1DEF

PEPTIDE DEFORMYLASE CATALYTIC CORE (RESIDUES 1-147), NMR, 9 STRUCTURES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 375-386

  • DOI: 10.1006/jmbi.1996.0521
  • Primary Citation of Related Structures:  
    1DEF

  • PubMed Abstract: 
  • Escherichia coli peptide deformylase, a member of the zinc metalloproteases family, is made up of an active core domain composed of 147 residues and of an additional and dispensable C-terminal tail of 21 residues. The three-dimensional structure of the catalytic core could be studied by NMR ...

    Escherichia coli peptide deformylase, a member of the zinc metalloproteases family, is made up of an active core domain composed of 147 residues and of an additional and dispensable C-terminal tail of 21 residues. The three-dimensional structure of the catalytic core could be studied by NMR. 1H and 15N NMR resonances assignments were obtained by two-dimensional and three-dimensional heteronuclear spectroscopy. The structure could be calculated using a set of 1015 restraints for the 147 residues of the enzyme. The overall structure is composed of a series of antiparallel beta-strands which surround two perpendicular alpha-helices. The C-terminal helix contains the HEXXH motif, which is crucial for activity. This helical arrangement and the way the histidines bind the zinc ion clearly are structurally reminiscent of the other members of the metalloprotease family, such as thermolysin or metzincins. Nevertheless, the overall arrangement of secondary and tertiary structures of peptide deformylase and the positioning of its third zinc ligand (a cysteine) are quite different from those of the other members of the family. These discrepancies, together with several biochemical differences, lead us to propose that peptide deformylase is the first example of a new class of the zinc-metalloproteases family. Studies of the interaction of peptide deformylase with either an inhibitor of the reaction or a product of the catalysed reaction, Met-Ala-Ser, as well as comparisons with the structures of other enzymes of the family, have enabled us to delineate the area corresponding to their binding site. The structural basis of the specificity of recognition of the formyl group is discussed in the context of the protease superfamily.


    Related Citations: 
    • 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
    • Mapping of the Active Site Zinc Ligands of Peptide Deformylase
      Meinnel, T., Lazennec, C., Blanquet, S.
      (1995) J Mol Biol 254: 175
    • 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

    Organizational Affiliation

    Laboratoire de Biochimie URA 1970 du Centre National de la Recherche Scientifique, Ecole Polytechnique, Palaiseau, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PEPTIDE DEFORMYLASEA147Escherichia coliMutation(s): 0 
Gene Names: FMS (CODONS 1-147)
EC: 3.5.1.31 (PDB Primary Data), 3.5.1.88 (UniProt)
UniProt
Find proteins for P0A6K3 (Escherichia coli (strain K12))
Explore P0A6K3 
Go to UniProtKB:  P0A6K3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 
  • OLDERADO: 1DEF Olderado

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-04-21
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance