein |
| Biological source | Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3) |
| Total number of polymer chains | 2 |
| Total formula weight | 86576.73 |
| Authors | Torelli, A.T.,Fenwick, M.K.,Zhang, Y.,Dong, M.,Kathiresan, V.,Carantoa, J.D.,Dzikovski, B.,Lancaster, K.M.,Freed, J.H.,Hoffman, B.M.,Lin, H.,Ealick, S.E. (deposition date: 2017-12-18, release date: 2018-04-11, Last modification date: 2023-10-04) |
| Primary citation | Dong, M.,Kathiresan, V.,Fenwick, M.K.,Torelli, A.T.,Zhang, Y.,Caranto, J.D.,Dzikovski, B.,Sharma, A.,Lancaster, K.M.,Freed, J.H.,Ealick, S.E.,Hoffman, B.M.,Lin, H. Organometallic and radical intermediates reveal mechanism of diphthamide biosynthesis. Science, 359:1247-1250, 2018 Cited by PubMed Abstract: 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. PubMed: 29590073DOI: 10.1126/science.aao6595 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.301 Å) |
Structure validation
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