6Q2D

Crystal structure of Methanobrevibacter smithii Dph2 in complex with Methanobrevibacter smithii elongation factor 2

Summary for 6Q2D

• Entry DOI: 10.2210/pdb6q2d/pdb
• Descriptor: 2-(3-amino-3-carboxypropyl)histidine synthase, Elongation factor 2, IRON/SULFUR CLUSTER (3 entities in total)
• Functional Keywords: radical, s-adenosylmethionine, enzyme, iron sulfur cluster, transferase
• Biological source: Methanobrevibacter smithii; More
• Total number of polymer chains: 4
• Total formula weight: 240509.75

Authors

Fenwick, M.K.,Dong, M.,Lin, H.,Ealick, S.E. (deposition date: 2019-08-07, release date: 2019-10-16, Last modification date: 2023-10-11)

Primary citation

Fenwick, M.K.,Dong, M.,Lin, H.,Ealick, S.E.
The Crystal Structure of Dph2 in Complex with Elongation Factor 2 Reveals the Structural Basis for the First Step of Diphthamide Biosynthesis.
Biochemistry, 58:4343-4351, 2019

PubMed Abstract: Elongation factor 2 (EF-2), a five-domain, GTP-dependent ribosomal translocase of archaebacteria and eukaryotes, undergoes post-translational modification to form diphthamide on a specific histidine residue in domain IV prior to binding the ribosome. The first step of diphthamide biosynthesis in archaebacteria is catalyzed by Dph2, a homodimeric radical -adenosylmethionine (SAM) enzyme having a noncanonical architecture. Here, we describe a 3.5 Å resolution crystal structure of the () Dph2 homodimer bound to two molecules of EF-2, one of which is ordered and the other largely disordered. EF-2 is bound to both protomers of Dph2, with domain IV bound to the active site of one protomer and domain III bound to a surface α-helix of an adjacent protomer. The histidine substrate of domain IV is inserted into the active site, which reveals for the first time the architecture of the Dph2 active site in complex with its target substrate. We also determined a high-resolution crystal structure of isolated Dph2 bound to 5'-methylthioadenosine that shows a conserved arginine residue preoriented by conserved phenylalanine and aspartate residues for binding the carboxylate group of SAM. Mutagenesis experiments suggest that the arginine plays an important role in the first step of diphthamide biosynthesis.

PubMed: 31566354
DOI: 10.1021/acs.biochem.9b00718

Experimental method

X-RAY DIFFRACTION (3.45 Å)