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Impact of the dynamics of the catalytic arginine on nitrite and chlorite binding by dimeric chlorite dismutase

DOI: 10.1016/j.jinorgbio.2021.111689 DOI Help

Authors: Ilenia Serra (University of Antwerp) , Daniel Schmidt (University of Natural Resources and Life Sciences) , Vera Pfanzagl (University of Natural Resources and Life Sciences) , Georg Mlynek (University of Natural Resources and Life Sciences; Max Perutz Laboratories) , Stefan Hofbauer (University of Natural Resources and Life Science) , Kristina Djinovic-Carugo (Max Perutz Laboratories; University of Ljubljana) , Paul G. Furtmüller (University of Natural Resources and Life Sciences) , Inés García Rubio (University of Zaragoza; Centro Universitario de la Defensa) , Sabine Van Doorslaer (University of Antwerp) , Christian Obinger (University of Natural Resources and Life Sciences)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Journal Of Inorganic Biochemistry , VOL 9

State: Published (Approved)
Published: December 2021
Diamond Proposal Number(s): 20221

Abstract: Chlorite dismutases (Clds) are heme b containing oxidoreductases able to decompose chlorite to chloride and molecular oxygen. This work analyses the impact of the distal, flexible and catalytic arginine on the binding of anionic angulate ligands like nitrite and the substrate chlorite. Dimeric Cld from Cyanothece sp. PCC7425 was used as a model enzyme. We have investigated wild-type CCld having the distal catalytic R127 hydrogen-bonded to glutamine Q74 and variants with R127 (i) being arrested in a salt-bridge with a glutamate (Q74E), (ii) being fully flexible (Q74V) or (iii) substituted by either alanine (R127A) or lysine (R127K). We present the electronic and spectral signatures of the high-spin ferric proteins and the corresponding low-spin nitrite complexes elucidated by UV–visible, circular dichroism and electron paramagnetic resonance spectroscopies. Furthermore, we demonstrate the impact of the dynamics of R127 on the thermal stability of the respective nitrite adducts and present the X-ray crystal structures of the nitrite complexes of wild-type CCld and the variants Q74V, Q74E and R127A. In addition, the molecular dynamics (MD) and the binding modi of nitrite and chlorite to the ferric wild-type enzyme and the mutant proteins and the interaction of the oxoanions with R127 have been analysed by MD simulations. The findings are discussed with respect to the role(s) of R127 in ligand and chlorite binding and substrate degradation.

Journal Keywords: Chlorite dismutase; Catalytic arginine; Substrate adduct; X-ray crystallography; electron paramagnetic resonance; Molecular dynamics simulation

Diamond Keywords: Enzymes

Subject Areas: Biology and Bio-materials, Chemistry

Instruments: I04-Macromolecular Crystallography

Added On: 15/12/2021 08:44

Discipline Tags:

Biochemistry Catalysis Chemistry Structural biology Life Sciences & Biotech

Technical Tags:

Diffraction Macromolecular Crystallography (MX)