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PDBsum entry 1v77
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RNA binding protein
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PDB id
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1v77
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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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Biochem Biophys Res Commun
319:787-794
(2004)
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PubMed id:
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Crystal structure of the ribonuclease P protein Ph1877p from hyperthermophilic archaeon Pyrococcus horikoshii OT3.
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H.Takagi,
M.Watanabe,
Y.Kakuta,
R.Kamachi,
T.Numata,
I.Tanaka,
M.Kimura.
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ABSTRACT
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Ribonuclease P (RNase P) is a ribonucleoprotein complex involved in the
processing of pre-tRNA. Protein Ph1877p is one of essential components of the
hyperthermophilic archaeon Pyrococcus horikoshii OT3 RNase P [Biochem. Biophys.
Res. Commun. 306 (2003) 666]. The crystal structure of Ph1877p was determined at
1.8A by X-ray crystallography and refined to a crystallographic R factor of
22.96% (Rfree of 26.77%). Ph1877p forms a TIM barrel structure, consisting of
ten alpha-helices and seven beta-strands, and has the closest similarity to the
TIM barrel domain of Escherichia coli cytosine deaminase with a root-mean square
deviation of 3.0A. The protein Ph1877p forms an oblate ellipsoid, approximate
dimensions being 45Ax43Ax39A, and the electrostatic representation indicated the
presence of several clusters of positively charged amino acids present on the
molecular surface. We made use of site-directed mutagenesis to assess the role
of twelve charged amino acids, Lys42, Arg68, Arg87, Arg90, Asp98, Arg107,
His114, Lys123, Lys158, Arg176, Asp180, and Lys196 related to the RNase P
activity. Individual mutations of Arg90, Arg107, Lys123, Arg176, and Lys196 by
Ala resulted in reconstituted particles with reduced enzymatic activities
(32-48%) as compared with that reconstituted RNase P by wild-type Ph1877p. The
results presented here provide an initial step for definite understanding of how
archaeal and eukaryotic RNase Ps mediate substrate recognition and process
5'-leader sequence of pre-tRNA.
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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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A.Perederina,
O.Esakova,
C.Quan,
E.Khanova,
and
A.S.Krasilnikov
(2010).
Eukaryotic ribonucleases P/MRP: the crystal structure of the P3 domain.
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EMBO J,
29,
761-769.
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PDB code:
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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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W.Y.Chen,
D.K.Pulukkunat,
I.M.Cho,
H.Y.Tsai,
and
V.Gopalan
(2010).
Dissecting functional cooperation among protein subunits in archaeal RNase P, a catalytic ribonucleoprotein complex.
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Nucleic Acids Res,
38,
8316-8327.
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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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C.D.Amero,
W.P.Boomershine,
Y.Xu,
and
M.Foster
(2008).
Solution structure of Pyrococcus furiosus RPP21, a component of the archaeal RNase P holoenzyme, and interactions with its RPP29 protein partner.
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Biochemistry,
47,
11704-11710.
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PDB code:
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K.Hada,
T.Nakashima,
T.Osawa,
H.Shimada,
Y.Kakuta,
and
M.Kimura
(2008).
Crystal structure and functional analysis of an archaeal chromatin protein Alba from the hyperthermophilic archaeon Pyrococcus horikoshii OT3.
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Biosci Biotechnol Biochem,
72,
749-758.
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PDB code:
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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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H.Y.Tsai,
D.K.Pulukkunat,
W.K.Woznick,
and
V.Gopalan
(2006).
Functional reconstitution and characterization of Pyrococcus furiosus RNase P.
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Proc Natl Acad Sci U S A,
103,
16147-16152.
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M.H.Lamers,
R.E.Georgescu,
S.G.Lee,
M.O'Donnell,
and
J.Kuriyan
(2006).
Crystal structure of the catalytic alpha subunit of E. coli replicative DNA polymerase III.
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Cell,
126,
881-892.
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PDB codes:
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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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S.Xiao,
J.Hsieh,
R.L.Nugent,
D.J.Coughlin,
C.A.Fierke,
and
D.R.Engelke
(2006).
Functional characterization of the conserved amino acids in Pop1p, the largest common protein subunit of yeast RNases P and MRP.
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RNA,
12,
1023-1037.
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H.Takagi,
Y.Kakuta,
T.Okada,
M.Yao,
I.Tanaka,
and
M.Kimura
(2005).
Crystal structure of archaeal toxin-antitoxin RelE-RelB complex with implications for toxin activity and antitoxin effects.
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Nat Struct Mol Biol,
12,
327-331.
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PDB code:
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M.Dlakić
(2005).
3D models of yeast RNase P/MRP proteins Rpp1p and Pop3p.
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RNA,
11,
123-127.
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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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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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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
