2DEF

PEPTIDE DEFORMYLASE CATALYTIC CORE (RESIDUES 1-147), NMR, 20 STRUCTURES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: LOWEST DIANA TARGET FUNCTION 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Solution structure of nickel-peptide deformylase.

Dardel, F.Ragusa, S.Lazennec, C.Blanquet, S.Meinnel, T.

(1998) J.Mol.Biol. 280: 501-513

  • DOI: 10.1006/jmbi.1998.1882

  • PubMed Abstract: 
  • In the accompanying paper, we report that zinc is unlikely to be the co-factor supporting peptide deformylase activity in vivo. In contrast, nickel binding promotes full enzyme activity. The three-dimensional structure of the resulting nickel-contain ...

    In the accompanying paper, we report that zinc is unlikely to be the co-factor supporting peptide deformylase activity in vivo. In contrast, nickel binding promotes full enzyme activity. The three-dimensional structure of the resulting nickel-containing peptide deformylase (catalytic domain, residues 1 to 147) was solved by NMR using a 13C-15N-doubly labelled protein sample. A set of 2261 restraints could be collected, with an average of 15.4 per amino acid. The resolution, which shows a good definition for the position of most side-chains, is greatly improved compared to that previously reported for the zinc-containing, inactive form. A comparison of the two stuctures indicates however that both share the same 3D organization. This shows that the nature of the bound metal is the primary determinant of the hydrolytic activity of this enzyme. Site-directed mutagenesis enabled us to determine the conserved residues of PDF involved in the structure of the active site. In particular, a buried arginine appears to be critical for the positioning of Cys90, one of the metal ligands. Furthermore, the 3D structure of peptide deformylase was compared to thermolysin and metzincins. Although the structural folds are very different, they all display a common structural motif involving an alpha-helix and a three-stranded beta-sheet. These conserved structural elements build a common scaffold which includes the active site, suggesting a common hydrolytic mechanism for these proteases. Finally, an invariant glycine shared by both PDF and metzincins enables us to extend the conserved motif from HEXXH to HEXXHXXG.


    Related Citations: 
    • Evidence that Peptide Deformylase and Methionyl-tRNA(Fmet) Formyltransferase are Encoded within the Same Operon in Escherichia Coli
      Meinnel, T.,Blanquet, S.
      (1993) J.Bacteriol. 175: 7737
    • Mapping of the Active Site Zinc Ligands of Peptide Deformylase
      Meinnel, T.,Lazennec, C.,Blanquet, S.
      (1995) J.Mol.Biol. 254: 175
    • The C-Terminal Domain of Peptide Deformylase is Disordered and Dispensable for Activity
      Meinnel, T.,Lazennec, C.,Dardel, F.,Schmitter, J.M.,Blanquet, S.
      (1996) FEBS Lett. 385: 91
    • A New Subclass of the Zinc Metalloproteases Superfamily Revealed by the Solution Structure of Peptide Deformylase
      Meinnel, T.,Blanquet, S.,Dardel, F.
      (1996) J.Mol.Biol. 262: 375


    Organizational Affiliation

    Unité Mixte de Recherche, Ecole Polytechnique, Palaiseau cedex, F-91128, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PEPTIDE DEFORMYLASE
A
147Escherichia coli (strain K12)Gene Names: def (fms)
EC: 3.5.1.88
Find proteins for P0A6K3 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6K3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI

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

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: LOWEST DIANA TARGET FUNCTION 
  • Olderado: 2DEF Olderado
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-03-18
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance