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PDBsum entry 1krs
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Aminoacyl-tRNA synthetase
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PDB id
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1krs
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References listed in PDB file
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Key reference
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Title
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Solution structure of the anticodon-Binding domain of escherichia coli lysyl-Trna synthetase and studies of its interaction with tRNA(lys).
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Authors
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S.Commans,
P.Plateau,
S.Blanquet,
F.Dardel.
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Ref.
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J Mol Biol, 1995,
253,
100-113.
[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
92%.
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Abstract
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A protein domain corresponding to residues 31 to 149 of the E. coli Lysyl-tRNA
synthetase species corresponding to the lysS gene was expressed and
15N-labelled. 1H and 15N NMR resonance assignments for this domain were obtained
by two-dimensional and three-dimensional homonuclear and heteronuclear
spectroscopy. Using distance geometry and simulated annealing, a
three-dimensional structure could be calculated using 701 NOE and 86 dihedral
angle restraints. It is composed of a five-stranded antiparallel beta-barrel
capped by three alpha-helices at its ends. This structure closely resembles that
of the N-terminal domain of the other E. coli lysyl-tRNA synthetase species
expressed from the lysU gene and is highly homologous to the fold observed for
the corresponding region of aspartyl-tRNA synthetase. It is shown that the
isolated N-terminal fragment of lysyl-tRNA synthetase can interact with
tRNA(Lys) as well as with poly (U), which mimics the anticodon sequence. Amino
acid residues involved in these interactions were identified and, in the case of
poly-U, a number of specific protein-RNA contacts were characterized. Specific
recognition of tRNA(Lys) involves a cluster of four structurally well-defined
aromatic residues, anchored on the beta-strands, and basic residues located on
the surrounding loops. This organization is reminiscent of other RNA binding
proteins, such as the U1A small nuclear ribonucleoprotein.
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Figure 3.
Figure 3. LysN structure contains a five-stranded
b-barrel. One face of the b-barrel features a cluster of
aromatic residues the side-chains of which are reasonably
well-defined in the solution structure. Shown are the
backbones of the 16 best conformers (red) and the
minimized mean structure (yellow), together with the
side-chains (in blue and white) of Phe85, Tyr98, His139 and
Phe129, from top to bottom. The side-chain of Gln96,
which is correctly defined, is also indicated.
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Figure 4.
Figure 4. Superposition of the
1
H-
15
N HSQC spectrum of LysN (black) with that of a tRNA
Lys
/LysN mixture of (0.25/1
stoichiometry; red), at 298 K, in 40 mM potassium phosphate (pH 7.0). Only peaks which show a significant broadening
and/or shift are labelled.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1995,
253,
100-113)
copyright 1995.
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Secondary reference #1
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Title
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Homology of lyss and lysu, The two escherichia coli genes encoding distinct lysyl-Trna synthetase species.
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Authors
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F.LéVêque,
P.Plateau,
P.Dessen,
S.Blanquet.
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Ref.
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Nucleic Acids Res, 1990,
18,
305-312.
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PubMed id
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