K. Kurita et al., IDENTIFICATION OF A REGION OF BACILLUS-SUBTILIS FFH, A HOMOLOG OF MAMMALIAN SRP54 PROTEIN, THAT IS ESSENTIAL FOR BINDING TO SMALL CYTOPLASMIC RNA, The Journal of biological chemistry, 271(22), 1996, pp. 13140-13146
Bacillus subtilis Ffh and scRNA are homologues of mammalian SRP54 and
SR9 RNA, respectively, which are components of the eukaryotic signal r
ecognition particle (SR9). Ffh (446 amino acids) interacts with scRNA
to form a stable complex in vivo. Here, we identified an RNA-binding d
omain of Ffh. The results obtained using a series of deletion mutants
show that amino acid positions 364 to 432 in the C-terminal region of
Ffh correlates with its ability to bind RNA. The amino acid sequence o
f this region is well conserved among members of the SRP54 protein fam
ily. This sequence contains two hydrophobic regions (h2, 364 to 391, a
nd h3, 416 to 435), separated by the positively charged amino acid mot
if, (398)RRKRIAKGSG(407). Among the basic amino acid residues in this
region, Arg-401 was essential for binding to scRNA, but Arg-399 and Ly
s-400 were not. The co-existence of Arg-398 and Lye-404 was necessary
for the same affinity as wild type Ffh. The two glycine residues of th
e (405)GSG(407) were also essential. MH23 peptide (91 amino acids) enc
ompassing from 356 to 446, consisting of h2-RRKRIAKGSG-h3, bound scRNA
with the same affinity as wild type Ffh, whereas a 24-amino acid synt
hetic peptide (392)DIINASRRKRIAKGSGTSVQEVNR(415) did not. The region c
ontaining two hydrophobic segments separated by the positively charged
motif is the minimal requirement of Ffh for RNA binding.