1BS7

PEPTIDE DEFORMYLASE AS NI2+ CONTAINING FORM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of peptide deformylase and identification of the substrate binding site.

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

(1998) J Biol Chem 273: 11413-11416

  • DOI: 10.1074/jbc.273.19.11413
  • Primary Citation of Related Structures:  
    1BS7, 1ICJ

  • PubMed Abstract: 
  • Peptide deformylase is an essential metalloenzyme required for the removal of the formyl group at the N terminus of nascent polypeptide chains in eubacteria. The Escherichia coli enzyme uses Fe2+ and nearly retains its activity on substitution of the ...

    Peptide deformylase is an essential metalloenzyme required for the removal of the formyl group at the N terminus of nascent polypeptide chains in eubacteria. The Escherichia coli enzyme uses Fe2+ and nearly retains its activity on substitution of the metal ion by Ni2+. We have solved the structure of the Ni2+ enzyme at 1.9-A resolution by x-ray crystallography. Each of the three monomers in the asymmetric unit contains one Ni2+ ion and, in close proximity, one molecule of polyethylene glycol. Polyethylene glycol is shown to be a competitive inhibitor with a KI value of 6 mM with respect to formylmethionine under conditions similar to those used for crystallization. We have also solved the structure of the inhibitor-free enzyme at 2.5-A resolution. The two structures are identical within the estimated errors of the models. The hydrogen bond network stabilizing the active site involves nearly all conserved amino acid residues and well defined water molecules, one of which ligates to the tetrahedrally coordinated Ni2+ ion.


    Related Citations: 
    • Iron Center, Substrate Recognition and Mechanism of Peptide Deformylase
      Becker, A., Schlichting, I., Kabsch, W., Groche, D., Schultz, S., Wagner, A.F.
      (1998) Nat Struct Biol 5: 1053
    • Isolation and Crystallization of Functionally Competent Escherichia Coli Peptide Deformylase Forms Containing Either Iron or Nickel in the Active Site
      Groche, D., Becker, A., Schlichting, I., Kabsch, W., Schultz, S., Wagner, A.F.V.
      (1998) Biochem Biophys Res Commun 246: 342

    Organizational Affiliation

    Max-Planck-Institut für medizinische Forschung, Abteilung Biophysik, Jahnstrasse 29, 69120 Heidelberg, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (PEPTIDE DEFORMYLASE)ABC168Escherichia coliMutation(s): 0 
Gene Names: def
EC: 3.5.1.31 (PDB Primary Data), 3.5.1.88 (UniProt)
Find proteins for P0A6K3 (Escherichia coli (strain K12))
Explore P0A6K3 
Go to UniProtKB:  P0A6K3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NI
Query on NI

Download CCD File 
A, B, C
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.4α = 90
b = 64β = 123
c = 84.5γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
XSCALEdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-08-27
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance