6BXO

Crystal structure of Candidatus Methanoperedens nitroreducens Dph2 with 4Fe-4S cluster and SAH

6BXO の概要

• エントリーDOI: 10.2210/pdb6bxo/pdb
• 分子名称: Diphthamide biosynthesis enzyme Dph2, IRON/SULFUR CLUSTER, S-ADENOSYL-L-HOMOCYSTEINE, ... (4 entities in total)
• 機能のキーワード: diphthamide biosynthesis, radical sam enzyme, biosynthetic protein
• 由来する生物種: Candidatus Methanoperedens nitroreducens
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 74390.77

構造登録者

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. (登録日: 2017-12-18, 公開日: 2018-04-11, 最終更新日: 2024-10-23)

主引用文献

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

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

実験手法

X-RAY DIFFRACTION (1.655 Å)