Structural modeling of RNase P RNA of the hyperthermophilic archaeon Pyrococcus horikoshii OT3

Christian Zwieb, Yuji Nakao, Takashi Nakashima, Hisanori Takagi, Shuichiro Goda, Ebbe Sloth Andersen, Yoshimitsu Kakuta, Makoto Kimura

Research output: Contribution to journalArticle

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Abstract

Ribonuclease P (RNase P) is a ubiquitous trans-acting ribozyme that processes the 5' leader sequence of precursor tRNA (pre-tRNA). The RNase P RNA (PhopRNA) of the hyperthermophilic archaeon Pyrococcus horikoshii OT3 is central to the catalytic process and binds five proteins (PhoPop5, PhoRpp21, PhoRpp29, PhoRpp30, and PhoRpp38) which contribute to the enzymatic activity of the holoenzyme. Despite significant progress in determining the crystal structure of the proteins, the structure of PhopRNA remains elusive. Comparative analysis of the RNase P RNA sequences and existing crystallographic structural information of the bacterial RNase P RNAs were combined to generate a phylogenetically supported three-dimensional (3-D) model of the PhopRNA. The model structure shows an essentially flat disk with 16 tightly packed helices and a conserved face suitable for the binding of pre-tRNA. Moreover, the structure in solution was investigated by enzymatic probing and small-angle X-ray scattering (SAXS) analysis. The low resolution model derived from SAXS and the comparative 3-D model have similar overall shapes. The 3-D model provides a framework for a better understanding of structure-function relationships of this multifaceted primordial ribozyme.

Original languageEnglish
Pages (from-to)517-522
Number of pages6
JournalBiochemical and Biophysical Research Communications
Volume414
Issue number3
DOIs
Publication statusPublished - Oct 28 2011

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Pyrococcus horikoshii
Ribonuclease P
Archaea
RNA
Catalytic RNA
RNA Precursors
X ray scattering
X-Rays
Holoenzymes
Model structures
Proteins
Crystal structure

All Science Journal Classification (ASJC) codes

  • Biophysics
  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

Structural modeling of RNase P RNA of the hyperthermophilic archaeon Pyrococcus horikoshii OT3. / Zwieb, Christian; Nakao, Yuji; Nakashima, Takashi; Takagi, Hisanori; Goda, Shuichiro; Andersen, Ebbe Sloth; Kakuta, Yoshimitsu; Kimura, Makoto.

In: Biochemical and Biophysical Research Communications, Vol. 414, No. 3, 28.10.2011, p. 517-522.

Research output: Contribution to journalArticle

Zwieb, Christian ; Nakao, Yuji ; Nakashima, Takashi ; Takagi, Hisanori ; Goda, Shuichiro ; Andersen, Ebbe Sloth ; Kakuta, Yoshimitsu ; Kimura, Makoto. / Structural modeling of RNase P RNA of the hyperthermophilic archaeon Pyrococcus horikoshii OT3. In: Biochemical and Biophysical Research Communications. 2011 ; Vol. 414, No. 3. pp. 517-522.
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