5y7m | pdb_00005y7m
Crystal structure of PhoRpp38 bound to a K-turn in P12.1 helix
Structural highlights
Function[RL7A_PYRHO] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA, box C/D and box C'/D' sRNAs (By similarity). When added to reconstituted ribonuclease P (RNase P) it increases the optimum temperature to that of the partially purified enzyme and causes a 5-fold increase in apparent Vmax. Binds the RNase P catalytic RNA.[1] [2] Publication Abstract from PubMedA 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 A resolution. In this study, the crystal structure of PhoRpp38 in complex with the K-turn in P12.2 was improved to 2.1 A resolution and the structure of PhoRpp38 in complex with the K-turn in P12.1 was also determined at a resolution of 3.1 A. 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 A. 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. Crystal structures of the archaeal RNase P protein Rpp38 in complex with RNA fragments containing a K-turn motif.,Oshima K, Gao X, Hayashi S, Ueda T, Nakashima T, Kimura M Acta Crystallogr F Struct Biol Commun. 2018 Jan 1;74(Pt 1):57-64. doi:, 10.1107/S2053230X17018039. Epub 2018 Jan 1. PMID:29372908[3] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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