Peptide deformylase
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In enzymology, a peptide deformylase (EC ) is an enzyme that removes the formyl group from the N terminus of nascent polypeptide chains in eubacteria, mitochondria and chloroplasts.
Peptide deformylases are metaloenzymes monomers and bind a metal cofactor, typically Fe(II) or Zn, in an active site. Cofactor identity impacts catalytic efficiency.
There are two types of peptide deformylases, types I and II, which differ in structure mainly in the outer surface of the protein.
Human gene PDF (gene) possesses this activity.
Function
Peptide deformylase removes the formyl group from the N terminus of nascent polypeptides as they are synthesized by the ribosome. The function of peptide deformylase can be described by the following equation, where formyl-L-methionyl peptide and water react under the formation of formate and methionyl peptide:
H2O + formyl-L-methionyl peptide ⇌ {\displaystyle \rightleftharpoons } methionyl peptide + formate
This reaction takes place on the surface of the ribosome, where the C-terminal alpha-helix of the peptide deformylase interacts with a grove between ribosomal proteins uL22 and bL32, and rRNA.
For its function this enzyme belongs to the family of hydrolases, those acting on carbon-nitrogen bonds other than peptide bonds, specifically in linear amides. The systematic name of this enzyme class is formyl-L-methionyl peptide amidohydrolase.
Structural studies
As of late 2007, 34 structures have been solved for this class of enzymes, with PDB accession codes , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , and .