5V3D

Crystal structure of fosfomycin resistance protein from Klebsiella pneumoniae with bound fosfomycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.539 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure and Dynamics of FosA-Mediated Fosfomycin Resistance in Klebsiella pneumoniae and Escherichia coli.

Klontz, E.H.Tomich, A.D.Gunther, S.Lemkul, J.A.Deredge, D.Silverstein, Z.Shaw, J.F.McElheny, C.Doi, Y.Wintrode, P.L.MacKerell, A.D.Sluis-Cremer, N.Sundberg, E.J.

(2017) Antimicrob. Agents Chemother. 61: --

  • DOI: 10.1128/AAC.01572-17
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Fosfomycin exhibits broad-spectrum antibacterial activity and is being reevaluated for the treatment of extensively drug-resistant pathogens. Its activity in Gram-negative organisms, however, can be compromised by expression of FosA, a metal-dependen ...

    Fosfomycin exhibits broad-spectrum antibacterial activity and is being reevaluated for the treatment of extensively drug-resistant pathogens. Its activity in Gram-negative organisms, however, can be compromised by expression of FosA, a metal-dependent transferase that catalyzes the conjugation of glutathione to fosfomycin, rendering the antibiotic inactive. In this study, we solved the crystal structures of two of the most clinically relevant FosA enzymes: plasmid-encoded FosA3 from Escherichia coli and chromosomally encoded FosA from Klebsiella pneumoniae (FosAKP). The structure, molecular dynamics, catalytic activity, and fosfomycin resistance of FosA3 and FosAKP were also compared to those of FosA from Pseudomonas aeruginosa (FosAPA), for which prior crystal structures exist. E. coli TOP10 transformants expressing FosA3 and FosAKP conferred significantly greater fosfomycin resistance (MIC, >1,024 μg/ml) than those expressing FosAPA (MIC, 16 μg/ml), which could be explained in part by the higher catalytic efficiencies of the FosA3 and FosAKP enzymes. Interestingly, these differences in enzyme activity could not be attributed to structural differences at their active sites. Instead, molecular dynamics simulations and hydrogen-deuterium exchange experiments with FosAKP revealed dynamic interconnectivity between its active sites and a loop structure that extends from the active site of each monomer and traverses the dimer interface. This dimer interface loop is longer and more extended in FosAKP and FosA3 than in FosAPA, and kinetic analyses of FosAKP and FosAPA loop-swapped chimeric enzymes highlighted its importance in FosA activity. Collectively, these data yield novel insights into fosfomycin resistance that could be leveraged to develop new strategies to inhibit FosA and potentiate fosfomycin activity.


    Organizational Affiliation

    Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fosfomycin resistance protein
A, B
145Klebsiella pneumoniae 30660/NJST258_1Mutation(s): 0 
Find proteins for A0A0E1CQ35 (Klebsiella pneumoniae 30660/NJST258_1)
Go to UniProtKB:  A0A0E1CQ35
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

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A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
FCN
Query on FCN

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

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Download CCD File 
B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.539 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 40.071α = 90.00
b = 47.155β = 90.00
c = 149.517γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
XDSdata reduction
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-08-30
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Database references