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 language | English |
|---|---|
| Pages (from-to) | 57-64 |
| Number of pages | 8 |
| Journal | Acta Crystallographica Section F: Structural Biology Communications |
| Volume | 74 |
| Issue number | 1 |
| DOIs | |
| Publication status | Published - Jan 2018 |
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All Science Journal Classification (ASJC) codes
- Biophysics
- Structural Biology
- Biochemistry
- Genetics
- Condensed Matter Physics
Cite this
Crystal structures of the archaeal RNase P protein Rpp38 in complex with RNA fragments containing a K-turn motif. / Oshima, Kosuke; Gao, Xuzhu; Hayashi, Seiichiro; Ueda, Toshifumi; Nakashima, Takashi; Kimura, Makoto.
In: Acta Crystallographica Section F: Structural Biology Communications, Vol. 74, No. 1, 01.2018, p. 57-64.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - Crystal structures of the archaeal RNase P protein Rpp38 in complex with RNA fragments containing a K-turn motif
AU - Oshima, Kosuke
AU - Gao, Xuzhu
AU - Hayashi, Seiichiro
AU - Ueda, Toshifumi
AU - Nakashima, Takashi
AU - Kimura, Makoto
PY - 2018/1
Y1 - 2018/1
N2 - 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.
AB - 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.
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U2 - 10.1107/S2053230X17018039
DO - 10.1107/S2053230X17018039
M3 - Article
C2 - 29372908
AN - SCOPUS:85041057869
VL - 74
SP - 57
EP - 64
JO - Acta Crystallographica Section F:Structural Biology Communications
JF - Acta Crystallographica Section F:Structural Biology Communications
SN - 1744-3091
IS - 1
ER -