A three-dimensional model of RNase P in the hyperthermophilic archaeon Pyrococcus horikoshii OT3

Xuzhu Gao, Kosuke Oshima, Toshifumi Ueda, Takashi Nakashima, Makoto Kimura

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Ribonuclease P (RNase P) is an endoribonuclease involved in maturation of the 5′-end of tRNA. We found previously that RNase P in the hyperthermophilic archaeon Pyrococcus horikoshii OT3 consists of a catalytic RNase P RNA (PhopRNA) and five protein cofactors designated PhoPop5, PhoRpp21, PhoRpp29, PhoRpp30, and PhoRpp38. The crystal structures of the five proteins have been determined, a three-dimensional (3-D) model of PhopRNA has been constructed, and biochemical data, including protein-RNA interaction sites, have become available. Here, this information was combined to orient the crystallographic structures of the proteins relative to their RNA binding sites in the PhopRNA model. Some alterations were made to the PhopRNA model to improve the fit. In the resulting structure, a heterotetramer composed of PhoPop5 and PhoRpp30 bridges helices P3 and P16 in the PhopRNA C-domain, thereby probably stabilizing a double-stranded RNA structure (helix P4) containing catalytic Mg2+ ions, while a heterodimer of PhoRpp21 and PhoRpp29 locates on a single-stranded loop connecting helices P11 and P12 in the specificity domain (S-domain) in PhopRNA, probably forming an appropriate conformation of the precursor tRNA (pre-tRNA) binding site. The fifth protein PhoRpp38 binds each kink-turn (K-turn) motif in helices P12.1, P12.2, and P16 in PhopRNA. Comparison of the structure of the resulting 3-D model with that of bacterial RNase P suggests transition from RNA-RNA interactions in bacterial RNase P to protein-RNA interactions in archaeal RNase P. The proposed 3-D model of P. horikoshii RNase P will serve as a framework for further structural and functional studies on archaeal, as well as eukaryotic, RNase Ps.

Original languageEnglish
Pages (from-to)1063-1068
Number of pages6
JournalBiochemical and Biophysical Research Communications
Volume493
Issue number2
DOIs
Publication statusPublished - Nov 18 2017

Fingerprint

Pyrococcus horikoshii
Ribonuclease P
Archaea
RNA
Proteins
Binding Sites
Endoribonucleases
Double-Stranded RNA
RNA Precursors
Ribonucleases
Transfer RNA
Conformations
Crystal structure
Ions

All Science Journal Classification (ASJC) codes

  • Biophysics
  • Biochemistry
  • Molecular Biology
  • Cell Biology

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A three-dimensional model of RNase P in the hyperthermophilic archaeon Pyrococcus horikoshii OT3. / Gao, Xuzhu; Oshima, Kosuke; Ueda, Toshifumi; Nakashima, Takashi; Kimura, Makoto.

In: Biochemical and Biophysical Research Communications, Vol. 493, No. 2, 18.11.2017, p. 1063-1068.

Research output: Contribution to journalArticle

Gao, Xuzhu ; Oshima, Kosuke ; Ueda, Toshifumi ; Nakashima, Takashi ; Kimura, Makoto. / A three-dimensional model of RNase P in the hyperthermophilic archaeon Pyrococcus horikoshii OT3. In: Biochemical and Biophysical Research Communications. 2017 ; Vol. 493, No. 2. pp. 1063-1068.
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