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PDBsum entry 1fl0
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RNA binding protein
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PDB id
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1fl0
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Structure of the emapii domain of human aminoacyl-Trna synthetase complex reveals evolutionary dimer mimicry.
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Authors
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L.Renault,
P.Kerjan,
S.Pasqualato,
J.Ménétrey,
J.C.Robinson,
S.Kawaguchi,
D.G.Vassylyev,
S.Yokoyama,
M.Mirande,
J.Cherfils.
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Ref.
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EMBO J, 2001,
20,
570-578.
[DOI no: ]
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PubMed id
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Abstract
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The EMAPII (endothelial monocyte-activating polypeptide II) domain is a
tRNA-binding domain associated with several aminoacyl-tRNA synthetases, which
becomes an independent domain with inflammatory cytokine activity upon apoptotic
cleavage from the p43 component of the multisynthetase complex. It comprises a
domain that is highly homologous to bacterial tRNA-binding proteins (Trbp),
followed by an extra domain without homology to known proteins. Trbps, which may
represent ancient tRNA chaperones, form dimers and bind one tRNA per dimer. In
contrast, EMAPII domains are monomers. Here we report the crystal structure at
1.14 Angstroms of human EMAPII. The structure reveals that the Trbp-like domain,
which forms an oligonucleotide-binding (OB) fold, is related by degenerate
2-fold symmetry to the extra-domain. The pseudo-axis coincides with the dyad
axis of bacterial TtCsaA, a Trbp whose structure was solved recently. The
interdomain interface in EMAPII mimics the intersubunit interface in TtCsaA, and
may thus generate a novel OB-fold-based tRNA-binding site. The low sequence
homology between the extra domain of EMAPII and either its own OB fold or that
of Trbps suggests that dimer mimicry originated from convergent evolution rather
than gene duplication.
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Figure 1.
Figure 1 Structure of EMAPII. (A) Overall view of human
EMAPII/p43. The five  -strands
of the OB fold are in violet, the linker region in orange and
the C-terminal domain in yellow. The His-tag in the C-terminus
is shown as a dotted line. (B) Alignment of sequences of
selected p43 (Hs, Homo sapiens; Dm, Drosophila melanogaster; Eo,
Euplotes octocarinatus; At, Arabidopsis thaliana) and
p43-related proteins (Sc, Saccharomyces cerevisiae; Os, Oriza
sativa; Tp, Treponema pallidum; Ec, E.coli; Aa, A.aeolicus; Tt,
T.thermophilus). Helices (rectangles) and strands (arrows) are
coloured as in (A). Amino acids conserved in >50% of sequences
are boxed in black. Hydrophobic residues at the domain interface
are on a yellow background. The conserved motif in the
C-terminal domain is highlighted in red.
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Figure 2.
Figure 2 The internal pseudo-dyad in human EMAPII coincides with
the 2-fold axis in bacterial CsaA. (A) Stereoview of EMAPII (in
violet) superimposed onto itself (in orange), with
superimposable regions shown as thick lines. The pseudo 2-fold
axis is shown by an arrow. (B) The C-terminus domain of EMAPII
(in yellow) is related by 2-fold symmetry to a subset of the OB
fold (in dark violet). (C) Crystal structure of CsaA from
T.thermophilus (Kawaguchi et al., 2001). A subset of the
N-terminus of the symmetrical subunit (in yellow) matches the
C-terminus domain of EMAPII. Orientations in (A), (B) and (C)
are as in Figure 1A. (D) Structure-based sequence alignment of
the C-terminal domain of EMAPII with its N-terminus domain and
with the symmetry-related subunit of CsaA. Helices and strands
are on a coloured background, with helices boxed. The C-domain
of EMAPII is superimposable as a continuous peptide. Dots
indicate residues of EMAPII (N-terminal domain) or CsaA
(symmetry-related subunit) that superimpose with the C-terminus
domain within a 2.5 Å cutoff; numbers indicate the length of
non-superposable intervening sequences.
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(2001,
20,
570-578)
copyright 2001.
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