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Literature summary for 3.5.1.88 extracted from
- Peptide deformylases from Vibrio parahaemolyticus phage and bacteria display similar deformylase activity and inhibitor binding clefts (2018), Biochim. Biophys. Acta, 1866, 348-355 .
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| recombinant expression in Escherichia coli strains PAL421Tr (PDF knockout) and Rosetta2(DE3)pLysS | Escherichia coli |
| recombinant expression in Escherichia coli strains PAL421Tr (PDF knockout) and Rosetta2(DE3)pLysS | Vibrio phage VP16T |
Crystallization (Commentary)
| Crystallization (Comment) | Organism |
|---|---|
| purified recombinant apoenzyme, from 28% PEG 1000, and 100 mM sodium acetate, pH 5.5, for complex formation the crystals are soaked with actinonin by adding the ligand to the drop, X-ray diffraction structure determination and analysis | Vibrio phage VP16T |
General Stability
| General Stability | Organism |
|---|---|
| elimination of the divalent cation from the enzyme destabilizes the enzyme | Vibrio phage VP16T |
Inhibitors
| Inhibitors | Comment | Organism | Structure |
|---|---|---|---|
| actinonin | competitive inhibitor, binding in a two-step mechanism, determination and comparison of the three-dimensional structure of Escherichia coli PDF bound to actinonin | Escherichia coli |  |
| actinonin | competitive inhibitor, binding in a two-step mechanism, determination and comparison of the three-dimensional structure of Vp16 PDF bound to actinonin | Vibrio phage VP16T | |
| EDTA | - |
Vibrio phage VP16T | |
KM Value [mM]
| KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| additional information | - |
additional information | Michaelis-Menten kinetics | Escherichia coli | |
| additional information | - |
additional information | Michaelis-Menten kinetics | Vibrio phage VP16T | |
| 0.2 | - |
formyl-Met-Ala-Ser | pH 4.5, 37°C, recombinant enzyme with bound Ni2+ | Escherichia coli | |
| 1 | - |
formyl-Met-Ala-Ser | pH 7.5, 37°C, recombinant enzyme with bound Ni2+, Ni-Vp16 PDF1B | Vibrio phage VP16T | |
| 3 | - |
formyl-Met-Ala-Ser | pH 7.5, 37°C, recombinant enzyme with bound Zn2+, Zn-Vp16 PDF1B | Vibrio phage VP16T | |
| 70 | - |
formyl-Met-Ala-Ser | pH 4.5, 37°C, recombinant enzyme with bound Zn2+ | Escherichia coli | |
Metals/Ions
| Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|
| additional information | elimination of the divalent cation from the enzyme destabilizes the enzyme | Vibrio phage VP16T | |
| Ni2+ | activates | Vibrio phage VP16T | |
| Ni2+ | activates, highly preferred divalent cation | Escherichia coli | |
| Zn2+ | activates, far less effective than Ni2+ | Escherichia coli | |
| Zn2+ | activates, less effective than Ni2+ | Vibrio phage VP16T | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Escherichia coli | P0A6K3 | - |
- |
| Vibrio phage VP16T | Q6VT21 | isolated from Vibrio parahaemolyticus strain 16 | - |
Purification (Commentary)
| Purification (Comment) | Organism |
|---|---|
| recombinant enzyme from Escherichia coli strains PAL421Tr and Rosetta2(DE3)pLysS by cation exchange chromatography and gel filtration or dialysis, in presence of Ni2+ | Escherichia coli |
| the optimized purification protocol provides strong improvement of Vp16 PDF specific activity to values similar to those of bacterial PDFs, recombinant enzyme from Escherichia coli strains PAL421Tr and Rosetta2(DE3)pLysS by cation exchange chromatography and gel filtration or dialysis, in presence of Ni2+ | Vibrio phage VP16T |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| formyl-Met-Ala-Lys + H2O | - |
Vibrio phage VP16T | formate + Met-Ala-Lys | - |
? | |
| formyl-Met-Ala-Ser + H2O | - |
Escherichia coli | formate + Met-Ala-Ser | - |
? | |
| formyl-Met-Ala-Ser + H2O | - |
Vibrio phage VP16T | formate + Met-Ala-Ser | - |
? | |
| formyl-Met-Lys-Leu + H2O | - |
Vibrio phage VP16T | formate + Met-Lys-Leu | - |
? | |
| formyl-Met-Pro-Ala + H2O | - |
Vibrio phage VP16T | formate + Met-Pro-Ala | - |
? | |
| formyl-Met-Ser-Asn + H2O | - |
Vibrio phage VP16T | formate + Met-Ser-Asn | - |
? | |
| formyl-Met-Thr-Thr + H2O | - |
Vibrio phage VP16T | formate + Met-Thr-Thr | - |
? | |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| EcPDF | - |
Escherichia coli |
| ECPDF1B | - |
Escherichia coli |
- |
Escherichia coli | |
- |
Vibrio phage VP16T | |
| PDF1B | - |
Vibrio phage VP16T |
| Vp 16 PDF1B | - |
Vibrio phage VP16T |
| Vp16 PDF | - |
Vibrio phage VP16T |
| Vp16T | - |
Vibrio phage VP16T |
Temperature Optimum [°C]
| Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
|---|---|---|---|
| 37 | - |
assay at | Escherichia coli |
| 37 | - |
assay at | Vibrio phage VP16T |
Temperature Stability [°C]
| Temperature Stability Minimum [°C] | Temperature Stability Maximum [°C] | Comment | Organism |
|---|---|---|---|
| 60 | - |
Tm of purified recombinant enzyme in presence of divalent metal ions (Ni2+) | Escherichia coli |
| 61.5 | - |
Tm of purified recombinant enzyme in absence of divalent metal ions and presence of EDTA | Vibrio phage VP16T |
| 67.7 | - |
Tm of purified recombinant enzyme in presence of divalent metal ions (Ni2+) | Vibrio phage VP16T |
| 68 | - |
Tm of purified recombinant enzyme in presence of divalent metal ions (Ni2+) and inhibitor actinonin | Escherichia coli |
| 80 | - |
Tm of purified recombinant enzyme in presence of divalent metal ions (Ni2+) and inhibitor actinonin | Vibrio phage VP16T |
Turnover Number [1/s]
| Turnover Number Minimum [1/s] | Turnover Number Maximum [1/s] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 2.6 | - |
formyl-Met-Ala-Ser | pH 7.5, 37°C, recombinant enzyme with bound Zn2+, Zn-Vp16 PDF1B | Vibrio phage VP16T | |
| 5.3 | - |
formyl-Met-Ala-Ser | pH 7.5, 37°C, recombinant enzyme with bound Ni2+, Ni-Vp16 PDF1B | Vibrio phage VP16T | |
| 5.6 | - |
formyl-Met-Ala-Ser | pH 4.5, 37°C, recombinant enzyme with bound Zn2+ | Escherichia coli | |
| 34 | - |
formyl-Met-Ala-Ser | pH 4.5, 37°C, recombinant enzyme with bound Ni2+ | Escherichia coli | |
pH Optimum
| pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|
| 4.5 | - |
assay at | Escherichia coli |
| 7.5 | - |
assay at | Vibrio phage VP16T |
pI Value
| Organism | Comment | pI Value Maximum | pI Value |
|---|---|---|---|
| Vibrio phage VP16T | sequence calculation | - |
7 |
General Information
| General Information | Comment | Organism |
|---|---|---|
| evolution | the bacteriophage Vp16 PDF enzyme is a representative member of the C-terminally truncated viral PDFs, Vp16 PDF belongs to subtype 1B | Vibrio phage VP16T |
| evolution | the Escherichia coli PDF isozyme belongs to subtype 1B | Escherichia coli |
| additional information | Vibrio parahaemolyticus phage Vp16T and Escherichia coli PDFs display an identical substrate binding mode | Escherichia coli |
| additional information | Vp16 and Escherichia coli PDFs display an identical substrate binding mode | Vibrio phage VP16T |
| physiological function | encoded phage PDFs might be important for viral fitness | Vibrio phage VP16T |
kcat/KM [mM/s]
| kcat/KM Value [1/mMs-1] | kcat/KM Value Maximum [1/mMs-1] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 0.08 | - |
formyl-Met-Ala-Ser | pH 4.5, 37°C, recombinant enzyme with bound Zn2+ | Escherichia coli | |
| 0.867 | - |
formyl-Met-Ala-Ser | pH 7.5, 37°C, recombinant enzyme with bound Zn2+, Zn-Vp16 PDF1B | Vibrio phage VP16T | |
| 5.3 | - |
formyl-Met-Ala-Ser | pH 7.5, 37°C, recombinant enzyme with bound Ni2+, Ni-Vp16 PDF1B | Vibrio phage VP16T | |
| 170 | - |
formyl-Met-Ala-Ser | pH 4.5, 37°C, recombinant enzyme with bound Ni2+ | Escherichia coli | |
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