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PDBsum entry 2d3w
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Biosynthetic protein
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PDB id
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2d3w
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References listed in PDB file
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Key reference
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Title
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Crystal structure of escherichia coli sufc, An abc-Type atpase component of the suf iron-Sulfur cluster assembly machinery.
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Authors
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S.Kitaoka,
K.Wada,
Y.Hasegawa,
Y.Minami,
K.Fukuyama,
Y.Takahashi.
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Ref.
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FEBS Lett, 2006,
580,
137-143.
[DOI no: ]
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PubMed id
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Abstract
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SufC is an ATPase component of the SUF machinery, which is involved in the
biosynthesis of Fe-S clusters. To gain insight into the function of this
protein, we have determined the crystal structure of Escherichia coli SufC at
2.5A resolution. Despite the similarity of the overall structure with
ABC-ATPases (nucleotide-binding domains of ABC transporters), some key
differences were observed. Glu171, an invariant residue involved in ATP
hydrolysis, is rotated away from the nucleotide-binding pocket to form a
SufC-specific salt bridge with Lys152. Due to this salt bridge, D-loop that
follows Glu171 is flipped out to the molecular surface, which may sterically
inhibit the formation of an active dimer. Thus, the salt bridge may play a
critical role in regulating ATPase activity and preventing wasteful ATP
hydrolysis. Furthermore, SufC has a unique Q-loop structure on its surface,
which may form a binding site for its partner proteins, SufB and/or SufD.
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Figure 2.
Fig. 2. A ribbon representation of the overall structure of
E. coli SufC. The catalytic α/β domain is shown in green and
the α-helical domain in blue. The motifs conserved in
ABC-ATPases are depicted by different colors: Walker A motif,
red; Walker B motif, magenta; ABC signature motif, yellow;
Q-loop, orange; and D-loop, dark blue. The side chains of Lys152
and Glu171, which are involved in a salt bridge between the
catalytic and helical domains, are represented by stick models
in blue and magenta, respectively.
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Figure 4.
Fig. 4. The dimer model of E. coli SufC and the
conservation of the surface residues among the SufC orthologs.
(A) A ribbon representation of the SufC dimer with the D-loops
at the interface highlighted by thick lines. The model was
obtained by superimposing two SufC structures onto the ATP-bound
HlyB (H662A) dimer (PDB: 1XEF). Two ATP molecules at the
interface of the HlyB dimer are included in the model (black
sticks). The ABC signature motifs are shown in yellow. (B) A
ConSurf image in the same orientation as in (A) for the SufC
family. Conserved residues are shown in magenta, whereas
variable sites are shown in white and highly variable sites in
blue. (C) The ConSurf surface rotated 90° relative to the
y-axis of the images shown in (A) and (B).
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The above figures are
reprinted
by permission from the Federation of European Biochemical Societies:
FEBS Lett
(2006,
580,
137-143)
copyright 2006.
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