Peptide deformylase

 

In prokaryotes, proteins are synthesised with an N-terminal formylmethionine which is removed by peptide deformylase. Eukaryotes do not use this enzyme, so it represents a potential drug target for the treatment of bacterial infections.

 

Reference Protein and Structure

Sequence
P0A6K3 UniProt (3.5.1.88) IPR023635 (Sequence Homologues) (PDB Homologues)
Biological species
Escherichia coli K-12 (Bacteria) Uniprot
PDB
1bsz - PEPTIDE DEFORMYLASE AS FE2+ CONTAINING FORM (NATIVE) IN COMPLEX WITH INHIBITOR POLYETHYLENE GLYCOL (1.9 Å) PDBe PDBsum 1bsz
Catalytic CATH Domains
3.90.45.10 CATHdb (see all for 1bsz)
Cofactors
Iron(2+) (1) Metal MACiE
Click To Show Structure

Enzyme Reaction (EC:3.5.1.88)

water
CHEBI:15377ChEBI
+
N-formyl-L-methionyl group
CHEBI:49298ChEBI
→
formate
CHEBI:15740ChEBI
+
L-methioniniumyl group
CHEBI:64731ChEBI
Alternative enzyme names: Polypeptide deformylase, PDF,

Enzyme Mechanism

Introduction

Glu133 abstracts a proton from the metal activated water molecule in the first step of this reaction. Computational studies have suggested that the nucleophilic attack of the resulting hydroxide ion occurs in a concerted manner. The nitrogen of the peptide bond then abstracts the proton from Glu133, making it a better leaving group for the final step. In this final step, the oxyanion collapses, eliminating methionine, which dissociates from the active site first. The formic acid is displaced by an incoming water molecule.

Catalytic Residues Roles

UniProt PDB* (1bsz)
Glu134 Glu1133(133)C Acts as the general acid/base during the course of the reaction. hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
Cys91, His133, His137 Cys1090(90)C, His1132(132)C, His1136(136)C Form part of the iron binding site. metal ligand
Gln51, Gly46 (main-N), Leu92 (main-N) Gln1050(50)C, Gly1045(45)C (main-N), Leu1091(91)C (main-N) Act to stabilise the negatively charged intermediates formed during the course of the reaction. hydrogen bond acceptor, hydrogen bond donor, electrostatic stabiliser
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

proton transfer, bimolecular nucleophilic addition, coordination to a metal ion, unimolecular elimination by the conjugate base, native state of enzyme regenerated

References

  1. Wu XH et al. (2007), J Phys Chem B, 111, 6236-6244. Theoretical Study of the Catalytic Mechanism and Metal-Ion Dependence of Peptide Deformylase. DOI:10.1021/jp068611m. PMID:17497768.
  2. Fell JS et al. (2015), Theor Chem Acc, 134,Electronic effects on the reaction mechanism of the metalloenzyme peptide deformylase. DOI:10.1007/s00214-015-1674-y.
  3. Hao B et al. (1999), Biochemistry, 38, 4712-4719. Structural Basis for the Design of Antibiotics Targeting Peptide Deformylase†,‡. DOI:10.1021/bi982594c. PMID:10200158.
  4. Becker A et al. (1998), Nat Struct Biol, 5, 1053-1058. Iron center, substrate recognition and mechanism of peptide deformylase. DOI:10.1038/4162. PMID:9846875.
  5. Rajagopalan PT et al. (1997), Biochemistry, 36, 13910-13918. Purification, Characterization, and Inhibition of Peptide Deformylase fromEscherichia coli†. DOI:10.1021/bi971155v. PMID:9374870.
  6. Chan MK et al. (1997), Biochemistry, 36, 13904-13909. Crystal Structure of theEscherichia coliPeptide Deformylase†,‡. DOI:10.1021/bi9711543. PMID:9374869.
  7. Meinnel T et al. (1997), J Mol Biol, 267, 749-761. Structure-function relationships within the peptide deformylase family. Evidence for a conserved architecture of the active site involving three conserved motifs and a metal ion. DOI:10.1006/jmbi.1997.0904. PMID:9126850.

Step 1. Glu133 deprotonates iron bound water. The activated water initiates a nucleophilic attack on the peptide substrate.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Gln1050(50)C hydrogen bond donor, hydrogen bond acceptor
Glu1133(133)C hydrogen bond acceptor
Cys1090(90)C metal ligand
His1132(132)C metal ligand
His1136(136)C metal ligand
Glu1133(133)C proton acceptor

Chemical Components

proton transfer, ingold: bimolecular nucleophilic addition, coordination to a metal ion

Step 2. The amide of the peptide bond abstracts a proton from Glu133.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Gln1050(50)C hydrogen bond donor, hydrogen bond acceptor, electrostatic stabiliser
Gly1045(45)C (main-N) hydrogen bond acceptor, activator
Glu1133(133)C hydrogen bond donor
Leu1091(91)C (main-N) hydrogen bond donor
Cys1090(90)C metal ligand
His1132(132)C metal ligand
His1136(136)C metal ligand
Glu1133(133)C proton donor

Chemical Components

proton transfer

Step 3. The oxyanion collapses, eliminating methionine. L-methionine dissociates from the active site first. Then water displaces formic acid to regenerate the starting state.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Gln1050(50)C hydrogen bond donor, hydrogen bond acceptor, electrostatic stabiliser
Gly1045(45)C (main-N) hydrogen bond acceptor
Leu1091(91)C (main-N) hydrogen bond donor, electrostatic stabiliser
Cys1090(90)C metal ligand
His1132(132)C metal ligand
His1136(136)C metal ligand

Chemical Components

ingold: unimolecular elimination by the conjugate base, native state of enzyme regenerated
Download: Image, Marvin File

Step 1. Glu133 deprotonates iron bound water. The activated water initiates a nucleophilic attack on the peptide substrate.

Step 2. The amide of the peptide bond abstracts a proton from Glu133.

Step 3. The oxyanion collapses, eliminating methionine. L-methionine dissociates from the active site first. Then water displaces formic acid to regenerate the starting state.

Products.

Contributors

Gemma L. Holliday, Gail J. Bartlett, Daniel E. Almonacid, Atlanta Cook, Craig Porter