5XTM

Crystal structure of PhoRpp38 bound to a K-turn in P12.2 helix

5XTM の概要

• エントリーDOI: 10.2210/pdb5xtm/pdb
• 関連するPDBエントリー: 5Y7M
• 分子名称: 50S ribosomal protein L7Ae, RNA (47-MER), MAGNESIUM ION, ... (4 entities in total)
• 機能のキーワード: rna-protein complex, rnase p, kink turn, rna binding protein, rna binding protein-rna complex, rna binding protein/rna
• 由来する生物種: Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3); 詳細
• 細胞内の位置: Cytoplasm : P62009
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 60805.73

構造登録者

Oshima, K.,Kimura, M. (登録日: 2017-06-20, 公開日: 2018-02-07, 最終更新日: 2023-11-22)

主引用文献

Oshima, K.,Gao, X.,Hayashi, S.,Ueda, T.,Nakashima, T.,Kimura, M.
Crystal structures of the archaeal RNase P protein Rpp38 in complex with RNA fragments containing a K-turn motif.
Acta Crystallogr F Struct Biol Commun, 74:57-64, 2018

PubMed 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 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.

PubMed: 29372908
DOI: 10.1107/S2053230X17018039

実験手法

X-RAY DIFFRACTION (2.1 Å)