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Literature summary for 1.13.11.18 extracted from
- Structural and biochemical analyses indicate that a bacterial persulfide dioxygenase-rhodanese fusion protein functions in sulfur assimilation (2017), J. Biol. Chem., 292, 14026-14038 .
Activating Compound
| Activating Compound | Comment | Organism | Structure |
|---|---|---|---|
| ascorbate | addition of 2.5 mM ascorbate to the standard assay results in an 20% increase in the PDO-specific activity | Paraburkholderia phytofirmans |  |
| GSH | GSH is slightly activating by about 1.3fold | Paraburkholderia phytofirmans | |
| additional information | no effect by thiosulfate | Paraburkholderia phytofirmans |
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| recombinant expression of wild-type and mutant enzymes in Escherichia coli strain BL21 | Paraburkholderia phytofirmans |
Crystallization (Commentary)
| Crystallization (Comment) | Organism |
|---|---|
| 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
| Protein Variants | Comment | Organism |
|---|---|---|
| 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
| Inhibitors | Comment | Organism | Structure |
|---|---|---|---|
| additional information | no effect by thiosulfate | Paraburkholderia phytofirmans | |
| sulfite | sulfite build up can potentially inhibit PDO activity | Paraburkholderia phytofirmans | |
KM Value [mM]
| KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| additional information | - |
additional information | kinetics of sulfur-transfer reaction | Paraburkholderia phytofirmans | |
| 0.037 | - |
S-sulfanylglutathione | recombinant mutant C314S, pH 7.4, 22°C | Paraburkholderia phytofirmans | |
| 0.07 | - |
S-sulfanylglutathione | recombinant wild-type enzyme, pH 7.4, 22°C | Paraburkholderia phytofirmans | |
| 0.13 | - |
O2 | recombinant wild-type enzyme, pH 7.4, 22°C | Paraburkholderia phytofirmans | |
Metals/Ions
| Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|
| 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]
| Molecular Weight [Da] | Molecular Weight Maximum [Da] | Comment | Organism |
|---|---|---|---|
| 40000 | - |
gel filtration, recombinant wild-type enzyme | Paraburkholderia phytofirmans |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| 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 | ? | - |
? | |
| S-sulfanylglutathione + O2 | Paraburkholderia phytofirmans | - |
sulfite + glutathione + H+ | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Paraburkholderia phytofirmans | - |
- |
- |
Purification (Commentary)
| Purification (Comment) | Organism |
|---|---|
| recombinant wild-type and mutant enzymes from Escherichia coli strain BL21 by nickel affinity chromatography and dialysis | Paraburkholderia phytofirmans |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| 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 | ? | - |
? | |
| additional information | cysteine persulfide and thiosulfate are no substrates | Paraburkholderia phytofirmans | ? | - |
? | |
| S-sulfanylglutathione + O2 | - |
Paraburkholderia phytofirmans | sulfite + glutathione + H+ | - |
? | |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| monomer | 1 * 41500, about, sequence calculation | Paraburkholderia phytofirmans |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| BpPRF | - |
Paraburkholderia phytofirmans |
| PDO | - |
Paraburkholderia phytofirmans |
| PRF | - |
Paraburkholderia phytofirmans |
Temperature Optimum [°C]
| Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
|---|---|---|---|
| 22 | - |
assay at | Paraburkholderia phytofirmans |
Temperature Stability [°C]
| Temperature Stability Minimum [°C] | Temperature Stability Maximum [°C] | Comment | Organism |
|---|---|---|---|
| 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]
| Turnover Number Minimum [1/s] | Turnover Number Maximum [1/s] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 5 | - |
S-sulfanylglutathione | recombinant mutant C314S, pH 7.4, 22°C | Paraburkholderia phytofirmans | |
| 143 | - |
O2 | recombinant wild-type enzyme, pH 7.4, 22°C | Paraburkholderia phytofirmans | |
| 143 | - |
S-sulfanylglutathione | recombinant wild-type enzyme, pH 7.4, 22°C | Paraburkholderia phytofirmans | |
pH Optimum
| pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|
| 7.4 | - |
assay at | Paraburkholderia phytofirmans |
General Information
| General Information | Comment | Organism |
|---|---|---|
| evolution | enzyme persulfide dioygenase, PDO, is a member of the 2His-1Asp mononuclear iron-containing enzyme superfamily | Paraburkholderia phytofirmans |
| 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 |
| 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]
| kcat/KM Value [1/mMs-1] | kcat/KM Value Maximum [1/mMs-1] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 14 | - |
S-sulfanylglutathione | recombinant mutant C314S, pH 7.4, 22°C | Paraburkholderia phytofirmans | |
| 1100 | - |
O2 | recombinant wild-type enzyme, pH 7.4, 22°C | Paraburkholderia phytofirmans | |
| 2043 | - |
S-sulfanylglutathione | recombinant wild-type enzyme, pH 7.4, 22°C | Paraburkholderia phytofirmans | |
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