NMR structure of the N-terminal domain of Saccharomyces cerevisiae RNase HI reveals a fold with a strong resemblance to the N-terminal domain of ribosomal protein L9

In addition to the conserved and well-defined RNase H domain, eukaryotic RN ases HI possess either one or two copies of a small N-terminal domain. The solution structure of one of the N-terminal domains from Saccharomyces cere visiae RNase HI, determined using NMR spectroscopy, is presented. The 46 re sidue motif comprises a three-stranded antiparallel beta-sheet and two shor t alpha-helices which pack onto opposite faces of the beta-sheet. Conserved residues involved in packing the alpha-helices onto the beta-sheet form th e hydrophobic core of the domain. Three highly conserved and solvent expose d residues are implicated in RNA binding, W22, K38 and K39. The beta-beta-a lpha-beta-alpha topology of the domain differs from the structures of known RNA binding domains such as the double-stranded RNA binding domain (dsRBD) , the hnRNP K homology (KH) domain and the RNP motif. However, structural s imilarities exist between this domain and the N-terminal domain of ribosoma l protein L9 which binds to 23 S ribosomal RNA. (C) 1999 Academic Press.