Literature summary for 3.5.1.88 extracted from

Fieulaine, S.; Desmadril, M.; Meinnel, T.; Giglione, C.
Understanding the highly efficient catalysis of prokaryotic peptide deformylases by shedding light on the determinants specifying the low activity of the human counterpart (2014), Acta Crystallogr. Sect. D, 70, 242-252.

Cloned(Commentary)

Cloned (Comment)	Organism
sequence comparison, recombinant expression of C-terminally His6-tagged human-like PDF protein, composed of 197 residues	Homo sapiens

Crystallization (Commentary)

Crystallization (Comment)	Organism
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	Homo sapiens

Crystallization (Comment)

Organism

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

Homo sapiens

Protein Variants

Protein Variants	Comment	Organism
C50G	site-directed mutagenesis	Homo sapiens
C50G/E115L	site-directed mutagenesis, the mutant shows increased activity compared to the wild-type enzyme	Homo sapiens
E115L	site-directed mutagenesis, the mutant shows increased activity compared to the wild-type enzyme	Homo sapiens

Inhibitors

Inhibitors	Comment	Organism	Structure
actinonin	binding structure to the enzyme, overview	Homo sapiens

Localization

Localization	Comment	Organism	GeneOntology No.	Textmining
mitochondrion	-	Homo sapiens	5739	-

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Zn2+	dependent on	Homo sapiens

Molecular Weight [Da]

Molecular Weight [Da]	Molecular Weight Maximum [Da]	Comment	Organism
22300	-	2 * 22300, recombinant enzyme, in solution, mainly, SDS-PAGE	Homo sapiens
46100	-	recombinant enzyme, gel filtration	Homo sapiens

Organism

Organism	UniProt	Comment	Textmining
Homo sapiens	Q9HBH1	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant C-terminally His6-tagged truncated enzyme by nickel affinity and anion exchange chromatography, followed by gel filtration and ultrafiltration to homogeneity	Homo sapiens

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
formyl-Met-Ala-Ser + H2O	-	Homo sapiens	formate + Met-Ala-Ser	-	?

Subunits

Subunits	Comment	Organism
dimer	2 * 22300, recombinant enzyme, in solution, mainly, SDS-PAGE	Homo sapiens

Synonyms

Synonyms	Comment	Organism
PDF	-	Homo sapiens

Temperature Stability [°C]

Temperature Stability Minimum [°C]	Temperature Stability Maximum [°C]	Comment	Organism
45	-	Tm value of the truncated human PDF-like protein	Homo sapiens

General Information

General Information	Comment	Organism
evolution	peptide deformylases constitute a large subfamily of hydrolytic enzymes related to the thermolysin-metzincin HEXXH motif-containing family of metalloproteases. Peptide deformylases are classified into four subtypes based on the structural and sequence similarity of specific conserved domains. All PDFs share a similar three-dimensional structure, are functionally interchangeable in vivo and display similar properties in vitro, indicating that their molecular mechanism has been conserved during evolution. The human mitochondrial enzyme is the only exception as despite its conserved fold it reveals a unique substrate-binding pocket together with an unusual kinetic behaviour, structural basis, overview	Homo sapiens
additional information	enzyme structure comparison to plant enzyme from Arabidopsis thaliana, overview. A cysteine residue is involved in metal coordination within the active site, together with the two histidines from the thermolysin-metzincin HEXXH motif. The natural product tripeptide Met-Ala-Ser does not change the unfolding process of the protein, binding structure of the peptide to the enzyme, overview	Homo sapiens
physiological function	the enzyme is essential and involved in the essential removal of the formyl group from the N-terminal methionine during the early phase of protein translation, barely after the nascent chain has emerged from the ribosome	Homo sapiens