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PDBsum entry 1d6t
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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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The structure of ribonuclease p protein from staphylococcus aureus reveals a unique binding site for single-Stranded RNA.
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Authors
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C.Spitzfaden,
N.Nicholson,
J.J.Jones,
S.Guth,
R.Lehr,
C.D.Prescott,
L.A.Hegg,
D.S.Eggleston.
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Ref.
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J Mol Biol, 2000,
295,
105-115.
[DOI no: ]
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PubMed id
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Abstract
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Ribonuclease P (RNaseP) catalyses the removal of the 5'-leader sequence from
pre-tRNA to produce the mature 5' terminus. The prokaryotic RNaseP holoenzyme
consists of a catalytic RNA component and a protein subunit (RNaseP protein),
which plays an auxiliary but essential role in vivo by binding to the 5'-leader
sequence and broadening the substrate specificity of the ribozyme.We determined
the three-dimensional high-resolution structure of the RNaseP protein from
Staphylococcus aureus (117 amino acid residues) by nuclear magnetic resonance
(NMR) spectroscopy in solution. The protein has an alphabeta-fold, similar to
the ribonucleoprotein domain. We used small nucleic acid molecules as a model
for the 5'-leader sequence to probe the propensity for generic single-stranded
RNA binding on the protein surface. The NMR results reveal a contiguous
interaction site, which is identical with the previously identified leader
sequence binding site in RNaseP holoenzyme. The conserved arginine-rich motif
does not bind single-stranded RNA. It is likely that this peptide segment binds
selectively to double-stranded sections of P RNA, which are conformationally
more rigid. Given the essentiality of RNaseP for the viability of the organism,
knowledge of the S. aureus protein structure and insight into its interaction
with RNA will help us to develop RNaseP and RNaseP protein as targets for novel
antibiotics against this pathogen.
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Figure 3.
Figure 3. Solution structure of S. aureus RNaseP protein.
(a) Superposition of the 20 conformers with the lowest DYANA
target function of RNaseP protein from S. aureus (blue) and from
B. subtilis (red; [Stams et al 1998]). The N, C^a and C'
positions of residues 8-9, 13-35 and 42-113, which are well
ordered in the NMR structure, were considered for superposition,
but for clarity only C^a is shown. (b) Schematic drawing of the
NMR-structure of RNaseP protein. Regular secondary structures
are represented as arrows (b-sheet) or ribbon (a-helix).
Individual side-chains are shown for residues with a high level
of phylogenetic conservation according to the sequence alignment
in Figure 4 (red, 100 %; yellow, > 70 %).
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Figure 6.
Figure 6. Substrate binding surface of RNaseP protein as
defined by NMR spectroscopy. A C^a plot of the RNaseP protein
structure is superimposed with the electrostatic potential
surface of the residues in the interaction site as characterised
by chemical shift perturbation. Purple cylinders indicate the
position of the a-helices. The position of potential
hydrogen-bonding donors and electrostatic charges within the
binding site and at the edge of the b-sheet are indicated. The
molecule is rotated by approximately 30° compared to Figure
3(b) to show the partial involvement of helix 3 in ligand
interactions.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2000,
295,
105-115)
copyright 2000.
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