Crystal structure of the human heterogeneous ribonucleoprotein A18 RNA-recognition motif

Abstract

The heterogeneous ribonucleoprotein A18 (hnRNP A18) is upregulated in hypoxic regions of various solid tumors and promotes tumor growth via the coordination of mRNA transcripts associated with pro-survival genes. Thus, hnRNP A18 represents an important therapeutic target in tumor cells. Presented here is the first X-ray crystal structure to be reported for the RNA-recognition motif of hnRNP A18. By comparing this structure with those of homologous RNA-binding proteins (i.e. hnRNP A1), three residues on one face of an antiparallel β-sheet (Arg48, Phe50 and Phe52) and one residue in an unstructured loop (Arg41) were identified as likely to be involved in protein-nucleic acid interactions. This structure helps to serve as a foundation for biophysical studies of this RNA-binding protein and structure-based drug-design efforts for targeting hnRNP A18 in cancer, such as malignant melanoma, where hnRNP A18 levels are elevated and contribute to disease progression.

Keywords: RNA-binding protein; RNA-recognition motif; crystal structure; heterogeneous ribonucleoprotein A18; hnRNP A18; tumor growth.

Figure 1

Ribbon diagram of the hnRNP A18 RRM crystal structure viewed from the front (a) and rear (b) with helices in blue and the β-sheet in green.

Figure 2

An overlay and alignment of the RRM of hnRNP A18 (green) and the first RRM of hnRNP A1 (gray; PDB entry 1u1q). All atoms align with an r.m.s.d. of 1.23 Å. The second RRM domain of hnRNP A1 has been omitted for clarity.

Figure 3

The electron-density map for the β-sheet of the hnRNP A18 RRM (a); the conserved RNA-binding residues of the hnRNP A18 RRM are highlighted in (b). For clarity, only strands β1 and β3 are in green in (a) and the RNA-binding residues are in green in (b). Electron-density maps are displayed at 2.0σ.

Figure 4

(a) The interactions between hnRNP A1 (gray) and RNA (yellow) (PDB entry 1u1q). (b) Overlay of hnRNP A1 with hnRNP A18 (green) showing the conserved RNA-binding residues. Arg55 in hnRNP A1 forms a salt bridge with the phosphate of the sugar backbone of the nucleotide. Phe17 and Phe59 form π-stacking interactions with the purine bases of the nucleotide. Phe57 interacts hydrophobically with the sugar rings of both nucleic acids. Arg41 in hnRNP A18 is also poised to form a salt bridge with the phosphate of the sugar backbone. Pro49 instead occupies this same position in hnRNP A1.