Synthesis of 5-Hydroxyectoine from Ectoine: Crystal Structure of the Non-Heme Iron(II) and 2-Oxoglutarate-Dependent Dioxygenase EctD
Figure 5
Binding of 2-oxoglutarate by PhyH-like enzymes.
(A) PhyH, (B) SyrB2 and (C) PtlH (PDB code: 2RDN) and (D) EctD. The Fe2+ ion is shown as a blue sphere, water molecules are shown as red spheres. Side chains of residues involved in 2-oxoglutarate binding or in Fe2+ coordination are represented as sticks. Secondary structure elements are indicated as ribbons. The positioning of Phe-143 residue in the EctD structure makes in all likelihood an interaction via its aromatic side chain with 2-oxoglutarate. However, the conformation of the Phe-143 side chain shown in this figure must be regarded as tentative as it is poorly defined in the electron density map (in contrast to the Phe-143 main chain atoms). In addition, the actual orientation of the Arg-259 side chain in the EctD crystal structure is not in a position enabling its guanidino function to salt bridge the 5-carboxylate of a bound 2-oxoglutarate. However, a position allowing this interaction can easily be achieved through torsion around rotatable single bonds within the side chain of this Arg residue. It also should be noted that the DSBH β-strand II of PhyH is largely disordered in the crystal structure of this protein. In the EctD structure, the corresponding β-strand also strongly deviates from ideal β-strand geometry.