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Structure and interactions with RNA of the N-terminal UUAG-specific RNA-binding domain of hnRNP D0.

Nagata T, Kurihara Y, Matsuda G, Saeki J, Kohno T, Yanagida Y, Ishikawa F, Uesugi S, Katahira M
J Mol Biol 287 221-37 (1999)
Cited: 32 times
EuropePMC logo PMID: 10080887

Abstract

Heterogeneous nuclear ribonucleoprotein (hnRNP) D0 has two ribonucleoprotein (RNP)-type RNA-binding domains (RBDs), each of which can bind solely to the UUAG sequence specifically. The structure of the N-terminal RBD (RBD1) determined by NMR is presented here. It folds into a compact alphabeta structure comprising a four-stranded antiparallel beta-sheet packed against two alpha-helices, which is characteristic of the RNP-type RBDs. Special structural features of RBD1 include N-capping boxes for both alpha-helices, a beta-bulge in the second beta-strand, and an additional short antiparallel beta-sheet coupled with a beta-turn-like structure in a loop. Two hydrogen bonds which restrict the positions of loops were identified. Backbone resonance assignments for RBD1 complexed with r(UUAGGG) revealed that the overall folding is maintained in the complex. The candidate residues involved in the interactions with RNA were identified by chemical shift perturbation analysis. They are located in the central and peripheral regions of the RNA-binding surface composed of the four-stranded beta-sheet, loops, and the C-terminal region. It is suggested that non-specific interactions with RNA are performed by the residues in the central region of the RNA-binding surface, while specific interactions are performed by those in the peripheral regions. It was also found that RBD1 has the ability to inhibit the formation of the quadruplex structure.

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  3. A circular RNA circ-DNMT1 enhances breast cancer progression by activating autophagy. Du WW, Yang W, Li X, Awan FM, Yang Z, Fang L, Lyu J, Li F, Peng C, Krylov SN, Xie Y, Zhang Y, He C, Wu N, Zhang C, Sdiri M, Dong J, Ma J, Gao C, Hibberd S, Yang BB. Oncogene 37 5829-5842 (2018)
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  8. Structural characterization of Set1 RNA recognition motifs and their role in histone H3 lysine 4 methylation. Trésaugues L, Dehé PM, Guérois R, Rodriguez-Gil A, Varlet I, Salah P, Pamblanco M, Luciano P, Quevillon-Cheruel S, Sollier J, Leulliot N, Couprie J, Tordera V, Zinn-Justin S, Chàvez S, van Tilbeurgh H, Géli V. J Mol Biol 359 1170-1181 (2006)
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  13. High precision NMR structure of YhhP, a novel Escherichia coli protein implicated in cell division. Katoh E, Hatta T, Shindo H, Ishii Y, Yamada H, Mizuno T, Yamazaki T. J Mol Biol 304 219-229 (2000)
  14. Structure of the C-terminal RNA-binding domain of hnRNP D0 (AUF1), its interactions with RNA and DNA, and change in backbone dynamics upon complex formation with DNA. Katahira M, Miyanoiri Y, Enokizono Y, Matsuda G, Nagata T, Ishikawa F, Uesugi S. J Mol Biol 311 973-988 (2001)
  15. Protein kinase A enhances, whereas glycogen synthase kinase-3 beta inhibits, the activity of the exon 2-encoded transactivator domain of heterogeneous nuclear ribonucleoprotein D in a hierarchical fashion. Tolnay M, Juang YT, Tsokos GC. Biochem J 363 127-136 (2002)
  16. Origin of higher affinity to RNA of the N-terminal RNA-binding domain than that of the C-terminal one of a mouse neural protein, musashi1, as revealed by comparison of their structures, modes of interaction, surface electrostatic potentials, and backbone dynamics. Miyanoiri Y, Kobayashi H, Imai T, Watanabe M, Nagata T, Uesugi S, Okano H, Katahira M. J Biol Chem 278 41309-41315 (2003)
  17. Elucidation of the mode of interaction in the UP1-telomerase RNA-telomeric DNA ternary complex which serves to recruit telomerase to telomeric DNA and to enhance the telomerase activity. Nagata T, Takada Y, Ono A, Nagata K, Konishi Y, Nukina T, Ono M, Matsugami A, Furukawa A, Fujimoto N, Fukuda H, Nakagama H, Katahira M. Nucleic Acids Res 36 6816-6824 (2008)
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  21. Structural basis for the recognition of transiently structured AU-rich elements by Roquin. Binas O, Tants JN, Peter SA, Janowski R, Davydova E, Braun J, Niessing D, Schwalbe H, Weigand JE, Schlundt A. Nucleic Acids Res 48 7385-7403 (2020)
  22. Analysis of the structural determinants for RNA binding of the human protein AUF1/hnRNP D. Moraes KC, Lee WH, Kobarg J. Biol Chem 383 831-837 (2002)
  23. In-vitro dual binding activity of a evolutionarily related subgroup of hnRNP proteins. Bandiera A, Medic N, Akindahunsi AA, Manzini G. Mol Cell Biochem 268 121-127 (2005)
  24. The Complete Chloroplast Genome of Plukenetia volubilis Provides Insights Into the Organelle Inheritance. Villanueva-Corrales S, García-Botero C, Garcés-Cardona F, Ramírez-Ríos V, Villanueva-Mejía DF, Álvarez JC. Front Plant Sci 12 667060 (2021)


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