Crystal structures of the archaeal RNase P protein Rpp38 in complex with RNA fragments containing a K-turn motif

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

Research output: Contribution to journalArticlepeer-review

4 Citations (Scopus)

Abstract

A characteristic feature of archaeal ribonuclease P (RNase P) RNAs is that they have extended helices P12.1 and P12.2 containing kink-turn (K-turn) motifs to which the archaeal RNase P protein Rpp38, a homologue of the human RNase P protein Rpp38, specifically binds. PhoRpp38 from the hyperthermophilic archaeon Pyrococcus horikoshii is involved in the elevation of the optimum temperature of the reconstituted RNase P by binding the K-turns in P12.1 and P12.2. Previously, the crystal structure of PhoRpp38 in complex with the K-turn in P12.2 was determined at 3.4 resolution. In this study, the crystal structure of PhoRpp38 in complex with the K-turn in P12.2 was improved to 2.1 resolution and the structure of PhoRpp38 in complex with the K-turn in P12.1 was also determined at a resolution of 3.1 . Both structures revealed that Lys35, Asn38 and Glu39 in PhoRpp38 interact with characteristic G·A and A·G pairs in the K-turn, while Thr37, Asp59, Lys84, Glu94, Ala96 and Ala98 in PhoRpp38 interact with the three-nucleotide bulge in the K-turn. Moreover, an extended stem-loop containing P10-P12.2 in complex with PhoRpp38, as well as PhoRpp21 and PhoRpp29, which are the archaeal homologues of the human proteins Rpp21 and Rpp29, respectively, was affinity-purified and crystallized. The crystals thus grown diffracted to a resolution of 6.35 . Structure determination of the crystals will demonstrate the previously proposed secondary structure of stem-loops including helices P12.1 and P12.2 and will also provide insight into the structural organization of the specificity domain in P. horikoshii RNase P RNA.Experimental structures of the archaeal RNase P protein PhoRpp38 in complex with K-turns of PhopRNA reveal how the protein recognizes the 3nt bulge and tandem G·A and A·G pairs. Moreover, the extended stem-loop containing P10-P12.2 in complex with PhoRpp21, PhoRpp29 and PhoRpp38 was crystallized.

Original languageEnglish
Pages (from-to)57-64
Number of pages8
JournalActa Crystallographica Section F: Structural Biology Communications
Volume74
Issue number1
DOIs
Publication statusPublished - Jan 2018

All Science Journal Classification (ASJC) codes

  • Biophysics
  • Structural Biology
  • Biochemistry
  • Genetics
  • Condensed Matter Physics

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