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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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References listed in PDB file
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Key reference
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Title
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Crystal structure of the ribonuclease p protein ph1877p from hyperthermophilic archaeon pyrococcus horikoshii ot3.
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Authors
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H.Takagi,
M.Watanabe,
Y.Kakuta,
R.Kamachi,
T.Numata,
I.Tanaka,
M.Kimura.
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Ref.
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Biochem Biophys Res Commun, 2004,
319,
787-794.
[DOI no: ]
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PubMed id
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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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