3LZC

Crystal structure of Dph2 from Pyrococcus horikoshii

Summary for 3LZC

• Entry DOI: 10.2210/pdb3lzc/pdb
• Related: 3LZD
• Descriptor: Dph2 (2 entities in total)
• Functional Keywords: diphthamide biosynthesis, radical sam enzyme, gene triplication, biosynthetic protein
• Biological source: Pyrococcus horikoshii
• Total number of polymer chains: 2
• Total formula weight: 85076.58

Authors

Zhang, Y.,Zhu, X.,Torelli, A.T.,Lee, M.,Dzikovski, B.,Koralewski, R.M.,Wang, E.,Freed, J.,Krebs, C.,Lin, H.,Ealick, S.E. (deposition date: 2010-03-01, release date: 2010-06-23, Last modification date: 2024-02-21)

Primary citation

Zhang, Y.,Zhu, X.,Torelli, A.T.,Lee, M.,Dzikovski, B.,Koralewski, R.M.,Wang, E.,Freed, J.,Krebs, C.,Ealick, S.E.,Lin, H.
Diphthamide biosynthesis requires an organic radical generated by an iron-sulphur enzyme.
Nature, 465:891-896, 2010

PubMed Abstract: Archaeal and eukaryotic translation elongation factor 2 contain a unique post-translationally modified histidine residue called diphthamide, which is the target of diphtheria toxin. The biosynthesis of diphthamide was proposed to involve three steps, with the first being the formation of a C-C bond between the histidine residue and the 3-amino-3-carboxypropyl group of S-adenosyl-l-methionine (SAM). However, further details of the biosynthesis remain unknown. Here we present structural and biochemical evidence showing that the first step of diphthamide biosynthesis in the archaeon Pyrococcus horikoshii uses a novel iron-sulphur-cluster enzyme, Dph2. Dph2 is a homodimer and each of its monomers can bind a [4Fe-4S] cluster. Biochemical data suggest that unlike the enzymes in the radical SAM superfamily, Dph2 does not form the canonical 5'-deoxyadenosyl radical. Instead, it breaks the C(gamma,Met)-S bond of SAM and generates a 3-amino-3-carboxypropyl radical. Our results suggest that P. horikoshii Dph2 represents a previously unknown, SAM-dependent, [4Fe-4S]-containing enzyme that catalyses unprecedented chemistry.

PubMed: 20559380
DOI: 10.1038/nature09138

Experimental method

X-RAY DIFFRACTION (2.261 Å)