The Structures of Frataxin Oligomers Reveal the Mechanism for the Delivery and Detoxification of Iron

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Defects in the mitochondrial protein frataxin are responsible for Friedreich ataxia, a neurodegenerative and cardiac disease that affects 1:40,000 children. Here, we present the crystal structures of the iron-free and iron-loaded frataxin trimers, and a single-particle electron microscopy reconstruction of a 24 subunit oligomer. The structures reveal fundamental aspects of the frataxin mechanism. The trimer has a central channel in which one atom of iron binds. Two conformations of the channel with different metal-binding affinities suggest that a gating mechanism controls whether the bound iron is delivered to other proteins or transferred to detoxification sites. The trimer constitutes the basic structural unit of the 24 subunit oligomer. The architecture of this oligomer and several features of the trimer structure demonstrate striking similarities to the iron-storage protein ferritin. The data reveal how stepwise assembly provides frataxin with the structural flexibility to perform two functions: metal delivery and detoxification.

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Structure 14, 1535–1546, October 2006 ª2006 Elsevier Ltd All rights reserved DOI 10.1016/j.str.2006.08.010
The Structures of Frataxin Oligomers
Reveal the Mechanism for the Delivery
and Detoxification of Iron
Tobias Karlberg,
Ulrika Schagerlo
Oleksandr Gakh,
Sungjo Park,
Ulf Ryde,
Martin Lindahl,
Kirstin Leath,
Elspeth Garman,
Grazia Isaya,
and Salam Al-Karadaghi
Department of Molecular Biophysics
Department of Theoretical Chemistry
Center for Chemistry and Chemical Engineering
Lund University
P.O. Box 124
SE-221 00 Lund
Departments of Pediatric & Adolescent Medicine
and Biochemistry & Molecular Biology
Mayo Clinic College of Medicine
Rochester, Minnesota 55905
Department of Biochemistry
University of Oxford
South Parks Road
Oxford, OX1 3QU
United Kingdom
Defects in the mitochondrial protein frataxin are re-
sponsible for Friedreich ataxia, a neurodegenerative
and cardiac disease that affects 1:40,000 children.
Here, we present the crystal structures of the iron-
free and iron-loaded frataxin trimers, and a single-
particle electron microscopy reconstruction of a 24
subunit oligomer. The structures reveal fundamental
aspects of the frataxin mechanism. The trimer has a
central channel in which one atom of iron binds. Two
conformations of the channel with different metal-
binding affinities suggest that a gating mechanism
controls whether the bound iron is delivered to other
proteins or transferred to detoxification sites. The tri-
mer constitutes the basic structural unit of the 24 sub-
unit oligomer. The architecture of this oligomer and
several features of the trimer structure demonstrate
striking similarities to the iron-storage protein ferritin.
The data reveal how stepwise assembly provides fra-
taxin with the structural flexibility to perform two func-
tions: metal delivery and detoxification.
The ability to incorporate iron into prosthetic groups and
proteins is essential for the biogenesis of many vital en-
zymes in all organisms (Al-Karadaghi et al., 2006; Lill
et al., 1999). However, in the presence of atmospheric
oxygen at neutral pH, ferrous iron (Fe
) is readily
oxidized to the ferric form (Fe
) with a decrease in sol-
ubility from %10
M(Williams, 1982). In
addition, Fe
can interact with hydrogen peroxide,
a byproduct of oxygen metabolism, and catalyze the
generation of highly toxic hydroxyl radicals, which ulti-
mately results in oxidative damage to proteins, mem-
branes, and DNA (Halliwell, 1978). Thus, to maintain an
adequate supply of iron, cells require molecular mecha-
nisms to overcome both the limited bioavailability and
potential toxicity of this transition metal. A well-charac-
terized mechanism is the one utilized by the ferritins,
a conserved family of proteins that assemble into hollow
particles able to accommodate large amounts of iron,
which play a critical role in iron detoxification and stor-
age in the cytoplasm and other cellular compartments
(Chasteen and Harrison, 1999). In mitochondria of
most tissues, another highly conserved protein, frataxin,
has been recently shown to perform the dual function of
making Fe
bioavailable and detoxifying surplus iron
(reviewed in Al-Karadaghi et al., 2006).
The function of frataxin has been the subject of in-
tense investigation ever since defects in this protein
were linked to Friedreich ataxia, a progressive disease
of children and adolescents characterized by neurolog-
ical impairment, cardiomyopathy, and diabetes mellitus
(Campuzano et al., 1996). In vivo frataxin promotes the
biosynthesis of heme (Schoenfeld et al., 2005; Zhang
et al., 2005) as well as the assembly and repair of iron-
sulfur clusters (Bulteau et al., 2004; Duby et al., 2002;
Gerber et al., 2003). This correlates well with the ability
of frataxin to deliver Fe
to ferrochelatase, the enzyme
that catalyzes the last step of heme biosynthesis (O’Neill
et al., 2005a; Park et al., 2003; Yoon and Cowan, 2004);
to the iron-sulfur cluster scaffold protein IscU, which ini-
tiates the assembly of iron-sulfur clusters (Layer et al.,
2006; Yoon and Cowan, 2003); and to the [3Fe-4S]
form of mitochondrial aconitase, which yields the active
enzyme (Bulteau et al., 2004). In vivo frataxin
also plays a primary role in the protection against oxida-
tive stress (Gakh et al., 2006; Schultz et al., 2000; Thier-
bach et al., 2005; Vazquez-Manrique et al., 2006). This is
consistent with the ability of frataxin to catalyze the
oxidation of Fe
to Fe
, by using O
or H
as the
oxidant, and to promote the conversion of Fe
to a
stable protein-bound mineral (Bou-Abdallah et al.,
2004; Nichol et al., 2003; O’Neill et al., 2005a; Park
et al., 2002).
Biochemical studies have shown that self-assembly is
a central part of the mechanism of iron detoxification by
frataxin. Thus, the bacterial frataxin homolog, CyaY,
forms a tetramer when Fe
is added anaerobically,
while larger oligomers are formed in the presence of
and atmospheric O
(Bou-Abdallah et al., 2004;
Layer et al., 2006). Using this mechanism, CyaY seques-
ters w25 atoms of iron per subunit in a polynuclear Fe
hydroxo(oxo) mineral. Assembly of yeast frataxin also
depends on the presence of iron, and it proceeds
according to the progression a / a
/ a
/ a
/ a
(Adamec et al., 2000; Gakh et al., 2002). The
48 subunit oligomer can store w50–75 iron atoms per
subunit in 1–2 nm cores, which are structurally similar
to ferrihydrite, the main biomineral formed by vertebrate
ferritins (Park et al., 2003; Nichol et al., 2003). Inter-
actions leading to stepwise assembly of yeast frataxin
*Correspondence: (G.I.), (S.A-K.)
Page 1
oligomers have been suggested to be mediated by
alignment and complexation of ferrihydrite crystallites,
formed at separate mineralization sites (Park et al.,
2003). Indeed, yeast frataxin oligomers readily disas-
semble into monomers upon reduction of their ferric
iron cores (Park et al., 2003). Unlike CyaY and yeast fra-
taxin, human frataxin assembles in an iron-independent
manner via stable subunit-subunit interactions medi-
ated by the nonconserved N-terminal region of the pro-
tein (O’Neill et al., 2005b). Like yeast frataxin, the human
protein has ferroxidase activity and forms iron cores
structurally similar to ferrihydrite (Nichol et al., 2003).
Although the three-dimensional structures of the
monomers of CyaY, yeast, and human frataxin have
been determined (Adinolfi et al., 2002; Cho et al., 2000;
Cook et al., 2006; Dhe-Paganon et al., 2000; He et al.,
2004), the molecular mechanism that enables frataxin
to function in both iron delivery and detoxification re-
mains elusive. In light of the high degree of amino acid
sequence conservation among frataxins from different
organisms and the fact that self-assembly is a conserved
property of the protein, we screened for point mutations
that would enable yeast frataxin to form stable oligo-
mers in an iron-independent manner, similar to human
frataxin. Here, iron-free and iron-loaded trimers and
a 24 subunit oligomer formed by an Y73A variant of
yeast frataxin were characterized by X-ray crystallogra-
phy and single-particle electron microscopy (EM) recon-
struction. The data suggest a conserved mechanism in
which the trimer is the basic functional unit of frataxin re-
sponsible for Fe
binding and delivery to other proteins,
while higher-order oligomers provide a basic structure
suitable for iron detoxification and storage.
Results and Discussion
Preparation of Stable Oligomers of Yeast Frataxin
The yeast frataxin monomer assembles stepwise in an
iron-dependent manner (Adamec et al., 2000). Trimer
was suggested to represent the functional unit of yeast
frataxin, but the instability of this species hampered
structural studies (Park et al., 2002; unpublished data).
In contrast, the human frataxin monomer assembles in
an iron-independent manner via stable protein-protein
interactions (O’Neill et al., 2005b). However, human fra-
taxin particles are not suitable for structural studies due
to their tendency to polymerize (Cavadini et al., 2002).
We therefore screened for point mutations that would
enable the yeast frataxin monomer to oligomerize in an
iron-independent manner. The mature form of the pro-
tein (i.e., lacking the mitochondrial matrix-targeting pep-
tide) (Branda et al., 1999) was subjected to site-directed
mutagenesis whereby residues conserved between
yeast and human frataxin were replaced by alanine res-
idues; then, mutant proteins were expressed in E. coli
and bacterial cell extracts analyzed by size-exclusion
chromatography as described (Gakh et al., 2006; O’Neill
et al., 2005b). Mutations in two regions (N terminus and
strands b2–b3) resulted in proteins that oligomerized
during expression in E. coli, yielding trimer and lower
levels of larger oligomers. The trimer and a 24 subunit
oligomer formed by one of these proteins (Y73A) were
further characterized, as described below.
Crystal Structure of the Trimer
The Y73A yeast frataxin crystallized in space group I2
The structure was solved by molecular replacement by
using the structures of CyaY (Cho et al., 2000) and hu-
man frataxin (Dhe-Paganon et al., 2000) monomers as
search models. The NMR structure of the yeast frataxin
monomer available at that time (He et al., 2004) did not
give a satisfactory molecular-replacement solution.
The trimer structure was refined to the crystallographic
R factor of 0.23 (R
= 0.28). The mature form of the pro-
tein used in this study consisted of 123 amino acid res-
idues (52–174). Of these, the first 9 and the last 2 were
disordered in the electron density map and could not
be modeled. The final refinement statistics are pre-
sented in Table 1.
The overall arrangement of monomers in the trimer
structure is almost flat, with dimensions of 75 A
75 A
3 30 A
(Figures 1A and 1B). Each subunit is folded
into an a/b sandwich with two a helices (a2, a3) packed
against a five-stranded (b1–b5), antiparallel, twisted
b sheet. Two additional b strands (b6, b7) build up
a b hairpin almost perpendicular to strand b 5. A short he-
lix at the protein N terminus (a1), together with a 7 resi-
due extended coil region connected to helix a2, build
up an N-terminal extension that interacts with the neigh-
boring monomer within the trimer (Figures 1A and 1B).
The overall fold of each subunit is similar to that reported
earlier for different monomeric forms of the protein, al-
though with some important deviations. Helix a2is
about two turns shorter in the trimer structure, suggest-
ing that oligomerization involves partial unfolding of this
element. Moreover, the N-terminal extension, which is
highly flexible in the yeast frataxin monomer (Cook
et al., 2006), is stabilized within the trimer by the interac-
tions between neighboring subunits (Figure 1B).
Table 1. Crystallographic Data Collection and Refinement
Native Fe(II)-Loaded
Data Collection
Beamline I911-2 ID23-1
Space group I2
Wavelength (A
) 1.0516 0.97625
Cell dimensions:
a, b, c (A
121.22, 121.22,
123.80, 123.80,
Resolution range (A
) 20–3.0 (3.2–3.0) 25–3.6 (3.8–3.6)
Completeness (%) 98.3 (94.7) 99.6 (99.4)
I/s(I) > 3 (%) 86.3 (61.1) 95.6 (83.2)
Multiplicity 11.6 (11.9) 22.8 (22.4)
0.051 (0.22) 0.036 (0.11)
Solvent content (%) 77.2 78.6
0.230 (0.276)
Rmsd bond
distances (A
Rmsd bond
angles (
= SjI
2 <I>j/SI, where I
is an individual intensity measure-
ment and <I> is the average intensity for this reflection.
= SjF
2 F
, where F
and F
are the observed and
calculated structure factor amplitudes, respectively. R
is the
same as R
, but it is calculated on 5% of the data excluded
from refinement.
Page 2
The plane of the b sheet in each subunit is inclined
with an angle of about 30
relative to the plane of the tri-
mer. Solvent-accessible parts of helix a3 and strand b7,
the hairpin loop between strands b6 and b7, and the loop
between strands b5 and b6 create one surface of the tri-
mer (Figure 1A). The opposite surface is created by ele-
ments from two different subunits, with the N-terminal
extension of one subunit packed against the b sheet sur-
face of the next, which, in turn, contributes helix a2,
strands b1–b3, and the loop between b3 and b4 to the
surface (Figure 1B).
The Role of the N-Terminal Region
The N-terminal region of each subunit appears to play
a crucial role in the stabilization of the trimer. In each
monomer, the N-terminal region is anchored to the
core structure at the base (Figure 2A) and through helix
a1, which interacts with the b sheet of another subunit
(Figure 2B). Figure 2C shows a 3F
2 2F
electron den-
sity map superimposed on the N-terminal region. At
the base, the conformation of the N-terminal extension
is stabilized by an extensive network of interactions be-
tween the main chain carbonyls of A72, H74, and E75
and the amide groups of H74, E76, and D78, respec-
tively, and between the side chains of H74, E76, and
D78 and the side chains of D79, R141, and K123, respec-
tively (Figure 2A). Interactions of helix a1 with the b sheet
of another subunit include residues P62, E64, V65, and
L68 from helix a1 and residues T110, E112, T118, and
V120 from the b sheet (Figure 2B). Hydrophobic residues
P62, V65, and L68 in the N-terminal extension are di-
rectly packed against residues T110 and T118 (Fig-
ure 2B). Only the side chain of T118 and the carbonyl
oxygen of E64 are at hydrogen-bonding distance from
each other.
Interestingly, the N-terminal extension also plays
a major role in the packing of trimers within the crystals,
where two monomers from neighboring trimers pack
with their b sheets facing each other. The N-terminal ex-
tension is responsible for the interactions within the
crystal lattice and is sandwiched between the structural
elements (not shown). Similar interactions may be re-
sponsible for the packing of trimers within the 24 subunit
oligomer (see below).
The Channel at the 3-Fold Axis of the Trimer
The trimer is further stabilized by interactions between
the loops around a central channel at the 3-fold axis
(Figures 1A and 1B). On one surface of the trimer, the
b hairpin loop between strands b6 and b7 (residues
S151–G155), the C terminus of strand b5, and the loop
between strands b5 and b6 (residues L144–W149) build
up a unique helical structural element (shown in red in
Figures 1A and 3A). Three such elements are arranged
around the 3-fold axis of the trimer, with the loop be-
tween strands b5 and b6 of one subunit packed against
the hairpin loop of the next subunit (Figure 3A). Two pu-
tative hydrogen bonds between subunits, one between
the carbonyl oxygen of L152 and the amide group of
G147 and the other between the side chain of N146
and the carbonyl oxygen of Q154, contribute to the
stabilization of the loops (Figure 3A). The side chains
of L145, V150, and L152 from the three subunits are ex-
posed to the solvent and together create a hydrophobic
edge around the entrance to the channel (Figure 3A). In
the sequence of human frataxin, L145, which is closer to
the surface, is replaced by a threonine, L152 is replaced
by a serine, while V150 is conserved (Figure 4). Each
subunit contributes an invariant aspartate residue
(D143, at the end of strand b5); the three D143 residues
are located approximately in the middle of the channel,
with their side chains directed toward the opening at
the opposite end (Figure 3
On the other surface of the trimer, the channel opening
is built up by residues between G117 and D143, which
belong to strands b3, b4, and b5 (Figures 1B and 3B).
Figure 1. Overall Architecture of the Yeast Frataxin Trimer in Ribbon
(A) Suggested outer surface of the trimer with the exposed helices
a2 and a3 (shown in yellow). Loops and b strands are shown in
brown or red.
(B) Suggested inner surface of the trimer. The N-terminal exten-
sion, which contributes to the stabilization of the trimer, is shown
in green.
The Structures of Frataxin Oligomers
Page 3
This is the most highly conserved stretch of amino acids
within eukaryotic frataxin sequences (Figure 4). Resi-
dues K123–I130 build up part of strands b3 and b4 and
the loop between them. The strands are sharply bent
by w80
relative to the plane of the central b sheet, while
the loop between them (residues P125–K128) extends
into the putative exit of the channel. Several interactions
may contribute to the stabilization of this loop. Among
them is a putative hydrogen bond between the side
chain of D143 and the amide of Q129 of the same sub-
unit. Additional interactions involve putative hydrogen
bonds between the side chain of Q129 and the carbonyl
oxygen of P126 of the next subunit, and between the
side chains of N127 of one subunit and E75 of another
(Figure 3B). Residues P126 and Q129 are invariant in
all frataxin sequences (Figure 4).
Difference electron density maps show that, within the
same crystallographic structure, loop P125–K128 may
exist in two alternative conformations, which approxi-
mately have the same occupancy (w0.5) (Figure 3C). In
the second conformation, the tip of the loop is displaced
by about 8 A
. This brings residues N127 and Q129 in
contact with the opposite subunit (Figure 3C). New inter-
actions are formed between N127 and Q129, and be-
tween D143 and the side chains of N127 and Q129 of
the same subunit. The interactions between N127 and
E75 and between Q129 and P126 are not present in
this conformation. The peptide unit of P126 is flipped,
resulting in the carbonyl oxygen pointing toward the
interior of the channel, a direction opposite to that ob-
served in the first conformation (Figure 3C). A shift of
the side chain of K128 creates a positively charged lid
at the channel opening (Figure 3C).
The channel is funnel shaped, with openings of w15 A
and w4A
at the two sides of the trimer, and with increas-
ing acidity toward the latter (Figures 5A–5D). In analogy
with the channels at the 3-fold axis of ferritin shells
(Grant et al., 1998; Hempstead et al., 1994; Stillman
et al., 2001), the larger and smaller openings may serve
as an entrance and exit, respectively, for iron ions. How-
ever, while the entrance to the ferritin channel is lined by
basic residues, the putative entrance to the frataxin
channel is lined by hydrophobic residues (Figures 3A
and 5C), which may serve not only to guide ions into
the channel, but also to provide a docking surface for
the proteins that interact with frataxin (Bulteau et al.,
2004; Park et al., 2003; Yoon and Cowan, 2003).
The Crystal Structure of the Iron-Loaded Trimer
Iron loading of the frataxin trimer was achieved by aero-
bic incubation of the purified oligomer with Fe
at a
molar ratio of two iron atoms per monomer, followed
by isolation of the iron-loaded trimer by size-exclusion
chromatography. A stoichiometric ratio of 0.9 (60.1)
Figure 2. Stabilization of the Trimer by the N-Terminal Extension
(A) Interactions at the base of the N-terminal extension.
(B) Interactions of helix a1 of one subunit of the trimer with the b sheet of another subunit.
(C) Stereoview showing a 3F
2 2F
density map (blue) contoured at the 1.3s level superimposed on helix a1.
Page 4
iron atoms per iron-loaded trimer was measured by
using particle-induced X-ray emission (microPIXE)
(Garman and Grime, 2005), whereas there was no mea-
surable iron in the unloaded control. The iron-loaded
trimer was crystallized at conditions similar to those of
the iron-free complex, and diffraction data were col-
lected to a resolution of 3.6 A
. Despite the low resolution
of the data, the difference electron density clearly shows
a high sigma peak (electron density is visible up to the
level of 5s; Figure 5C) at the center of the channel at
the 3-fold axis of the trimer. The presence of one iron
atom per trimer is in agreement with the microPIXE
results. Three additional peaks, which most probably
correspond to solvent molecules, are positioned at
from the center of the density (Figures 5C and
5D). This distance is within the range expected for
metal-solvent bond distances. Interestingly, in the pres-
ence of iron, the P125–K128 loop is present only in the
first of the two conformations described above. The
metal binds close to the suggested entrance at w4A
from the side chains of the three D143 residues (Figures
5C and 5D). It cannot be excluded that additional solvent
molecules, not visible at the present resolution of the
data, bridge the interactions between the iron and pro-
tein groups. Owing to the hydrophobic lid formed by
V150, L152, and especially L145, the iron atom is fully
enclosed within the channel (Figure 5C).
Calculations of the electrostatic potential and corre-
sponding metal-binding energies in the central pore of
the frataxin trimer indicate that the change in the confor-
mation of the P125–K128 loop may affect the iron-
binding properties of the channel, with the second con-
formation demonstrating higher metal-binding affinity
(Figure 6; also see Experimental Procedures). This is in
apparent contrast with the fact that in the structure of
the iron-loaded trimer the P125–K128 loop is present
in the first, low-affinity binding conformation. A possible
explanation is that upon iron binding the interaction
between D143 and the metal prevents D143 from con-
tributing to the stabilization of the second, high-affinity
binding conformation, favoring a shift to the low-affinity
conformation. This may facilitate iron delivery to pro-
teins docked at the channel entrance, while conditions
that stabilize the second conformation, which remain
to be identified, may promote iron passage through
the channel. The suggested channel exit appears to be
Figure 3. Stereoview of the Structure of the
Central Channel
(A) Putative channel entrance. The helical
structural motif from each monomer is shown
in red.
(B) The first conformation of the proposed
channel exit. The residues that contribute to
the structure and stabilization of the trimer
are shown as sticks. In (A) and (B), the elec-
tron density contoured at the 1.3s level is
shown superimposed on the model.
(C) The second conformation of the proposed
channel exit. The teal ribbon model with
amino acid side chains (shown as sticks) rep-
resents the second conformation of the chan-
nel exit. The structure of the first conforma-
tion shown as a brown ribbon model is
superimposed to demonstrate the two posi-
tions of the P125–K128 loop.
The Structures of Frataxin Oligomers
Page 5
connected to negatively charged patches on the side of
each subunit (Figure 5B). The residues forming the
patches, D78, D79, D82, D86, E89, E90, and E93 from
helix a2, and D101 from strand b1, are conserved in eu-
karyotic sequences (Figure 4). NMR iron titrations of mo-
nomeric frataxins have implicated these residues in iron
binding (Cook et al., 2006; Nair et al., 2004). In addition,
site-directed mutagenesis has shown that they com-
prise functionally distinct sites that are involved in iron
oxidation and mineralization, and that they are impor-
tant for iron detoxification in vivo (Gakh et al., 2006).
Each patch is lined by hydrophobic and positively
charged residues (H74, H106, K123), which together
with the side chain of K128 (in the high-affinity binding
conformation of the P125–K128 loop), may serve in lead-
ing metal ions from the channel exit directly to the detox-
ification sites. The putative ferroxidation site is in close
vicinity of the channel exit and entails an arrangement
of residues (H74, D78, D79, D82, and H83) reminiscent
of the di-iron site of ribonucleotide reductase (Nordlund
and Eklund, 1995)(Figure 5E). The residues constituting
this site have a different arrangement in the trimer com-
pared to the monomer structure of yeast frataxin (Cook
et al., 2006), due to the partial unfolding of helix a2, im-
plying that trimer formation is needed for the formation
of a functional ferroxidation site.
Position of Pathogenic Frataxin Point Mutations
Defects in frataxin are linked to the neurodegenerative
disease Friedreich ataxia (Campuzano et al., 1996).
Most patients carry large GAA trinucleotide repeat ex-
pansions in the first intron of the frataxin gene that ham-
per transcriptional elongation, causing a severe reduc-
tion in the levels of frataxin. About 4% of the patients
carry an expansion in one allele and a point mutation
in the other allele (Campuzano et al., 1996). While the
majority of the pathogenic point mutations affect the
hydrophobic core of the structure (L84S, I130F, L132P,
W149G, L158H, and L158F, yeast numbering), four mu-
tations are likely to destabilize formation of the trimeric
complex (Figure 7). These include G107V, W131R,
R141C (G130V, W155R, and R165C, human numbering),
and D122Y at a position that corresponds to P100 in
yeast. P100 is located in the loop between helix a2 and
strand b1, at the tip of the subunit close to the surface
against which helix a1 is packed. G107 is located in
a loop between strands b1 and b2. Its carbonyl oxygen
makes a putative hydrogen bond with the amide group
of K123, thus contributing to the stabilization of the con-
formation of the regions between K123 and I130. K123 is
also involved in interactions with the N-terminal ex-
tension through a putative hydrogen bond with D78.
Moreover, W131, which is exposed to the surface of
the central b sheet, is involved in interactions with the
N-terminal extension. Another mutation, R141C, may
disrupt a putative hydrogen bond to the carbonyl of
P125, which may affect the conformation of the loop at
the channel exit. Solution studies of the effect of these
mutations, in combination with a rational design of com-
pounds that stabilize the frataxin trimer, might offer
a new opportunity for the treatment of Friedreich ataxia.
EM Single-Particle Reconstruction
of the 24 Subunit Oligomer
The 24 subunit oligomer formed by yeast frataxin Y73A
was reconstructed from 4,000 particles at a resolution
of 19 A
(Figures 8A and 8B). The reconstruction shows
a cubic shape in which the trimer represents the basic
structural unit, with the center of each trimer positioned
at the 3-fold axis of the cube (Figure 8C). Docking of the
trimer into the reconstruction (Figure 8D) shows that the
particle is primarily stabilized by interactions between
Figure 4. Alignment of Frataxin Sequences
The amino acid sequences of frataxin from yeast, human, mouse, and Drosophila are aligned with the bacterial CyaY frataxin homologs from
S. typhimurium, E. coli, and P. aeruginosa. Residues conserved only in eukaryotic or bacterial sequences are marked in green and blue, respec-
tively; invariant residues are marked in red. The positions of secondary structural elements are shown along the sequence. The overall sequence
identity is 40% between the yeast and human sequences, and it is 28% between the 106 overlapping residues (68–174) of the yeast and E. coli
sequences. This figure was generated with Alscript (Barton, 1993). The sequences are identified by their Swiss-Prot entry names.
Page 6
the N termini of subunits from neighboring trimers
(Figure 8E). The best fit is obtained with the N termini
pointing toward the interior of the complex. This location
of the N termini places the suggested entrance to the
channel on the outside of the particle (Figure 8F), while
the exit and the oxidation and mineralization sites are
located in the interior. Ongoing reconstruction of iron-
loaded oligomers shows that the packing of trimers de-
limits a cavity for iron deposition (unpublished data).
This architecture is in agreement with the iron-storage
function of frataxin and is remarkably reminiscent of
the iron-storage protein ferritin (Grant et al., 1998;
Hempstead et al., 1994; Stillman et al., 2001)(Figure 8F).
Concluding Remarks
A reduction in the levels of frataxin is responsible for
Friedreich ataxia, a fatal neurodegenerative and cardiac
disease (Campuzano et al., 1996). Frataxin is an iron-
binding protein required for the maintenance of mito-
chondrial iron balance in humans and other eukaryotes,
owing to its roles in the delivery of iron to the heme and
iron-sulfur cluster biosynthetic pathways and the detox-
ification of surplus iron (reviewed in Al-Karadaghi et al.,
2006). The mechanism that enables frataxin to perform
such essential functions has been eagerly pursued but
has remained elusive even after different structures of
monomeric frataxins were solved. The structures of olig-
omeric frataxin species described here suggest that
self-assembly provides the protein with the means to
bind iron and either transfer it to other proteins or detox-
ify and store it.
Whereas the assembly of yeast frataxin and CyaY is
driven by the binding and oxidation of iron (Layer
et al., 2006; Park et al., 2003), assembly of human fra-
taxin occurs in an iron-independent manner via sub-
unit-subunit interactions mediated by the protein N
Figure 5. Potential Functional Sites and
Metal Binding to the Central Channel of the
(A and B) Electrostatic surface-potential dis-
tribution for the suggested outer (A) and inner
(B) surfaces of the frataxin trimer. Red and
blue denote negative and positive potentials,
respectively. The residues constituting one
of the three proposed ferroxidation sites are
shown as sticks in (B).
(C) Top view of the channel with bound iron.
The F
2 F
difference electron density map
contoured at the 4s level (magenta) is shown
superimposed on the 3F
2 2F
density map
(blue). The bound iron (shown as a blue
sphere) is located w6A
from the entrance
to the channel, as defined by the side chain
of L145. The red spheres correspond to sol-
vent molecules.
(D) Cross-section through the central channel
showing the electrostatic-potential distribu-
tion within the channel. The bound iron and
surrounding solvent molecules are shown
as spheres.
(E) The proposed ferroxidation site of frataxin
viewed with an electrostatic-potential sur-
face. Distances (A
) between the side chains
are indicated in the figure.
The Structures of Frataxin Oligomers
Page 7
terminus (O’Neill et al., 2005b). The Y73A variant used in
the present work was identified by screening for point
mutations that would enable yeast frataxin to form sta-
ble oligomers in an iron-independent manner like human
frataxin. Similar variants found in the screen included
single substitutions at the base of the N-terminal exten-
sion, H74A and D78A, and double substitutions in the
b sheet, V108A/T110A and T118A/V120A. These muta-
tions probably induce conformational changes that fa-
vor the interaction of the N-terminal extension of one
subunit with the b sheet of another, thereby facilitating
oligomerization. The N-terminal region of human frataxin
is 18 residues longer than that of the yeast protein and
has a significantly different amino acid sequence,
whereas CyaY only has a short stretch of amino acids
upstream of helix a2(Figure 4). Thus, we speculate
that different N-terminal regions reflect different modes
by which frataxin assembly can be induced and regu-
lated in different organisms.
We have shown that one atom of iron binds in the chan-
nel at the 3-fold axis of the trimer. The two possible con-
formations of the channel suggest that a gated mecha-
nism controls whether the iron stays in the channel or
is transferred to the detoxification sites at the channel
exit. Because a single iron atom is delivered to ferroche-
latase during heme synthesis, IscU during iron-sulfur
cluster assembly, and aconitase during [3Fe-4S]
repair, the trimer could be a suitable source of metal in
all of these processes in which frataxin has been impli-
cated as the iron donor. In addition, the relatively large
hydrophobic surface that lines the entrance to the chan-
nel may enable the trimer to interact with structurally
different proteins. The reconstruction of a 24 subunit
oligomer further shows that the trimer is the building
block of larger frataxin complexes. It also reveals striking
similarities in the structural organization of frataxin olig-
omers and the iron-storage protein ferritin, despite the
lack of any apparent evolutionary relationship between
these two protein families. It can also be expected that
the organization of the iron core of frataxin will be re-
miniscent of the iron core of ferritin (Nichol et al., 2003).
Together these data suggest that self-assembly pro-
vides frataxin with the structural features required to
perform both iron delivery and iron detoxification. The
insights gained from this work provide a framework to
identify natural factors or develop compounds that
enhance frataxin activity by modulating its oligomeriza-
tion behavior.
Experimental Procedures
Protein Preparation and Crystallization
The mutant Y73A frataxin from S. cerevisiae (residues 52–174 of the
yeast frataxin sequence, corresponding to the mature form of the
protein) (Branda et al., 1999) was recombinantly expressed in
E. coli and purified with a modification of a previously described pro-
cedure (Cavadini et al., 2002). Briefly, bacterial lysate (w 25 ml at
26 mg/ml total protein) was applied to a Macro-Prep DEAE column
(16 mm 3 50 cm) (Bio-Rad), and protein was eluted with a 1 l linear
gradient, from 50 to 525 mM NaCl, in 20 mM Tris-HCl (pH 8.0) at
a flow rate of 10 ml/min. Most Y73A frataxin was eluted in two sep-
arate pools, a low-salt pool (300–380 mM NaCl) containing a
, and
a high-salt pool (440–510 mM) containing a
. Each DEAE pool
was diluted to 600 ml and loaded onto a Macro-Prep High Q column
(Bioscale MT20) (Bio-Rad), and the protein was eluted with a 500 ml
linear NaCl gradient as described above at a flow rate of 5 ml/min.
Two High Q pools were obtained, a
(w410–510 mM NaCl) and a
(w200–290 mM NaCl). Each pool was concentrated to 1 ml, loaded
onto a Sephacryl 300 column (16 mm 3 60 cm) (Amersham-Biosci-
ences), and eluted with 120 ml of 10 mM HEPES-KOH (pH 7.3),
100 mM NaCl at a flow rate of 0.4 ml/min. Fractions containing trimer
) or a 24 subunit oligomer (a
) were pooled and applied to a Mono
Q HR5/5 column (Amersham-Biosciences) and eluted with a linear
gradient, from 100 to 450 mM NaCl, at flow rate of 1ml/min. Fractions
Figure 6. Calculated Metal Binding Energy along the 3-Fold Symme-
try Axis of the Trimer
Electrostatic interaction energies with a +2-charged ion were calcu-
lated for each of the two conformations of the P125–K128 loop as
described in Experimental Procedures. The red and blue plots
show the metal-binding energies for the first and second configura-
tions, respectively, along the 3-fold-symmetry axis of the trimer. The
position of the two plots along the 3-fold axis is defined by the Mol-
Script y coordinate (y coord, in angstroms from the unit cell origin).
The position of the metal-binding energy in the first configuration of
the channel (red plot) is in agreement with the position of the metal
ion in the iron-loaded structure (w6A
from the side chain of L145).
Figure 7. Position of Pathogenic FRDA Mutations
Residues that are mutated in some Friedreich ataxia patients are
mapped on one subunit of the trimer. See Results for details.
Page 8
containing a
(w200–250 mM NaCl) or a
(w280–310 mM NaCl)
were concentrated and buffer exchanged to 10 mM HEPES-KOH
(pH 7.3).
Trimer crystals were grown by vapor diffusion in a hanging drop
at 15
C. Crystallization drops were made by mixing 3 ml of a protein
solution at a concentration of 7 mg/ml in 10 mM KOH-HEPES
(pH 7.3) with 3 ml of a reservoir solution containing 0.1 M Bis-Tris
(pH 5.5), 2.0 M ammonium sulfate, and 4% (v/v) g-butyrolactone.
Crystals appeared after 5 days. The best crystals had dimensions
of w0.15 mm 3 0.15 mm 3 0.15 mm. The crystals belonged to space
group I2
3. Iron loading of frataxin trimer was achieved by incubating
the purified oligomer with ferrous iron at a molar ratio of two iron
atoms per monomer for 2 hr at 30
C, followed by isolation of the
iron-loaded trimer by size-exclusion chromatography. Crystals in
space group I2
3 were obtained in the same manner as for the
metal-free trimer.
Data Collection and Structure Determination
For data collection, 25% glycerol was used as cryoprotectant, and
crystals were mounted on a rayon loop and flash frozen directly in
Figure 8. Electron Microscopic Model of a 24
Subunit Frataxin Oligomer
(A) EM images of the 24 subunit oligomer in
1% uranyl acetate negative stain on the re-
corded micrograph.
(B) A comparison between projection images
of the reconstructed model (to the left) and
the class averages (to the right). See Experi-
mental Procedures for details.
(C) View approximately along the 2-fold axis,
which relates two trimers. A total of eight tri-
mers make the oligomer.
(D) Packing of trimers docked into the EM re-
construction. The trimers (green and purple)
are shown in surface representation.
(E) A stereoview showing interactions be-
tween the N termini of two subunits from
neighboring trimers packed within the 24
subunit particle.
(F) Surface representation of frataxin (left)
and horse-spleen ferritin (right) 24-meric olig-
omers viewed along the 3-fold axis, repre-
sented with the same scale. The width of
the particles is 115 A
and 130 A
, respectively.
Trimers are colored according to their elec-
trostatic surface potentials.
The Structures of Frataxin Oligomers
Page 9
a stream of boiled-off nitrogen gas held at 100 K. A native data set to
3.0 A
resolution (I2
3) was collected with a MAR Research CCD de-
tector at MAX II synchrotron laboratory stations I711 and I911-2 in
Lund, Sweden (Cerenius et al., 2000; Mammen et al., 2004). The res-
olution of the data could not be improved at the higher-energy Swiss
Light Source synchrotron. A data set of the iron-loaded trimer was
collected with an ADSC CCD detector at beamline ID23-1, ESRF
synchrotron facility in Grenoble, France, to a resolution of 3.6 A
3). All data sets were processed with the XDS package (Kabsch,
1993). The structure was solved by molecular replacement with the
program Phaser (McCoy et al., 2005) by using a combination of the
solved crystal structures of human frataxin and the E. coli homolog,
CyaY (Cho et al., 2000; Dhe-Paganon et al., 2000), as a search probe.
The model was built by using the graphical program O (Jones et al.,
1991) and was refined with CNS (Brunger et al., 1998). The progress
of refinement was followed by decreasing R and R
values. Data
collection and refinement statistics are shown in Table 1.
Particle-Induced X-Ray Emission Measurements
The particle-induced X-ray emission (microPIXE) measurements
were carried out at the National Ion Beam Centre, University of Sur-
rey, UK on a beamline arranged as described by Grime et al. (1991).
Small volumes (0.2 ml) of the unloaded and iron-loaded protein con-
centrated to 20 mg/ml in Tris-HCl buffer (pH 7.3) were each pipetted
onto two separate 2 mm thick mylar films stretched over three alumi-
num target holders and dried, as described (Garman, 1999). A
2.5 MeV proton beam of 3 mm diameter was used to induce charac-
teristic X-ray emission from the dried liquid droplet under vacuum.
The X-rays were detected in a solid-state lithium-drifted silicon de-
tector with high energy resolution. The proton beam was then
scanned spatially in the x and y dimensions. Using the data collec-
tion software, spatial maps of all elements heavier than sodium
that were present in the sample were obtained. Quantitative infor-
mation was obtained by collecting spectra at four separate selected
points on the drop and also at a point on the backing foil. These
spectra were analyzed with GUPIX (Johansson et al., 1995) to ex-
tract the areal density of each element of interest in the sample
with respect to the sulfur peak from the methionines and cysteines
in the protein. The sulfur signal provides a very convenient internal
calibration, allowing the number of iron atoms per protein monomer,
and hence per trimer, to be obtained.
Calculation of Metal Interaction Energies in the Channel
along the 3-Fold Axis
Calculations of the electrostatic potential in the central pore of the
frataxin trimer were performed by solving the Poisson-Boltzmann
equation with the program MEAD (Macroscopic Electrostatics with
Atomic Detail) (Bashford, 1997; Bashford and Gerwert, 1992). The
electrostatic potential was calculated for each of the two different
conformations of the P125–K128 loop present in the iron-free struc-
ture of the trimer. The protein was described as a volume with a di-
electric constant of 4, dissolved in water with a dielectric constant of
80. All atoms in the protein were assigned a partial charge, taken
from the AMBER 2003 force field (Case et al., 2004; Cornell et al.,
1995). Aspartate and glutamic acid residues were assumed to be
negatively charged, and lysine and arginine residues were assumed
to be positively charged. Based on the presumed hydrogen bond
pattern, the surroundings, and the solvent exposure, we let H74,
H83, and H106 be doubly protonated and therefore positively
charged, whereas H95 was protonated on the N
atom. Several ad-
ditional calculations were made with different assignments of the
histidine residues, e.g., all residues protonated on the N
atom or
all residues doubly protonated, as well as different ionic strength
values. These variations had some influence on the absolute value
of the potential, but the shapes and positions of the two curves
shown in Figure 6 were not affected. Hydrogen atoms were added
and optimized by AMBER 8 (Case et al., 2004) before the MEAD
calculations. All atoms were assigned PARSE radii (Sitkoff et al.,
1994), and the solvent probe radius was 1.4 A
(water). The electro-
static potential was calculated along the 3-fold symmetry axis by
using a 0.5 A
grid with at least twice the size of the protein (251
grid points). The calculations were run at 300 K. The electrostatic
potential was used to calculate the electrostatic interaction energies
with a +2 ion along the 3-fold symmetry axis of the trimer, which were
obtained by multiplying the electrostatic potential at any given posi-
tion along the 3-fold axis by the charge of the metal ion. The energies
in Figure 6 exclude the solvation energy of the unbound metal ion,
which will reduce the binding energies by a constant factor for
both curves. In Figure 6, the position of the two curves along the
3-fold axis of the trimer is defined by the y coordinate of the PDB files
used to calculate the electrostatic potential.
EM Data Collection and Image Processing
Protein solution (2 ml of 0.2 mg/ml) was applied to carbon-coated,
glow-discharged copper grids (400-mesh, Electron Microscopy Sci-
ences, USA) and was allowed to adsorb for 1 min. Excess solution
was blotted, and the grids were subsequently stained with either
1% uranyl acetate in water (2 ml for 10 s) or 1% phosphor tungsten
acid in 20 mM phosphate buffer (pH 6.9) (2 ml for 1 min). Images
were acquired with a Philips CM120 equipped with a Gatan GIF
100 energy filter and Gatan 791 CCD camera (1024 3 1024 pixels)
at a magnification of 52,400-fold (sampling distance 4.67 A
). The im-
age processing was performed with the Eman software package
(Ludtke et al., 1999), applying octahedral point group symmetry.
The iterative classification procedure converged after 8 cycles of
reclassifications, and 4000 particles out of the 5400 were used for
calculating the final reconstruction. The resolution of the frataxin
oligomer was determined to 19 A
according to the 0.5 Fourier shell
correlation criteria. Strict damping of the FSC curve in high-
resolution shells was observed, which, together with the compari-
son between class averages and projections, is an indication that
the envelope of the classification process is not limiting. The dock-
ing of the X-ray structure into the EM reconstruction was done in
Chimera (Pettersen et al., 2004). The modification of the trimeric
X-ray structure was done in O (Jones et al., 1991). The final recon-
struction of the 24 subunit oligomer was evaluated by comparing
class averages with projection images in the same angular orienta-
tion of the interpolated model (Figure 8B). The image pairs revealed
the same structural features, an indication of the reconstruction be-
ing in a global minimum, rather than trapped in a local one. An initial
reconstruction was performed without any symmetry. The result
reveals a cubic shape of the molecule, vindicating our use of octahe-
dral symmetry (result not shown). Several independent reconstruc-
tions aligning on either point group symmetry or varying reference
models gave similar results. To induce a better fit to the EM model,
the monomer had to be tilted by an angle of about 12
compared to
its position in the X-ray model. The tilt did not introduce any notable
changes in the internal interactions within the trimeric structure, and
the size of the channel was conserved.
We acknowledge MAX-lab and the European Synchrotron Radiation
Facility for provision of synchrotron radiation facilities, and we thank
the National Center for High-Resolution Electron Microscopy elec-
tron biomicroscopy unit. This work was supported by grants from
the Swedish Research Council to S.A.-K. and from the National Insti-
tutes of Health/National Institute on Aging (AG15709) and the Frie-
dreich Ataxia Research Alliance (FARA) to G.I.
Received: March 21, 2006
Revised: August 21, 2006
Accepted: August 28, 2006
Published: October 10, 2006
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The Structures of Frataxin Oligomers
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Accession Numbers
Atomic coordinates for the reported crystal structures have been
deposited in the Protein Data Bank with accession number 2FQL.
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    • "It is firmly established that the Na + , Cl-and SO42-ions preferentially interact with waters [15, 16] , and so should be excluded from the protein solvation shell of both the Nstate and D-state. Indeed, the analysis of several frataxin X-ray structures, from different sources (pdb id: 2fql [17], 1ekg [18], 1ew4 [19]), revealed no interaction between the N-state of the protein and sulfate, chloride or sodium ions, even though these ions are very abundant in the crystallization conditions. Since the protein-solvent interactions involve always water molecules , the same assumption made in the case of pure water should hold in aqueous solutions of NaCl and Na 2 SO 4 . "
    [Show abstract] [Hide abstract] ABSTRACT: Both sodium chloride and sodium sulfate are able to stabilize yeast frataxin, causing an overall increase of its thermodynamic stability curve, with a decrease in the cold denaturation temperature and an increase in the hot denaturation one. The influence of low concentrations of these two salts on yeast frataxin stability can be assessed by the application of a theoretical model based on scaled particle theory. First developed to figure out the mechanism underlying cold denaturation in water, this model is able to predict the stabilization of globular proteins provided by these two salts. The densities of the salt solutions and their temperature dependence play a fundamental role.
    Full-text · Article · Jul 2015
    • "E. coli 2bzt (NMR) [56] CyaY bacterial frataxin Inhibitor of cluster assembly E. coli 1ew4 (X-ray) [141] CyaY bacterial frataxin–iron complex Iron delivery protein? E. coli 1soy (NMR) [142] YFH1 yeast frataxin Iron delivery protein Saccharomyces cerevisiae 1xaq (NMR) [143] YFH1 yeast frataxin (trimeric) Iron delivery protein Saccharomyces cerevisiae 2fql (X-ray) [144] YFH1 yeast frataxin (trimeric) Iron delivery protein Saccharomyces cerevisiae 3oeq (X-ray) [145] YFH1 yeast frataxin (trimeric, cobalt complex) Iron delivery protein Saccharomyces cerevisiae 3oer (X-ray) [145] YFH1 yeast frataxin (trimeric, Fe 2+ complex) Iron delivery protein Saccharomyces cerevisiae 4ec2 (X-ray) [146] FRDA (frataxin) Enhances desulfurase activity Homo sapiens 1ekg (X-ray) [147] FRDA (frataxin) Enhances desulfurase activity Homo sapiens 1ly7 (NMR) [148] HscA(390–615)–peptide complex Chaperone (DnaK-type protein) substrate binding domain with bound IscU peptide stable IscU variant D39A was used in both studies, which eliminated this potential ligand. "
    [Show abstract] [Hide abstract] ABSTRACT: Proteins containing iron-sulfur (Fe-S) clusters arose early in evolution and are essential to life. Organisms have evolved machinery consisting of specialized proteins that operate together to assemble Fe-S clusters efficiently so as to minimize cellular exposure to their toxic constituents: iron and sulfide ions. To date, the best studied system is the iron sulfur cluster (isc) operon of Escherichia coli, and the eight ISC proteins it encodes. Our investigations over the past five years have identified two functional conformational states for the scaffold protein (IscU) and have shown that the other ISC proteins that interact with IscU prefer to bind one conformational state or the other. From analyses of the NMR spectroscopy-derived network of interactions of ISC proteins and small-angle X-ray scattering (SAXS), chemical crosslinking experiments, and functional assays, we have constructed working models for Fe-S cluster assembly and delivery. Future work is needed to validate and refine what has been learned about the E. coli system and to extend these findings to the homologous Fe-S cluster biosynthetic machinery of yeast and human mitochondria. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
    Full-text · Article · Nov 2014
    • "By simple fitting, the curve allows to extract the thermodynamic parameters of the unfolding transitions and to measure the percentage of folded protein at the maximal stability temperature (Pastore et al., 2007; Martin et al., 2008; Sanfelice et al., 2014). This is only around 60–70% (Pastore et al., 2007) a value which cannot solely be explained by the presence of an N-terminal mitochondrial import signal (He et al., 2004; Karlberg et al., 2006 ). This observation suggests the possibility that Yfh1 exists in a partially unfolded state also at room temperature. "
    [Show abstract] [Hide abstract] ABSTRACT: Yfh1, the yeast ortholog of frataxin, is a protein of limited thermodynamic stability which undergoes cold denaturation at temperatures above the water freezing point. We have previously demonstrated that its stability is strongly dependent on ionic strength and that monovalent or divalent cations are able to considerably stabilize the fold. Here, we present a study of the folded state and of the structural determinants that lead to the strong salt dependence. We demonstrate by nuclear magnetic resonance that, at room temperature, Yfh1 exists as an equilibrium mixture of a folded species and a folding intermediate in slow exchange equilibrium. The equilibrium completely shifts in favor of the folded species by the addition of even small concentrations of salt. We demonstrate that Yfh1 is destabilized by a localized energetic frustration arising from an "electrostatic hinge" made of negatively charged residues mapped in the β-sheet. Salt interactions at this site have a "frustration-relieving" effect. We discuss the consequences of our findings for the function of Yfh1 and for our understanding of protein folding stability.
    Full-text · Article · Sep 2014
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