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6BXM

Crystal structure of Candidatus Methanoperedens nitroreducens Dph2 with 4Fe-4S cluster and SAM/cleaved SAM

Summary for 6BXM
Entry DOI10.2210/pdb6bxm/pdb
DescriptorDiphthamide biosynthesis enzyme Dph2, IRON/SULFUR CLUSTER, S-ADENOSYLMETHIONINE, ... (6 entities in total)
Functional Keywordsdiphthamide biosynthesis, radical sam enzyme, biosynthetic protein
Biological sourceCandidatus Methanoperedens nitroreducens
Total number of polymer chains2
Total formula weight74420.84
Authors
Fenwick, M.K.,Torelli, A.T.,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: 2023-11-15)
Primary citationDong, 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: 29590073
DOI: 10.1126/science.aao6595
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (2.252 Å)
Structure validation

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数据于2024-11-06公开中

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