3G6N

Crystal structure of an EfPDF complex with Met-Ala-Ser


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of an EfPDF complex with Met-Ala-Ser based on crystallographic packing.

Nam, K.H.Kim, K.H.Kim, E.E.Hwang, K.Y.

(2009) Biochem.Biophys.Res.Commun. 381: 630-633

  • DOI: 10.1016/j.bbrc.2009.02.113

  • PubMed Abstract: 
  • PDF (peptide deformylase) plays a critical role in the production of mature proteins by removing the N-formyl polypeptide of nascent proteins in the prokaryote cell system. This protein is essential for bacterial growth, making it an attractive targe ...

    PDF (peptide deformylase) plays a critical role in the production of mature proteins by removing the N-formyl polypeptide of nascent proteins in the prokaryote cell system. This protein is essential for bacterial growth, making it an attractive target for the design of new antibiotics. Accordingly, PDF has been evaluated as a drug target; however, architectural mechanism studies of PDF have not yet fully elucidated its molecular function. We recently reported the crystal structure of PDF produced by Enterococcus faecium [K.H. Nam, J.I. Ham, A. Priyadarshi, E.E. Kim, N. Chung, K.Y. Hwang, "Insight into the antibacterial drug design and architectural mechanism of peptide recognition from the E. faecium peptide deformylase structure", Proteins 74 (2009) 261-265]. Here, we present the crystal structure of the EfPDF complex with MAS (Met-Ser-Ala), thereby not only delineating the architectural mechanism for the recognition of mimic-peptides by N-terminal cleaved expression peptide, but also suggesting possible targets for rational design of antibacterial drugs. In addition to their implications for drug design, these structural studies will facilitate elucidation of the architectural mechanism responsible for the peptide recognition of PDF.


    Organizational Affiliation

    Korea University, Seoul, South Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptide deformylase
A, B
191Enterococcus faeciumMutation(s): 0 
Gene Names: def (def_2)
EC: 3.5.1.88
Find proteins for Q842S4 (Enterococcus faecium)
Go to UniProtKB:  Q842S4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
peptide (Met)(Ala)(Ser)
F, G
3N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
A, B
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.225 
  • Space Group: P 64 2 2
Unit Cell:
Length (Å)Angle (°)
a = 148.688α = 90.00
b = 148.688β = 90.00
c = 141.902γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-02-07 
  • Released Date: 2009-03-03 
  • Deposition Author(s): Hwang, K.Y., Nam, K.H.

Revision History 

  • Version 1.0: 2009-03-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance