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Literature summary for 3.5.1.88 extracted from

  • Lin, P.; Hu, T.; Hu, J.; Yu, W.; Han, C.; Zhang, J.; Qin, G.; Yu, K.; Gotz, F.; Shen, X.; Jiang, H.; Qu, D.
    Characterization of peptide deformylase homologs from Staphylococcus epidermidis (2010), Microbiology, 156, 3194-3202.
    View publication on PubMed

Cloned(Commentary)

Cloned (Comment) Organism
expressed in Escherichia coli BL21(DE3) cells Staphylococcus epidermidis

Crystallization (Commentary)

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 [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

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 [Da] Molecular Weight Maximum [Da] Comment Organism
21800
-
1 * 21800, gel filtration Staphylococcus epidermidis

Natural Substrates/ Products (Substrates)

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

Organism UniProt Comment Textmining
Staphylococcus epidermidis Q5HPX6 isoform PDF-2; strain ATCC35984/RP62A
-
Staphylococcus epidermidis Q5HQ78 isoform PDF-1; strain ATCC35984/RP62A
-

Purification (Commentary)

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 and Products (Substrate)

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

Subunits Comment Organism
monomer 1 * 21800, gel filtration Staphylococcus epidermidis

Synonyms

Synonyms Comment Organism
PDF-1 isoform Staphylococcus epidermidis
PDF-2 isoform without peptide deformylase activity Staphylococcus epidermidis

Turnover Number [1/s]

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 [mM/s]

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