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Literature summary extracted from

  • Grzela, R.; Nusbaum, J.; Fieulaine, S.; Lavecchia, F.; Desmadril, M.; Nhiri, N.; Van Dorsselaer, A.; Cianferani, S.; Jacquet, E.; Meinnel, T.; Giglione, C.
    Peptide deformylases from Vibrio parahaemolyticus phage and bacteria display similar deformylase activity and inhibitor binding clefts (2018), Biochim. Biophys. Acta, 1866, 348-355 .
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
3.5.1.88 recombinant expression in Escherichia coli strains PAL421Tr (PDF knockout) and Rosetta2(DE3)pLysS Escherichia coli
3.5.1.88 recombinant expression in Escherichia coli strains PAL421Tr (PDF knockout) and Rosetta2(DE3)pLysS Vibrio phage VP16T

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
3.5.1.88 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

EC Number General Stability Organism
3.5.1.88 elimination of the divalent cation from the enzyme destabilizes the enzyme Vibrio phage VP16T

Inhibitors

EC Number Inhibitors Comment Organism Structure
3.5.1.88 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
3.5.1.88 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
3.5.1.88 EDTA
-
 Vibrio phage VP16T

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
3.5.1.88 additional information
-
 additional information Michaelis-Menten kinetics Escherichia coli
3.5.1.88 additional information
-
 additional information Michaelis-Menten kinetics Vibrio phage VP16T
3.5.1.88 0.2
-
 formyl-Met-Ala-Ser pH 4.5, 37°C, recombinant enzyme with bound Ni2+ Escherichia coli
3.5.1.88 1
-
 formyl-Met-Ala-Ser pH 7.5, 37°C, recombinant enzyme with bound Ni2+, Ni-Vp16 PDF1B Vibrio phage VP16T
3.5.1.88 3
-
 formyl-Met-Ala-Ser pH 7.5, 37°C, recombinant enzyme with bound Zn2+, Zn-Vp16 PDF1B Vibrio phage VP16T
3.5.1.88 70
-
 formyl-Met-Ala-Ser pH 4.5, 37°C, recombinant enzyme with bound Zn2+ Escherichia coli

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
3.5.1.88 additional information elimination of the divalent cation from the enzyme destabilizes the enzyme Vibrio phage VP16T
3.5.1.88 Ni2+ activates Vibrio phage VP16T
3.5.1.88 Ni2+ activates, highly preferred divalent cation Escherichia coli
3.5.1.88 Zn2+ activates, far less effective than Ni2+ Escherichia coli
3.5.1.88 Zn2+ activates, less effective than Ni2+ Vibrio phage VP16T

Organism

EC Number Organism UniProt Comment Textmining
3.5.1.88 Escherichia coli P0A6K3
-
-
3.5.1.88 Vibrio phage VP16T Q6VT21 isolated from Vibrio parahaemolyticus strain 16
-

Purification (Commentary)

EC Number Purification (Comment) Organism
3.5.1.88 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
3.5.1.88 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)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.5.1.88 formyl-Met-Ala-Lys + H2O
-
 Vibrio phage VP16T formate + Met-Ala-Lys
-
 ?
3.5.1.88 formyl-Met-Ala-Ser + H2O
-
 Escherichia coli formate + Met-Ala-Ser
-
 ?
3.5.1.88 formyl-Met-Ala-Ser + H2O
-
 Vibrio phage VP16T formate + Met-Ala-Ser
-
 ?
3.5.1.88 formyl-Met-Lys-Leu + H2O
-
 Vibrio phage VP16T formate + Met-Lys-Leu
-
 ?
3.5.1.88 formyl-Met-Pro-Ala + H2O
-
 Vibrio phage VP16T formate + Met-Pro-Ala
-
 ?
3.5.1.88 formyl-Met-Ser-Asn + H2O
-
 Vibrio phage VP16T formate + Met-Ser-Asn
-
 ?
3.5.1.88 formyl-Met-Thr-Thr + H2O
-
 Vibrio phage VP16T formate + Met-Thr-Thr
-
 ?

Synonyms

EC Number Synonyms Comment Organism
3.5.1.88 EcPDF
-
 Escherichia coli
3.5.1.88 ECPDF1B
-
 Escherichia coli
3.5.1.88 PDF
-
 Escherichia coli
3.5.1.88 PDF
-
 Vibrio phage VP16T
3.5.1.88 PDF1B
-
 Vibrio phage VP16T
3.5.1.88 Vp 16 PDF1B
-
 Vibrio phage VP16T
3.5.1.88 Vp16 PDF
-
 Vibrio phage VP16T
3.5.1.88 Vp16T
-
 Vibrio phage VP16T

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
3.5.1.88 37
-
 assay at Escherichia coli
3.5.1.88 37
-
 assay at Vibrio phage VP16T

Temperature Stability [°C]

EC Number Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
3.5.1.88 60
-
 Tm of purified recombinant enzyme in presence of divalent metal ions (Ni2+) Escherichia coli
3.5.1.88 61.5
-
 Tm of purified recombinant enzyme in absence of divalent metal ions and presence of EDTA Vibrio phage VP16T
3.5.1.88 67.7
-
 Tm of purified recombinant enzyme in presence of divalent metal ions (Ni2+) Vibrio phage VP16T
3.5.1.88 68
-
 Tm of purified recombinant enzyme in presence of divalent metal ions (Ni2+) and inhibitor actinonin Escherichia coli
3.5.1.88 80
-
 Tm of purified recombinant enzyme in presence of divalent metal ions (Ni2+) and inhibitor actinonin Vibrio phage VP16T

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
3.5.1.88 2.6
-
 formyl-Met-Ala-Ser pH 7.5, 37°C, recombinant enzyme with bound Zn2+, Zn-Vp16 PDF1B Vibrio phage VP16T
3.5.1.88 5.3
-
 formyl-Met-Ala-Ser pH 7.5, 37°C, recombinant enzyme with bound Ni2+, Ni-Vp16 PDF1B Vibrio phage VP16T
3.5.1.88 5.6
-
 formyl-Met-Ala-Ser pH 4.5, 37°C, recombinant enzyme with bound Zn2+ Escherichia coli
3.5.1.88 34
-
 formyl-Met-Ala-Ser pH 4.5, 37°C, recombinant enzyme with bound Ni2+ Escherichia coli

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
3.5.1.88 4.5
-
 assay at Escherichia coli
3.5.1.88 7.5
-
 assay at Vibrio phage VP16T

pI Value

EC Number Organism Comment pI Value Maximum pI Value
3.5.1.88 Vibrio phage VP16T sequence calculation
-
 7

General Information

EC Number General Information Comment Organism
3.5.1.88 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
3.5.1.88 evolution the Escherichia coli PDF isozyme belongs to subtype 1B Escherichia coli
3.5.1.88 additional information Vibrio parahaemolyticus phage Vp16T and Escherichia coli PDFs display an identical substrate binding mode Escherichia coli
3.5.1.88 additional information Vp16 and Escherichia coli PDFs display an identical substrate binding mode Vibrio phage VP16T
3.5.1.88 physiological function encoded phage PDFs might be important for viral fitness Vibrio phage VP16T

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
3.5.1.88 0.08
-
 formyl-Met-Ala-Ser pH 4.5, 37°C, recombinant enzyme with bound Zn2+ Escherichia coli
3.5.1.88 0.867
-
 formyl-Met-Ala-Ser pH 7.5, 37°C, recombinant enzyme with bound Zn2+, Zn-Vp16 PDF1B Vibrio phage VP16T
3.5.1.88 5.3
-
 formyl-Met-Ala-Ser pH 7.5, 37°C, recombinant enzyme with bound Ni2+, Ni-Vp16 PDF1B Vibrio phage VP16T
3.5.1.88 170
-
 formyl-Met-Ala-Ser pH 4.5, 37°C, recombinant enzyme with bound Ni2+ Escherichia coli