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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

Engineering

Engineering on EC 3.5.1.88 - peptide deformylase

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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
G41A
the mutant shows strongly reduced Km and kcat values compared to the wild type enzyme
G41M
the kcat/Km value is reduced by three orders of magnitude due to large decrease in the kcat value (to 1%) compared to the wild type enzyme
G41Q
the kcat/Km value is reduced by three orders of magnitude due to large decrease in the kcat value (to 0.4%) compared to the wild type enzyme
I130A
the mutant protein exhibits strongly reduced kcat and Km values but shows no change in overall stability compared to the wild type
I130F
the mutant protein exhibits strongly reduced kcat and Km values but shows no change in overall stability compared to the wild type
I42A
the mutant shows increased Km and reduced kcat values compared to the wild type enzyme
I42F
the mutant shows increased Km and reduced kcat values compared to the wild type enzyme
I42N
the mutant shows decreased Km and kcat values compared to the wild type enzyme
I42W
the mutant shows decreased Km and kcat values compared to the wild type enzyme
Y178A
the mutant shows an increase in Km for f-MTA substrate
Y178F
mutant shows a decrease in Km as well as an increase in kcat, indicating tighter binding of the substrate
F134C
-
the mutation alters the enzyme activity (nearly 2fold higher Km and increased kcat value as compared with the wild type enzyme) and affects protein stability
F134C/R137S
-
the mutation alters the enzyme activity (nearly 10fold higher Km, increased kcat and 27% decrease in the kcat/Km value as compared with the wild type enzyme) and is 6.3fold more resistant towards inhibitor GM6001 as the wild type enzyme
R137S
-
the mutation alters the enzyme activity (nearly 2fold higher Km and increased kcat value as compared with the wild type enzyme) and affects protein stability
F134C
-
the mutation alters the enzyme activity (nearly 2fold higher Km and increased kcat value as compared with the wild type enzyme) and affects protein stability
-
F134C/R137S
-
the mutation alters the enzyme activity (nearly 10fold higher Km, increased kcat and 27% decrease in the kcat/Km value as compared with the wild type enzyme) and is 6.3fold more resistant towards inhibitor GM6001 as the wild type enzyme
-
R137S
-
the mutation alters the enzyme activity (nearly 2fold higher Km and increased kcat value as compared with the wild type enzyme) and affects protein stability
-
C129A
-
turnover-number is 86% of that of the wild-type enzyme, Km-value for N-formyl-Met-Ala is 1.3fold higher than the Km-value of the wild-type enzyme
E133A
-
10000000fold reduction in activity
E133C
-
mutant fails to produce soluble protein
E133D
-
modest reduction in activity, less than 10fold for most of the substrates tested
E133Q
-
mutant fails to produce soluble protein
E88F
-
turnover-number is 0.36% of that of the wild-type enzyme, Km-value for N-formyl-Met-Ala is 1.1fold higher than the Km-value of the wild-type enzyme
I128A
-
Km-value for N-formyl-Met-Ala is 8.4fold higher than the Km-value of the wild-type enzyme
I128F
-
turnover-number is 0.13% of that of the wild-type enzyme, Km-value for N-formyl-Met-Ala is 37% of the Km-value of the wild-type enzyme
I128R
-
turnover-number is 0.6% of that of the wild-type enzyme, Km-value for N-formyl-Met-Ala is 6fold higher than the Km-value of the wild-type enzyme
I128S
-
turnover-number is 11% of that of the wild-type enzyme, Km-value for N-formyl-Met-Ala is 1.25fold higher than the Km-value of the wild-type enzyme
I130F
-
turnover-number is 58% of that of the wild-type enzyme, Km-value for N-formyl-Met-Ala is 77% of the Km-value of the wild-type enzyme
I44F
-
turnover-number is 3.8% of that of the wild-type enzyme, Km-value for N-formyl-Met-Ala is 35% of the Km-value of the wild-type enzyme
I86A
-
turnover-number is 8.9% of that of the wild-type enzyme, Km-value for N-formyl-Met-Ala is 1.fold higher than the Km-value of the wild-type enzyme
I86F
-
turnover-number is 3.3% of that of the wild-type enzyme, Km-value for N-formyl-Met-Ala is 65% of the Km-value of the wild-type enzyme
L125A
-
turnover-number is 2.9% of that of the wild-type enzyme, Km-value for N-formyl-Met-Ala is 3fold higher than the Km-value of the wild-type enzyme
L125W
-
turnover-number is 0.9% of that of the wild-type enzyme, Km-value for N-formyl-Met-Ala is 1.9fold higher than the Km-value of the wild-type enzyme
L126F
-
turnover-number is 113% of that of the wild-type enzyme, Km-value for N-formyl-Met-Ala is 1.5fold higher than the Km-value of the wild-type enzyme
L91E
-
the ratio of turnover number to Km-value for the substrate formyl-Met-Leu-p-nitroanilide is decreased 10fold
C50G
site-directed mutagenesis
C50G/E115L
site-directed mutagenesis, the mutant shows increased activity compared to the wild-type enzyme
E115L
site-directed mutagenesis, the mutant shows increased activity compared to the wild-type enzyme
E173L
-
the ratio of turnover number to Km-value for the substrate formyl-Met-Leu-p-nitroanilide is increased 3.7fold. The ratio of turnover number to Km-value for the substrate formyl-Met-Ala-His-Ala-Ala-Gln is increased 3.5fold. The ratio of turnover number to Km-value for the substrate formyl-Met-Thr–Gln-Ser-His is increased 1.5fold. The ratio of turnover number to Km-value for the substrate formyl-Met-Thr-Met-His-Thr-Thr is increased 2.4fold
C102A
high level expression but no enzyme activity
C102S
high level expression but no enzyme activity
C106S
C59S
site-directed mutagenesis, unaltered IC50 value for H2O2 compared to the wild-type enzyme
C68S
site-directed mutagenesis, the mutant protein exhibits 32fold reduced IC50s for H2O2 compared to wild-type mPDF
DELTA182-197
-
deletion mutant, amino acids 182-197 were removed from the carboxy-terminal end, inactive
G151A
-
the mutant shows wild type activity
G151D
-
the mutant shows 1.5 times the activity of the wild type enzyme against N-formyl-Met-Ala-Ser and deformylates N-formyl-Met-Leu-Phe with higher efficiency than the wild type enzyme. The mutation increases deformylase thermostability (2fold higher activity at 50°C compared with wild type activity at 30°C) and completely loses its activity upon incubating with 200 mM H2O2
G49C
-
the mutant retains nearly 36.1% activity compared to the wild type enzyme
G49P
-
the mutant is almost completely inactive
H148A
-
inactive mutant
H152A
-
inactive mutant
L107E
-
the mutant retains less than 10% activity compared to the wild type enzyme
M145C
site-directed mutagenesis, the mutant shows reduced enzyme activity and increased sensitivity to H2O2 compared to the wild-type enzyme
M145S
site-directed mutagenesis, the mutant shows higly reduced enzyme activity and increased sensitivity to H2O2 compared to the wild-type enzyme
R77A
-
mutant, constructed to demonstrate that the three arginines are important for the activity of mPDF
R77D
-
mutant, constructed to demonstrate that the three arginines are important for the activity of mPDF
R77K
-
mutant, constructed to demonstrate that the three arginines are important for the activity of mPDF
R77K/R78K/R79K
-
mutant, constructed to demonstrate that the three arginines are important for the activity of mPDF
R78A
-
mutant, constructed to demonstrate that the three arginines are important for the activity of mPDF
R78D
-
mutant, constructed to demonstrate that the three arginines are important for the activity of mPDF
R78K
-
mutant, constructed to demonstrate that the three arginines are important for the activity of mPDF
R79A
-
mutant, constructed to demonstrate that the three arginines are important for the activity of mPDF
R79D
-
mutant, constructed to demonstrate that the three arginines are important for the activity of mPDF
R79k
-
mutant, constructed to demonstrate that the three arginines are important for the activity of mPDF
R77A
-
mutant, constructed to demonstrate that the three arginines are important for the activity of mPDF
-
R77D
-
mutant, constructed to demonstrate that the three arginines are important for the activity of mPDF
-
R77K
-
mutant, constructed to demonstrate that the three arginines are important for the activity of mPDF
-
R78A
-
mutant, constructed to demonstrate that the three arginines are important for the activity of mPDF
-
R79k
-
mutant, constructed to demonstrate that the three arginines are important for the activity of mPDF
-
G151A
-
the mutant shows wild type activity
-
G151D
-
the mutant shows 1.5 times the activity of the wild type enzyme against N-formyl-Met-Ala-Ser and deformylates N-formyl-Met-Leu-Phe with higher efficiency than the wild type enzyme. The mutation increases deformylase thermostability (2fold higher activity at 50°C compared with wild type activity at 30°C) and completely loses its activity upon incubating with 200 mM H2O2
-
G49C
-
the mutant retains nearly 36.1% activity compared to the wild type enzyme
-
G49P
-
the mutant is almost completely inactive
-
L107E
-
the mutant retains less than 10% activity compared to the wild type enzyme
-
Ndelta57PfPDF Cdelta234
-
PfPDF variant with truncations of the first aminoterminal 57 acid residues and carboxyl terminus to amino acid residue S234
C130M/V63C
site-directed mutagenesis, the mutant shows reduced enzyme activity and decreased sensitivity to H2O2 compared to the wild-type enzyme
additional information