Premium
Crystal structures of the archaeal RNase P protein Rpp38 in complex with RNA fragments containing a K‐turn motif
Author(s) -
Oshima Kosuke,
Gao Xuzhu,
Hayashi Seiichiro,
Ueda Toshifumi,
Nakashima Takashi,
Kimura Makoto
Publication year - 2018
Publication title -
acta crystallographica section f
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.572
H-Index - 37
ISSN - 2053-230X
DOI - 10.1107/s2053230x17018039
Subject(s) - rnase p , turn (biochemistry) , ribonuclease , structural motif , crystal structure , crystallography , pyrococcus horikoshii , rna , ribonuclease iii , biology , stereochemistry , chemistry , biochemistry , rna interference , gene
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. Pho Rpp38 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 Pho Rpp38 in complex with the K‐turn in P12.2 was determined at 3.4 Å resolution. In this study, the crystal structure of Pho Rpp38 in complex with the K‐turn in P12.2 was improved to 2.1 Å resolution and the structure of Pho Rpp38 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 Pho Rpp38 interact with characteristic G·A and A·G pairs in the K‐turn, while Thr37, Asp59, Lys84, Glu94, Ala96 and Ala98 in Pho Rpp38 interact with the three‐nucleotide bulge in the K‐turn. Moreover, an extended stem‐loop containing P10–P12.2 in complex with Pho Rpp38, as well as Pho Rpp21 and Pho Rpp29, 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.