7ATI

Crystal structure of dimeric chlorite dismutase variant Q74V (CCld Q74V) from Cyanothece sp. PCC7425

Summary for 7ATI

• Entry DOI: 10.2210/pdb7ati/pdb
• Descriptor: Chlorite dismutase, GLYCEROL, PROTOPORPHYRIN IX CONTAINING FE, ... (5 entities in total)
• Functional Keywords: chlorite dismutase, heme enzyme, oxidoreductase
• Biological source: Cyanothece sp. (strain PCC 7425 / ATCC 29141)
• Total number of polymer chains: 2
• Total formula weight: 45601.54

Authors

Schmidt, D.,Mlynek, G.,Djinovic-Carugo, K.,Obinger, C. (deposition date: 2020-10-30, release date: 2021-02-17, Last modification date: 2024-01-31)

Primary citation

Schmidt, D.,Serra, I.,Mlynek, G.,Pfanzagl, V.,Hofbauer, S.,Furtmuller, P.G.,Djinovic-Carugo, K.,Van Doorslaer, S.,Obinger, C.
Arresting the Catalytic Arginine in Chlorite Dismutases: Impact on Heme Coordination, Thermal Stability, and Catalysis.
Biochemistry, 60:621-634, 2021

PubMed Abstract: Chlorite dismutases (Clds) are heme -containing oxidoreductases that can decompose chlorite to chloride and molecular oxygen. They are divided in two clades that differ in oligomerization, subunit architecture, and the hydrogen-bonding network of the distal catalytic arginine, which is proposed to switch between two conformations during turnover. To understand the impact of the conformational dynamics of this basic amino acid on heme coordination, structure, and catalysis, Cld from sp. PCC7425 was used as a model enzyme. As typical for a clade 2 Cld, its distal arginine 127 is hydrogen-bonded to glutamine 74. The latter has been exchanged with either glutamate (Q74E) to arrest R127 in a salt bridge or valine (Q74V) that mirrors the setting in clade 1 Clds. We present the X-ray crystal structures of Q74V and Q74E and demonstrate the pH-induced changes in the environment and coordination of the heme iron by ultraviolet-visible, circular dichroism, and electron paramagnetic resonance spectroscopies as well as differential scanning calorimetry. The conformational dynamics of R127 is shown to have a significant role in heme coordination during the alkaline transition and in the thermal stability of the heme cavity, whereas its impact on the catalytic efficiency of chlorite degradation is relatively small. The findings are discussed with respect to (i) the flexible loop connecting the N-terminal and C-terminal ferredoxin-like domains, which differs in clade 1 and clade 2 Clds and carries Q74 in clade 2 proteins, and (ii) the proposed role(s) of the arginine in catalysis.

PubMed: 33586945
DOI: 10.1021/acs.biochem.0c00910

Experimental method

X-RAY DIFFRACTION (1.51 Å)