2DE2

Crystal structure of desulfurization enzyme DSZB

Summary for 2DE2

• Entry DOI: 10.2210/pdb2de2/pdb
• Related: 2DE3 2DE4
• Descriptor: DIBENZOTHIOPHENE DESULFURIZATION ENZYME B, ACETATE ION, GLYCEROL, ... (4 entities in total)
• Functional Keywords: alpha-beta, hydrolase
• Biological source: Rhodococcus sp.
• Total number of polymer chains: 1
• Total formula weight: 39782.26

Authors

Lee, W.C.,Ohshiro, T.,Matsubara, T.,Izumi, Y.,Tanokura, M. (deposition date: 2006-02-08, release date: 2006-08-01, Last modification date: 2024-03-13)

Primary citation

Lee, W.C.,Ohshiro, T.,Matsubara, T.,Izumi, Y.,Tanokura, M.
Crystal structure and desulfurization mechanism of 2'-hydroxybiphenyl-2-sulfinic acid desulfinase.
J.Biol.Chem., 281:32534-32539, 2006

PubMed Abstract: The desulfurization of dibenzothiophene in Rhodococcus erythropolis is catalyzed by two monooxygenases, DszA and DszC, and a desulfinase, DszB. In the last step of this pathway, DszB hydrolyzes 2'-hydroxybiphenyl-2-sulfinic acid into 2-hydroxybiphenyl and sulfite. We report on the crystal structures of DszB and an inactive mutant of DszB in complex with substrates at resolutions of 1.8A or better. The overall fold of DszB is similar to those of periplasmic substrate-binding proteins. In the substrate complexes, biphenyl rings of substrates are recognized by extensive hydrophobic interactions with the active site residues. Binding of substrates accompanies structural changes of the active site loops and recruits His(60) to the active site. The sulfinate group of bound substrates forms hydrogen bonds with side chains of Ser(27), His(60), and Arg(70), each of which is shown by site-directed mutagenesis to be essential for the activity. In our proposed reaction mechanism, Cys(27) functions as a nucleophile and seems to be activated by the sulfinate group of substrates, whereas His(60) and Arg(70) orient the syn orbital of sulfinate oxygen to the sulfhydryl hydrogen of Cys(27) and stabilize the negatively charged reaction intermediate. Cys, His, and Arg residues are conserved in putative proteins homologous to DszB, which are presumed to constitute a new family of desulfinases.

PubMed: 16891315
DOI: 10.1074/jbc.M602974200

Experimental method

X-RAY DIFFRACTION (1.8 Å)