Peptide deformylase (PDF) is an essential metalloenzyme required for the removal of the formyl group at the N-terminus of nascent polypeptide chains in eubacteria [PMID:9846875] EC: 3.5.1.88. The enzyme acts as a monomer and binds a single zinc ion, catalysing the reaction:: N-formyl-L-methionine + H₂O = formate + methionyl peptide Catalytic efficiency strongly depends on the identity of the bound metal [PMID:9565550].

The structure of these enzymes is known [PMID:8845003, PMID:9665852]. PDF, a member of the zinc metalloproteases family, comprises an active core domain of 147 residues and a C-terminal tail of 21 residue. The 3D fold of the catalytic core has been determined by X-ray crystallography and NMR. Overall, the structure contains a series of anti-parallel beta- strands that surround two perpendicular alpha-helices. The C-terminal helix contains the characteristic HEXXH motif of metalloenzymes, which is crucial for activity. The helical arrangement, and the way the histidine residues bind the zinc ion, is reminiscent of other metalloproteases, such as thermolysin or metzincins. However, the arrangement of secondary and tertiary structures of PDF, and the positioning of its third zinc ligand (a cysteine residue), are quite different. These discrepancies, together with notable biochemical differences, suggest that PDF constitutes a new class of zinc-metalloproteases. [PMID:8845003].