5XDG

Crystal structure of tertiary complex of TdsC from Paenibacillus sp. A11-2 with FMN and dibenzothiophene sulfoxide

Summary for 5XDG

• Entry DOI: 10.2210/pdb5xdg/pdb
• Related: 5XB8 5XDB 5XDC 5XDD 5XDE
• Descriptor: Thermophilic dibenzothiophene desulfurization enzyme C, FLAVIN MONONUCLEOTIDE, SULFATE ION, ... (6 entities in total)
• Functional Keywords: monooxygenase, fmn binding protein, tetramer, oxidoreductase
• Biological source: Paenibacillus sp. A11-2
• Total number of polymer chains: 4
• Total formula weight: 186547.87

Authors

Hino, T.,Hamamoto, H.,Ohshiro, T.,Nagano, S. (deposition date: 2017-03-28, release date: 2017-08-09, Last modification date: 2024-03-27)

Primary citation

Hino, T.,Hamamoto, H.,Suzuki, H.,Yagi, H.,Ohshiro, T.,Nagano, S.
Crystal structures of TdsC, a dibenzothiophene monooxygenase from the thermophile Paenibacillus sp. A11-2, reveal potential for expanding its substrate selectivity.
J. Biol. Chem., 292:15804-15813, 2017

PubMed Abstract: Sulfur compounds in fossil fuels are a major source of environmental pollution, and microbial desulfurization has emerged as a promising technology for removing sulfur under mild conditions. The enzyme TdsC from the thermophile sp. A11-2 is a two-component flavin-dependent monooxygenase that catalyzes the oxygenation of dibenzothiophene (DBT) to its sulfoxide (DBTO) and sulfone (DBTO) during microbial desulfurization. The crystal structures of the apo and flavin mononucleotide (FMN)-bound forms of DszC, an ortholog of TdsC, were previously determined, although the structure of the ternary substrate-FMN-enzyme complex remains unknown. Herein, we report the crystal structures of the DBT-FMN-TdsC and DBTO-FMN-TdsC complexes. These ternary structures revealed many hydrophobic and hydrogen-bonding interactions with the substrate, and the position of the substrate could reasonably explain the two-step oxygenation of DBT by TdsC. We also determined the crystal structure of the indole-bound enzyme because TdsC, but not DszC, can also oxidize indole, and we observed that indole binding did not induce global conformational changes in TdsC with or without bound FMN. We also found that the two loop regions close to the FMN-binding site are disordered in apo-TdsC and become structured upon FMN binding. Alanine substitutions of Tyr-93 and His-388, which are located close to the substrate and FMN bound to TdsC, significantly decreased benzothiophene oxygenation activity, suggesting their involvement in supplying protons to the active site. Interestingly, these substitutions increased DBT oxygenation activity by TdsC, indicating that expanding the substrate-binding site can increase the oxygenation activity of TdsC on larger sulfur-containing substrates, a property that should prove useful for future microbial desulfurization applications.

PubMed: 28768765
DOI: 10.1074/jbc.M117.788513

Experimental method

X-RAY DIFFRACTION (1.747 Å)