Structures of an extradiol catechol dioxygenase – C23O64, from 3-nitrotoluene degrading Diaphorobacter sp. strain DS2 in substrate-free, substrate-bound and substrate analog-bound states

• Published in: Experimental Results 2020-01, Vol.1, Article e48
• Main Authors: Mishra, Keerti, Arya, Chetan Kumar, Subramanian, Ramaswamy, Ramanathan, Gurunath
• Format: Article
• Language: English
• Subjects: Amino acids; aromatic ring cleavage; Catechol 2,3-dioxygenase; Diaphorobacter sp. strain DS2; Enzymes; extradiol dioxygenases; Geometry; Ligands; Mononuclear iron-containing enzymes; Proteins; Scholarships & fellowships
• ISSN: 2516-712X; 2516-712X
• DOI: 10.1017/exp.2020.50

This manuscript reports structure–function studies of Catechol 2,3-dioxygenase ( C23O64 ), which is the second enzyme in the metabolic degradation pathway of 3-nitrotoluene by Diaphorobacter sp. strain DS2. The recombinant protein is a ring cleavage enzyme for 3-methylcatechol and 4-methylcatechol products formed after dioxygenation of the aromatic ring. Here we report the substrate-free, substrate-bound, and substrate-analog bound crystal structures of C23O64. The protein crystallizes in the P6(2)22 space-group. The structures were determined by molecular replacement and refined to resolutions of 2.4, 2.4, 2.2 Å, respectively. A comparison of the structures with related extradiol dioxygenases showed 22 conserved residues. A comparison of the active site pocket with catechol 2,3-dioxygenase ( LapB) from Pseudomonas sp KL28 and homoprotocatechuate 2,3-dioxygenase (HPCD) from Brevibacterium fuscum shows significant similarities to suggest that the mechanism of enzyme action is similar to HPCD .