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Literature summary extracted from

  • 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 (2017), J. Biol. Chem., 292, 14026-14038 .
    View publication on PubMedView publication on EuropePMC

Activating Compound

EC Number Activating Compound Comment Organism Structure
1.13.11.18 ascorbate addition of 2.5 mM ascorbate to the standard assay results in an 20% increase in the PDO-specific activity Paraburkholderia phytofirmans
1.13.11.18 GSH GSH is slightly activating by about 1.3fold Paraburkholderia phytofirmans
1.13.11.18 additional information no effect by thiosulfate Paraburkholderia phytofirmans

Cloned(Commentary)

EC Number Cloned (Comment) Organism
1.13.11.18 recombinant expression of wild-type and mutant enzymes in Escherichia coli strain BL21 Paraburkholderia phytofirmans

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
1.13.11.18 wild-type PRF and sulfurtransferase-inactivated C314S mutant with and without glutathione, X-ray diffraction structure determination and analysis at 1.8 A, 2.4 A, and 2.7 A resolution,respectively Paraburkholderia phytofirmans

Protein Variants

EC Number Protein Variants Comment Organism
1.13.11.18 C314S site-directed mutagenesis, structure comparison with wild-type enzyme. C314S BpPRF exhibits a 29fold lower kcat and an 5fold higher Km for GSSH than the wild-type Paraburkholderia phytofirmans

Inhibitors

EC Number Inhibitors Comment Organism Structure
1.13.11.18 additional information no effect by thiosulfate Paraburkholderia phytofirmans
1.13.11.18 sulfite sulfite build up can potentially inhibit PDO activity Paraburkholderia phytofirmans

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
1.13.11.18 additional information
-
 additional information kinetics of sulfur-transfer reaction Paraburkholderia phytofirmans
1.13.11.18 0.037
-
 S-sulfanylglutathione recombinant mutant C314S, pH 7.4, 22°C Paraburkholderia phytofirmans
1.13.11.18 0.07
-
 S-sulfanylglutathione recombinant wild-type enzyme, pH 7.4, 22°C Paraburkholderia phytofirmans
1.13.11.18 0.13
-
 O2 recombinant wild-type enzyme, pH 7.4, 22°C Paraburkholderia phytofirmans

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
1.13.11.18 Fe2+ required, the PDO domain active site contains a mononuclear non-heme iron coordinated by His58, His114, and Asp133 comprising a 2His:1Asp facial triad. The remaining coordination sites are occupied by water molecules giving an octrahedral geometry around ferrous iron. The wild-type enzyme contains 0.60 mol iron per mol of enzyme, the mutant C314S 0.46 mol iron/mol enzyme Paraburkholderia phytofirmans

Molecular Weight [Da]

EC Number Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
1.13.11.18 40000
-
 gel filtration, recombinant wild-type enzyme Paraburkholderia phytofirmans

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
1.13.11.18 additional information Paraburkholderia phytofirmans BpPRF is a bifunctional enzyme that uses the rhodanese domain to preferentially catalyze sulfur transfer from thiosulfate to GSH to form sulfite and GSSH and uses the PDO domain to oxidize GSSH to sulfite ?
-
 ?
1.13.11.18 S-sulfanylglutathione + O2 Paraburkholderia phytofirmans
-
 sulfite + glutathione + H+
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
1.13.11.18 Paraburkholderia phytofirmans
-
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
1.13.11.18 recombinant wild-type and mutant enzymes from Escherichia coli strain BL21 by nickel affinity chromatography and dialysis Paraburkholderia phytofirmans

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.13.11.18 additional information BpPRF is a bifunctional enzyme that uses the rhodanese domain to preferentially catalyze sulfur transfer from thiosulfate to GSH to form sulfite and GSSH and uses the PDO domain to oxidize GSSH to sulfite Paraburkholderia phytofirmans ?
-
 ?
1.13.11.18 additional information cysteine persulfide and thiosulfate are no substrates Paraburkholderia phytofirmans ?
-
 ?
1.13.11.18 S-sulfanylglutathione + O2
-
 Paraburkholderia phytofirmans sulfite + glutathione + H+
-
 ?

Subunits

EC Number Subunits Comment Organism
1.13.11.18 monomer 1 * 41500, about, sequence calculation Paraburkholderia phytofirmans

Synonyms

EC Number Synonyms Comment Organism
1.13.11.18 BpPRF
-
 Paraburkholderia phytofirmans
1.13.11.18 PDO
-
 Paraburkholderia phytofirmans
1.13.11.18 PRF
-
 Paraburkholderia phytofirmans

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
1.13.11.18 22
-
 assay at Paraburkholderia phytofirmans

Temperature Stability [°C]

EC Number Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
1.13.11.18 50
-
 the Tm value for the isolated rhodanese domain (55°C) is slightly higher than for wild-type (50°C) and the enzyme mutant C314S (51.6°C) Paraburkholderia phytofirmans

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
1.13.11.18 5
-
 S-sulfanylglutathione recombinant mutant C314S, pH 7.4, 22°C Paraburkholderia phytofirmans
1.13.11.18 143
-
 O2 recombinant wild-type enzyme, pH 7.4, 22°C Paraburkholderia phytofirmans
1.13.11.18 143
-
 S-sulfanylglutathione recombinant wild-type enzyme, pH 7.4, 22°C Paraburkholderia phytofirmans

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
1.13.11.18 7.4
-
 assay at Paraburkholderia phytofirmans

General Information

EC Number General Information Comment Organism
1.13.11.18 evolution enzyme persulfide dioygenase, PDO, is a member of the 2His-1Asp mononuclear iron-containing enzyme superfamily Paraburkholderia phytofirmans
1.13.11.18 additional information residue Cys314, located in the rhodanese-active site, is captured in its persulfidated Cys-SSH form. The PDO-active site is located at the bottom of a large pocket framed on one side by a positively charged ridge comprising residues Arg193-Lys216 and by Tyr176 on the other Paraburkholderia phytofirmans
1.13.11.18 physiological function natural fusions between the non-heme iron containing PDO and rhodanese, a thiol sulfurtransferase, exist in some bacteria, e.g. in Burkholderia phytofirmans. The two active sites in PRF are distant and do not show evidence of direct communication. The Burkholderia phytofirmans PRF exhibits robust PDO activity and preferentially catalyzes sulfur transfer in the direction of thiosulfate to sulfite and glutathione persulfide, while sulfur transfer in the reverse direction is detectable only under limited turnover conditions. Burkholderia phytofirmans PRF is poised to metabolize thiosulfate to sulfite in a sulfur assimilation pathway rather than in sulfide stress response Paraburkholderia phytofirmans

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
1.13.11.18 14
-
 S-sulfanylglutathione recombinant mutant C314S, pH 7.4, 22°C Paraburkholderia phytofirmans
1.13.11.18 1100
-
 O2 recombinant wild-type enzyme, pH 7.4, 22°C Paraburkholderia phytofirmans
1.13.11.18 2043
-
 S-sulfanylglutathione recombinant wild-type enzyme, pH 7.4, 22°C Paraburkholderia phytofirmans