3LZC image
Entry Detail
PDB ID:
3LZC
Title:
Crystal structure of Dph2 from Pyrococcus horikoshii
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2010-03-01
Release Date:
2010-06-23
Method Details:
Experimental Method:
Resolution:
2.26 Å
R-Value Free:
0.24
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Dph2
Chain IDs:A, B
Chain Length:378
Number of Molecules:2
Biological Source:Pyrococcus horikoshii
Primary Citation
Diphthamide biosynthesis requires an organic radical generated by an iron-sulphur enzyme.
Nature 465 891 896 (2010)
PMID: 20559380 DOI: 10.1038/nature09138

Abstact

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.

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