Peptide deformylase

In enzymology, a peptide deformylase (EC 3.5.1.88) 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 PDB: 1IX1​, PDB: 1LM4​, PDB: 1LM6​, PDB: 1LME​, PDB: 1LQW​, PDB: 1LQY​, PDB: 1LRU​, PDB: 1LRY​, PDB: 1N5N​, PDB: 1Q1Y​, PDB: 1S17​, PDB: 1SV2​, PDB: 1SZZ​, PDB: 1V3Y​, PDB: 1VEV​, PDB: 1VEY​, PDB: 1VEZ​, PDB: 1WS0​, PDB: 1WS1​, PDB: 1XEM​, PDB: 1XEN​, PDB: 1XEO​, PDB: 1Y6H​, PDB: 1ZXZ​, PDB: 1ZY0​, PDB: 1ZY1​, PDB: 2AI7​, PDB: 2AI8​, PDB: 2AI9​, PDB: 2AIA​, PDB: 2AIE​, PDB: 2EW5​, PDB: 2EW6​, and PDB: 2EW7​.