extra loop of seryl-tRNA is recognized by the enzyme, but not the anticodon loop. A conserved N-terminal
domain of the protein forms a coiled-coil region that is involved in RNA recognition.
10.9.4 Small Interfering RNA Recognition
Small interfering RNAs (siRNA) play an important role in gene regulation in eukaryotes (Section 5.7.2).
These RNAs are bound by specific protein complexes and target the cleavage of complementary RNA
transcripts. The crystal structure of a 16-mer siRNA duplex with the recognition domain (PIWI) has been
reported. The structure shows how the RNA is recognized for length and without sequence preference. The
guide siRNA strand (antisense strand) binds by use of a divalent metal ion to help place the complementary
mRNA strand in a position to reach the putative catalytic site where degradation takes place (Figure 10.24).^69
Web Resources
There are many useful databases of structural and functional information of protein–nucleic acid comple-
xes. Among these are the NDB: a database of nucleic acids and protein–nucleic acid complexes^70.
http://ndbserver.rutgers.edu
Protein–Nucleic Acid Interactions 421
Figure 10.24 PIWI–siRNA complex. The domain is shown in red, the duplex composed of the siRNA guide strand
and target mRNA strand is shown in black. The manganese ion is shown in black, situated in the bind-
ing pocket for the first residue of the guide strand