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

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 Å resolution. In this study, the crystal structure of PhoRpp38 in complex with the K‐turn in P12.2 was improved to 2.1 Å resolution and the structure of PhoRpp38 in complex with the K‐turn in P12.1 was also determined at a resolution of 3.1 Å. 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 Å. 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.