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PDBsum entry 1d6t
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* Residue conservation analysis
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Enzyme class:
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E.C.3.1.26.5
- ribonuclease P.
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Reaction:
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Endonucleolytic cleavage of RNA, removing 5'-extra-nucleotide from tRNA precursor.
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DOI no:
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J Mol Biol
295:105-115
(2000)
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PubMed id:
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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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C.Spitzfaden,
N.Nicholson,
J.J.Jones,
S.Guth,
R.Lehr,
C.D.Prescott,
L.A.Hegg,
D.S.Eggleston.
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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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Selected figure(s)
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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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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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P.D.Olson,
L.J.Kuechenmeister,
K.L.Anderson,
S.Daily,
K.E.Beenken,
C.M.Roux,
M.L.Reniere,
T.L.Lewis,
W.J.Weiss,
M.Pulse,
P.Nguyen,
J.W.Simecka,
J.M.Morrison,
K.Sayood,
O.A.Asojo,
M.S.Smeltzer,
E.P.Skaar,
and
P.M.Dunman
(2011).
Small Molecule Inhibitors of Staphylococcus aureus RnpA Alter Cellular mRNA Turnover, Exhibit Antimicrobial Activity, and Attenuate Pathogenesis.
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PLoS Pathog,
7,
e1001287.
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L.B.Lai,
A.Vioque,
L.A.Kirsebom,
and
V.Gopalan
(2010).
Unexpected diversity of RNase P, an ancient tRNA processing enzyme: challenges and prospects.
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FEBS Lett,
584,
287-296.
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O.Esakova,
and
A.S.Krasilnikov
(2010).
Of proteins and RNA: the RNase P/MRP family.
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RNA,
16,
1725-1747.
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T.Honda,
T.Hara,
J.Nan,
X.Zhang,
and
M.Kimura
(2010).
Archaeal homologs of human RNase P protein pairs Pop5 with Rpp30 and Rpp21 with Rpp29 work on distinct functional domains of the RNA subunit.
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Biosci Biotechnol Biochem,
74,
266-273.
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K.L.Anderson,
and
P.M.Dunman
(2009).
Messenger RNA Turnover Processes in Escherichia coli, Bacillus subtilis, and Emerging Studies in Staphylococcus aureus.
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Int J Microbiol,
2009,
525491.
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L.A.Kirsebom,
and
S.Trobro
(2009).
RNase P RNA-mediated cleavage.
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IUBMB Life,
61,
189-200.
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Y.Xu,
C.D.Amero,
D.K.Pulukkunat,
V.Gopalan,
and
M.P.Foster
(2009).
Solution structure of an archaeal RNase P binary protein complex: formation of the 30-kDa complex between Pyrococcus furiosus RPP21 and RPP29 is accompanied by coupled protein folding and highlights critical features for protein-protein and protein-RNA interactions.
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J Mol Biol,
393,
1043-1055.
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PDB code:
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J.K.Smith,
J.Hsieh,
and
C.A.Fierke
(2007).
Importance of RNA-protein interactions in bacterial ribonuclease P structure and catalysis.
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Biopolymers,
87,
329-338.
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M.Gösringer,
and
R.K.Hartmann
(2007).
Function of heterologous and truncated RNase P proteins in Bacillus subtilis.
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Mol Microbiol,
66,
801-813.
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S.Niranjanakumari,
J.J.Day-Storms,
M.Ahmed,
J.Hsieh,
N.H.Zahler,
R.A.Venters,
and
C.A.Fierke
(2007).
Probing the architecture of the B. subtilis RNase P holoenzyme active site by cross-linking and affinity cleavage.
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RNA,
13,
521-535.
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A.V.Kazantsev,
and
N.R.Pace
(2006).
Bacterial RNase P: a new view of an ancient enzyme.
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Nat Rev Microbiol,
4,
729-740.
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C.Roberts,
K.L.Anderson,
E.Murphy,
S.J.Projan,
W.Mounts,
B.Hurlburt,
M.Smeltzer,
R.Overbeek,
T.Disz,
and
P.M.Dunman
(2006).
Characterizing the effect of the Staphylococcus aureus virulence factor regulator, SarA, on log-phase mRNA half-lives.
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J Bacteriol,
188,
2593-2603.
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D.Evans,
S.M.Marquez,
and
N.R.Pace
(2006).
RNase P: interface of the RNA and protein worlds.
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Trends Biochem Sci,
31,
333-341.
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R.C.Wilson,
C.J.Bohlen,
M.P.Foster,
and
C.E.Bell
(2006).
Structure of Pfu Pop5, an archaeal RNase P protein.
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Proc Natl Acad Sci U S A,
103,
873-878.
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PDB code:
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S.C.Walker,
and
D.R.Engelke
(2006).
Ribonuclease P: the evolution of an ancient RNA enzyme.
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Crit Rev Biochem Mol Biol,
41,
77.
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A.H.Buck,
A.B.Dalby,
A.W.Poole,
A.V.Kazantsev,
and
N.R.Pace
(2005).
Protein activation of a ribozyme: the role of bacterial RNase P protein.
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EMBO J,
24,
3360-3368.
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E.Sharin,
A.Schein,
H.Mann,
Y.Ben-Asouli,
and
N.Jarrous
(2005).
RNase P: role of distinct protein cofactors in tRNA substrate recognition and RNA-based catalysis.
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Nucleic Acids Res,
33,
5120-5132.
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M.Kifusa,
H.Fukuhara,
T.Hayashi,
and
M.Kimura
(2005).
Protein-protein interactions in the subunits of ribonuclease P in the hyperthermophilic archaeon Pyrococcus horikoshii OT3.
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Biosci Biotechnol Biochem,
69,
1209-1212.
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J.Hsieh,
A.J.Andrews,
and
C.A.Fierke
(2004).
Roles of protein subunits in RNA-protein complexes: lessons from ribonuclease P.
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Biopolymers,
73,
79-89.
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J.J.Day-Storms,
S.Niranjanakumari,
and
C.A.Fierke
(2004).
Ionic interactions between PRNA and P protein in Bacillus subtilis RNase P characterized using a magnetocapture-based assay.
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RNA,
10,
1595-1608.
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L.S.Harlow,
A.Kadziola,
K.F.Jensen,
and
S.Larsen
(2004).
Crystal structure of the phosphorolytic exoribonuclease RNase PH from Bacillus subtilis and implications for its quaternary structure and tRNA binding.
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Protein Sci,
13,
668-677.
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PDB codes:
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T.A.Hall,
and
J.W.Brown
(2004).
Interactions between RNase P protein subunits in archaea.
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Archaea,
1,
247-254.
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T.Numata,
I.Ishimatsu,
Y.Kakuta,
I.Tanaka,
and
M.Kimura
(2004).
Crystal structure of archaeal ribonuclease P protein Ph1771p from Pyrococcus horikoshii OT3: an archaeal homolog of eukaryotic ribonuclease P protein Rpp29.
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RNA,
10,
1423-1432.
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PDB code:
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A.V.Kazantsev,
A.A.Krivenko,
D.J.Harrington,
R.J.Carter,
S.R.Holbrook,
P.D.Adams,
and
N.R.Pace
(2003).
High-resolution structure of RNase P protein from Thermotoga maritima.
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Proc Natl Acad Sci U S A,
100,
7497-7502.
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PDB code:
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D.J.Sidote,
and
D.W.Hoffman
(2003).
NMR structure of an archaeal homologue of ribonuclease P protein Rpp29.
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Biochemistry,
42,
13541-13550.
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PDB code:
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E.Hartmann,
and
R.K.Hartmann
(2003).
The enigma of ribonuclease P evolution.
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Trends Genet,
19,
561-569.
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H.W.Choe,
D.G.Jeong,
J.H.Park,
R.Schlesinger,
J.Labahn,
K.P.Hofmann,
and
G.Büldt
(2003).
Preliminary X-ray characterization of the ribonuclease P (C5 protein) from Escherichia coli: expression, crystallization and cryoconditions.
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Acta Crystallogr D Biol Crystallogr,
59,
350-352.
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W.P.Boomershine,
C.A.McElroy,
H.Y.Tsai,
R.C.Wilson,
V.Gopalan,
and
M.P.Foster
(2003).
Structure of Mth11/Mth Rpp29, an essential protein subunit of archaeal and eukaryotic RNase P.
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Proc Natl Acad Sci U S A,
100,
15398-15403.
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PDB code:
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A.A.Krivenko,
A.V.Kazantsev,
C.Adamidi,
D.J.Harrington,
and
N.R.Pace
(2002).
Expression, purification, crystallization and preliminary diffraction analysis of RNase P protein from Thermotoga maritima.
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Acta Crystallogr D Biol Crystallogr,
58,
1234-1236.
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F.Houser-Scott,
S.Xiao,
C.E.Millikin,
J.M.Zengel,
L.Lindahl,
and
D.R.Engelke
(2002).
Interactions among the protein and RNA subunits of Saccharomyces cerevisiae nuclear RNase P.
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Proc Natl Acad Sci U S A,
99,
2684-2689.
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J.H.Lee,
H.Kim,
J.Ko,
and
Y.Lee
(2002).
Interaction of C5 protein with RNA aptamers selected by SELEX.
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Nucleic Acids Res,
30,
5360-5368.
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M.Jovanovic,
R.Sanchez,
S.Altman,
and
V.Gopalan
(2002).
Elucidation of structure-function relationships in the protein subunit of bacterial RNase P using a genetic complementation approach.
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Nucleic Acids Res,
30,
5065-5073.
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S.Xiao,
F.Scott,
C.A.Fierke,
and
D.R.Engelke
(2002).
Eukaryotic ribonuclease P: a plurality of ribonucleoprotein enzymes.
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Annu Rev Biochem,
71,
165-189.
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C.H.Henkels,
J.C.Kurz,
C.A.Fierke,
and
T.G.Oas
(2001).
Linked folding and anion binding of the Bacillus subtilis ribonuclease P protein.
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Biochemistry,
40,
2777-2789.
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S.M.Sharkady,
and
J.M.Nolan
(2001).
Bacterial ribonuclease P holoenzyme crosslinking analysis reveals protein interaction sites on the RNA subunit.
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Nucleic Acids Res,
29,
3848-3856.
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J.C.Kurz,
and
C.A.Fierke
(2000).
Ribonuclease P: a ribonucleoprotein enzyme.
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Curr Opin Chem Biol,
4,
553-558.
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S.Altman,
V.Gopalan,
and
A.Vioque
(2000).
Varieties of RNase P: a nomenclature problem?
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RNA,
6,
1689-1694.
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W.A.Ziehler,
J.J.Day,
C.A.Fierke,
and
D.R.Engelke
(2000).
Effects of 5' leader and 3' trailer structures on pre-tRNA processing by nuclear RNase P.
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Biochemistry,
39,
9909-9916.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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Links
