PDBsum entry: 1bs5

Hydrolase

PDB id: 1bs5

Contents

Protein chains

168 a.a. *

Ligands

SO4 ×2

Metals

_ZN ×3

Waters ×132

* Residue conservation analysis

PDB id:

1bs5

Name:

Hydrolase

Title:

Peptide deformylase as zn2+ containing form

Structure:

Protein (peptide deformylase). Chain: a, b, c. Synonym: pdf. Engineered: yes. Other_details: pdf protein from escherichia coli is crystallized as zn2+ containing form

Source:

Escherichia coli. Organism_taxid: 562. Strain: jm109. Cellular_location: cytoplasma. Gene: def. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Monomer (from PDB file)

Resolution:

2.50Å R-factor: 0.208 R-free: 0.258

Authors:

A.Becker,I.Schlichting,W.Kabsch,D.Groche,S.Schultz, A.F.V.Wagner

Key ref:

A.Becker et al. (1998). Iron center, substrate recognition and mechanism of peptide deformylase. Nat Struct Biol, 5, 1053-1058. PubMed id: 9846875 DOI: 10.1038/4162

Date:

01-Sep-98 Release date: 27-Aug-99

Protein chains

P0A6K3  (DEF_ECOLI) -  Peptide deformylase

Seq: 169 a.a.

Struc: 168 a.a.

Enzyme reactions

• Enzyme class: E.C.3.5.1.88 - Peptide deformylase.
• Reaction: Formyl-L-methionyl peptide + H₂O = formate + methionyl peptide
• Cofactor: Fe(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 Gene Ontology (GO) functional annotation 

• Biological process: translation (3 terms)
• Biochemical function: protein binding (7 terms)

reference

DOI no: 10.1038/4162

Nat Struct Biol 5:1053-1058 (1998)

PubMed id: 9846875

Iron center, substrate recognition and mechanism of peptide deformylase.

A.Becker, I.Schlichting, W.Kabsch, D.Groche, S.Schultz, A.F.Wagner.

ABSTRACT

Eubacterial proteins are synthesized with a formyl group at the N-terminus which is hydrolytically removed from the nascent chain by the mononuclear iron enzyme peptide deformylase. Catalytic efficiency strongly depends on the identity of the bound metal. We have determined by X-ray crystallography the Fe2+, Ni2+ and Zn2+ forms of the Escherichia coli enzyme and a structure in complex with the reaction product Met-Ala-Ser. The structure of the complex, with the tripeptide bound at the active site, suggests detailed models for the mechanism of substrate recognition and catalysis. Differences of the protein structures due to the identity of the bound metal are extremely small and account only for the observation that Zn2+ binds more tightly than Fe2+ or Ni2+. The striking loss of catalytic activity of the Zn2+ form could be caused by its reluctance to change between tetrahedral and five-fold metal coordination believed to occur during catalysis. N-terminal formylation and subsequent deformylation

Selected figure(s)

Figure 1.
Figure 1. a, Omit map of Met-Ala-Ser in the PDF−Ni/MAS structure contoured at 1 . Figure prepared with BobScript^25. b, Stereo-view of superimposed C -traces of the three crystallographically independent copies of peptide deformylase in complex with the reaction product Met-Ala-Ser. The numbers refer to amino acid residues. The transformations for optimal superposition were determined from equivalent C -atoms using molecule A as a reference and applied to the Ni^2+ ion (marked as Ni) and the peptide as well. Molecule complexes A, B, C are shown in green, magenta, blue, respectively. c, Active site of PDF−Ni (monomer A) with bound catalytic product Met-Ala-Ser, ordered water molecules W1, W2 and the Ni^2+ ion. d, A hypothetical model of PDF with bound substrate formyl-Met-Ala-Ser.

Figure 2.
Figure 2. Peptide deformylase in complex with the reaction product Met-Ala-Ser. a, Peptide binding scheme; Gly 45, Glu 88, Gly 89, His 132 and Glu 133 are conserved residues. Dashed lines indicate hydrogen bonds. Mean distances between donor and acceptor atoms as observed in the three crystallographically independent monomers are given in Å . The distance between the N-terminal amino group of the peptide to the Ni^2+-ion is 3.9 Å. b, Protein atoms (white, carbon; red, oxygen; dark blue, nitrogen; green, sulphur) and catalytic metal (magenta, Ni^2+) are depicted as space-filling spheres. Met-Ala-Ser is in ball-and-stick representation with carbon atoms and bonds colored yellow. Water molecules W1, W2 are shown as small light blue spheres. Figure prepared using MOLSCRIPT^26 and Raster3D^27.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (1998, 5, 1053-1058) copyright 1998.

Figures were selected by an automated process.