5VE3

Crystal structure of wild-type persulfide dioxygenase-rhodanese fusion protein from Burkholderia phytofirmans

Summary for 5VE3

• Entry DOI: 10.2210/pdb5ve3/pdb
• Related: 5VE4 5VE5
• Descriptor: BpPRF, FE (III) ION (3 entities in total)
• Functional Keywords: persulfide dioxygenase, rhodanese, oxidoreductase, transferase
• Biological source: Paraburkholderia phytofirmans (strain DSM 17436 / LMG 22146 / PsJN)
• Total number of polymer chains: 2
• Total formula weight: 82701.32

Authors

Motl, N.,Skiba, M.A.,Smith, J.L.,Banerjee, R. (deposition date: 2017-04-03, release date: 2017-07-19, Last modification date: 2024-10-09)

Primary citation

Motl, N.,Skiba, M.A.,Kabil, O.,Smith, J.L.,Banerjee, R.
Structural and biochemical analyses indicate that a bacterial persulfide dioxygenase-rhodanese fusion protein functions in sulfur assimilation.
J. Biol. Chem., 292:14026-14038, 2017

PubMed Abstract: Hydrogen sulfide (HS) is a signaling molecule that is toxic at elevated concentrations. In eukaryotes, it is cleared via a mitochondrial sulfide oxidation pathway, which comprises sulfide quinone oxidoreductase, persulfide dioxygenase (PDO), rhodanese, and sulfite oxidase and converts HS to thiosulfate and sulfate. Natural fusions between the non-heme iron containing PDO and rhodanese, a thiol sulfurtransferase, exist in some bacteria. However, little is known about the role of the PDO-rhodanese fusion (PRF) proteins in sulfur metabolism. Herein, we report the kinetic properties and the crystal structure of a PRF from the Gram-negative endophytic bacterium The crystal structures of wild-type PRF and a sulfurtransferase-inactivated C314S mutant with and without glutathione were determined at 1.8, 2.4, and 2.7 Å resolution, respectively. We found that the two active sites are distant and do not show evidence of direct communication. The PRF exhibited robust PDO activity and preferentially catalyzed sulfur transfer in the direction of thiosulfate to sulfite and glutathione persulfide; sulfur transfer in the reverse direction was detectable only under limited turnover conditions. Together with the kinetic data, our bioinformatics analysis reveals that PRF is poised to metabolize thiosulfate to sulfite in a sulfur assimilation pathway rather than in sulfide stress response as seen, for example, with the PRF or sulfide oxidation and disposal as observed with the homologous mammalian proteins.

PubMed: 28684420
DOI: 10.1074/jbc.M117.790170

Experimental method

X-RAY DIFFRACTION (1.793 Å)