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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

Crystallization

Crystallization on EC 3.5.1.88 - peptide deformylase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystals of AtPDF1Bt were grown by hanging drop vapor diffusion. The structure is determined a resolution of 2.4 A
purified recombinant enzyme, X-ray diffraction structure determination and analysis at 1.95 A resolution
-
sitting drop vapor diffusion method, using 15%-20% (w/v) PEG-3350 and either 0.1 or 0.2 M zinc acetate
using the sitting drop vapor diffusion method, two crystal forms diffract with a resolution of 2.8-2.9 A, third form yield a data set at 3.4 A resolution
-
inhibitor free structure, 1.7 A resolution - peptide deformylase-actinonin complex, 2.0 A resolution
-
inhibitor free structure, resolution range 50-1.7 A - peptide deformylase-actinonin complex, resolution 50-2.0 A
-
sitting-drop vapor diffusion method, crystallization of a BcPDF2-actinonin complex. BcPDF2 is found as a dimer in the crystal form with two additional actinonin bound at that interface
-
purified recombinant detagged enzyme, hanging drop vapour diffusion method, mixing of 900 nl of 6 mg/ml protein in 20 mM Tris–HCl pH 8.0, 20 mM NaCl, 3 mM 2-mercaptoethanol, with 900 nl reservoir solution containing 2 M zinc acetate dihydrate, 20% w/v PEG 3350, pH 6.4, and euilibration against 1 ml reservoir solution, microseeding and buffer optimization, 4 days, X-ray diffraction structure determination and analysis at 2.9 A resolution
-
PDF in complex with malonic acid, sitting drop vapor diffusion method, using 2.0 M Na-malonic acid, pH 4.0, at 22°C
the crystal structure of peptide deformylase in complex with Met-Ala-Ser is determined to 2.5 A
crystallographic analysis of the complex between the ribosome-interacting helix of the enzyme and the ribosome at 3.7 A resolution reveals that the enzyme orients its active site towards the ribosomal tunnel exit for efficient co-translational processing of emerging nascent chains
-
Fe2+-, Ni2+- and Zn2+-bound enzyme, Met-Ala-Ser-tripeptide bound to the substrate binding-site
-
Fe2+-, Ni2+- and Zn2+-bound forms, hanging and sitting drop vapour diffusion techniques
-
hanging-drop method, zinc-containing enzyme
PDB IDs 1DFF and 1BS7
PDF of Escherichia coli with Ni2+ replacing the native Fe2+, hanging drop vapour diffusion method, using 20.5% (w/v) PEG 4000, 0.1 M sodium acetate, pH 4.0
sitting drop vapor diffusion method
structure of the catalytically active enzyme in the nickel-bound form at 2.5-A resolution and at 1.9-A resolution in complex with the competitive inhibitor polyethylene glycol molecule
-
vapor diffusion method
vapour diffusion method. Crystallization of protein and protein-inhibitor complexes with N-formyl-H-hydroxy-3-phenylpropylamine, N-hydroxy-N-[3-(6-methyl pyridine-2-yl)propyl] formamide or N-formyl-N-hydroxy-2-(3-benzoylphenoxy)ethylamine
-
vapour diffusion method. Crystallization of protein and protein-inhibitor complexes with N-formyl-H-hydroxy-3-phenylpropylamine, N-hydroxy-N-[3-(6-methyl pyridine-2-yl)propyl] formamide or N-formyl-N-hydroxy-2-(3-benzoylphenoxy)ethylamine
-
apo-HpPDF, HpPDF - N-trans-caffeoyltyramine complex, HpPDF - (E)-N-phenethyl-3-(3,4-diacetoxyphenyl)acrylamide complex
ligand-free enzyme, and complxed with inhibitors actinonin and caffeic acid phenethyl ester, hanging drop vapour diffusion method, condition screening, using 0.1 M HEPES, pH 7.5, 70% v/v MPD, mixing of 0.001 ml protein and reservoir solution each, and equilibration against 0.5 ml of reservoir solution, 17°C, X-ray diffraction structure determination and analysis at 1.66-1.70 A resolution
-
PBD ID 3G5K
purified recombinant C-terminally His6-tagged truncated enzyme free or complexed with inhibitor actinonin or natural product peptide Met-Ala-Ser, PEG 5000 MME or PEG 6000 are employed as a precipitant, crystallization with or without 15 mM actinonin, free crystal soaking in 10 mM Met-Ala-Ser, usage of 15% PEG 5000 MME or PEG 6000, 100 mM MES buffer pH 5.5, 20% glycerol for cryoprotection, X-ray diffraction structure determination and analysis at 2.0-2.4 A resolution, molecular replacement
the structures of peptide deformylase and of peptide deformylase in complex with actinonin are determined at 1.7 A
cocrystallization of enzyme with actinonin, diffraction-quality crystals belong to space group P2(1), with unit-cell parameters a = 87.5 A, b = 119.1 A, c = 95.8 A, beta = 111.6°
-
crystallization of enzyme in Zn-bound form, hanging-drop vapour-diffusion method at 4°C, 2.2 A resolution, the enzyme is observed to be a dimer in crystals
-
hanging drop method, five LiPDF structures, resolution from 2.3-3.1 A
hanging-drop vapour-diffusion method, two crystal forms
structures of several complexes of Mycobacterium tuberculosis peptide deformylase with the inhibitors are determined at 2.0 to 1.4 A
2.2 A, cocrystallized with a synthesized inhibitor - 2.8 A resolution of the unliganded PfPDF
-
sitting drop vapor diffusion method
-
sitting-drop vapour-diffusion method, crystals grown from either native or SeMet-substituted protein, 2.8 A resolution with ten subunits per asymmetric unit
-
unusual type of noncrystallographic symmetry
-
crystallization in presence of the inhibitor actinonin using polyethylene glycol 4000 as precipitant, hanging-drop vapour-diffusion method at 4°C. The crystal belongs to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 68.75 A, b = 74,46 A, c = 77.18 A. The asymmetric unit contains two subunits of peptide deformylase, with a corresponding crystal volume per protein mass of 2.45 A Da and a solvent content of 49.8%
-
sitting drop vapor diffusion method
vapor diffusion method
crystal structure of Staphylococcus aureus peptide deformylase, SaPDF, in complex with its inhibitor actinonin at 1.9 A resolution
-
Ni-peptide deformylase from Pseudomonas aeruguinosa was co-crystallized with inhibitor
-
purified recombinant His6-tagged enzyme in complex with four hydroxamate inhibitors, hanging drop vapour-diffusion method, mixing of 30 mg/ml protein in 20 mM Tris-HCl, pH 7.5, and 120 mM NaCl, with reservoir solution consisting of 23% w/v PEG 4000, 50 mM Tris-HCl pH 8.5, 15% v/v glycerol, 100 mM MgCl2, 20mM CaCl2, X-ray diffraction structure determination and analysis at resolutions of 1.90-2.30 A
-
sitting drop vapor diffusion method
sitting-drop vapour-diffusion method, structure determination to 1.9 A resolution
-
sitting-drop vapour-diffusion method. Preparation of diffraction-quality Se-Met crystals of peptide deformylase that belong to space group C222(1) with unit cell parameters of a = 94.1 A, b = 121.9 A, c = 47.6 A, 1.9 resolution. Preparation of crystals with the inhibitors thiorphan, actinonin and PONU-172550. The thiorphan and actinonin co-crystals belong to space group C222(1). Repeated attempts to generate a complex structure of peptide deformylase with PNU-172550 from the orthorhombic space group are unsuccessful. Crystallization screening identifies an alternate C2 crystal form with unit cell dimensions of a = 93.4, b = 42.5, c = 104.1 A, beta = 93°
-
vapor diffusion method
vapour diffusion method. Crystallization of protein and protein-inhibitor complexes with N-formyl-H-hydroxy-3-phenylpropylamine, N-hydroxy-N-[3-(6-methyl pyridine-2-yl)propyl] formamide or N-formyl-N-hydroxy-2-(3-benzoylphenoxy)ethylamine
-
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
purified recombinant enzyme mutant S2A in apoform, hanging drop vapour diffusion method, mixing of 0.001 ml of 14-17 mg/ml protein in 50 mM HEPES-NaOH, pH 7.5, 0.1 M NaCl, and 0.1 mM NiCl2, with 0.001 ml of reservoir solution containing 5-15% PEG 8000, 0.2-0.5 M zinc acetate, and 0.1 M imidazole, pH 7.5, or 0.1 M sodium cacodylate, pH 6.5, at 18-20°C, stable crystals of apo-SaPDF are soaked by adding ligands to the drop to a final concentration of 16-32 mM, X-ray diffraction structure determination and analysis
sitting drop vapor diffusion method
vapour diffusion method. Crystallization of protein and protein-inhibitor complexes with N-formyl-H-hydroxy-3-phenylpropylamine, N-hydroxy-N-[3-(6-methyl pyridine-2-yl)propyl] formamide or N-formyl-N-hydroxy-2-(3-benzoylphenoxy)ethylamine
-
purified recombinant enzyme, X-ray diffraction structure determination and analysis at 1.95 A resolution, comparison to the crystal structure of the Arabidopsis thaliana chloroplast PDF enzyme
sitting drop vapor diffusion method
by the hanging drop vapour-diffusiuon method using PEG 4000 as a precipitant
-
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
native peptide deformylase crystals diffract to 2.7 A resolution
-
purified enzyme in complex with product peptides Met-Ala-Ser and Met-Ala, with inhibitor actinonin, and with six fragment chemical compounds bound in the substrate-binding pocket, X-ray diffraction structure determination and analysis at 1.9 A resolution