7O9J

Crystal structure of DyP-type peroxidase from Dictyostelium discoideum in complex with an activated form of oxygen

Summary for 7O9J

• Entry DOI: 10.2210/pdb7o9j/pdb
• Descriptor: DyPA, PROTOPORPHYRIN IX CONTAINING FE, 1,2-ETHANEDIOL, ... (6 entities in total)
• Functional Keywords: dye decolorizing-type peroxidase, dictyostelium discoideum, b-type dyp, hydrolase
• Biological source: Dictyostelium discoideum (Slime mold)
• Total number of polymer chains: 2
• Total formula weight: 72404.76

Authors

Rai, A.,Fedorov, R.,Manstein, D.J. (deposition date: 2021-04-16, release date: 2021-07-14, Last modification date: 2024-01-31)

Primary citation

Rai, A.,Klare, J.P.,Reinke, P.Y.A.,Englmaier, F.,Fohrer, J.,Fedorov, R.,Taft, M.H.,Chizhov, I.,Curth, U.,Plettenburg, O.,Manstein, D.J.
Structural and Biochemical Characterization of a Dye-Decolorizing Peroxidase from Dictyostelium discoideum .
Int J Mol Sci, 22:-, 2021

PubMed Abstract: A novel cytoplasmic dye-decolorizing peroxidase from was investigated that oxidizes anthraquinone dyes, lignin model compounds, and general peroxidase substrates such as ABTS efficiently. Unlike related enzymes, an aspartate residue replaces the first glycine of the conserved GXXDG motif in DyPA. In solution, DyPA exists as a stable dimer with the side chain of Asp146 contributing to the stabilization of the dimer interface by extending the hydrogen bond network connecting two monomers. To gain mechanistic insights, we solved the DyPA structures in the absence of substrate as well as in the presence of potassium cyanide and veratryl alcohol to 1.7, 1.85, and 1.6 Å resolution, respectively. The active site of DyPA has a hexa-coordinated heme iron with a histidine residue at the proximal axial position and either an activated oxygen or CN molecule at the distal axial position. Asp149 is in an optimal conformation to accept a proton from HO during the formation of compound I. Two potential distal solvent channels and a conserved shallow pocket leading to the heme molecule were found in DyPA. Further, we identified two substrate-binding pockets per monomer in DyPA at the dimer interface. Long-range electron transfer pathways associated with a hydrogen-bonding network that connects the substrate-binding sites with the heme moiety are described.

PubMed: 34200865
DOI: 10.3390/ijms22126265

Experimental method

X-RAY DIFFRACTION (1.7 Å)