Peptide deformylase
Escherichia coli peptide deformylase structure
Identifiers
EC no.3.5.1.88
Databases
IntEnzIntEnz view
BRENDABRENDA entry
ExPASyNiceZyme view
KEGGKEGG entry
MetaCycmetabolic pathway
PRIAMprofile
PDB structuresRCSB PDB PDBe PDBsum
Gene OntologyAmiGO / QuickGO
Search
PMCarticles
PubMedarticles
NCBIproteins

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.[1]

Peptide deformylases are metaloenzymes monomers and bind a metal cofactor, typically Fe(II) or Zn, in an active site. Cofactor identity impacts catalytic efficiency.[2]

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) posesses 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 methionyl peptide + formate
Activity of peptide deformylase
Activity of peptide deformylase

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.[3]

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 1IX1, 1LM4, 1LM6, 1LME, 1LQW, 1LQY, 1LRU, 1LRY, 1N5N, 1Q1Y, 1S17, 1SV2, 1SZZ, 1V3Y, 1VEV, 1VEY, 1VEZ, 1WS0, 1WS1, 1XEM, 1XEN, 1XEO, 1Y6H, 1ZXZ, 1ZY0, 1ZY1, 2AI7, 2AI8, 2AI9, 2AIA, 2AIE, 2EW5, 2EW6, and 2EW7.

See also

References

  1. Escobar-Alvarez S, Goldgur Y, Yang G, Ouerfelli O, Li Y, Scheinberg DA (April 2009). "Structure and activity of human mitochondrial peptide deformylase, a novel cancer target". Journal of Molecular Biology. 387 (5): 1211–1228. doi:10.1016/j.jmb.2009.02.032. PMC 2782631. PMID 19236878.
  2. Becker A, Schlichting I, Kabsch W, Schultz S, Wagner AF (May 1998). "Structure of peptide deformylase and identification of the substrate binding site". The Journal of Biological Chemistry. 273 (19): 11413–11416. doi:10.1074/jbc.273.19.11413. PMID 9565550.
  3. McGrath H, Černeková M, Kolář MH (December 2022). "Binding of the peptide deformylase on the ribosome surface modulates the exit tunnel interior". Biophysical Journal. 121 (23): 4443–4451. Bibcode:2022BpJ...121.4443M. doi:10.1016/j.bpj.2022.11.004. PMC 9748369. PMID 36335428.

Further reading

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