The Gram-positive pathogen Staphylococcus aureus is a leading cause of global morbidity and mortality. Like many multi-drug-resistant organisms, S. aureus contains antibiotic-modifying enzymes that facilitate resistance to a multitude of antimicrobial compounds. FosB is a Mn(2+)-dependent fosfomycin-inactivating enzyme found in S. aureus that catalyzes nucleophilic addition of either l-cysteine (l-Cys) or bacillithiol (BSH) to the antibiotic, resulting in a modified compound with no bactericidal properties. The three-dimensional X-ray crystal structure of FosB from S. aureus (FosB(Sa)) has been determined to a resolution of 1.15 Å. Cocrystallization of FosB(Sa) with either l-Cys or BSH results in a disulfide bond between the exogenous thiol and the active site Cys9 of the enzyme. An analysis of the structures suggests that a highly conserved loop region of the FosB enzymes must change conformation to bind fosfomycin. While two crystals of FosB(Sa) contain Zn(2+) in the active site, kinetic analyses of FosB(Sa) indicated that the enzyme is inhibited by Zn(2+) for l-Cys transferase activity and only marginally active for BSH transferase activity. Fosfomycin-treated disk diffusion assays involving S. aureus Newman and the USA300 JE2 methicillin-resistant S. aureus demonstrate a marked increase in the sensitivity of the organism to the antibiotic in either the BSH or FosB null strains, indicating that both are required for survival of the organism in the presence of the antibiotic. This work identifies FosB as a primary fosfomycin-modifying pathway of S. aureus and establishes the enzyme as a potential therapeutic target for increased efficacy of fosfomycin against the pathogen.
The Gram-positive pathogen Staphylococcus aureus is a leading cause of global morbidity and mortality. Like many multi-drug-resistant organisms, S. aureus contains antibiotic-modifying enzymes that facilitate resistance to a multitude of antimicrobial compounds. FosB is a Mn(2+)-dependent fosfomycin-inactivating enzyme found in S. aureus that catalyzes nucleophilic addition of either l-cysteine (l-Cys) or bacillithiol (BSH) to the antibiotic, resulting in a modified compound with no bactericidal properties. The three-dimensional X-ray crystal structure of FosB from S. aureus (FosB(Sa)) has been determined to a resolution of 1.15 Å. Cocrystallization of FosB(Sa) with either l-Cys or BSH results in a disulfide bond between the exogenous thiol and the active site Cys9 of the enzyme. An analysis of the structures suggests that a highly conserved loop region of the FosB enzymes must change conformation to bind fosfomycin. While two crystals of FosB(Sa) contain Zn(2+) in the active site, kinetic analyses of FosB(Sa) indicated that the enzyme is inhibited by Zn(2+) for l-Cys transferase activity and only marginally active for BSH transferase activity. Fosfomycin-treated disk diffusion assays involving S. aureus Newman and the USA300 JE2 methicillin-resistant S. aureus demonstrate a marked increase in the sensitivity of the organism to the antibiotic in either the BSH or FosB null strains, indicating that both are required for survival of the organism in the presence of the antibiotic. This work identifies FosB as a primary fosfomycin-modifying pathway of S. aureus and establishes the enzyme as a potential therapeutic target for increased efficacy of fosfomycin against the pathogen.
The Gram-positive
pathogen Staphylococcus aureus is a leading cause
of global morbidity
and mortality.[1,2] This organism innocuously colonizes
the anterior nares of nearly one-third of the world’s population
and is commonly associated with commensal colonization of the skin.[3,4]S. aureus poses a serious risk to public health
because of its prevalence as a commensal organism, its ability to
cause a multitude of diseases, and the increasing incidence of antibiotic-resistant
strains like methicillin-resistant S. aureus (MRSA).
Herein, we characterize the resistance mechanism of MRSA to the antibiotic
fosfomycin.Fosfomycin is a safe, broad-spectrum antibiotic
that is effective
against both Gram-negative and Gram-positive bacteria. It is most
often prescribed for the treatment of urinary tract and gastrointestinal
infections.[5−8] Fosfomycin has few human side effects and is excreted from the body
in its unmetabolized, active form. Therefore, it can be administered
in a single 3 g dose in the clinical setting. Fosfomycin inhibits
cell wall biogenesis by covalently binding to an active site cysteine
of MurA, the enzyme responsible for the first committed step in peptidoglycan
biosynthesis, a historically important target for antimicrobial agents.
A significant disadvantage of the effectiveness of fosfomycin has
been the emergence of pathogens that contain fosfomycin-modifying
enzymes.FosB, a Mn2+-dependent fosfomycin-inactivating
enzyme
found in Gram-positive organisms such as S. aureus, is one of three related enzymes (FosA, FosB, and FosX) that confer
resistance to the antibiotic.[9−16] The enzyme catalyzes nucleophilic addition of bacillithiol (BSH),
a unique low-molecular weight (LMW) thiol native to Gram-positive
bacteria,[17] to C1 of fosfomycin, resulting
in a modified, inactive compound (Figure 1).
FosB was originally characterized as a Mg2+-dependent l-cysteine (l-Cys) transferase.[18] However, the synthesis of BSH has allowed further investigation
into the thiol preference of the FosB enzymes, and kinetic analyses
indicate a preference of the FosB enzymes for BSH over l-Cys
as the cosubstrate for nucleophilic addition to the antibiotic.[19]
Figure 1
Reaction catalyzed by the fosfomycin resistance protein,
FosB.
FosB is a thiol-dependent fosfomycin-inactivating enzyme found in S. aureus that catalyzes nucleophilic addition of either l-cysteine or bacillithiol to C1 of the antibiotic, resulting
in a modified compound with no bactericidal properties.
Reaction catalyzed by the fosfomycin resistance protein,
FosB.
FosB is a thiol-dependent fosfomycin-inactivating enzyme found in S. aureus that catalyzes nucleophilic addition of either l-cysteine or bacillithiol to C1 of the antibiotic, resulting
in a modified compound with no bactericidal properties.BSH was first identified in 2009 and isolated from S. aureus and Deinococcus radiodurans (Figure 2).[20] It is the α-anomeric
glycoside of l-cysteinyl-d-glucosaminyl-l-malate and is a significant LMW thiol found in S. aureus. Like mycothiol in mycobacteria and glutathione in Gram-negative
bacteria, BSH serves as the LMW thiol responsible for detoxification
of xenobiotics in Gram-positive organisms.[21] Recently, the BSH-dependent detoxification of rifamycin in S. aureus Newman was shown to result in the mercapturic
acid form of the antibiotic, an end compound that is analogous to
the products of the mycothiol- and glutathione-dependent detoxification
pathways for their respective organisms.[21] Furthermore, BSH knockout strains of both S. aureus and Bacillus subtilis, along with FosB knockout
strains of B. subtilis, show increased sensitivity
to fosfomycin.[17,22]
Figure 2
Structure of bacillithiol.
Structure of bacillithiol.In this report, we present five three-dimensional
X-ray structures
of FosB from S. aureus (FosB). Two of the structures contain Zn2+ and sulfate
in the active site of the enzyme: one determined by single-wavelength
anomalous dispersion (SAD) phasing to 1.42 Å resolution and the
other by molecular replacement to 1.15 Å resolution. In addition
to the FosB·Zn2+·sulfate
structures, we provide structures of FosB cocrystallized with either l-Cys or BSH. Cocrystallization
of FosB with the exogenous thiol results
in removal of the metal and formation of a disulfide bond to the active
site Cys9 of the enzyme. In three of the five structures, an alternate
conformation of an important active site loop region of the enzyme
that provides insight into the mechanism of the FosB enzymes is observed.
In addition, we present kinetic analyses to demonstrate that FosBthiol transferase activity is inhibited
by Zn2+ at physiological concentrations (∼100 μM).
Finally, we provide disk diffusion assays to show that S.
aureus inactivated for FosB in both the Newman and USA300
JE2 strain backgrounds exhibits increased susceptibility to fosfomycin.
Thus, this report contains the crystal structure of the fosfomycin
resistance enzyme from S. aureus and demonstrates
that the enzyme is required for resistance of the pathogen to the
antibiotic.
Materials and Methods
General Materials
Buffer salts were
purchased from
Research Products International Corp. (RPI) and used without further
purification. All crystallization materials were from Hampton Research.
Metals were obtained as their chloride salts from J. T. Baker. l-Cysteine was purchased from Sigma Life Sciences. Fosfomycin
disodium salt was from MP Biomedicals, LLC. BSH was synthesized as
bacillithiol disulfide (BSSB) by the Vanderbilt Chemical Synthesis
Core and reduced to BSH prior to use according to published procedures.[19] pET28 (FosB) was
from Platinum PCR SuperMix, and custom primers were ordered from Invitrogen
(Carlsbad, CA). Restriction enzymes were from New England Biolabs
(Ipswich, MA). The pET20b(+) vector was from EMB Chemicals, Inc. (Gibbstown,
NJ). XL1-Blue supercompetent cells and BL21-Gold (DE3) cells were
from Agilent Technologies (Santa Clara, CA).
Protein Expression and
Purification for Crystallography and
Kinetics
N-Terminal Intein-Tagged FosB
Intein-tagged FosB was expressed
and purified for crystallography as previously described.[19] Intein-tagged FosB was dialyzed into 25 mM HEPES (pH 7.5) containing 50 mM NaCl.
N-Terminal Six-His-Tagged FosB
The six-HisFosB gene was
amplified from the FosB-pET28 plasmid
previously prepared[19] using primers containing
restriction sites for NdeI and EcoRI. To prepare the N-terminal six-histidine-tagged FosB construct, the forward primer was 5′-GC
GGG GCC GGG GGT ATA CAT ATG CAT CAT CAT CAT CAT CAC TTA AAA TCT ATT AAT C-3′ and the reverse primer
was 5′-GCC GGC GCC CGG AAT TCG CTT
ATT TGT AAA ATG-3′. The underlined parts of primer
sequences are complementary to the nucleotide sequences of the FosB-pET28 gene, whereas the 5′-overhanging
ends of primers contain recognition sites for restriction endonucleases
(bold) and are designed to facilitate cloning.The polymerase
chain reaction (PCR) solution consisted of 200 ng of pET28(FosB), each primer at 10 μM, and 45 μL
of Platinum PCR SuperMix. For PCR, 35 cycles were performed with a
temperature profile of 30 s at 95 °C, 30 s at 55 °C, and
1 min at 72 °C in an Applied Biosystems (Foster City, CA) 2720
thermal cycler. The amplification products were analyzed by electrophoresis
on a 0.8% agarose gel stained with ethidium bromide.The amplification
products (1 μg) and pET20b vector (1 μg)
were digested with NdeI and EcoRI.
The digested DNA was analyzed by electrophoresis as previously described;
the corresponding bands on the gel were excised, and the DNA was extracted
with a QIAquick Gel Extraction Kit (Qiagen). Purified histidine-tagged FosB and nontagged FosB were each ligated into
pET20b NdeI–EcoRI sites. Escherichia coli XL1-Blue supercompetent cells were transformed
with the ligation mixture, and four colonies were assayed for the
presence of the FosB gene fragment by plasmid extraction and plasmid DNA sequencing.The new pET-20b expression plasmid containing the gene encoding
six-His-tagged FosB was transformed into E. coli BL21(DE3) cells. The
cells were plated on LB-agar containing 100 μg/mL ampicillin
and incubated at 37 °C for approximately 16 h. Single colonies
were isolated from the LB-agar plates and used to inoculate 2 mL LB
(Gibco) starter cultures (three cultures for a total of 6 mL) containing
80 μg/mL ampicillin. After incubation at 37 °C for ∼8
h with shaking, 1 mL of starter growth was used to inoculate 1 L of
Terrific Broth containing 80 μg/mL ampicillin (6 L total). The
1 L cultures were grown at 37 °C while being shaken for approximately
12 h (or until the OD600 reached ∼1) and then induced
with 0.5 mM IPTG. Upon induction with IPTG, the temperature was reduced
to 25 °C and the cells were allowed to grow for an additional
4–5 h. The cells were harvested by centrifugation at 5000g for 15 min.The E. coli cell pellet
was resuspended in 2 mL
of His tag lysis buffer [50 mM sodium phosphate (pH 8.0), 300 mM sodium
chloride, and 10 mM imidazole] per gram of cell pellet. Lysozyme was
added to the slurry at a concentration of 1 mg/mL, and the mixture
was stirred at 4 °C for 1 h. After the mixture had been stirred
for 1 h, 5 mg of DNase and RNase were added, and the slurry was stirred
at 4 °C for an additional 1 h. The slurry was sonicated to ensure
complete lysing of cells and the lysate cleared by centrifugation
at 35000g for 30 min.The cleared lysate containing
the six-His-tagged FosB protein of
interest was added to a nickel-NTA purification column. The column
was washed with 50 mM NaH2PO4 (pH 8.0) containing
300 mM NaCl and 20 mM imidazole to remove any protein impurities.
Finally, the six-His-tagged FosB protein was eluted form the nickel-NTA
column with 50 mM NaH2PO4 (pH 8.0), containing
300 mM NaCl and 250 mM imidazole. Following elution from the column,
the FosB protein was dialyzed into 20 mM HEPES (pH 7.5) for crystallization
trials.
Protein Crystallization
N-Terminal
Intein-Tagged FosB
Crystals
of intein-tagged FosB with
the exogenous l-Cys-Cys9disulfide bond were grown using
the hanging drop vapor diffusion method at 303 K by mixing 3 μL
of protein solution [20 mg/mL in 25 mM HEPES buffer (pH 7.5), 50 mM
NaCl, 10 mM MgCl2, 10 mM l-Cys, and 10 mM fosfomycin]
and 3 μL of reservoir solution [Hampton Research Index 68, 0.1
M HEPES (pH 7.5), 200 mM ammonium sulfate, and 25% (w/v) polyethylene
glycol (PEG) 3350] in a Hampton Research VDX plate. Apo crystals of
intein-tagged FosB were grown via the
same approach with the addition of 10 mM tris(2-carboxyethyl)phosphine
(TCEP) to the initial protein solution. These crystals were cryoprotected
with 25% ethylene glycol in 75% mother liquor.
N-Terminal
Six-His-Tagged FosB
Initial
crystals of six-His-tagged FosB (Figure
S1 of the Supporting Information) were
grown using the hanging drop vapor diffusion method at 303
K by mixing 3 μL of protein solution [8 mg/mL in 20 mM HEPES
buffer (pH 7.5)] and 3 μL of reservoir solution [Hampton Research
Index 67, 0.1 M Bis-Tris (pH 6.5), 200 mM ammonium sulfate, and 25%
(w/v) PEG 3350] in a Hampton Research VDX plate. The final optimized
conditions for each crystal are as follows. The FosB crystals with Zn2+ and sulfate used for SAD phasing
and molecular replacement were obtained after mixing equal volumes
(3 μL) of protein solution [7.5 mg/mL in 20 mM HEPES buffer
(pH 7.5) and 5 mM fosfomycin] and reservoir solution [0.1 M Bis-Tris
(pH 6.5), 200 mM ammonium sulfate, and 16% (w/v) PEG 3350]. The FosB crystals with bacillithiol were obtained
after mixing equal volumes (3 μL) of protein solution [7.5 mg/mL
in 20 mM HEPES buffer (pH 7.5), 5 mM fosfomycin, and 5 mM BSH] and
reservoir solution [0.1 M Bis-Tris, 200 mM ammonium sulfate, and 16%
(w/v) PEG 3350]. All crystals were cryoprotected in 30% glycerol and
70% mother liquor and frozen in liquid nitrogen prior to collection
of the diffraction data.
Data Collection and Refinement
Diffraction data for
all crystals were collected at 100 K on either the LS-CAT 21-ID beamline
at the APS synchrotron facility or the Bruker-Nonius Microstar rotating
anode X-ray generator at Vanderbilt University. The collected diffraction
data sets from LS-CAT 21-ID were processed with HKL2000,[23] whereas those collected on the Bruker instrument
were processed with Bruker-AXS (2010) PROTEUM2 version 2010.11 (Bruker-AXS,
Madison, WI). Phasing of the diffraction data was done either by SAD
phasing using SHELXD/E[24] or by molecular
replacement using PHASER.[25] For SAD phasing,
the presence of anomalous scatterers was confirmed and the peak wavelength
was determined by X-ray fluorescence. In the case of SAD phasing,
the initial model was constructed using ARPwARP.[26] For molecular replacement, the first model output and refined
from ARPwARP was used as the initial search model. Manual model building
for each structure was performed using Coot model building software.[27] Waters were placed with the Coot routine, Find
Waters. The final models were obtained by iterative cycles of model
building in Coot and structure refinement using Refmac5[28] in the CCP4 suite of programs (Collaborative
Computational Project, 1994). All protein figures were prepared with
Chimera.[29] Data collection and refinement
statistics are listed in Table 1.
Table 1
Data Collection and Refinement Statistics
FosB·Zn·sulfate SAD
FosB·Zn·sulfate MR
FosB·BS-Cys9
FosB·l-Cys-Cys9
apo
FosB
Protein Data Bank entry
4NAY
4NAZ
4NB0
4NB1
4NB2
space group
C2
C2
P1
P1
P1
unit cell parameters
a (Å)
62.49
62.62
40.93
40.88
40.61
b (Å)
62.91
62.81
44.88
44.92
44.83
c (Å)
44.91
45.05
46.87
46.35
45.67
α
(deg)
90.00
90.00
110.91
61.19
119.30
β
(deg)
121.91
122.08
115.24
65.04
106.79
γ
(deg)
90.00
90.00
98.27
82.5
97.92
Data Collection
temperature (K)
100
100
100
100
100
wavelength (Å)
1.2823
1.0781
1.1272
1.5412
1.5412
resolution (Å)a
40.56–1.42 (1.44–1.42)
40.53–1.15 (1.17–1.15)
39.27–1.62 (1.65–1.62)
39.19–1.80 (1.85–1.80)
38.88–1.89 (1.94–1.89)
no. of unique reflections
27859
49038
32205
23472
18192
completeness (%)a
99.9 (100)
93.6 (89.2)
96.3 (93.9)
97.4 (80.7)
90.0 (80.3)
Rmerge (%)b
5.2 (40.2)
3.9 (29.9)
3.2 (35.3)
6.0 (22.5)
5.5 (34.3)
I/σ
50.8 (4.1)
37.1 (3.1)
24.1 (2.0)
14.4 (2.7)
25.3 (3.6)
redundancy
7.1 (6.0)
3.8 (3.1)
2.0 (2.0)
3.6 (1.3)
2.5 (1.3)
Refinement
Rwork/Rfree (%)c
12.95/16.64
13.44/16.22
18.87/22.44
19.47/24.35
18.56/24.08
average B factor (Å2)
all atoms
19.27
16.96
23.78
20.37
22.97
protein
18.26
15.35
23.49
20.46
22.57
water
29.50
28.76
27.60
21.36
28.36
no. of atoms
protein
1244
1375
2204
2218
2245
water
101
136
119
99
162
root-mean-square deviation
from ideal
bond lengths (Å)
0.025
0.025
0.023
0.019
0.020
bond angles
(deg)
2.28
2.28
2.22
1.96
2.03
Ramachandran
plot (%)d
most favored
110
110
194
202
195
allowed
7
9
22
15
21
disallowed
0
0
0
0
0
Values
in parentheses are for the
highest-resolution shell.
Rmerge = ∑(|I – I̅|)/∑I ×
100.
Rwork = ∑|Fo – Fc|/∑Fo ×
100,
where Fo is the observed structure factor
amplitude and Fc is the calculated structure
factor amplitude.
Values
are numbers of residues.
Values
in parentheses are for the
highest-resolution shell.Rmerge = ∑(|I – I̅|)/∑I ×
100.Rwork = ∑|Fo – Fc|/∑Fo ×
100,
where Fo is the observed structure factor
amplitude and Fc is the calculated structure
factor amplitude.Values
are numbers of residues.
Continuous 31P NMR Activity Assays with Zn2+
FosB (0.5 μM) was equilibrated
for 5 min with 100 μM ZnCl2 and 8 mM fosfomycin in
20 mM HEPES (pH 7.0). The reaction was initiated by addition of 1.8
mM BSH or l-Cys, and the mixture was transferred to an NMR
tube and allowed to react at room temperature. At various time points,
a 31P with 1H decoupling NMR spectrum was collected
using Bruker AV-400 MHz NMR. The analysis of the data was completed
according to the method previously described.[19]
Time Point High-Performance Liquid Chromatography (HPLC) Activity
Assays with Mn2+ and Mn2+ with Zn2+
FosB (0.5 μM) was equilibrated
for 5 min with either 10 μM MnCl2 or 10 μM
MnCl2 and 100 μM ZnCl2 and 4 mM fosfomycin
in 20 mM HEPES (pH 7.0). The reaction was initiated by addition of
1.6 mM BSH or 1.8 mM l-Cys and the mixture allowed to react
at room temperature. At various time points, a 20 μL aliquot
of the reaction mixture was quenched by addition of 40 μL of
5% (w/v) trichloroacetic acid followed by vortexing. Addition of 15
μL of 0.8 M NaOH returned the pH to 7.0. An internal standard
(20 μL of 0.4 mM serine) was added, and the mixture was diluted
to 100 μL with 20 mM HEPES (pH 7.0). A 20 μL aliquot of
the quench was added to 55 μL of borate buffer and mixed with
25 μL of the AQC reagent (Waters, Milford, MA) solubilized according
to the manufacturer’s directions. Derivatization reaction mixtures
were incubated at 55 °C for 10 min followed by dilution with
400 μL of 70 mM NaOAc containing 7 mM triethylamine, adjusted
to pH 5.0 with phosphoric acid (mobile phase A).Derivatized
samples were analyzed on an Agilent 1260 Infinity HPLC System using
fluorescence detection with excitation at 250 nm and emission at 395
nm. Samples were injected onto a 250 mm × 4.6 mm Kinetex C-18
column with a particle size of 5 μm and a pore size of 100 Å
(Phenomenex, Torrance, CA) and equilibrated with 90% mobile phase
A and 10% mobile phase B [80% (v/v) acetonitrile]. Samples were eluted
using a flow rate of 1 mL/min and the following gradient of mobile
phase B: 10% from 0 to 6 min, 10 to 12% from 6 to 12 min, 12 to 15%
from 12 to 15 min, 15 to 40% from 15 to 19 min, and 40 to 100% from
19 to 22 min. BS-fosfomycin, l-Cys-fosfomycin, and serine
had retention times of 4.0, 4.7, and 7.5 min, respectively. The amount
of product formed was quantified as previously described.[30]
Disk Diffusion Assay
Soft agar was
inoculated with
an overnight culture of Newman or USA300 JE2 methicillin-resistant S. aureus isolate and poured over a tryptic soy agar plate.
Four sterile Whatman paper discs were placed on top of the cooled
soft agar. The indicated amounts of fosfomycin were added to each
disk from a 50 mg/mL stock. The plates were incubated overnight at
37 °C.
Results
Crystal Structure Determination
and Modeling
FosB with Zinc
and Sulfate, SAD
Phasing [Protein Data Bank (PDB) entry 4NAY]
The crystal structure of the
FosB·Zn2+·sulfate
complex was refined to 1.42 Å resolution (Figure 3). An X-ray fluorescence scan of the crystal prior to collection
of the diffraction data indicated the presence of Zn2+ (Figure
S2 of the Supporting Information). Subsequently,
the diffraction data were collected at a wavelength of 1.28 Å,
the Kα absorption edge of Zn2+, and the
initial phases were determined using Zn2+ SAD phasing.
This crystal indexed into the C2 space group. Unit
cell content analysis of the data indicated one subunit of FosB and one metal ion per asymmetric unit.
The anomalous density map, contoured at 5σ, is displayed in
Figure 3 and outlines the location of the Zn2+metal ions used in the model. The final model consists of
amino acids 1–91 and 102–138 with a sulfate ion coordinated
to the metal.
Figure 3
Overall crystal structure of FosB from S. aureus with Zn2+ and sulfate in the active site. The structure
was determined by SAD phasing from the Zn2+ Kα edge. The red and blue color scheme indicates each subunit of the
homodimer of the enzyme after the symmetry operation has been applied
to the coordinate file. The anomalous density map (magenta) around
the Zn2+ metal ions (purple) is contoured at 5σ and
clearly marks the location of the metal within the structure. Final
refinement yielded an Rwork of 12.95%
and an Rfree of 16.64%.
Overall crystal structure of FosB from S. aureus with Zn2+ and sulfate in the active site. The structure
was determined by SAD phasing from the Zn2+ Kα edge. The red and blue color scheme indicates each subunit of the
homodimer of the enzyme after the symmetry operation has been applied
to the coordinate file. The anomalous density map (magenta) around
the Zn2+metal ions (purple) is contoured at 5σ and
clearly marks the location of the metal within the structure. Final
refinement yielded an Rwork of 12.95%
and an Rfree of 16.64%.
FosB with Zinc
and Sulfate, Molecular
Replacement (PDB entry 4NAZ)
After the initial crystal structure of the
FosB·Zn2+·sulfate
had been determined by SAD phasing, another data set was collected
on a second crystal at a wavelength of 1.078 Å to achieve higher
resolution. The second data set, determined by molecular replacement
using PDB entry 4NAY, resulted in a 1.15 Å resolution structure of FosB with Zn2+ and sulfate in the active
site (Figure S3 of the Supporting Information). Zn2+ was used to model the metal ion density in the
active site given that the enzyme was expressed, purified, and crystallized
under the same conditions as PDB entry 4NAY. This crystal also indexed into the C2 space group with one subunit of FosB per asymmetric unit. The final model consists of amino acids
1–91 and 102–139 with a sulfate ion coordinated to the
metal.
FosB with a Bacillithiol–Cys9
Disulfide Bond (PDB entry 4NB0)
Cocrystallization of FosB with BSH resulted in a crystal structure of the enzyme with
a BS-Cys9disulfide bond (Figures S4 and S5 of the Supporting Information). X-ray fluorescence scans of the crystal
prior to collection of the diffraction data did not indicate the presence
of any metals (Figures S6 and S7 of the Supporting
Information). This crystal indexed into the P1 space group, rather than C2, and had both subunits
of the homodimer in the asymmetric unit. The structure was determined
by molecular replacement using a homodimer model of the enzyme created
from PDB entry 4NAZ. The final resolution of this structure is 1.62 Å, and the
final model consists of amino acids 1–53, 62–91, 102–128,
and 133–138 for subunit A and 1–53, 63–129, and
135–138 for subunit B.
FosB with an l-Cysteine–Cys9
Disulfide Bond (PDB entry 4NB1)
Cocrystallization of FosB with l-Cys resulted in a crystal structure with an l-Cys–Cys9disulfide bond similar to that with BSH (Figures
S8 and S9 of the Supporting Information). This crystal also indexed into the P1 space group,
was determined by molecular replacement, and had a final resolution
of 1.62 Å. The final model consists of amino acids 1–52,
61–92, 102–127, and 131–139 for subunit A and 1–53, 64–128, and
134–138 for subunit B.
FosB Apo Structure (PDB entry 4NB2)
Cocrystallization
of FosB with l-Cys and TCEP
reduced the exogenous disulfide bond and yielded an apo structure
of the enzyme (Figure S10 of the Supporting Information). The resultant structure indexed into the P1 space
group and had a final resolution of 1.62 Å. The final model consists
of amino acids 1–56, 62–91, 102–126, and 132–138
for subunit A and 1–53, 63–128, and 135–138 for
subunit B.
Overall Structure of FosB
Similar to the FosB enzymes from Bacillus
cereus(31) and Bacillus
anthracis, FosB and FosB, respectively, FosB belongs
to the vicinal oxygen chelate (VOC) superfamily of enzymes. Although
amino acids 92–101 are not observed in PDB entry 4NAY or 4NAZ and are observed
in only one subunit of PDB entries 4NB0, 4NB1, and 4NB2, the three-dimensional domain-swapped
arrangement of sequential βαβββ motifs
that define the VOC superfamily is still evident in the overall structure
(Figure 3 and Figures S3, S4, S8, and S10 of
the Supporting Information).[32] The protein residues that constitute the metal
binding site in FosB are His7, His66,
and Glu115, the same as those in FosB.[31] In the FosB·Zn2+·sulfate structures (PDB entries 4NAY and 4NAZ), the Zn2+ adopts a tetrahedral coordination geometry with a sulfateoxygen
occupying the fourth coordination site of the metal. However, the
sulfate molecule, in either structure, is oriented in a position opposite
to that observed in FosB,[31] with the second of the sulfateoxygenshydrogen
bonded to the non-metal-coordinated Oε atom of Glu115
(Figure 4, left). In FosB (PDB entry 4JH2), the sulfate is oriented in a position that superimposes the phosphonate
moiety of fosfomycin, and the non-metal-coordinated Oε atom of Glu115 is hydrogen bonded to a highly conserved water molecule
(Figure 4, right).
Figure 4
Sulfate molecule of FosB (left) oriented
in a position opposite that observed in FosB (right).[31] In FosB, the second of the sulfate oxygens is hydrogen
bonded to the non-metal-coordinated Oε atom of Glu115.
In FosB, the non-metal-coordinated Oε atom of Glu115 is hydrogen bonded to a highly conserved
water molecule. Cys9 in the FosB structure
is observed in two conformations, pointed toward or away from the
metal. The occupancy of the two conformations is correlated to the
occupancy of Zn2+ and the coordinated sulfate molecule
such that the occupancy of Cys9 pointed away from the metal is approximately
the same as that for the metal and the coordinated sulfate molecule.
Sulfate molecule of FosB (left) oriented
in a position opposite that observed in FosB (right).[31] In FosB, the second of the sulfateoxygens is hydrogen
bonded to the non-metal-coordinated Oε atom of Glu115.
In FosB, the non-metal-coordinated Oε atom of Glu115 is hydrogen bonded to a highly conserved
water molecule. Cys9 in the FosB structure
is observed in two conformations, pointed toward or away from the
metal. The occupancy of the two conformations is correlated to the
occupancy of Zn2+ and the coordinated sulfate molecule
such that the occupancy of Cys9 pointed away from the metal is approximately
the same as that for the metal and the coordinated sulfate molecule.
Alternate Conformation
of the Fosfomycin–Phosphonate
Binding Loop
In PDB entries 4NB0 (FosB with
a BS–Cys9disulfide bond), 4NB1 (FosB with
an l-Cys–Cys9disulfide bond), and 4NB2 (FosB apo structure), amino acids ∼90–101
are observed in a conformation different from that found in either
FosB or FosB (Figure 5, left). The two different
conformations can be described as open, for FosB, and closed, for both FosB and
FosB (PDB entry 4IR0, not shown), the
difference being the absence and presence of fosfomycin, respectively.
In the structures of FosB with the open
loop conformation, the loop region is wrapped around a sulfate molecule
(Figure 5 and Figures S4, S8, and S10 of the Supporting Information). Of the approximately
11 residues that compose the loop region, eight are conserved throughout
all the FosB enzymes (Figure 6). The three
nonconserved residues are solvent-exposed in the closed conformation
of the loop in the FosB (PDB entry 4JH6) or FosB (PDB entry 4IR0) structure. The conserved residues of
the loop region constitute important structural features of the enzyme.
In the closed conformation, they form one side of the fosfomycin binding
cage with several hydrogen bonding interactions to the antibiotic
and also form one side of the BSH binding pocket. Most importantly,
the open residues of FosB can be morphed
into the positions of fosfomycin-bound FosB to completely form the important substrate binding structural
features (Figure 5, right).
Figure 5
Superposition of FosB (cyan) and
FosB (red) (left). In the FosB structure (PDB entry 4JH6), Mn2+ and fosfomycin are
bound in the active site and the conserved phosphonate binding loop
is observed in the closed conformation. In the FosB structure (PDB entry 4NB2), there is no metal or antibiotic bound in the active
site. Therefore, the phosphonate binding loop is observed in the open
conformation. Superpostion of FosB and
FosB with the phosphonate binding loop
morphed into the closed conformation (right). The conserved fosfomycin
cage residues align after the FosB structure
has been morphed into the FosB structure.
Figure 6
Sequence alignment of the phosphonate binding
loop residues. Eight
of the 11 residues are conserved throughout the FosB enzymes. The
nonconserved residues are all solvent-exposed.
Superposition of FosB (cyan) and
FosB (red) (left). In the FosB structure (PDB entry 4JH6), Mn2+ and fosfomycin are
bound in the active site and the conserved phosphonate binding loop
is observed in the closed conformation. In the FosB structure (PDB entry 4NB2), there is no metal or antibiotic bound in the active
site. Therefore, the phosphonate binding loop is observed in the open
conformation. Superpostion of FosB and
FosB with the phosphonate binding loop
morphed into the closed conformation (right). The conserved fosfomycin
cage residues align after the FosB structure
has been morphed into the FosB structure.Sequence alignment of the phosphonate binding
loop residues. Eight
of the 11 residues are conserved throughout the FosB enzymes. The
nonconserved residues are all solvent-exposed.
Kinetic Analysis
A detailed mechanistic investigation
of divalent metal activation of FosB has been reported.[33] The results indicated
that FosB is activated by Zn2+ and has the following metal ion activation order: Zn2+ > Ni2+ > Mn2+ > Mg2+ ∼
Fe2+ ∼ Co2+ ∼ Cu2+ ∼
Ca2+. However, this result is contradictory to the metal
activation of all other fosfomycin resistance enzymes from the VOC
superfamily, including FosA, FosX, FosB, and FosB, in which Zn2+ effectively inhibits any transferase activity.[7,8,12,18,19,31] Therefore, when we
obtained the crystal structure of FosB with Zn2+ in the active site, we were compelled to confirm
the reported results.[33]Our time
course kinetic analyses, shown in Figure 7,
indicate that FosB is inhibited for l-Cys transferase activity and only marginally active for BSH
transferase activity at physiological concentrations of Zn2+ (∼100 μM)[34] with an apparent kcatBSH of 0.17 s–1. In addition, we found that 10 μM Mn2+ activates
FosB for BSH transferase activity with
an apparent kcatBSH of 5.98
s–1. These results are consistent with other reports
for VOC class fosfomycin resistance enzymes.[7,8,12,18,19,31] By comparison, the
apparent kcat for l-Cys transferase
activity of FosB activated by physiological
concentrations of Mn2+ (∼10 μM)[34] is 0.05 s–1, indicating that
FosB has a preference for BSH in agreement
with published results.[19,33] Finally, we found that
100 μM Zn2+ inhibits the reaction when the mixture
is supplemented with 10 μM Mn2+ for either l-Cys or BSH transferase activity. The apparent kcatBSH is 0.08 s–1, whereas
the apparent kcat could not be determined, similar to inhibition by Zn2+ alone.
Figure 7
Time course of FosB-catalyzed addition
of BSH or l-Cys to fosfomycin in the presence of Mn2+ or Zn2+. Reactions were conducted at 25 °C in 20
mM HEPES (pH 7.0) with 4 mM fosfomycin and 0.50 μM enzyme in
the presence of (red diamonds) 1.6 mM BSH and 10 μM Mn2+, (red circles) 1.6 mM BSH and 10 μM Zn2+, (blue
circles) 1.6 mM BSH, 10 μM Mn2+, and 100 μM
Zn2+, (black squares) 1.8 mM l-Cys and 10 μM
Mn2+, (blue squares) 1.8 mM l-Cys and 10 μM
Zn2+, or (green triangles) 1.8 mM l-Cys, 10 μM
Mn2+, and 100 μM Zn2+.
Time course of FosB-catalyzed addition
of BSH or l-Cys to fosfomycin in the presence of Mn2+ or Zn2+. Reactions were conducted at 25 °C in 20
mM HEPES (pH 7.0) with 4 mM fosfomycin and 0.50 μM enzyme in
the presence of (red diamonds) 1.6 mM BSH and 10 μM Mn2+, (red circles) 1.6 mM BSH and 10 μM Zn2+, (blue
circles) 1.6 mM BSH, 10 μM Mn2+, and 100 μM
Zn2+, (black squares) 1.8 mM l-Cys and 10 μM
Mn2+, (blue squares) 1.8 mM l-Cys and 10 μM
Zn2+, or (green triangles) 1.8 mM l-Cys, 10 μM
Mn2+, and 100 μM Zn2+.
Disk Diffusion Assays
Our kinetic
analysis, in addition
to the previous kinetic analyses,[19,31] has demonstrated
that FosB enzymes have a preference for BSH over l-Cys for
nucleophilic addition to fosfomycin in vitro. Furthermore,
the pathway for detoxification of xenobiotics (including fosfomycin)
involving BSH has been characterized for S. aureus in vivo.[21] While BSH null S. aureus exhibited an increase in sensitivity to fosfomycin for both the
Newman[17] and USA300 JE2 strains, the question
of whether FosB null S. aureus exhibits a similar
increase in sensitivity to the antibiotic remained. To answer this, bshA, which encodes the glycosyltransferase involved in
BSH biosynthesis, and fosB knockout strains of both
Newman and USA300 JE2 S. aureus were obtained from
the Network on Antimicrobial Resistance in S. aureus (NARSA), and Kirby-Bauer disk diffusion assays were conducted on
the prepared cultures to test their sensitivity to fosfomycin. As
anticipated, both the BSH and FosB null strains of USA300 JE2 and
Newman show a substantial increase in their sensitivity to the antibiotic
as evidenced by the increased zone of clearing (Figure 8 and Figure S11 of the Supporting Information, summarized in Table 2). Furthermore, the
zone of clearing of the BshA null mutant is comparable to that of
the FosB null mutant, indicating that both BSH and the FosB enzyme
are required for optimal survival of S. aureus when
it is treated with fosfomycin.
Figure 8
Fosfomycin disk diffusion
assays for USA300 JE2 (MRSA). The amount
of fosfomycin on each disk is shown in red: (left) wild-type MRSA,
(center) BshA knockout MRSA, and (right) FosB knockout MRSA.
Table 2
Disk Diffusion Zones
of Clearing (millimeters)
for MRSA
strain
10 μg
25 μg
50 μg
100 μg
WT USA300 JE2
17
18
21
24
BshA
KO
34
33
40
40
Fosb
KO
35
33
37
40
WT
Newman
22
24
28
30
BshA
KO
35
37
40
40
Fosb
KO
34
34
39
37
Fosfomycin disk diffusion
assays for USA300 JE2 (MRSA). The amount
of fosfomycin on each disk is shown in red: (left) wild-type MRSA,
(center) BshA knockout MRSA, and (right) FosB knockout MRSA.
Discussion
Structural
Interpretation of FosB
The
139-amino acid FosB enzyme reported here is conserved
throughout the S. aureus genome sequences available
in UniProt, including the USA300 JE2 (MRSA) and Newman (NCTC 8325)
strains. Thus, the reported three-dimensional structures are representative
of the same resistance enzyme from both strains of the pathogen.FosB crystallized with Zn2+ in the active site of the enzyme, as did FosB from B. cereus (FosB).[31] The Zn2+ in the active site is most likely a result of
the nutrient rich Terrific Broth used during protein expression. Having
Zn2+ in the active site is fortuitous because, of the first-row
transition metals found in most biological macromolecules, Zn2+ has the greatest electron density and is therefore one of
the best anomalous scatterers. Thus, Zn2+ gives a very
strong X-ray fluorescence signal (Figure S2 of the Supporting Information) and is an excellent metal for SAD
phasing of the data. The anomalous scattering density map shown in
Figure 3 establishes the location of the metal
ion in the active site of the enzyme. However, at a given wavelength,
several metals will give an anomalous signal, and the correct metal
need not be assigned to determine the structure by SAD methods. Thus,
we have used Zn2+ to model the anomalous electron density,
but we recognize that the metal may not be homogeneously distributed
throughout the entire crystal.Although both FosB and FosB were crystallized
with fosfomycin coordinated to
the metal, we have been unable to obtain a fosfomycin-coordinated
structure of FosB even though the antibiotic
was present in the crystallization solution at a concentration of
5 mM. This is due to the crystallization conditions requiring high
concentrations of ammonium sulfate (200 mM) that compete with fosfomycin
for binding in the active site of the enzyme. Sulfate molecules have
been observed in the active sites of other VOC class fosfomycin resistance
enzymes,[12,15,31] as the sulfate
ion is isoelectronic with the phosphonate moiety of the antibiotic.Neither the metal nor the sulfate in PDB entries 4NAY and 4NAZ has an occupancy
of 100% in the structures. Rather, Cys9 in the FosB structure is observed in two conformations (Figure 4, left). They can be described as pointing toward
or away from the metal ion binding site of the enzyme. The occupancy
of the two conformations (∼50/50) is correlated to the occupancy
of Zn2+ and the coordinated sulfate molecule such that
the occupancy of Cys9 pointed away from the metal is approximately
the same as that for the metal and the coordinated sulfate molecule.
The conformation pointed away from the metal binding site is the same
as that observed for FosB from B. cereus(31) and FosB from B. anthracis (PDB
entry 4IR0).
The functional significance of these two conformations is currently
not known and may simply be a steric consequence resulting from the
metal vacancy.The most important feature of the structures
reported here is the
loop region composed of amino acids 90–100. In the structures
of FosB and FosB, the loop region is observed in a conformation that encloses
the hydrophilic phosphonate end of the polar antibiotic and represents
one side of the “fosfomycin cage” structure of the enzyme.[31] The fosfomycin cage is composed of residues
Tyr39, Trp46, Ala48, Tyr64, Arg94, Asp100, Tyr105, and Arg124, all
of which are conserved (FosB of Figure 5, or see Figure 9 of ref (31) for greater detail), and is the structural feature
that locks the antibiotic in the active site properly positioning
C1 for nucleophilic attack by l-Cys or BSH. In FosB, the residues are highly dynamic as evidenced by
the complete lack of electron density for the region in either PDB
entry 4NAY or 4NAZ, suggesting a high
degree of flexibility. In PDB entries 4NB0, 4NB1, and 4NB2, electron density for the residues is
observed, but the loop is in a conformation that can be described
as “open” relative to FosB or FosB (Figure 5 and Figures S4, S8, S10, and S12 of the Supporting
Information).In both the FosB and FosB structures, the phosphonate
moiety of fosfomycin
is directly coordinated by Arg94 of the loop and/or cage, which also
forms a salt bridge with Asp100 giving rigidity to the cage (see Figure
9 of ref (31)). Arg96
is hydrogen bonded to Tyr105 and to a highly conserved water molecule
that is hydrogen bonded to the non-metal-coordinated Oε atom of Glu115. The water molecule coordinated to the Oε atom of Glu115 is also hydrogen bonded to one phosphonateoxygen
and Arg124 of the cage. It has been observed in every deposited structure
of FosB to date (Figure 4, Right). However,
its position is approximately 5 Å from C1 of the antibiotic in
FosB, and given that nucleophilic addition
of the thiol proceeds via direct SN2 substitution to C1,
the functional relevance of the conserved water in the active site
of FosB has remained unclear. In PDB entries 4NAY and 4NAZ, both the water
and fosfomycin are absent, and the sulfate is positioned “backward”
relative to FosB (PDB entry 4JH2), with one oxygen
coordinated to the metal and another coordinated to the second Oε atom of Glu155, where the conserved water molecule
is expected (Figure 4, left). As a result,
the residues of the loop region have nothing to coordinate and are
highly dynamic, leading to inhomogeneity in the crystal and no observed
electron density.In PDB entries 4NB0, 4NB1, and 4NB2, where the open
conformation of the loop is observed, the residues of the loop are
wrapped around a sulfate molecule forming five hydrogen bond interactions
and demonstrating the propensity of the loop to coordinate sulfate
or perhaps the isoelectronic phosphonate end of fosfomycin (Figure 5 and Figures S4, S8, S10, and S12 of the Supporting Information). The open conformation
of the phosphonate binding loop in the structures of FosB presented here points to an important functional
aspect of the enzyme. In both the FosB and FosB structures, only a narrow
access channel leading to C1 of the antibiotic is observed. In FosB, the cross-sectional area of the access
channel at its most narrow point is approximately 15 Å2 (Figure S13 of the Supporting Information), whereas the cross-sectional area of the phosphonate end of fosfomycin
is 19 Å2 (Figure S14 of the Supporting
Information). Moreover, the narrow channel is optimized to
accommodate the l-cysteinyl domain of BSH and contains conserved
residues involved in the catalytic mechanism of the FosB enzymes.
This raises the question of how fosfomycin enters the interior active
site of FosB.We think the answer lies in opening and closing
of the loop region.
The loop must be open to allow fosfomycin to enter the interior cavity
of FosB. The hydrophobic methyl end of the antibiotic would thermodynamically
favor the hydrophobic side of the fosfomycin cage of the enzyme. Once
bound, the loop closes around the antibiotic holding it in place directly
at the end of the access channel poised for nucleophilic attack by
the thiol. Loop closure could incorporate the unexplained water molecule,
and a combination of hydrogen bonds to the water and to the antibiotic
would hold the loop in its closed position forming the final side
of the BSH binding pocket (see Figure 7 of ref (31)). This ordered substrate
binding mechanism involving the loop is consistent with substrate
binding studies of FosB that have indicated
the antibiotic must bind first followed by nucleophilic attack of
the thiol cosubstrate.[33]When FosB was cocrystallized with
either BSH or l-Cys, a disulfide bond formed between the
exogenous thiol and Cys9 of the enzyme (Figures S5 and S9 of the Supporting Information). When the disulfide bond
is present in the structure, the metal is removed from the active
site of the enzyme. The conformation of Cys9 in the disulfide bond
is that pointed away from the metal binding site, as in FosB and FosB. The crystals
containing the unnatural disulfide bonds belong to a space group (P1) different from that of those that contain Zn2+ and sulfate (C2). In PDB entry 4NB1, the density for
exogenous l-Cys is very clear. However, in PDB entry 4NB0, the density for
BSH is not complete (Figure S5 of the Supporting
Information). This has been observed before in a structure
of FosB (PDB entry 4JH9) in which the highly
flexible glucosamine–malate moiety of the BSH molecule is not
homogeneous in the crystal. The same situation has most likely occurred
in the current structure. Nevertheless, given that the crystallization
conditions are the same for PDB entry 4NAZ (C2) and PDB entry 4NB0 (P1) except for addition of BSH, this suggests that a significant change
occurred in the enzyme prior to crystallization, indicating that the
dilsulfide bond likely formed in solution before the crystals grew,
i.e., opening of the phosphonate binding loop. The disulfide bond
between l-Cys or BSH and Cys9 is unique to FosB and was never observed in FosB even though the crystallization conditions for FosB included the same concentration of either thiol.[31]Cocrystallization of FosB with tris(2-carboxyethyl)phosphine
(TCEP) and l-Cys prevented formation of the disulfide bond
in the crystal. This resulted in an apo structure of the enzyme with
no metals or exogenous ligands in the active site [PDB entry 4NB2 (Figure S5 of the Supporting Information)]. This crystal indexed
also into the P1 space group even though the disulfide
bond was not present. The significance of this structure is that it
maintains the open loop conformation even in the absence of any exogenous
ligands in the active site of FosB.
Thus, the P1 space group appears to be the result
of the open conformation of the phosphonate binding loop.
Kinetic Analysis
of FosB
Initial kinetic analyses
of FosB indicated
that the enzyme is activated by Zn2+ and has the following
divalent metal ion activation order: Zn2+ > Ni2+ > Mn2+ > Mg2+ ∼ Fe2+ ∼
Co2+ ∼ Cu2+ ∼ Ca2+.[33] However, other fosfomycin resistance enzymes
of the VOC superfamily, including FosA, FosX, FosB, and FosB, are effectively inhibited
by Zn2+.[7,8,12,18,19,31] Thus, finding Zn2+ in the active site
of the FosB structure prompted us to
reassess the divalent metal activation and/or inactivation of the
enzyme. Our kinetic analysis in Figure 7 was
never intended to be a full kinetic report for FosB as we meant to test and confirm the activation of FosB by Zn2+. Nonetheless, as might
have been expected given the activation of other VOC class fosfomycin
resistance enzymes, we found that FosB is inhibited by Zn2+ for l-Cys transferase activity
and only marginally active for BSH transferase activity at physiological
concentrations (∼100 μM).[34] The apparent kcatBSH is only
0.17 s–1. By comparison, the apparent kcatBSH of FosB when it is activated by physiological concentrations of Mn2+ (∼10 μM) is 5.98 s–1, a >35-fold
increase. More interestingly, our kinetic assays involving physiological
concentrations of both Zn2+ and Mn2+ demonstrate
that FosB is inhibited for either l-Cys or BSH transferase activity, similar to inhibition by
Zn2+ alone.Our kinetic results are in contrast to
the published results for FosB specifically[33] but consistent with all other reports for this
class of enzymes in which they are activated by Mn2+ and
inhibited by Zn2+.[7,8,12,18,19,31] Given that active site residues for each
class are conserved, especially among the FosB enzymes, we believe
that inhibition of FosB by physiological
concentrations of Zn2+ is correct. It is noteworthy to
point out that the published report used concentrations of Zn2+ as high as 10 mM in their activation studies, which is physiologically
irrelevant. Moreover, an explanation for why this class of enzymes
is inhibited by Zn2+ and activated by Mn2+ has
been presented.[31]Roberts et al.
demonstrated that increasing concentrations of BSH
(0.5–5 mM) appeared to inhibit activation of FosB by Zn2+, at least until the concentration
of Zn2+ had eclipsed that of BSH.[33] They concluded that the enzyme and BSH were competing for complexation
with Zn2+ and that BSH is therefore a sufficiently strong
Zn2+ chelator to demetalate the enzyme. While BSH is likely
an effective M2+ chelator by the nature of its functional
substituents, our crystals of FosB with
disulfide bonds in the active site suggest an alternative explanation.
The crystallization conditions presented here [100 mM Bis-Tris (pH
6.5), 5 mM fosfomycin, and 5 mM BSH or 100 mM HEPES (pH 7.5), 10 mM
fosfomycin, and 10 mM l-Cys] are similar to the kinetic assay
conditions used by Roberts et al. [50 mM HEPES (pH 7.0), 25 mM fosfomycin,
and 0.5–5 mM BSH]. Furthermore, the change in crystallographic
space group, from C2 to P1, indicates
that the disulfide bond formed in solution prior to crystal formation.
Thus, inhibition of FosB by millimolar
concentrations of exogenous thiol may be due to formation of the thiol–Cys9dilsulfide bond and steric removal of the metal rather than demetaltion
of the enzyme by the substrate. As a final point, if the BSH were
in a strong complex with Zn2+, the thiol would be one of
the coordinating ligands, and it would not be able to serve as a nucleophilic
substrate for FosB. This line of thinking
is what prompted our kinetic experiment with both Zn2+ and
Mn2+. Even if all the Zn2+ (100 μM) is
in complex with BSH, there is still excess free BSH (1.8 mM) in solution
to serve as the nucleophilic substrate for FosB activated by Mn2+ (10 μM). Because the reaction
does not proceed, we can conclude that either (1) Zn2+ and
Mn2+ are in complex with BSH and there is no free metal
to activate the enzyme or (2) Zn2+ is competing with Mn2+ in the active site of FosB and inhibiting the enzyme. Only the latter conclusion is plausible
given that the reaction proceeds as it should in the presense of Mn2+ and BSH only.The interplay between Mn2+ and Zn2+ for the
activation and/or inactivation of FosB is interesting given the importance of acquisition of these two
metals for survival of the organism and the concurrent resistance
to fosfomycin. The concentrations of Mn2+ and Zn2+ are very tightly regulated within pathogens like S. aureus. Mn2+-dependent superoxide dismutase is encoded by many
pathogens to defend against superoxide,[35,36] while an estimated
4–8% of all proteins encoded in the genome of bacteria are
Zn2+-binding proteins.[37] Host
limitation of nutrient divalent metals is an essential component of
the inate immune response to infection by S. aureus and other pathogens. In the process of nutritional immunity, neutrophils
respond to the infection and deplete the pathogen of vital metals
required for proliferation. Specifically, calprotectin binds both
Mn2+ and Zn2+ in an effort to starve the pathogen
of the nutrient metals. It is estimated that 40–50% of the
protein composition of neutrophil cytoplasm is calprotectin.[38−40] To combat the nutritional immunity of the host, S. aureus has evolved high-affinty Mn2+ and Zn2+ transporters
to sequester the required metals necessary for proliferation.[41,42]
Function of FosBin Vivo
Regardless of the metal activation and/or inactivation
of FosB, we were interested in the requirement
of the enzyme for survival of the pathogen in general. BSH null strains
of B. subtilis and S. aureus have
been examined for their sensitivity to fosfomycin.[17,22] The results consistently demonstrate that BSH is necessary for detoxification
of xenobiotics from Gram-positive organisms and that BSH is required
for resistance of the organisms to fosfomycin. The disk diffusion
assays presented here show that FosB knockout S. aureus USA300 JE2 (Figure 8) and Newman (Figure
S11 of the Supporting Information) strains
demonstrate an increase in susceptibility to fosfomycin similar to
that of the BSH null cells. While BshA knockout strains have been
examined in the aforementioned BSH null studies, we included them
in our experiment for direct comparison to the FosB knockouts. BshA,
along with BshB and BshC, is involved in BSH biosynthesis. The zone
of clearing for BshA knockout USA300 JE2 cells treated with 100 μg
of fosfomycin in our experiment is 40 mm. This result is consistent
with the published values of 39, 40, and 39 mm for BshA, BshB, and
BshC knockouts, respectively, of USA300 JE2 treated with 350 μg
of fosfomycin.[22] While the published data
use an amount of fosfomycin more than 3-fold greater than ours, we
point out that our results reach a maximal zone of clearing between
25 and 50 μg, and the zone of clearing at 50 μg is the
same as that for 100 or 350 μg. Thus, there appears to be a
maximal effectiveness of fosfomycin reached for disk diffusion assays
somewhere between 25 and 50 μg of the antibiotic. Nevertheless,
the zones of clearing for the FosB knockout strains are the same as
those for the BshA knockouts, indicating that both the FosB enzyme
and BSH are equally important for the resistance of MRSA to the antibiotic
fosfomycin and therefore validate FosB as a potential therapeutic
drug target.The fact that both BshA and FosB knockout strains
of S. aureus Newman and USA300 JE2 have equally increased
susceptibility to fosfomycin suggests that the thiol-dependent FosB
detoxification pathway for fosfomycin is the primary resistance mechanism
of the organism to the antibiotic. The MIC values for BSH null USA300
JE2 are reported to be 10–20 μg/mL.[33] Because the FosB null strains demonstrate a similar increase
in sensitivity to fosfomycin, we can predict that the MIC value for
fosfmycin in the FosB knockout USA300 JE2 is likely to be approximately
the same (10–20 μg/mL). The reported maximal serum drug
concentration (Cmax) of fosfomycin following
the standard 3 g oral dose is 22–32 mg/L within 2–2.5
h of treatment.[43] Thus, we might expect
fosfomycin to be an effective treatment against multi-drug-resistant S. aureus if the FosB enzyme could be targeted therapeutically
at least in a synergistic approach using multiple available antibiotics
in addition to a FosB inhibitor.
Conclusion
We
have obtained the first three-dimensional structures of FosB
from S. aureus, the enzyme responsible for resistance
of the pathogen to the antibiotic fosfomycin. FosB catalyzes nucleophilic addition of BSH to the antibiotic and
represents the sole fosfomycin inactivating pathway of the organism
from the USA300 JE2 or Newman strains. The new structures provide
insight into the functional role of the fosfomycin–phosphonate
binding loop of the enzyme. The loop probably functions as a door
that opens and closes to allow the antibiotic to enter the active
site of the enzyme. Once closed, the loop completes important structural
features that bind and secure both cosubstrates. Contrary to previous
results,[33] we have demonstrated that FosB is inhibited by Zn2+, as are
all other reported VOC superfamily fosfomycin resistance enzymes.
Given the similarity of the susceptibility of the BSH and FosB null
strains of MRSA, we can predict the MIC values of FosB null MRSA to
be 10–20 μg/mL, below the reported serum concentration
of fosfomycin following the standard 3 g dose. Therefore, if FosB could be targeted therpeutically, fosfomycin
could very well serve as a synergystic treatment for pathogens like
multi-drug-resistant strains of S. aureus.
Authors: Matthew J Kuehnert; Deanna Kruszon-Moran; Holly A Hill; Geraldine McQuillan; Sigrid K McAllister; Gregory Fosheim; Linda K McDougal; Jasmine Chaitram; Bette Jensen; Scott K Fridkin; George Killgore; Fred C Tenover Journal: J Infect Dis Date: 2005-12-15 Impact factor: 5.226
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