Selenoprotein synthesis in eukaryotes requires the selenocysteine
insertion sequence (SECIS) RNA, a hairpin in the 3′
untranslated region of selenoprotein mRNAs. The SECIS RNA is
recognized by the SECIS-binding protein 2 (SBP2), which is a
key player in this specialized translation machinery. The objective
of this work was to obtain structural insight into the SBP2-SECIS
RNA complex. Multiple sequence alignment revealed that SBP2
and the U4 snRNA-binding protein 15.5 kD/Snu13p share the same
RNA binding domain of the L7A/L30 family, also found in the
box H/ACA snoRNP protein Nhp2p and several ribosomal proteins.
In corollary, we have detected a similar secondary structure
motif in the SECIS and U4 RNAs. Combining the data of the crystal
structure of the 15.5 kD-U4 snRNA complex, and the SBP2/15.5
kD sequence similarities, we designed a structure-guided strategy
predicting 12 SBP2 amino acids that should be critical for SECIS
RNA binding. Alanine substitution of these amino acids followed
by gel shift assays of the SBP2 mutant proteins identified four
residues whose mutation severely diminished or abolished SECIS
RNA binding, the other eight provoking intermediate down effects.
In addition to identifying key amino acids for SECIS recognition
by SBP2, our findings led to the proposal that some of the
recognition principles governing the 15.5 kD-U4 snRNA interaction
must be similar in the SBP2-SECIS RNA complex.