5VB0

Crystal structure of fosfomycin resistance protein FosA3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1128/AAC.01572-17
  • Primary Citation of Related Structures:  
    5V3D, 5V91, 5VB0

  • 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-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 (FosA KP ). The structure, molecular dynamics, catalytic activity, and fosfomycin resistance of FosA3 and FosA KP were also compared to those of FosA from Pseudomonas aeruginosa (FosA PA ), for which prior crystal structures exist. E. coli TOP10 transformants expressing FosA3 and FosA KP conferred significantly greater fosfomycin resistance (MIC, >1,024 μg/ml) than those expressing FosA PA (MIC, 16 μg/ml), which could be explained in part by the higher catalytic efficiencies of the FosA3 and FosA KP 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 FosA KP 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 FosA KP and FosA3 than in FosA PA , and kinetic analyses of FosA KP and FosA PA 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fosfomycin resistance protein FosA3
A, B, C, D, E
A, B, C, D, E, F, G, H
144Escherichia coliMutation(s): 0 
Gene Names: 
UniProt
Find proteins for D7UQM0 (Escherichia coli)
Explore D7UQM0 
Go to UniProtKB:  D7UQM0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD7UQM0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI

Download Ideal Coordinates CCD File 
J [auth A]
K [auth A]
N [auth C]
O [auth C]
S [auth F]
J [auth A],
K [auth A],
N [auth C],
O [auth C],
S [auth F],
V [auth H]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
I [auth A]
L [auth B]
M [auth C]
P [auth D]
Q [auth E]
I [auth A],
L [auth B],
M [auth C],
P [auth D],
Q [auth E],
R [auth F],
T [auth G],
U [auth H]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.207 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.608α = 90
b = 87.608β = 90
c = 357.038γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-30
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Database references
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description