Cloned (Comment) | Organism |
---|---|
expressed in Escherichia coli BL21(DE3) cells | Staphylococcus epidermidis |
Crystallization (Comment) | Organism |
---|---|
Co2+-PDF1-complex hanging drop vapor diffusion method, using 0.2 M ammonium acetate, 0.1 M tri-sodium citrate dihydrate pH 5.6, and 30% (v/v) PEG 4000 | Staphylococcus epidermidis |
KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
---|---|---|---|---|---|
2.227 | - |
N-formyl-L-Met-L-Ala-L-Ser | Co2+-substituted PDF-1, in 50 mM HEPES, pH 7.5, at 37°C | Staphylococcus epidermidis |
Metals/Ions | Comment | Organism | Structure |
---|---|---|---|
Co2+ | Co2+-substituted isoform PDF-1 exhibits much higher enzymatic activity than that of Ni2+ and Zn2+ substituted PDF-1 | Staphylococcus epidermidis | |
additional information | Co2+-, Zn2+-, or Ni2+-substituted isoform PDF-2 exhibits no enzymatic activity | Staphylococcus epidermidis | |
Ni2+ | isoform PDF-1 shows much weaker binding ability towards Ni2+ than towards Co2+ and Zn2+ | Staphylococcus epidermidis | |
Zn2+ | compared with Co2+-substituted PDF-1, the enzymatic activity of Zn2+-substituted PDF-1 shows a 4fold decrease, PDF-1 binds more Zn2+ (1.36 mol Zn per mol protein) than Co2+ (0.87 mol Co per mol protein), though the activity of Zn-PDF is much lower | Staphylococcus epidermidis |
Molecular Weight [Da] | Molecular Weight Maximum [Da] | Comment | Organism |
---|---|---|---|
21800 | - |
1 * 21800, gel filtration | Staphylococcus epidermidis |
Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
---|---|---|---|---|---|---|
N-formyl-L-methionine-polypeptide + H2O | Staphylococcus epidermidis | - |
formate + L-methionine-polypeptide | - |
? |
Organism | UniProt | Comment | Textmining |
---|---|---|---|
Staphylococcus epidermidis | Q5HPX6 | isoform PDF-2; strain ATCC35984/RP62A | - |
Staphylococcus epidermidis | Q5HQ78 | isoform PDF-1; strain ATCC35984/RP62A | - |
Purification (Comment) | Organism |
---|---|
Ni-NTA column chromatography | Staphylococcus epidermidis |
Ni-NTA column chromatography, the purification buffers for PDFs expressed using Ni2+ fortified medium are compensated with 0.1 mM NiCl2 to avoid possible Ni2+ competition between Ni-NTA and PDFs | Staphylococcus epidermidis |
Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
---|---|---|---|---|---|---|
additional information | isoform PDF-2 exhibits no peptide deformylase activity | Staphylococcus epidermidis | ? | - |
? | |
N-formyl-L-Met-L-Ala-L-Ser + H2O | - |
Staphylococcus epidermidis | formate + L-Met-L-Ala-L-Ser | - |
? | |
N-formyl-L-methionine-polypeptide + H2O | - |
Staphylococcus epidermidis | formate + L-methionine-polypeptide | - |
? |
Subunits | Comment | Organism |
---|---|---|
monomer | 1 * 21800, gel filtration | Staphylococcus epidermidis |
Synonyms | Comment | Organism |
---|---|---|
PDF-1 | isoform | Staphylococcus epidermidis |
PDF-2 | isoform without peptide deformylase activity | Staphylococcus epidermidis |
Turnover Number Minimum [1/s] | Turnover Number Maximum [1/s] | Substrate | Comment | Organism | Structure |
---|---|---|---|---|---|
140 | - |
N-formyl-L-Met-L-Ala-L-Ser | Co2+-substituted PDF-1, in 50 mM HEPES, pH 7.5, at 37°C | Staphylococcus epidermidis |
kcat/KM Value [1/mMs-1] | kcat/KM Value Maximum [1/mMs-1] | Substrate | Comment | Organism | Structure |
---|---|---|---|---|---|
63 | - |
N-formyl-L-Met-L-Ala-L-Ser | Co2+-substituted PDF-1, in 50 mM HEPES, pH 7.5, at 37°C | Staphylococcus epidermidis |