3D41

Crystal structure of fosfomycin resistance kinase FomA from Streptomyces wedmorensis complexed with MgAMPPNP and fosfomycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure of Fosfomycin Resistance Kinase FomA from Streptomyces wedmorensis.

Pakhomova, S.Bartlett, S.G.Augustus, A.Kuzuyama, T.Newcomer, M.E.

(2008) J.Biol.Chem. 283: 28518-28526

  • DOI: 10.1074/jbc.M803709200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The fosfomycin resistance protein FomA inactivates fosfomycin by phosphorylation of the phosphonate group of the antibiotic in the presence of ATP and Mg(II). We report the crystal structure of FomA from the fosfomycin biosynthetic gene cluster of St ...

    The fosfomycin resistance protein FomA inactivates fosfomycin by phosphorylation of the phosphonate group of the antibiotic in the presence of ATP and Mg(II). We report the crystal structure of FomA from the fosfomycin biosynthetic gene cluster of Streptomyces wedmorensis in complex with diphosphate and in ternary complex with the nonhydrolyzable ATP analog adenosine 5'-(beta,gamma-imido)-triphosphate (AMPPNP), Mg(II), and fosfomycin, at 1.53 and 2.2 angstroms resolution, respectively. The polypeptide exhibits an open alphabetaalpha sandwich fold characteristic for the amino acid kinase family of enzymes. The diphosphate complex shows significant disorder in loops surrounding the active site. As a result, the nucleotide-binding site is wide open. Binding of the substrates is followed by the partial closure of the active site and ordering of the alpha2-helix. Structural comparison with N-acetyl-L-glutamate kinase shows several similarities in the site of phosphoryl transfer: 1) preservation of architecture of the catalytical amino acids of N-acetyl-L-glutamate kinase (Lys9, Lys216, and Asp150 in FomA); 2) good superposition of the phosphate acceptor groups of the substrates, and 3) good superposition of the diphosphate molecule with the beta- and gamma-phosphates of AMPPNP, suggesting that the reaction could proceed by an associative in-line mechanism. However, differences in conformations of the triphosphate moiety of AMPPNP molecules, the long distance (5.1 angstroms) between the phosphate acceptor and donor groups in FomA, and involvement of Lys18 instead of Lys9 in binding with the gamma-phosphate may indicate a different reaction mechanism. The present work identifies the active site residues of FomA responsible for substrate binding and specificity and proposes their roles in catalysis.


    Organizational Affiliation

    Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA. sveta@lsu.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FomA protein
A
286Streptomyces wedmorensisMutation(s): 0 
Gene Names: fomA
Find proteins for Q56187 (Streptomyces wedmorensis)
Go to UniProtKB:  Q56187
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download SDF File 
Download CCD File 
A
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
FCN
Query on FCN

Download SDF File 
Download CCD File 
A
FOSFOMYCIN
1,2-EPOXYPROPYLPHOSPHONIC ACID
C3 H7 O4 P
YMDXZJFXQJVXBF-STHAYSLISA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.193 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 85.656α = 90.00
b = 85.656β = 90.00
c = 78.979γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
AMoREphasing
HKL-2000data scaling
HKL-2000data reduction
MAR345dtbdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-08-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance