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PDBsum entry 1vgs
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Oxygen storage/transport
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PDB id
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1vgs
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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 an archaeal peroxiredoxin from the aerobic hyperthermophilic crenarchaeon aeropyrum pernix k1.
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Authors
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E.Mizohata,
H.Sakai,
E.Fusatomi,
T.Terada,
K.Murayama,
M.Shirouzu,
S.Yokoyama.
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Ref.
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J Mol Biol, 2005,
354,
317-329.
[DOI no: ]
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PubMed id
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Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
percentage match of
77%.
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Abstract
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Peroxiredoxins (Prxs) are thiol-dependent peroxidases that catalyze the
detoxification of various peroxide substrates such as H2O2, peroxinitrite, and
hydroperoxides, and control some signal transduction in eukaryotic cells. Prxs
are found in all cellular organisms and represent an enormous superfamily.
Recent genome sequencing projects and biochemical studies have identified a
novel subfamily, the archaeal Prxs. Their primary sequences are similar to those
of the 1-Cys Prxs, which use only one cysteine residue in catalysis, while their
catalytic properties resemble those of the typical 2-Cys Prxs, which utilize two
cysteine residues from adjacent monomers within a dimer in catalysis. We present
here the X-ray crystal structure of an archaeal Prx from the aerobic
hyperthermophilic crenarchaeon, Aeropyrum pernix K1, determined at 2.3 A
resolution (Rwork of 17.8% and Rfree of 23.0%). The overall subunit arrangement
of the A.pernix archaeal Prx is a toroid-shaped pentamer of homodimers, or an
(alpha2)5 decamer, as observed in the previously reported crystal structures of
decameric Prxs. The basic folding topology and the peroxidatic active site
structure are essentially the same as those of the 1-Cys Prx, hORF6, except that
the C-terminal extension of the A.pernix archaeal Prx forms a unique helix with
its flanking loops. The thiol group of the peroxidatic cysteine C50 is
overoxidized to sulfonic acid. Notably, the resolving cysteine C213 forms the
intra-monomer disulfide bond with the third cysteine, C207, which should be a
unique structural characteristic in the many archaeal Prxs that retain two
conserved cysteine residues in the C-terminal region. The conformational
flexibility near the intra-monomer disulfide linkage might be necessary for the
dramatic structural rearrangements that occur in the catalytic cycle.
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Figure 3.
Figure 3. Topology diagram of the A. pernix archaeal Prx.
The secondary structure was defined by the program DSSP.53 The
a-helices and the b-strands from the N-terminal domain are green
and orange, and those from the C-terminal domain are blue and
yellow, respectively. The beginnings and the ends of the
secondary structural elements are labeled. The positions of the
three redox-active cysteine residues (C[P]50, C207 and C[R]213)
are shown with red stars.
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Figure 8.
Figure 8. Ribbon diagrams of the peroxidatic active sites.
The typical 2-Cys Prx adopts (a) fully folded (PDB ID 1QMV)17
and (b) locally unfolded (1QQ2)16 conformations that are
correlated with the catalytic cycle. In the recycling step, a
dramatic structural rearrangement occurs in order to allow C[P]
and C[R] to react and form a disulfide, through the local
unfolding of the a2 region and the C-terminal domain. (c) The A.
pernix archaeal Prx structure in the fully folded conformation
(2CV4, this study). Multiple conformations of the flexible
region III (residues 197-206) from ten monomers are drawn in the
Figure. The intra-monomer C207-S-S-C[R]213 minimizes the
conformational flexibility of region III and suppresses the
structural rearrangement leading to the locally unfolded
conformation. (d) A model of the locally unfolded conformation
for the A. pernix archaeal Prx. The breakage of the
intra-monomer C207-S-S-C[R]213 by unknown electron donor(s)
would induce the structural rearrangement so that C[R]213-SH can
access and react with the C[P]50-SOH, to form the inter-monomer
C[P]50-S-S-C[R]213. Helices and b-strands of monomer A are blue
and cyan, and those of monomer B are red and pink.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2005,
354,
317-329)
copyright 2005.
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