5XBP

Oxygenase component of 3-nitrotoluene dioxygenase from Diaphorobacter sp. strain DS2

Replaces:  5BRC

Summary for 5XBP

• Entry DOI: 10.2210/pdb5xbp/pdb
• Descriptor: 3NT oxygenase alpha subunit, 3NT oxygenase beta subunit, FE (III) ION, ... (5 entities in total)
• Functional Keywords: rieske non-heme oxygenase, iron-sulfur clusters, oxidoreductase, nitroaromatic compounds degrader, metal binding protein
• Biological source: Diaphorobacter sp. DS2; More
• Total number of polymer chains: 6
• Total formula weight: 218313.33

Authors

Ramaswamy, S.,Kumari, A.,Singh, D.,Gurunath, R. (deposition date: 2017-03-21, release date: 2017-04-19, Last modification date: 2024-10-30)

Primary citation

Kumari, A.,Singh, D.,Ramaswamy, S.,Ramanathan, G.
Structural and functional studies of ferredoxin and oxygenase components of 3-nitrotoluene dioxygenase from Diaphorobacter sp. strain DS2.
PLoS ONE, 12:e0176398-e0176398, 2017

PubMed Abstract: 3-nitrotoluene dioxygenase (3NTDO) from Diaphorobacter sp. strain DS2 catalyses the conversion of 3-nitrotoluene (3NT) into a mixture of 3- and 4-methylcatechols with release of nitrite. We report here, X-ray crystal structures of oxygenase and ferredoxin components of 3NTDO at 2.9 Å and 2.4 Å, respectively. The residues responsible for nitrite release in 3NTDO were further probed by four single and two double mutations in the catalytic site of α-subunit of the dioxygenase. Modification of Val 350 to Phe, Ile 204 to Ala, and Asn258 to Val by site directed mutagenesis resulted in inactive enzymes revealing the importance of these residues in catalysis. Docking studies of meta nitrotoluene to the active site of 3NTDO suggested possible orientations of binding that favor the formation of 3-methylcatechol (3MC) over 4-methylcatechol energetically. The electron transfer pathway from ferredoxin subunit to the active site of the oxygenase subunit is also proposed.

PubMed: 28448625
DOI: 10.1371/journal.pone.0176398

Experimental method

X-RAY DIFFRACTION (2.9 Å)