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article

published online: 27 January 2013 | doi: 10.1038/nchembio.1168

A new structural paradigm in copper resistance in


Streptococcus pneumoniae
Yue Fu1,2, Ho-Ching Tiffany Tsui3, Kevin E Bruce3, Lok-To Sham3, Khadine A Higgins1, John P Lisher1,2,
Krystyna M Kazmierczak3, Michael J Maroney4, Charles E Dann III1,2, Malcolm E Winkler2,3 &
David P Giedroc1,2*

Copper resistance has emerged as an important virulence determinant of microbial pathogens. In Streptococcus pneumoniae,
copper resistance is mediated by the copper-responsive repressor CopY, CupA and the copper-effluxing P1B-type ATPase CopA.
We show here that CupA is a previously uncharacterized cell membrane–anchored Cu(I) chaperone and that a Cu(I) binding–
competent, membrane-localized CupA is obligatory for copper resistance. The crystal structures of the soluble domain of
CupA and the N-terminal metal-binding domain (MBD) of CopA (CopAMBD) reveal isostructural cupredoxin-like folds that each
harbor a binuclear Cu(I) cluster unprecedented in bacterial copper trafficking. NMR studies reveal unidirectional Cu(I) trans-
fer from the low-affinity site on the soluble domain of CupA to the high-affinity site of CopAMBD. However, copper binding by
© 2013 Nature America, Inc. All rights reserved.

CopAMBD is not essential for cellular copper resistance, consistent with a primary role of CupA in cytoplasmic Cu(I) sequestration
and/or direct delivery to the transmembrane site of CopA for cellular efflux.

C
opper is an essential transition metal in living organisms that contains considerable cell-associated copper20, and adaptation to
functions as a catalytic cofactor in electron transfer reactions, a high-Cu(I) environment may be important for invasive disease.
aerobic respiration, photosynthesis and oxidative stress resis- Total Cu(I) is replete in the nasopharynx and in lung tissues, and
tance and in a number of metabolic enzymes by virtue of its ability copA expression is induced in these tissues in intranasally infected
to undergo reversible oxidation from Cu(I) to Cu(II)1. This crucial mice18. Deletion of copA leads to poor kinetics of colonization in the
characteristic of copper chemistry also makes copper highly toxic as nasopharynx and delayed appearance and reduced bacterial loads
Cu(I), like ferrous iron, catalyzes the production of hydroxyl radical in the lung18; consistent with this, signature-tagged muta­genesis
(OH•) from endogenous hydrogen peroxide (H2O2) in the presence reveals that ΔcupA and ΔcopA strains are attenuated in a mouse
of cellular reductants, which is highly damaging to cellular lipids, model of lung infection and pneumonia21.
proteins and nucleic acids2. As such, the copper supply in mammals Bacterial copper chaperones are thought to function in copper
is tightly regulated. resistance by sequestering Cu(I) and buffering the metal to a very
Copper is also essential for proper development and functioning low concentration8,22. This function is enabled by a high affinity for
of the immune system3. An established feature of innate immunity Cu(I)23 and/or, as articulated in the copper trafficking hypothesis, the
to bacterial infection is host control of transition metal availabil- ability to donate copper to apo forms of copper-requiring proteins
ity. This has long been recognized for iron4, and only recently has or to membrane transporters that efflux the metal across the cell
control of manganese and zinc availability been linked to the host- membrane24. Copper transfer is facilitated by transient and specific
npg

pathogen interface5. In contrast, emerging evidence suggests that protein-protein interactions between often-isostructural donor and
copper may be used to kill microbial pathogens6 by inducing oxida- target proteins via a metal-ligand exchange reaction without disso-
tive stress or, in the absence of oxygen, by mediating dis­assembly of ciation of the metal into bulk solvent25–27. S. pneumoniae lacks the
enzyme-bound Fe-S clusters7. Cu(I) is also a highly competitive metal major characterized class of Cu(I) chaperone that is ubiquitous in
ion and will outcompete most other divalent metal ions at binding eukaryotes and some bacterial systems, exemplified by S. cerevisiae
sites in proteins8. In Mycobacterium tuberculosis and Staphylococcus or Synechocystis Atx1 (ref. 27) and Bacillus subtilis CopZ28.
aureus, copper stress induces a global stress response that mitigates In this report, we show that a structurally unprecedented copper
the effects of thiol oxidation, disrupting the redox status of the chaperone–copper effluxer pair jointly mediates resistance to cop-
cell9,10. Escherichia coli and Salmonella strains lacking the ability to per toxicity in the S. pneumoniae D39 strain. We show that CupA is a
efflux copper are more susceptible to copper toxicity11,12. Bacterial plasma membrane–anchored copper-binding protein whose mem-
pathogens have evolved multiple strategies to quickly mitigate the brane localization and high Cu(I) binding affinity are required for cel-
effects of copper toxicity with the same mechanisms likely used to lular copper resistance. The crystallographic structures of the soluble
maintain the cytoplasmic availability of weakly complexed or ‘free’ domain of CupA (sCupA) and CopAMBD reveal a new functional twist
copper to near-undetectable concentrations6,13–16. on the common cupredoxin fold long associated with iron import,
Copper resistance in the Gram-positive respiratory pathogen cytochrome oxidase assembly and electron transfer29–31. Although
S. pneumoniae is mediated by an operon encoding CopY, a Cu(I)- we establish that the sCupA is capable of transferring bound Cu(I)
dependent repressor17; CupA, of unknown function; and a Cu(I)- to the CopAMBD in a thermodynamically favorable and kinetically
effluxing P1B-type ATPase, CopA18. Although the intracellular facile reaction, it is not required for cellular copper resistance under
requirement for Cu(I) in S. pneumoniae is unknown19, S. pneumoniae conditions of copper stress. These findings suggest that the primary

Department of Chemistry, Indiana University, Bloomington, Indiana, USA. 2Interdisciplinary Graduate Program in Biochemistry, Indiana University,
1

Bloomington, Indiana, USA. 3Department of Biology, Indiana University, Bloomington, Indiana, USA. 4Department of Chemistry, University of
Massachusetts, Amherst, Massachusetts, USA. *e-mail: giedroc@indiana.edu

nature CHEMICAL BIOLOGY | vol 9 | March 2013 | www.nature.com/naturechemicalbiology 177


article Nature chemical biology doi: 10.1038/nchembio.1168
a 0.8 ∆copA
c 0.8 WT + 0.2 All CupAs are predicted to harbor a single transmembrane helix
– Cu mM Cu
0.6
∆cupA ∆cupA
0.6 cupA(∆(2–28))
that anchors CupA to the plasma membrane. To test this, we cre-
cupA(∆(2–28)-(C)-Flag) ated ΔcupA and ΔcopA S. pneumoniae D39 deletion strains and
D620 nm

D620 nm
0.4 0.4
tested growth on a rich (brain-heart infusion (BHI)) medium under
0.2 0.2 microaerophilic conditions in the presence of 0.2 mM or 0.5 mM
0
+ 0.2 mM Cu
0 added Cu(II) (Supplementary Table 1). Both strains show a marked
0 2 4 6 8
Time (h)
10 12 0 2 4
Time (h)
6 8
growth inhibition phenotype relative to the wild-type strain (Fig. 1a
PG
and Supplementary Fig. 4a,b) that can be rescued by ectopic
b d Wash Digestion Protoplast expression of CupA from a heterologous promoter (Fig. 1b). This
0.8 S P S P S P S P
WT + 0.2 mM Cu
Anti-Flag CopA- result rules out any unintended polar effect on the expression of the
∆cupA Flag
0.6 Fraction downstream copA gene due to deletion of cupA; in fact, the ΔcupA

Bo d
d

m
an l l
al
D620 nm

∆cupA//Pfcsk-cupA
strain accumulates a large amount of CopA protein (Supplementary

br Ce
e
un

e
as
ll w
et
0.4

pl
cr

Ce

to
Se

em
Fig. 5b). Strains expressing C-terminally Flag-tagged CupA or

Cy

m
0.2 PG
Wash Digestion Protoplast CopA are characterized by wild-type growth in the presence of
0 S P S P S P S P
0 2 4 6 8 10 12 Anti-Flag CupA- 0.2 mM or 0.5 mM copper (Supplementary Fig. 4c,d). In contrast,
Flag
Time (h) Fraction a strain expressing CopAD442A, which ablates the catalytic aspartic
Bo d
d

m
an l l
al

br Ce
e
un

e
as
ll w
acid residue in the ATPase domain of CopA (based on an alignment
et

pl
cr

Ce

to
Se

em
Cy
with Legionella CopA32), is indistinguishable from the ΔcopA strain
m
Figure 1 | Copper sensitivity phenotypes of mutant S. pneumoniae (Supplementary Fig. 4d). More notably, a strain expressing CupA
D39 strains. (a,b) ΔcupA and ΔcopA S. pneumoniae strains are highly lacking the N-terminal transmembrane domain, Δ(2–28)CupA
sensitive to copper toxicity (a), which can be reversed by expression of (denoted hereafter sCupA; Fig. 1c and Supplementary Fig. 5a),
cupA from a heterologous promoter (b). (c) Deletion of the single putative is also unable to grow under these conditions. These experiments
transmembrane helix abrogates copper resistance to an extent comparable established that a C-terminal Flag tag does not interfere with CupA
© 2013 Nature America, Inc. All rights reserved.

to inactivation of CopA(D442A) (compare to Supplementary Fig. 4d). or CopA function, thus allowing us to determine the subcellular
In all cases, two independent isolates of the same strain designation were localization of both CopA and CupA using a standard fractionation
constructed, and duplicate (or more) growth experiments were carried scheme followed by western blotting with Flag-specific (anti-Flag)
out with each of the two strains. WT, wild type. (d) Both CopA and antibody (Fig. 1d and Supplementary Fig. 6). These data reveal that
CupA localize to the cell membrane fraction. The results of subcellular both full-length CupA and CopA localize exclusively to the plasma
fractionation of copA-(C)-Flag (top) and cupA-(C)-Flag (bottom) with membrane in S. pneumoniae; furthermore, plasma membrane
visualization by anti-Flag western blotting are shown. Supernatants (S) localization of CupA is required for full copper resistance.
or pellets (P) are marked for centrifugation steps, and cell fractions are
indicated below the blots. PG, peptidoglycan. See Supplementary Figure 6 Copper binding by sCupA and CopAMBD
for additional experimental details and the full blot and Supplementary The experiments described above suggest that sCupA and CopAMBD
Tables 1 and 2 for strain details. bind Cu(I) directly as a means to effect copper resistance. To test
this, we carried out anaerobic titration experiments in which
Cu(I) was added to apo sCupA or apo CopAMBD in the presence
function of membrane-anchored CupA under copper stress is to of one of two specific Cu(I) chelators, bathocuprione disulfonate
chelate Cu(I) as soon as it enters the cytoplasm and not to function (BCS; log β2 = 19.8 for Cu(I)–BCS2) or bicinchoninic acid (BCA;
as an obligatory chaperone to the MBD of CopA. log β2 = 17.2 for Cu(I)–BCA2), thus allowing us to access a range of
KCu between 1012 M−1 and 1019 M−1 (ref. 34). A global analysis of two
RESULTS representative titrations at two protein concentrations is shown in
Both CupA and CopA localize to the plasma membrane Supplementary Figures 7 and 8, with parameter values compiled in
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A transcriptomic analysis of wild-type S. pneumoniae D39 and an Table 1. Titrations in which apo sCupA was titrated into a solution
isogenic markerless deletion strain, ΔcopY, reveals massive upregu- of Cu(I)–BCS2 or Cu(I)–BCA2 returned identical parameter values
lation of the expression of downstream genes cupA and copA, with (Supplementary Fig. 9). These titrations reveal that the stoichio­
the expression of virtually no other gene strongly affected upon copY metry of Cu(I) binding in both cases is approximately two per mono-
deletion (Supplementary Results, Supplementary Fig. 1). This mer. sCupA is characterized by stepwise affinity constants (KCu1
finding, coupled with a previous report of copper-induced expres- and KCu2) of 7.4 × 1017 M−1 and 6.2 × 1014 M−1, respectively, and the
sion of copY, cupA and copA, reveals that the cellular response to values for CopAMBD are 2.1 × 1016 M−1 and 2.7 × 1013 M−1, respectively
copper stress is mediated solely by the cop operon18. (Table 1). Thus, the putative chaperone sCupA binds Cu(I) 20- to
Although the core domain of CopA seems to be a prototypical 30-fold more tightly than the putative copper acceptor CopAMBD to
bacterial Cu(I)-effluxing CopA of known structure32, a ~100-residue each of the high- and low-affinity sites.
domain that has high sequence similarity to CupA can be found
at the N terminus of CopA. Notably, both domains contain four Crystallographic structures of sCupA and CopAMBD
conserved candidate ligands for Cu(I) arranged in a Cys-X36-Cys-X- To understand the structural basis for Cu(I) binding stoichiometry,
Met-X-Met (where X is any amino acid) sequence (Supplementary affinity and resistance, we solved the X-ray crystallographic
Fig. 2). Furthermore, the N terminus of CupA is predicted to con-
tain a single transmembrane helix. The high sequence similarity of
CupA and the N-terminal region of CopA is a hallmark of a cog- Table 1 | Cu(i) binding affinities for sCupA and CopAMBD
nate copper chaperone–MBD pair found in other bacterial species33. Protein log KCu1 (M−1) log KCu2 (M−1) log b2,Cu (M−2)
S. pneumoniae does not encode Atx1 or CopZ, and bioinformat- sCupA 17.9 (± 0.3) 14.8 (± 0.2)a 32.6 (±0.3)
ics analysis reveals that CupA is nearly always found in genomes
CopAMBD 16.3 (± 0.1) 13.4 (± 0.3) 29.8 (±0.3)
that lack a recognizable gene encoding CopZ or Atx1. Furthermore, Parameters (mean values ± s.d.) were measured via global analysis of multiple anaerobic CuCl
CupA is widely distributed, perhaps more so than CopZ and titrations using BCA or BCS as a competitor copper chelator (Supplementary Figs. 7–9) using a
Atx1, but clearly clustered in Lactobacillus and Streptococcus nonlinear least-squares fit to a stepwise two-Cu(I)–binding model in both cases.
a
Mean value from BCA and BCS titrations. Conditions: 25 mM HEPES, 0.2 M NaCl, pH 7.0, 22 °C.
(Supplementary Fig. 3).

1 78 nature chemical biology | vol 9 | March 2013 | www.nature.com/naturechemicalbiology


Nature chemical biology doi: 10.1038/nchembio.1168 article
s­ tructures of sCupA and CopAMBD to 1.45-Å and 1.50-Å resolution, with a single cysteine from the β2-β3 loop (Cys49 in CopAMBD and
respectively (Fig. 2a–f and Supplementary Table 3). Each structure Cys74 in sCupA) functioning as a bridging ligand to each copper
reveals an eight-stranded β-barrel harboring a binuclear Cu(I) cluster site, denoted S1 and S2. The S1 copper site is digonal bis-thiolato,
whereas the more solvent-exposed S2 site is best described as dis-
torted trigonal planar coordination by the three protein-derived
a b Cys...Cys-X-Met-X-Met
Cl– β3-β4 ligands, with a long axial coordination bond to a Cl− anion from
solution (or distorted trigonal pyramidal; Supplementary Fig. 10

Cu-binding loop
Cys74 S2 Met113
loop Cl–
Cys74
S1 S2 2.33 and Supplementary Table 4). A conserved Cys-Gly-Met-X-Met
Cys111 Met115
2.16 Å 2.25
motif position in the β7-β8 loop in each protein provides three of
2.32
β5 S1 the four donor atoms to the Cu(I) ions. The Cu-Cu distance is 3.15 Å
β4
2.18 Met113 Met115 in each case. Both sCupA and CopAMBD adopt a well-known cupre-
β1 Cys111 doxin fold, with Dali z-scores ranging from 10 to 12 for cupredoxins
β3
β6
of known structure (Supplementary Fig. 11). However, the metal-
β7-β8 loop
ligand disposition (Supplementary Table 4) is without precedent,
β2
β8
β7 c evidence that nature has adapted this ancient fold35 to perform Cu(I)
trafficking rather than electron transfer.
C
Despite adopting identical folds with identical Cu(I) coordina-
N tion chemistries, sCupA and CopAMBD have contrasting electrostatic
TM α-helix surface potentials around the Cu(I)-binding sites, with the sCupA
being largely negatively charged and the CopAMBD being largely pos-
itively charged in the vicinity of the Cu(I)-binding sites (Fig. 2g,h).
Electrostatic complementarity is an established feature of copper
d chaperone–MBD pairs, which allows the Cu(I) chelates of each pro-
© 2013 Nature America, Inc. All rights reserved.

Cl– tein to transiently dock and undergo ligand exchange and copper
transfer without dissociation of bound Cu(I) into solvent8,36.
Cu-binding loop

Cys49 S2 Met88
e Cys...Cys-X-Met-X-Met
S1 β3-β4
Cys86 Met90 loop Cl– The high- and low-affinity copper sites in sCupA and CopAMBD
β5 Cys49 S2 2.47 The copper trafficking hypothesis24 states that the copper transfer
β4 2.16 Å 2.23 2.24 moves from donor chaperone to target protein with or against a
β1
S1 ­relatively shallow thermodynamic gradient as defined by KCu, mea-
β6
β3 2.15 Met88 Met90 sured with purified proteins37,38. For the sCupA and the CopA MBD,
Cys86
the situation is complicated by the presence of two bound Cu(I) ions in
β2 N β7 each case, with no insight as to which site defines the high- and low-
β8
β7-β8 loop affinity Cu(I) sites in each case. We therefore used X-ray absorption
f
spectroscopy (XAS) and NMR spectroscopy to define the sequence
of Cu(I) binding, exploiting the fact that the stepwise Cu(I) affinities
C
differ by ~1,000-fold for both sCupA and CopAMBD (Table 1).
The addition of substoichiometric Cu(I) to sCupA and CopAMBD
CopA gives rise to the Cu(I) near-edge feature in the X-ray absorption
near-edge structure (XANES) spectrum whose intensity is con-
sistent with a low-coordination-number complex, either n = 2 or
n = 3 (Fig. 3). For Cu1 CopAMBD, the extended X-ray absorption fine
npg

structure (EXAFS) spectrum is best described by a model corre-


h sponding to a digonal bis-thiolato (2S) complex or a trigonal 2S, 1Br−
g
complex in NaBr; in NaCl, a three-coordinate 2S-Cl− fit with a long
Cu-Cl− bond (2.42 Å) is the best fit. These data and accompanying
Cu(I)-S− bond distances (2.18 Å) are consistent with Cu(I) binding
the two S1-site thiolate ligands Cys49 and Cys86 (Supplementary
Fig. 12 and Supplementary Table 5). For Cu1 sCupA, the spectra in
both NaBr and NaCl are consistent with an n = 3 complex; the best-
fit 2S, 1N/O complex is consistent, for example, with recruitment
of a solvent molecule into the anticipated 2S (Cys74, Cys111) com-
plex (Supplementary Table 6). As expected, XAS analysis of a Cu2
Figure 2 | Crystallographic structures of sCupA and CopAMBD. sCupA sample in NaBr gives rise to an average Cu(I) ­coordination
(a–c) Structure of sCupA. Ribbon representation with Cu(i)-coordinating environment that is consistent with the crystal structure, includ-
side chains shown in stick, Cu(i) ions as brown spheres (S1 and S2) and the ing the presence of bound Br− anion (Supplementary Table 7 and
Cl− ion as an silver sphere (a). TM, transmembrane. Close-up view of the Supplementary Fig. 12).
Cu(i) coordination complex of sCupA with metal-ligand bond distances We next examined Cu(I) binding to the apoproteins by moni-
(Å) (b). Solvent-accessible surface area (arbitrarily colored according to toring perturbations in the amide chemical shifts of uniformly
residue type) around the binuclear Cu(i) chelate (c). (d–f) Structure of 15
N,13C-labeled samples of sCupA and CopAMBD upon sequential
CopAMBD. Ribbon representation as in a (d). Close-up view of the Cu(i) filling each of the two Cu(I) sites (Supplementary Fig. 13). In each
coordination complex as in b (e). Solvent-accesssible surface area around case (but more so in CopAMBD), the β3-β4 and β7-β8 metal-binding
the Cu(i) complex as in c (f). (g,h) Electrostatic surface potentials loops in the apoproteins are conformationally exchange broadened,
(painted on the basis of surface potentials) of sCupA (g) and CopAMBD (h). indicative of substantial μs-ms dynamics in this region (Fig. 4), as
Structure statistics are compiled in Supplementary Table 3. The dashed recently found for another apo cupredoxin involved in electron
box represents the approximate location of Cu(i) chelate in g and h. transfer39. Stepwise addition of Cu(I) quenches this line broadening

nature CHEMICAL BIOLOGY | vol 9 | March 2013 | www.nature.com/naturechemicalbiology 179


article Nature chemical biology doi: 10.1038/nchembio.1168
a c a b
17 Met1 0.30 0.29

∆p.p.m.
∆p.p.m.
1.0

0.8 18 0 0
Normalized fluorescence

C (p.p.m.)
0.6
19

13
0.4

Met90
0.2 20
c d
CopAMBD Met88 CopAMBD 0.30 0.32
0

∆p.p.m.

∆p.p.m.
8,960 8,980 9,000 9,020 9,040 2.4 2.2 2.0 1.8
1
Energy (eV) H (p.p.m.) 0 0
b d
17 Met28
1.0
Met120
Met91
0.8 18
Normalized fluorescence

C (p.p.m.)

Met46
0.6
Met116
19
Figure 4 | NMR chemical shift perturbation analysis of sCupA and
13

0.4
CopAMBD induced by Cu(I) binding. Ribbon representation of the changes
0.2 20 Met115
in backbone amide chemical shift upon Cu(I) binding by (a,b) sCupA, with
© 2013 Nature America, Inc. All rights reserved.

sCupA Δp.p.m. (Cu1–apo) sCupA in (a) and Δp.p.m. (Cu2–Cu1) sCupA in (b), and
Met113 sCupA
0 (c,d) CopAMBD, with Δp.p.m. (Cu1–apo) CopAMBD in (c) and Δp.p.m. (Cu2–Cu1)
8,960 8,980 9,000 9,020 9,040 2.4 2.2 2.0 1.8 CopAMBD in (d). The ribbon is white for proline residues and black for those
1
Energy (eV) H (p.p.m.) resonances broadened beyond detection in the apo state in each case.
e Lys89 Tyr50
f
114 Cys74 Cys111 Tyr38
116 Ser47 Phe74 Met90
Lys89 Tyr50 Met90 Cys111
Phe109 indicative of direct ligation (Fig. 3c). For sCupA, addition of the
Tyr24 116 Cys111
N (p.p.m.)

first molar equivalent of Cu(I) results in a slight upfield shift of the


N (p.p.m.)

118 Ile16 Ile13 Phe109 Met115 Glu93


Tyr24 Lys51
Asn36 Ile99 Met115 Val85

120
Ala27 Glu68 Ile60 118 Cys74
Glu106
Asp76
Met116 13Cε−1Hε with few other changes in the spectrum; only
Glu106 Glu106 Asp76 Asp76
upon addition of the second molar equivalent of Cu(I) is there
15

15

Leu75 Cys74
Phe84 120
122 Cys49
CopA
MBD Leu75 Leu75
sCupA a strong downfield shift of the methyl resonances of Met113 and
8.2 8.0 7.8 7.6 7.4 7.2 8.0 7.8 7.6 7.4 7.2 7.0 Met115. Inspection of the sCupA structure reveals that Met116 is
1
H (p.p.m.)
1
H (p.p.m.) quite close to the S1 copper ion and thus reports on filling the digo-
nal bis-thiolato S1 site (Fig. 3d). We conclude that the high-affinity
Figure 3 | The methionine-rich S2 site is the low-affinity site on both Cu(I) site on both CopAMBD and sCupA is the bis-thiolato S1 site,
CopAMBD and sCupA, and Cu(I) is transferred only from the S2 site of with the more solvent-exposed methionine-rich S2 site being the
sCupA to the S1 site of apo MBD. (a,b) XANES of Cu1 CopAMBD (a) and low-affinity Cu(I) site in each protein.
Cu1 sCupA (b) in the presence of 0.2 M NaBr (red) or 0.2 M NaCl (blue).
(c,d) Overlay of the methionine thioether methyl (13Cε-1Hε) region of an Facile copper transfer from sCupA to CopAMBD
H,13C-HSQC spectrum for CopAMBD (c) and sCupA (d) acquired in the apo We next determined whether Cu(I) bound to the putative donor
npg

state (magenta), Cu1 state (green) and Cu2 states (blue). Cyan cross-peaks sCupA could be transferred to acceptor CopAMBD, taking advan-
result when apo MBD is mixed with 2.0 molar equivalents of Cu2 sCupA, tage of the distinct spectroscopic signatures of Cu(I) bound to each
as in c, or 1.0 molar equivalents of Cu2 sCupA, as in d. (e,f) Overlay of the of the two Cu(I) sites (Fig. 3c,d). We performed this experiment
backbone 1H,15N-HSQC spectra of CopAMBD (e) and sCupA (f), with the using an NMR-based strategy31 by mixing [13C,15N]sCupA with
same cross-peak color pattern as in panels c and d. unlabeled CopAMBD or unlabeled sCupA with [13C,15N]CopAMBD,
with sCupA loaded with two molar equivalents of Cu(I) as a copper
with the addition of the first Cu(I), inducing measurable perturba- donor. When unlabeled apo CopAMBD is mixed with stoichiometeric
tions beyond these loops and into nearby β-strands, such as the β7 Cu2 [13C,15N]sCupA, one Cu(I) is lost, specifically from the low-
strand; addition of the second Cu(I) gives rise to detectable pertur- affinity methionine-rich S2 site, as evidenced by a return of the
bations in the metal-binding loops only (Fig. 4). These perturbation 13
Cε-1Hε cross-peaks of Met113 and Met115 to their positions in
maps are fully consistent with Cys49 (CopAMBD) and Cys74 (sCupA) Cu1 sCupA (Fig. 3d). The same is evident on inspection of the
functioning as a bridging ligand as filling of both S1 and S2 ­copper 1
H,15N-HSQC spectrum of sCupA, with the Cu2 resonances lost and
sites in each induces backbone perturbations in both β3-β4 and the occurrence of concomitant superposition of the cross-peaks
β7-β8 loops. associated with bona fide Cu1 sCupA and those that result when
Although the Cu1 and Cu2 states of both sCupA and CopAMBD are Cu2 sCupA is mixed with apo CopAMBD (Fig. 3f). There is no trace
readily distinguished from one another (Supplementary Fig. 13), of apo sCupA in these spectra. Monitoring the same reaction with
they cannot be used to assign the high- and low-affinity sites. We excess (2:1) unlabeled copper-saturated sCupA and 13C,15N-labeled
therefore assigned the methionine 13Cε−1Hε groups of both sCupA apo CopAMBD reveals formation of only the bona fide Cu1 CopAMBD
and CopAMBD by 13C-edited NOESY spectroscopy, with direct with the S1 sites filled (Fig. 3c), with no evidence of the Cu2 or
Met-Cu(I) coordination expected to induce a strong downfield shift apo MBD in these mixtures (Fig. 3e). Thus, even in the presence
of the 13Cε chemical shift, as revealed by a 1H,13C-HSQC spectrum of excess copper bound to sCupA, only the high-affinity S1 site on
(Fig. 3c)40. Consistent with XAS, only upon addition of the ­second the CopAMDB is capable of accepting the Cu(I) from sCupA, and
molar equivalent of Cu(I) is there a strong downfield shift of the Cu(I) is donated from the more solvent-exposed lower-affinity
13
Cε-1Hε methyl cross-peaks of Met88 and Met90 of CopAMBD, S2 site on sCupA.

180 nature chemical biology | vol 9 | March 2013 | www.nature.com/naturechemicalbiology


Nature chemical biology doi: 10.1038/nchembio.1168 article
a 0.8 –Cu b 0.8 + 0.2 mM Cu c 0.8
+ 0.2 mM Cu copA WT
cupA WT cupA WT copA(C49S)
0.6 cupA(C74S) 0.6 0.6
cupA(2A) cupA(3A)

D620 nm
D620 nm
D620 nm

0.4 cupA(3A) 0.4 0.4


cupA(C74S,3A)
cupA(C74S)
∆cupA
0.2 0.2 cupA(2A) 0.2 ∆copA
cupA(C74S,3A)
∆cupA copA(D442A)
0 0 0
0 2 4 6 8 10 0 2 4 6 8 10 0 2 4 6 8 10
Time (h) Time (h) Time (h)

Figure 5 | Mutagenesis of Cu(I)-binding residues in CupA but not in CopAMBD partly or completely abrogates Cu(I) resistance of S. pneumoniae.
(a–c) Representative growth curves for the cupA missense strains in BHI with no additions (a), cupA missense strains in BHI with 0.2 mM Cu(ii) added (b)
and copA strains in BHI with 0.2 mM Cu(ii) added (c). Two independent isolates of the same strain designation were constructed and duplicate (or more)
growth experiments were carried out with each of the two strains. See Supplementary Tables 1 and 2 for strain details.

The reverse experiment was also done in which stoichiometric DISCUSSION


13
C,15N-labeled Cu1 CopAMBD was mixed with unlabeled apo sCupA. In this work, we define a new structural paradigm for copper traf-
There is no change in the spectrum (Supplementary Fig. 14), thus ficking and resistance characterized in the Gram-positive respi-
revealing that, despite the higher affinity, the S1 site on sCupA ratory pathogen S. pneumoniae. Soluble CupA and CopAMBD are
is unable to strip the MBD of its bound Cu(I) under these condi- isostructural and of opposite electrostatic surface potentials, and
tions. Efficient Cu(I) transfer is therefore preferentially unidirec- each harbors a binuclear Cu(I) cluster in the context of a new archi-
tional but may depend on the molar ratio of CupA and CopA in tecture not previously observed in bacterial copper trafficking. The
the membrane. Cu(I) binding affinities of sCupA and CopAMBD differ substantially
© 2013 Nature America, Inc. All rights reserved.

from one another, and although sCupA binds Cu(I) more tightly
Copper resistance requires copper binding by CupA overall than CopAMBD, copper transfer is preferentially down a
To further understand the essentiality of CupA for copper resistance, thermodynamic gradient, from the low-affinity S2 site of sCupA to
we characterized cupA allelic replacement strains using our structure the high-affinity S1 site of CopAMBD, as found in many other Cu(I)
as a guide (Fig. 2). Mutant cupA strains include the mutations M113A chaperone systems23,37,38. CupA therefore satisfies all established
and M115A (cupA(2A)), which abrogate binding to the S2 site only; criteria for designation as a copper chaperone33 but is to our
a Cu-coordinating β7-β8 loop triple mutant with mutations C111A, knowledge the first one known to be inserted into the plasma mem-
M113A and M115A) designated cupA(3A); a single bridging ligand brane, which itself is obligatory for copper resistance.
substitution of Cys74 (cupA(C74S)); and a quadruple mutant in This is to our knowledge the first instance where biological studies
which all of the metal ligands are substituted with nonliganding resi- establish that deletion or functional inactivation of the copper chaper-
dues (cupA(C74S,3A)). C74S sCupA binds a single molar equivalent one reduces copper resistance to a level identical to deletion or inacti-
of Cu(I) with a low affinity (KCu ~ 1012 M−1) but adopts a fold identical vation of the copper transporter itself. This requirement of the CupA
to that of wild-type sCupA with only local structural perturbations chaperone in copper resistance in S. pneumoniae was missed in the
near the substitution (Supplementary Fig. 15). previous report, which suggested that a S. pneumoniae strain encod-
In the absence of added copper, all cupA metal-liganding mutant ing a translationally terminated cupA gene only gave rise to a more
strains grow similarly to the wild-type strain (Fig. 5a). However, in the modest copper sensitivity phenotype18. We show here that CupA
presence of 0.2 mM Cu(II), growth of the cupA(3A) strain is inhibited protein in cupA missense strains that express CupA with diminished
but viable, whereas the cupA(2A), cupA(C74S) and cupA(C74S,3A) Cu(I)-binding affinities accumulates to a degree greater than that in
strains all largely fail to grow (Fig. 5b), despite the fact that these a wild-type background. A hyperaccumulation of both CupA and
npg

CupAs accumulate to an extent greater than that of wild-type CupA CopA in these cells may be reporting on hypersensitivity or continued
(Supplementary Fig. 5a). At 0.5 mM Cu(II), none of the mutant derepression of CopY-mediated transcription of the cop operon in a
cupA strains are able to grow (Supplementary Fig. 16b). In fact, the failed effort to resist the effects of increased cytoplasmic copper.
behavior of the cupA(C74S) strain is indistinguishable from that of a Although copper transfer from the S2 site of CupA to the S1 site
copA(D442A) strain expressing a catalytically inactive CopA (Fig. 5c). of CopAMBD occurs spontaneously, we suggest that this may occur
Notably, western blotting reveals that there is very high accumulation only under nonstressed or ‘housekeeping’ conditions as it is not
of CopA in both strains as well as in the ΔcupA strain (Supplementary strongly relevant to the cellular copper toxicity response. In fact,
Fig. 5b). Analysis of the total cell-associated metal content of these recent studies32,41 support a model in which the N-terminal MBD
strains by inductively coupled plasma (ICP)-MS reveals a substantial (not visualized in the crystallographic structure of Legionella CopA)
(approximately five-fold) increase in total cellular copper relative to has a regulatory role. Here, the MBD is thought to dock against the
wild-type cells 3 h after addition of 0.2 mM copper in the ΔcupA and actuator domain (Supplementary Fig. 17) and inhibit ATP hydro-
cupA(C74S) strains (Supplementary Table 8). lysis in the absence of Cu(I); metal binding by the MBD then dis-
In contrast, when a substitution that is analogous to C74S in CupA rupts this interaction, allosterically activating ATP hydrolysis and
is introduced into the CopAMBD in the copA gene (copA(C49S)), Cu(I) transport. It is known that the cytoplasmic copper chaper-
copper resistance is unaffected at both 0.2 mM (Fig. 5c) and 0.5 mM one Atx1 can deliver Cu(I) to either the N-terminal MBD, which
Cu(II) (Supplementary Fig. 16c). Consistent with this result, is not on-pathway for copper transfer, or the transmembrane site
Flag-tagged CopAC49S accumulates to a degree similar to that of directly42; the latter is hypothesized to occur via docking to the posi-
wild-type CopA rather than to that of copper-sensitive mutants tively charged platform region that surrounds the putative entry site
(Supplementary Fig. 5b). These experiments thus establish that a for copper transfer32. Thus, the negative electrostatic surface poten-
major function of CupA in copper stress resistance is most likely tial of sCupA is complementary to both the MBD and the platform
not to chaperone Cu(I) to the CopAMBD but instead to deliver cop- region of CopA and may facilitate transient docking and direct cop-
per directly to the transmembrane Cu(I)-binding sites in CopA for per delivery to either site (Supplementary Fig. 17).
efflux and/or to sequester Cu(I) during copper stress in an effort to Our data are consistent with recent experiments in Synechocystis
mitigate the effects of cellular copper toxicity. and in Listeria monocytogenes, which suggest that a primary role

nature CHEMICAL BIOLOGY | vol 9 | March 2013 | www.nature.com/naturechemicalbiology 181


article Nature chemical biology doi: 10.1038/nchembio.1168

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Such strict control of bioavailable Cu(I) in the cytoplasm might be CsoR and copper-metallochaperone CopZ modulate CopA-mediated copper
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42. González-Guerrero, M. & Arguello, J.M. Mechanism of Cu+-transporting Lawrence Berkeley National Laboratory is supported by the US Department of Energy and
ATPases: soluble Cu+ chaperones directly transfer Cu+ to transmembrane Indiana University. The Stanford Synchrotron Radiation Lightsource Structural Molecular
transport sites. Proc. Natl. Acad. Sci. USA 105, 5992–5997 (2008). Biology Program is supported by the US Department of Energy, Office of Biological
43. Chillappagari, S., Miethke, M., Trip, H., Kuipers, O.P. & Marahiel, M.A. and Environmental Research and by the NIH National Center for Research Resources,
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MBio. 3, e00293–e00311 (2012). from the National Institute of Biomedical Imaging and Bioengineering.
45. Ramos-Montañez, S., Kazmierczak, K.M., Hentchel, K.L. & Winkler, M.E.
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Author contributions
Y.F. carried out all protein purification, Cu(I) binding experiments and NMR studies, and
6390–6400 (2010).
solved the crystallographic structures of sCupA and CopAMBD, the latter in collaboration
46. Anjem, A. & Imlay, J.A. Mononuclear iron enzymes are primary targets of
with C.E.D. III., H.-C.T.T., K.E.B. and L.-T.S. K.M.K. constructed S. pneumoniae
hydrogen peroxide stress. J. Biol. Chem. 287, 15544–15556 (2012).
strains and carried out all cell culture and western blotting experiments under the
47. Lynch, J.P. III & Zhanel, G.G. Streptococcus pneumoniae: epidemiology and
direction of M.E.W. K.A.H. prepared samples for XAS and analyzed these spectra in
risk factors, evolution of antimicrobial resistance, and impact of vaccines.
collaboration with M.J.M., and J.P.L. made the ICP-MS measurements on cultures grown
Curr. Opin. Pulm. Med. 16, 217–225 (2010).
by K.E.B. D.P.G. conceived and directed the study, and wrote the manuscript.

Acknowledgments Competing financial interests


The authors gratefully acknowledge support from the US National Institutes of Health
The authors declare no competing financial interests.
(NIH; GM042569 to D.P.G., GM094472 to C.E.D. III, AI095814 to M.E.W. and GM069696
to M.J.M.), the Lilly Endowment (to M.E.W.) and an Indiana University Quantitative
and Chemical Biology Training Fellowship (to J.P.L.). We thank L. Christiansen for Additional information
assistance in strain construction, members of the Giedroc laboratory for help in Supplementary information is available in the online version of the paper. Reprints and
acquiring the NMR data and H. Hu and N. Giri from of the Maroney laboratory for XAS permissions information is available online at http://www.nature.com/reprints/index.
data collection. Crystallographic data collection at the Advanced Light Source at the html. Correspondence and requests for materials should be addressed to D.P.G.
© 2013 Nature America, Inc. All rights reserved.
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nature CHEMICAL BIOLOGY | vol 9 | March 2013 | www.nature.com/naturechemicalbiology 183


ONLINE METHODS Triton-X 100 was added to solubilize the cell pellets, and they were lysed for
Bacterial strains and growth conditions. S. pneumoniae serotype 2 strain 10 min at 95 °C with shaking at 500 r.p.m. followed by vigorous vortexing for
D39 and its derivatives were used in this study48. Strains containing antibiotic 20 s. Two hundred microliters of the lysed cell solution (equivalent to 0.75 mL
markers were constructed by transforming linear DNA amplicons synthesized total cell culture) was added to 2.8 mL of 2.5% (v/v) nitric acid for ICP-MS
by overlapping fusion PCR into competent pneumococcal cells49. Strains con- analysis. Analyses were performed using a PerkinElmer ELAN DRCII ICP-MS
taining markerless copY, cupA or copA and respective Flag-tagged alleles in essentially as described20. Germanium at 50 p.p.b. was added as an internal
native gene loci (Supplementary Table 1) were generated using the Pc-[kanR- standard using an EzyFit glass mixing chamber. Metal concentration per mg
rpsL+] (Janus cassette) allele replacement method49. ΔcopY and ΔcopA alleles protein were determined as follows: the metal concentration in μg/L (measured
in IU3566 (D39 ΔcopY) and IU5975 (D39 ΔcopA) strains were constructed by by ICP-MS) × 0.003-L sample = total μg metal in 0.75 mL of cell culture. The
deletion of the gene sequences except for the 60 bp at the 5′ and 3′ end. The μg metal × 1,000 × 2 gave the amount of metal in ng in the original 1.5 mL of
ΔcupA allele in IU5971 (D39 ΔcupA) was constructed by deletion of the cupA culture. Protein samples were resuspended in 100 μL buffer, and concentrations
gene sequence except for the 5′ 42 bp and 3′ 60 bp. All constructs were con- were determined in mg/mL using a Bradford assay (Biorad). Total protein in
firmed by DNA sequencing of the amplicon region used for transformation. 1.5 mL was calculated by multiplying by 0.1 to correct for the resuspension
Strains were grown on plates containing Trypticase Soy Agar II (Modified) volume. The final copper concentration is expressed as ng metal/mg protein.
(Becton-Dickinson; BD) and 5% (v/v) defibrinated sheep blood (TSAII BA)
and were incubated at 37 °C in an atmosphere of 5% CO2. For antibiotic selec- Construction of overexpression plasmids and protein purification. The pHis-
tions, TSAII BA plates were supplemented with 250 μg kanamycin/mL or parallel plasmid was used to subclone sCupA (residues 29–123 of the 123-
250 μg streptomycin/mL. For liquid cultures, strains were cultured statically in residue CupA) and the CopAMBD (residues 1–99 of CopA). These constructs,
BD Brain-Heart Infusion (BHI) broth at 37 °C in an atmosphere of 5% CO2. following TEV protease cleavage, yield a non-native glycine-alanine-methionine
To obtain growth curves, overnight cultures were obtained from frozen stock N-terminal sequence for sCupA (denoted residues 26–28 in the structure)
inoculums into 3 mL of BHI broth in 17-mm-diameter polystyrene plastic tubes and a single non-native N-terminal glycine in the case of CopAMBD (denoted
and serially diluted over five tubes. Overnight cultures still in log-phase growth Gly0). E. coli BL21 (DE3)–competent cells were transformed with the result-
were diluted to an optical density of 0.002 at 620 nm in BHI with or without ant plasmids. For unlabeled proteins, overnight cultures were inoculated into
0.2 or 0.5 mM CuSO4. Growth was monitored by optical density at 620 nm LB medium containing 100 μg/mL ampicillin. For the 15N- and 13C-labeled
© 2013 Nature America, Inc. All rights reserved.

using a Spectronic 20 Genesys spectrophotometer. proteins, overnight cultures were inoculated into M9 minimal medium
(pH 7.4) containing 100 μg/mL ampicillin, supplemented with 15NH4Cl (1 g/L)
Cell fractionation and subcellular localization of CupA and CopA in (Cambridge Isotope Laboratories) and [13C6]D-glucose (2.5 g/L) (Cambridge
S. pneumoniae D39. Biochemical fractionation of pneumococcal cells was Isotope Laboratories). For both media, the cells were grown at 37 °C to an
performed as described50 with strains IU6041 (cupA-(C)-Flag) and IU6044 D600 nm = 0.6 with IPTG added to a final concentration of 0.4 mM and cultures
(copA-(C)-Flag) in BHI supplemented with 0.3 mM CuSO4. continued at 16 °C for 20 h. The cells were harvested by centrifugation and
kept at −80 °C. All buffers in the purification were placed under argon using a
Western blotting to quantify cellular expression of CupA and CopA in Schlenk line immediately before use. For lysis, cells were resuspended in buffer R
various cupA or copA mutants. Whole-cell lysates were prepared using the (25 mM Tris, pH 8.0, 200 mM NaCl, 5 mM TCEP). The resuspended cells were
FastPrep method on cell cultures grown overnight in BHI and then diluted to lysed by a sonic dismembranator (Fisher). The recombinant proteins were puri-
an attenuance at 620 nm (D620 nm) of 0.0035 (cupA (C)-Flag, WT, copA (C)-Flag fied using HisTrap FF columns (GE Healthcare) using a gradient of imidazole
and copA (C49S)-(C)-Flag strains) or 0.005 (all other mutant strains) in 30 mL from 10 mM to 300 mM in buffer R. The appropriate fractions were pooled and
BHI and were allowed to grow to an optical density of 0.04 (cupA (C)-Flag, WT, subjected to TEV protease cleavage at for 16 °C for 36 h. The proteins were fur-
copA (C)-Flag and copA (C49S)-(C)-Flag strains) or 0.06 (all other strains), ther purified using HisTrap FF columns (GE Healthcare) and the Superdex 75
or approximately three doublings, at which time CuSO4 was added to a final 16/60 column (GE Healthcare). The purity of the proteins was estimated to
concentration of 0.2 mM. Two-and-a-half hours after addition of Cu, at an be >95%, as judged by SDS-PAGE. Protein concentration was determined by
optical density of ~0.25 for cupA-Flag strains (approximately two doublings A280 nm with an extinction coefficient of 4,595 M−1cm−1. The number of reduced
for copper-sensitive mutant alleles and approximately three doublings for WT thiols was 1.9 for sCupA and 1.7 for CopAMBD (2.0 expected). Mutants of sCupA
and cupA (C)-Flag) and at an D620 nm of ~0.5 for copA-Flag strains (approxi- and CopAMBD were generated using a standard site-directed mutagenesis
mately two doublings for copper-sensitive mutant alleles and approximately strategy (Stratagene), and mutant proteins were purified as described above.
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three doublings for WT, copA (C)-Flag and copA (C49S)-(C)-Flag), cells were
centrifuged at 14,500g for 5 min at 4 °C. Supernatants were removed, and Cu(I) binding affinity measurements. Bathocuproine disulfonate (BCS) and
pellets were placed on ice and suspended in 1.0 mL of cold 20 mM Tris pH 7.0 bicinchoninic acid (BCA) were used for Cu(I) binding affinity determination
and 8 μL of protease inhibitor cocktail set III (Calbiochem) and transferred to of sCupA and CopAMBD by direct Cu(I) titration into a mixture of chelator and
chilled Lysing Matrix B tubes (MP Biomedicals). Matrix tubes were secured apoprotein essentially as described previously or by titration of apoprotein into
in a 24 × 2 mL-tube adaptor in a FastPrep-24 instrument (MP Biomedicals) a ­chelator–copper complex34. Apoproteins were buffer exchanged into degassed
stored at 4 °C. Cells were disrupted by three consecutive runs of 40 s each at buffer B (25 mM HEPES, pH 7.0, 200 mM NaCl) in an anaerobic chamber. The
a speed setting of 6.0 m/s. Lysed cell mixtures were placed on ice and centri- Cu(I) stock was prepared by taking the supernatant following anaerobic dissolu-
fuged at 10,000g for 1 min at 4 °C. 100 μL of supernatant was transferred to a tion of solid CuCl into fully degassed buffer B (25 mM HEPES, pH 7.0, 200 mM
tube containing 100 μL of cold 2× Laemmli sample buffer (containing 5% (v/v) NaCl). The concentration of Cu(I) stock was determined by atomic absorption
of freshly added β-mercaptoethanol), boiled for 5 min and placed on ice. Gel spectroscopy (PerkinElmer AAS-400) with a typical stock concentration of
loading volumes were calculated to adjust for the slightly different cell culture ~10 mM. For direct Cu(I) titrations, the final solution to be titrated contained
densities. Visualization and relative quantification of Flag-tagged proteins were 20–30 μM sCupA or CopAMBD and 30–40 μM BCA or BCS in Buffer B. Each
achieved with western blotting with primary anti-Flag polyclonal antibody 120-μL aliquot of titration solution was mixed with increasing Cu(I) titrant.
(Sigma, F7425, 1:1,000 dilution) and an IVIS imaging system48. For apoprotein titrations, a concentrated stock solution of the apo sCupA was
titrated into a solution containing 27–40 μM Cu(I) and 80–162 μM BCS or 25–
Bioinformatics analysis. The sequences of CupA and B. subtilis CopZ and 35 μM Cu(I) and 170–285 μM BCA; under these conditions, all of the Cu(I) is bound
Synechocystis (sc) Atx1 were used as query in a pBLAST analysis against a as a Cu–BCS2 or Cu–BCA2 chelate, respectively, before addition of apo CupA.
nonredundant protein sequence database of all bacterial genomes. Criteria for In both experiments, the optical spectra of BCA or BCS were recorded from
designation as a CupA, CopZ or scAtx1 are shown in Supplementary Figure 3. 200 nm to 900 nm. Corrected spectra were obtained by subtracting the apo
sCupA (or CopAMBD) spectrum from each Cu(I)-addition spectrum and then
ICP-MS analysis. Aliquots (1.5 mL) of S. pneumoniae strains were centrifuged correcting for dilution. The A483 value was used to determine the concentration
and washed once with BHI containing 1 mM nitrilotriacetic acid (Aldrich) then of Cu(I)–BCS2 complex with an extinction coefficient of 13,500 M−1 cm−1. The
washed twice with PBS that had been treated overnight with Chelex-100 (Biorad) A562 value was used to determine the concentration of the Cu(I)–BCA2 complex
according to the manufacturer’s protocol. The cell pellets were dried overnight, with an extinction coefficient of 7,700 M−1 cm−1. All the data were fitted to the
400 μL of 2.5% v/v nitric acid (Ultrapure, Sigma-Aldrich) containing 0.1% v/v appropriate competition model using Dynafit51.

nature chemical biology doi:10.1038/nchembio.1168


Crystallization and crystal structure determination. Apo protein (sCupA or 3 GeV and 80–100 mA. Beamline optics consisted of a Si(220) double-crystal
CopAMBD) was first buffer exchanged to fully degassed buffer A (25 mM Tris, monochromator and two rhodium-coated mirrors. X-ray fluorescence was col-
pH 8.0, 200 mM NaCl) in an anaerobic glove box. A ~10 mM Cu(I) stock solu- lected using a 30-element Ge detector (Canberra). Scattering was minimized
tion was prepared by taking the supernatant from dissolution of solid CuCl using Soller slits and by placing a Z-1 filter between the sample chamber and
into fully degassed buffer B (25 mM HEPES, pH 7.0, 200 mM NaCl) with the the detector.
concentration of copper determined by atomic absorption spectroscopy. Cu(I)- The Cu1.8 sCupA sample was prepared by adding 1.8 molar equivalents of
loaded proteins were prepared by mixing apo protein with a freshly prepared CuBr to 3 mM sCupA in 25 mM HEPES (pH 7.0) and 200 mM NaBr and con-
Cu(I) stock in the glove box at a 1:2 protein:copper molar ratio. Cu(I)-sCupA centrated to 3 mM under anaerobic conditions. Sixty microliters were syringed
was crystallized by hanging drop vapor diffusion at 20 °C against a well buffer into a polycarbonate XAS holder wrapped in kapton tape and frozen in liquid
of 30% (w/v) PEG 3350, 0.1 M sodium citrate tribasic dihydrate pH 5.0 and nitrogen. The data were collected at beam line X3b at the NSLS, Brookhaven
Big CHAP Deoxy. The cryosolvent was prepared using 35% (w/v) polyethylene National Laboratories. The samples were loaded into an aluminum sample
glycerol 3350 in the well solution. Cu(I)-CopAMBD was crystallized by hanging holder, which was cooled to ~50 K using a helium displex cryostat. Data
drop vapor diffusion at 20 °C against a well buffer of 28% (w/v) polyethyl- were collected under ring conditions of 2.8 GeV and 120–300 mA using a
ene glycerol monomethyl ether 2000, 0.1 M Bis-Tris pH 6.5. The cryosolvent sagitally focusing Si(111) double-crystal monochromator. Harmonic rejection
was prepared by using 35% (w/v) polyethylene glycerol monomethyl ether was accomplished with a nickel-coated focusing mirror. X-ray fluorescence
2000 in the well solution. For CopAMBD, diffraction data for the native data set was collected using a 30-element Ge detector (Canberra). Scattering was
were collected at −160 °C on an R-AXIS IV+ detector at Indiana University, minimized by placing a Z-1 filter between the sample chamber and the
Bloomington. The space group of the crystal was P212121 with one monomer in detector. For all samples, XANES was collected from ± 200 eV relative to the
the asymmetric unit. All data were processed with HKL2000, and diffraction metal edge. The X-ray energy for the copper metal Kα-edge was internally
data for the initial phase determination were collected on ALS 4.2.2 (Advanced calibrated to the first inflection point, 8980.3 eV. EXAFS was collected to
Light Source, Lawrence Berkeley National Laboratory). Initial phases for the 15 k above the edge energy (Eo).
structure of CopAMBD were determined by single-wavelength anomalous dis-
persion (SAD) techniques from a data set collected on beamline 4.2.2 at the XAS data reduction and analysis. The XAS data shown (shown below) are the
Advanced Light Source with Cu(I) providing an anomalous signal for phas- average of eight scans. XAS data was analyzed using SixPack57. The SixPack
© 2013 Nature America, Inc. All rights reserved.

ing. The structure of CopAMBD was solved and auto-built with PHENIX52. fitting software builds on the IFEFFIT engine58,59. Each data set was background
Two Cu(I) atoms were found in the structure. Iterative rounds of model build- corrected and normalized. For EXAFS analysis, each data set was converted to
ing and refinement were carried out in Coot53 and PHENIX52, respectively. k-space using the relationship
Ramachandran statistics were 98% of the residues in the allowed region, 2%
1/ 2
generously allowed and 0% disallowed. For sCupA, diffraction data were col- k = 2me (E − E0 )/  2 
lected at Indiana University, Bloomington, as described above. The space group
of the crystal was P21212 with one monomer in the asymmetric unit. Following where me is the mass of the electron, ħ is Plank’s constant divided by 2π, and E0
processing with HKL2000, initial phases were calculated using a truncated is the threshold energy of the absorption edge. The threshold energy chosen
model of CopAMBD as a molecular replacement search model in PHENIX52 with for copper is 8,990 eV60. The best fits for the data sets were obtained using a
the structure refined as described above for CopAMBD. Ramachandran statistics Fourier transform of the data produced using data over the range k = 2–14 Å−1
for sCupA were 100% of the residues in the allowed region with 0% in the (Cu0.8 sCupA and Cu0.8 CopAMBD) or k = 2–12.5 Å−1 (Cu1.8 sCupA), where
generously allowed and disallowed regions. All structure-related figures were the upper limit was determined by the signal:noise ratio. Scattering para­
prepared using PyMOL (Delano Scientific). meters were generated using FEFF 8 (ref. 59). The first coordination sphere
was determined by setting the number of scattering atoms in each shell
NMR methods. Typical NMR sample solution conditions were 300–600 μM to integer values and systematically varying the combination of N/O and
15
N- and 13C-labeled sCupA or CopAMBD, pH 6.0, 50 mM sodium phosphate, S-donors (Supplementary Tables 5–7). To compare different models of the
50 mM NaCl, 0.02% (w/v) NaN3 and 10% (v/v) 2H2O, 25 °C. All NMR sam- same data set, IFEFFIT uses three goodness-of-fit parameters: χ2, reduced
ples were prepared in an anaerobic glove box. Apo state samples (sCupA and χ2 and the R-factor. χ2 is given by equation (1), where Nidp is the number of
CopAMBD) were prepared with 5 mM TCEP. Cu1 sCupA samples contained independent data points, Nε2 is the number of uncertainties to minimize,
0.9 molar equivalents of Cu(I), and Cu2 sCupA samples contained 1.9 molar Re(f i) is the real part of the EXAFS function and Im(f i) is the imaginary part
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equivalents of Cu(I). Cu1 CopAMBD samples contained 0.8 molar equivalents of of the EXAFS fitting function
Cu(I), and Cu2 CopAMBD samples contained 1.8 molar equivalents of Cu(I). NMR
spectra were acquired with a Varian DDR 800 MHz spectrometer equipped N idp N
∑{[Re( fi )] + [Im( fi )] }
2 2
c2 = (1)
with a cryogenic probe at the Indiana University METACyt Biomolecular Ne 2 i =1
NMR laboratory. The NMR spectra were processed using NMRPipe54 and ana-
lyzed using Sparky (T. D. Goddard and D. G. Kneller, SPARKY 3, University of Reduced χ2=χ2/(Nind−Nvarys), where Nvarys is the number of refining parameters
California–San Francisco). Chemical shifts are referenced relative to internal and represents the degrees of freedom in the fit. Additionally, IFEFFIT
2,2-dimethyl-2-silapentane-5-sulfonic acid (DSS). calculates the R-factor for the fit, which is given by equation (2), and is scaled
Sequential backbone resonance assignments of all six states (apo, Cu 1 to the magnitude of the data, making it proportional to χ2
and Cu2 states of sCupA and CopAMBD) were obtained using 1H-15N HSQC,
HADAMAC-2 (ref. 55) and triple-resonance CBCA(CO)NH, CBCANH,
N
HNCO and Best-HNCA56 spectra. The automatic backbone assignment server
∑{[Re( fi )] + [Im( fi )] }
2 2

PINE was used to aid in obtaining assignments. Methionine 13CH3 resonance R= i =1 (2)
N
∑{[Re(xdata i )] }
assignments of Cu2 sCupA were obtained from a 1H,13C HSQC experiment 2 2
 i )] + [ Im( xdata

using HCCH-TOCSY, HCCH-COSY and 13C-edited NOESY-HSQC experi- i =1
ments. The NOESY experiments were conducted using standard pulse
sequences from the Varian Biopack with τm = 100 ms. For the 13C -edited In comparing different models, the R-factor and reduced χ2 parameter were
NOESY-HSQC experiment, 1,024 × 200 ×70 data points were acquired. used to determine which model was the best fit for the data. The R-factor will
always generally improve with an increasing number of adjustable parameters,
XAS. sCupA and MBD were concentrated to 2 mM and 1.2 mM, respectively, whereas reduced χ2 will go through a minimum and then increase, indicating
in 25 mM HEPES (pH 7.0) and 200 mM NaCl or NaBr. CuCl or CuBr (0.8 that the model is overfitting the data.
molar equivalents) was added to both MBD and CupA anaerobically. Thirty
microliters of each sample was syringed into polycarbonate XAS holders that
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nature chemical biology doi:10.1038/nchembio.1168