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
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3.5.1.88
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actinonin
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medicine
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n-formylated
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deformylation
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eubacteria
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hydroxamic
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drug development
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formyltransferase
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oxazolidinone
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catarrhalis
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linezolid
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moraxella
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hexxh
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biotechnology
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synthesis
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agriculture
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molecular biology
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analysis
- 3.5.1.88
- actinonin
- medicine
-
n-formylated
-
deformylation
- eubacteria
-
hydroxamic
- drug development
-
formyltransferase
-
oxazolidinone
- catarrhalis
- linezolid
- moraxella
-
hexxh
- biotechnology
- synthesis
- agriculture
- molecular biology
- analysis
Reaction
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
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Metals Ions
Metals Ions on EC 3.5.1.88 - peptide deformylase
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Cd2+
the metal ion is bound in the active site, metalloprotease, metal binding and coordination structure of enzyme XoPDF
Co2+
Cu2+
Fe
Fe2+
Ni2+
Zn
Zn2+
additional information
Co2+
can replace Fe2+ without loss of activity, enhances stability
Co2+
enzymatic activity of Escherichia coli PDF is retained after replacement of the active-site Fe2+ ion with Co2+
Co2+
can replace Fe2+ without loss of activity, enhances stability
Co2+
the activity of Co2+-containing enzyme is higher than the activity of Zn2+-containing enzyme
Co2+
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Co2+ is an optimal metal for increasing the activity of purified thioredoxin-fused PDF
Co2+
can replace Fe2+ without loss of activity, enhances stability
Co2+
can replace Fe2+ without loss of activity, enhances stability
Co2+
Co2+-substituted isoform PDF-1 exhibits much higher enzymatic activity than that of Ni2+ and Zn2+ substituted PDF-1
Co2+
can replace Fe2+ without loss of activity, enhances stability
Co2+
can replace Fe2+ without loss of activity, enhances stability
Cu2+
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the enzyme is strongly activated by Cu2+ with 50% increase of activity at 0.05 mM
Fe
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enzyme form 2 contains up to 1.0 iron atom per polypeptide - 0.77 Fe2+ and 0.2 Fe3+ per polypeptide. The iron is likely coordinated by His132, His136 and Cys90 in the protein
Fe2+
bacterial PDF utilizes a Fe2+ ion as the catalytic metal ion. The Fe2+ ion in PDF is very unstable, and is rapidly and irreversibly oxidized to the Fe3+ ion through contact with atmospheric oxygen, resulting in an inactive enzyme. Addition of other divalent cations in vitro, such as Ni2+ or Co2+, result in better enzyme stability with very little loss of enzyme activity
Fe2+
required, irreversible oxidation to Fe3+ results in almost complete loss of activity
Fe2+
theoretically investigation of catalytic mechanism and metal specificity by studying both Fe2+-PDF and Zn2+-PDF. In both forms of PDF, the conserved Glu133 residue is protonated in the reactant complex, and acts as a general acid during the reaction. The initial reaction step is the nucleophilic attack of the metal-bound hydroxide on the carbonyl carbon of the substrate. Calculations indicate that the metal ion in Fe2+-PDF is always pentacoordinated during the reaction process, while that in Zn2+-PDF is only tetrahedrally coordinated and not bound to the substrate in the reactant complex. This difference in their metal coordination is suggested to account for the lower activity of Zn2+-PDF in comparison with Fe2+-PDF
Fe2+
bacterial PDF utilizes a Fe2+ ion as the catalytic metal ion. The Fe2+ ion in PDF is very unstable, and is rapidly and irreversibly oxidized to the Fe3+ ion through contact with atmospheric oxygen, resulting in an inactive enzyme. Addition of other divalent cations in vitro, such as Ni2+ or Co2+, result in better enzyme stability with very little loss of enzyme activity
Fe2+
required, catalytic metal ion, bound by Cys90, His132, and His136, metalloenzyme. Fe2+ leads to the lowest activation barriers for nucleophilic attack due to the ability of Fe2+ to act as a Lewis acid and thereby to more strongly coordinate to and activate the substrate carbonyl leading to a decrease in the energy barrier for the reaction. Fe2+ function analysis by using heteroscorpionate N2Sthiolate biomimetic ligand (L) complexed to Fe2+. The high-spin state for the Fe2+-L coordination complexes here has been shown to be the ground state. Reaction of Fe2+-L with formamide leading to formation of Fe2+-L-(formate) and ammonia
Fe2+
bacterial PDF utilizes a Fe2+ ion as the catalytic metal ion. The Fe2+ ion in PDF is very unstable, and is rapidly and irreversibly oxidized to the Fe3+ ion through contact with atmospheric oxygen, resulting in an inactive enzyme. Addition of other divalent cations in vitro, such as Ni2+ or Co2+, result in better enzyme stability with very little loss of enzyme activity
Fe2+
bacterial PDF utilizes a Fe2+ ion as the catalytic metal ion. The Fe2+ ion in PDF is very unstable, and is rapidly and irreversibly oxidized to the Fe3+ ion through contact with atmospheric oxygen, resulting in an inactive enzyme. Addition of other divalent cations in vitro, such as Ni2+ or Co2+, result in better enzyme stability with very little loss of enzyme activity
Fe2+
-
only Fe2+ and Co2+ ions are capable of supporting the enzyme activity of PDF
Fe2+
iron-containing enzyme variant, the apo-enzyme is enzymatically inactive, conserved metal ion coordinating Cys106 of mPDF
Fe2+
bacterial PDF utilizes a Fe2+ ion as the catalytic metal ion. The Fe2+ ion in PDF is very unstable, and is rapidly and irreversibly oxidized to the Fe3+ ion through contact with atmospheric oxygen, resulting in an inactive enzyme. Addition of other divalent cations in vitro, such as Ni2+ or Co2+, result in better enzyme stability with very little loss of enzyme activity
Fe2+
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required, irreversible oxidation to Fe3+ results in almost complete loss of activity
Fe2+
required, Fe2+ cofactor ion exhibits tetrahedral ligation to Cys156, His198, His202 and W1
Fe2+
the metal ion is positioned at the bottom of the pocket to enable the enzyme to carry out its catalytic function. The metal ion is tetrahedrally coordinated by three amino acid residues (Cys155, His196, and His200, respectively) and a water molecule
Fe2+
iron-containing enzyme variant, the apo-enzyme is enzymatically inactive, conserved metal ion coordinating Cys90 of sPDF, oxidation of Fe2+ to Fe3+ reduces the enzyme activity
Fe2+
required, irreversible oxidation to Fe3+ results in almost complete loss of activity
Fe2+
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the imidazole ring of histidine can combine with a metal ion such as iron. The activity of the iron form of the enzyme is higher than the nickel form
Fe2+
bacterial PDF utilizes a Fe2+ ion as the catalytic metal ion. The Fe2+ ion in PDF is very unstable, and is rapidly and irreversibly oxidized to the Fe3+ ion through contact with atmospheric oxygen, resulting in an inactive enzyme. Addition of other divalent cations in vitro, such as Ni2+ or Co2+, result in better enzyme stability with very little loss of enzyme activity
Fe2+
required, irreversible oxidation to Fe3+ results in almost complete loss of activity
Fe2+
required, irreversible oxidation to Fe3+ results in almost complete loss of activity
Fe2+
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Ni2+ or Co2+ leads to the retention of almost full catalytic activity
Ni2+
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enzyme nearly retains its activity on substitution of the naturally occuring Fe2+ by Ni2+
Ni2+
can replace Fe2+ without loss of activity, enhances stability
Ni2+
enzymatic activity of Escherichia coli PDF is retained after replacement of the active-site Fe2+ ion with Ni2+, the activity of the protein is not affected by Ni2+ concentrations up to 0.1 mM
Ni2+
can replace Fe2+ without loss of activity, enhances stability
Ni2+
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PdfA with Zn2+ substituted is much less active than the Ni2+ forms of the enzyme
Ni2+
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PdfB with Zn2+ substituted is much less active than the Ni2+ forms of the enzyme
Ni2+
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PdfC with Zn2+ substituted is as active as the Ni+ form for the fMA substrate and exhibits substrate specificity different from that of Ni2+ PdfC
Ni2+
can replace Fe2+ without loss of activity, enhances stability
Ni2+
can replace Fe2+ without loss of activity, enhances stability
Ni2+
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the imidazole ring of histidine can combine with a metal ion such as nickel. The activity of the iron form of the enzyme is higher than the nickel form
Ni2+
isoform PDF-1 shows much weaker binding ability towards Ni2+ than towards Co2+ and Zn2+
Ni2+
can replace Fe2+ without loss of activity, enhances stability
Ni2+
can replace Fe2+ without loss of activity, enhances stability
Zn2+
His132 and His136 bind Zn2+ through their Nepsilon1 imidazole nitrogens
Zn2+
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enzyme form 1 contains approximately 1.0 Zn2+ per polypeptide chain, the zinc-containing protein 1 is likely formed during iron depletion caused by overexpression
Zn2+
theoretically investigation of catalytic mechanism and metal specificity by studying both Fe2+-PDF and Zn2+-PDF. In both forms of PDF, the conserved Glu133 residue is protonated in the reactant complex, and acts as a general acid during the reaction. The initial reaction step is the nucleophilic attack of the metal-bound hydroxide on the carbonyl carbon of the substrate. Calculations indicate that the metal ion in Fe2+-PDF is always pentacoordinated during the reaction process, while that in Zn2+-PDF is only tetrahedrally coordinated and not bound to the substrate in the reactant complex. This difference in their metal coordination is suggested to account for the lower activity of Zn2+-PDF in comparison with Fe2+-PDF
Zn2+
the activity of Co2+-containing enzyme is higher than the activity of Zn2+-containing enzyme
Zn2+
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PdfA with Zn2+ substituted is much less active than the Ni2+ forms of the enzyme
Zn2+
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PdfB with Zn2+ substituted is much less active than the Ni2+ forms of the enzyme
Zn2+
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PdfC with Zn2+ substituted is as active as the Ni+ form for the fMA substrate and exhibits substrate specificity different from that of Ni2+ PdfC
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
Zn2+
the metal ion is bound in the active site, metalloprotease, metal binding and coordination structure of enzyme XoPDF
the metal ion in the active site of PDF is tetrahedrally ligated and bound to the two histidines from the HEPhiDH motif, as well to a cysteine and a water molecule
additional information
theoretical study of the catalytic mechanism and metal-ion dependence of peptide deformylase
additional information
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theoretical study of the catalytic mechanism and metal-ion dependence of peptide deformylase
additional information
preference for Fe2+ as the active site metal ion, versus, for example, Zn2+, Co2+, or N2+, despite Fe2+ being uncommon for this class of metalloenzymes and that PDF catalyzes a non-redox reaction. The difference in computed activation energies for deformylation between Fe2+, Co2+, and Zn2+ complexes with ligand L is fully consistent with experimental kinetics data for the Fe2+, Co2+, and Zn2+ forms of PDF as well as with the results from the earlier QM/MM computational studies
additional information
the metal ion in the active site of PDF is tetrahedrally ligated and bound to the two histidines from the HEPhiDH motif, as well to a cysteine and a water molecule
additional information
the metal ion in the active site of PDF is tetrahedrally ligated and bound to the two histidines from the HEPhiDH motif, as well to a cysteine and a water molecule
additional information
the metal ion in the active site of PDF is tetrahedrally ligated and bound to the two histidines from the HEPhiDH motif, as well to a cysteine and a water molecule
additional information
-
Zn2+ and Ni2+ are not capable of supporting the enzyme activity of PDF
additional information
the metal ion in the active site of PDF is tetrahedrally ligated and bound to the two histidines from the HEPhiDH motif, as well to a cysteine and a water molecule
additional information
-
the metal ion in the active site of PDF is tetrahedrally ligated and bound to the two histidines from the HEPhiDH motif, as well to a cysteine and a water molecule
additional information
the metal ion in the active site of PDF is tetrahedrally ligated and bound to the two histidines from the HEPhiDH motif, as well to a cysteine and a water molecule
additional information
the metal ion in the active site of PDF is tetrahedrally ligated and bound to the two histidines from the HEPhiDH motif, as well to a cysteine and a water molecule
additional information
Co2+-, Zn2+-, or Ni2+-substituted isoform PDF-2 exhibits no enzymatic activity
additional information
Co2+-, Zn2+-, or Ni2+-substituted isoform PDF-2 exhibits no enzymatic activity
additional information
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Co2+-, Zn2+-, or Ni2+-substituted isoform PDF-2 exhibits no enzymatic activity
additional information
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Co2+, Mg2+, Mn2+ do not significantly affect the enzyme activity
additional information
elimination of the divalent cation from the enzyme destabilizes the enzyme
additional information
comparisons to Escherichia coli metal binding structures with Co2+ and Fe2+
additional information
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comparisons to Escherichia coli metal binding structures with Co2+ and Fe2+