dsRBM1 and a proline-rich domain of RNA helicase A can form a composite binder to recognize a specific dsDNA.
The double-stranded RNA-binding motif (dsRBM) is a widely distributed motif frequently found within proteins with sequence non-specific RNA duplex-binding activity. In addition to the binding of double-stranded RNA, some dsRBMs also participate in complex formation via protein-protein interactions. Interestingly, a lot of proteins containing multiple dsRBMs have only some of their dsRBMs with the expected RNA duplex-binding competency proven, while the functions of the other dsRBMs remain unknown. We show here that the dsRBM1 of RNA helicase A (RHA) can cooperate with a C-terminal domain of proline-rich content to gain novel nucleic acid-binding activities. This integrated nucleic acid-binding module is capable of associating with the consensus sequences of the constitutive transport element (CTE) RNA of type D retrovirus against RNA duplex competitors. Remarkably, binding activity for double-stranded DNA corresponding to the consensus sequences of the cyclic-AMP responsive element also resides within this composite nucleic acid binder. It thus suggests that the dsRBM fold can be used as a platform for the building of a ligand binding module capable of non-RNA macromolecule binding with an accessory sequence, and functional assessment for a newly identified protein containing dsRBM fold should be more cautious.
D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001324:Autoantigens / Q000737:chemistry* / Q000378:metabolism*; D001483:Base Sequence; D001665:Binding Sites; D001667:Binding, Competitive; D016384:Consensus Sequence; D053487:DEAD-box RNA Helicases; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D008024:Ligands; D008969:Molecular Sequence Data; D009363:Neoplasm Proteins; D029543:Nucleocytoplasmic Transport Proteins; D011392:Proline / Q000737:chemistry*; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D012313:RNA / Q000378:metabolism; D020365:RNA Helicases / Q000737:chemistry* / Q000378:metabolism*; D015347:RNA Probes; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism; D011993:Recombinant Fusion Proteins / Q000032:analysis; D020218:Response Elements; D016415:Sequence Alignment
D001324:Autoantigens; D008024:Ligands; C122111:NXF1 protein, human; D009363:Neoplasm Proteins; D029543:Nucleocytoplasmic Transport Proteins; D011506:Proteins; D015347:RNA Probes; D016601:RNA-Binding Proteins; D011993:Recombinant Fusion Proteins; D012313:RNA; D004247:DNA; D011392:Proline; C098487:DHX9 protein, human; D053487:DEAD-box RNA Helicases; D020365:RNA Helicases