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Roles of distal aspartate and arginine of B-class dye-decolorizing peroxidase in heterolytic hydrogen peroxide cleavage

DOI: 10.1074/jbc.RA118.004773 DOI Help

Authors: Vera Pfanzagl (BOKU - University of Natural Resources and Life Sciences) , Kevin Nys (Univerity of Antwerp) , Marzia Bellei (University of Modena and Reggio Emilia) , Hanna Michlits (BOKU - University of Natural Resources and Life Sciences) , Georg Mlynek (University of Vienna) , Gianantonio Battistuzzi (University of Modena and Reggio Emilia) , Kristina Djinovic-Carugo (University of Vienna) , Sabine Van Doorslaer (Univerity of Antwerp) , Paul G. Furtmüller (BOKU - University of Natural Resources and Life Sciences) , Stefan Hofbauer (BOKU - University of Natural Resources and Life Sciences) , Christian Obinger (BOKU - University of Natural Resources and Life Sciences)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Journal Of Biological Chemistry

State: Published (Approved)
Published: August 2018
Diamond Proposal Number(s): 16011

Abstract: Dye-decolorizing peroxidases (DyPs) represent the most recently classified hydrogen peroxide dependent heme peroxidase family. Although widely distributed with more than 5000 annotated genes and hailed for their biotechnological potential detailed biochemical characterization of their reaction mechanism remains limited. Here, we present the high resolution crystal structures of wild-type B-class DyP from the pathogenic bacterium Klebsiella pneumoniae (KpDyP) (1.6 Å) and the variants D143A (1.3 Å), R232A (1.9 Å), and D143A/R232A (1.1 Å). We demonstrate the impact of elimination of the DyP-typical, distal residues Asp 143 and Arg 232 on (i) the spectral and redox properties, (ii) the kinetics of heterolytic cleavage of hydrogen peroxide, (iii) the formation of the low-spin (LS) cyanide complex as well as on (iv) the stability and reactivity of an oxoiron(IV)porphyrin π-cation radical (Compound I). Structural and functional studies reveal that the distal aspartate is responsible for deprotonation of H2O2 and for the poor oxidation capacity of Compound I. Elimination of the distal arginine promotes a collapse of the distal heme cavity including blocking of one access channel and a conformational change of the catalytic aspartate. We also provide evidence of formation of an oxoiron(IV)-type Compound II in KpDyP with absorbance maxima at 418, 527 and 553 nm. In summary, a reaction mechanism of the peroxidase cycle of B-class DyPs is proposed. Our observations challenge the idea that peroxidase activity toward conventional aromatic substrates is related to the physiological roles of B-class DyPs.

Journal Keywords: Compound I; Compound II; heme peroxidase; oxoiron; Klebsiella pneumonia; enzyme kinetics; electron paramagnetic resonance (EPR); site-directed mutagenesis; pre-steady-state kinetics; X-ray crystallography; heme

Diamond Keywords: Enzymes

Subject Areas: Biology and Bio-materials, Chemistry


Instruments: I24-Microfocus Macromolecular Crystallography

Other Facilities: ID30A-1 at ESRF

Added On: 09/08/2018 14:52

Documents:
jbc.RA118.004773.full.pdf

Discipline Tags:

Biochemistry Catalysis Chemistry Structural biology Biophysics Life Sciences & Biotech

Technical Tags:

Diffraction Macromolecular Crystallography (MX)