1LMH

Crystal Structure of S. aureus peptide deformylase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.180 

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This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of Type II peptide deformylase from Staphylococcus aureus

Baldwin, E.T.Harris, M.S.Yem, A.W.Wolfe, C.L.Vosters, A.F.Curry, K.A.Murray, R.W.Bock, J.H.Marshall, V.P.Cialdella, J.I.Merchant, M.H.Choi, G.Deibel Jr., M.R.

(2002) J Biol Chem 277: 31163-31171

  • DOI: 10.1074/jbc.M202750200
  • Primary Citation of Related Structures:  
    1LMH

  • PubMed Abstract: 
  • The first crystal structure of Class II peptide deformylase has been determined. The enzyme from Staphylococcus aureus has been overexpressed and purified in Escherichia coli and the structure determined by x-ray crystallography to 1.9 A resolution. The purified iron-enriched form of S ...

    The first crystal structure of Class II peptide deformylase has been determined. The enzyme from Staphylococcus aureus has been overexpressed and purified in Escherichia coli and the structure determined by x-ray crystallography to 1.9 A resolution. The purified iron-enriched form of S. aureus peptide deformylase enzyme retained high activity over many months. In contrast, the iron-enriched form of the E. coli enzyme is very labile. Comparison of the two structures details many differences; however, there is no structural explanation for the dramatic activity differences we observed. The protein structure of the S. aureus enzyme reveals a fold similar, but not identical to, the well characterized E. coli enzyme. The most striking deviation of the S. aureus from the E. coli structure is the unique conformation of the C-terminal amino acids. The distinctive C-terminal helix of the latter is replaced by a strand in S. aureus which wraps around the enzyme, terminating near the active site. Although there are no differences at the amino acid level near the active site metal ion, significant changes are noted in the peptide binding cleft which may play a role in the design of general peptide deformylase inhibitors.


    Organizational Affiliation

    Department of Structural Analytical and Medicinal Chemistry, Pharmacia, 301 Henrietta Street, Kalamazoo, MI 49007, USA. eric.t.baldwin@pharmacia.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (S.aureus peptide deformylase)A184Staphylococcus aureusMutation(s): 0 
Gene Names: defdef1pdf1
EC: 3.5.1.27 (PDB Primary Data), 3.5.1.88 (UniProt)
UniProt
Find proteins for P68826 (Staphylococcus aureus)
Explore P68826 
Go to UniProtKB:  P68826
Protein Feature View
Expand
  • 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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.180 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.131α = 90
b = 121.873β = 90
c = 47.579γ = 90
Software Package:
Software NamePurpose
SAINTdata scaling
SAINTdata reduction
MLPHAREphasing
CNXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-06-12
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance