5Y7M

Crystal structure of PhoRpp38 bound to a K-turn in P12.1 helix

Summary for 5Y7M

• Entry DOI: 10.2210/pdb5y7m/pdb
• Related: 5XTM
• Descriptor: 50S ribosomal protein L7Ae, RNA (52-MER), GUANOSINE-5'-TRIPHOSPHATE, ... (4 entities in total)
• Functional Keywords: rna binding protein, kink-turn rna, ribonuclease p
• Biological source: Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3); More
• Total number of polymer chains: 4
• Total formula weight: 64306.85

Authors

Oshima, K.,Kimura, M. (deposition date: 2017-08-01, release date: 2018-02-07, Last modification date: 2024-03-20)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (3.1 Å)