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3.5.1.88: peptide deformylase

This is an abbreviated version!
For detailed information about peptide deformylase, go to the full flat file.

Word Map on EC 3.5.1.88

Reaction

formyl-L-methionyl peptide
+
H2O
=
formate
+
methionyl peptide

Synonyms

AtDEF1.1, AtDEF1.2, AtDEF2, AtPDF1A, AtPDF1B, AtPDF1Bt, AtPDF2, BbPDF, BcPDF, BcPDF2, DEF, Def1, DEF2, deformylase, peptide N-formylmethionine, EC 3.5.1.27, EcPDF, ECPDF1B, EfPDF, HpPDF, HsPDF, hydrolase, aminoacyl-transfer ribonucleate, LiPDF, mPDF, Ni-peptide deformylase, PDF, PDF-1, PDF-2, PDF1A, PDF1B, PDF2, PdfA, PdfB, PdfC, peptide deformylase, peptide deformylase 1, peptide deformylase 1A, peptide deformylase 1B, peptide deformylase 2, Pf PDF, PfPDF, Polypeptide deformylase, SaPDF, sPDF, TbPDF1, TbPDF2, type I PDF, type II PDF, type II peptide deformylase, Vp 16 PDF1B, Vp16 PDF, Vp16T, XOO1075, XoPDF

ECTree

     3 Hydrolases
         3.5 Acting on carbon-nitrogen bonds, other than peptide bonds
             3.5.1 In linear amides
                3.5.1.88 peptide deformylase

General Stability

General Stability on EC 3.5.1.88 - peptide deformylase

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GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
additon of metal ions required during purification
-
denaturation with guanidinium hydrochloride, protein 1 unfolds at more than 3 M, protein 2 unfolds at 1.7 M
-
elimination of the divalent cation from the enzyme destabilizes the enzyme
enhanced in vitro stability by binding of Zn2+
-
enhanced stabilitiy in concentrated form
-
enhanced stability by binding of Co2+
-
extremely labile
-
limited proteolysis of AtPDF1B with trypsin results in the relatively slow formation of a lower molecular mass form (AtPDF1Bt) reduced by approximately 3 kDa. Although small reductions in molecular mass are observed after prolonged incubation, the proteolyzed AtPDF1B generated was largely resistant to further digestion. Recombinant AtPDF1B has a requirement for 0.5 M NaCl for solubility at concentrations of 0.5 mg/ml. After proteolysis with trypsin, AtPDF1B loses this characteristic and is soluble without NaCl at concentrations of 30 mg/ml
Ni2+ activates and stabilizes at 5 mM
Ni2+ and Co2+ increase stability compared to the Fe2+ enzyme
Ni2+ and Co2+ increases stability compared to the Fe2+ enzyme
Ni2+-bound enzyme fully stable, additional stabilization during purification by catalase
-
PDF has high activity in Tris buffer, but low activity in HEPES and NaH2PO4 buffers
-
the enzyme undergoes slow denaturation in the presence of varying concentrations of GdmCl. Abrupt reversal of the unfolding pathway is observed at low to moderate concentrations of the denaturant, but not at high concentration
-