1WDE

Crystal structure of the conserved hypothetical protein APE0931 from Aeropyrum pernix K1

Summary for 1WDE

• Entry DOI: 10.2210/pdb1wde/pdb
• Descriptor: Probable diphthine synthase (2 entities in total)
• Functional Keywords: structural genomics, conserved hypothetical protein, riken structural genomics/proteomics initiative, rsgi, transferase
• Biological source: Aeropyrum pernix
• Total number of polymer chains: 1
• Total formula weight: 31764.15

Authors

Kishishita, S.,Murayama, K.,Shirouzu, M.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2004-05-13, release date: 2004-11-13, Last modification date: 2024-10-16)

Primary citation

Kishishita, S.,Shimizu, K.,Murayama, K.,Terada, T.,Shirouzu, M.,Yokoyama, S.,Kunishima, N.
Structures of two archaeal diphthine synthases: insights into the post-translational modification of elongation factor 2.
Acta Crystallogr.,Sect.D, 64:397-406, 2008

PubMed Abstract: The target of diphtheria toxin is the diphthamide residue in translation elongation factor 2 (EF-2), which is generated by a three-step post-translational modification of a specific histidine residue in the EF-2 precursor. In the second modification step, an S-adenosylmethionine-dependent methyltransferase, diphthine synthase (DS), catalyzes the trimethylation of the EF-2 precursor. The homodimeric crystal structures of the archaeal diphthine synthases from Pyrococcus horikoshii OT3 and Aeropyrum pernix K1 have been determined. These structures share essentially the same overall fold as the cobalt-precorrin-4 methyltransferase CbiF, confirming that DS belongs to the dimeric class III family of methyltransferases. In the P. horikoshii DS dimer, only one of the two active sites binds the reaction product S-adenosyl-L-homocysteine (AdoHcy), while the other active site contains no ligand. This asymmetric AdoHcy binding may be a consequence of intra-domain and inter-domain movements upon binding of AdoHcy at one of the two sites. These movements disrupt the twofold dimeric symmetry of the DS dimer and probably cause lower AdoHcy affinity at the other binding site.

PubMed: 18391406
DOI: 10.1107/S0907444908000723

Experimental method

X-RAY DIFFRACTION (2 Å)