Figure 5.
Figure 5. Cartoon summarizing the structural consequences of
binding of Mg^2+GDP and GDP to NG. The three structures
suggest a pathway for stepwise release of Mg^2+ and GDP. GTPase
sequence motifs I, II and III interact with the magnesium and
phosphate groups. On release of Mg^2+ (or perhaps Mg^2+P[i])
they can form a network of hydrogen bonding interactions that
stabilizes the nucleotide-free protein. Gln 144 is adjacent to
the active site and can hydrogen bond the -phosphate
of the product GDP, thereby opening up the active site for
product release. The closing loop, depicted at the bottom of the
active site, packs against the bound nucleotide but on
nucleotide release moves away and becomes disordered. The
position of motif IV, which provides recognition of the guanine
base, is coupled to the position of the N domain. The concerted
action of the four elements presumably allows regulation of
binding and release, and can explain the low nucleotide affinity
of the SRP GTPase.
-phosphate
of the product GDP, thereby opening up the active site for
product release. The closing loop, depicted at the bottom of the
active site, packs against the bound nucleotide but on
nucleotide release moves away and becomes disordered. The
position of motif IV, which provides recognition of the guanine
base, is coupled to the position of the N domain. The concerted
action of the four elements presumably allows regulation of
binding and release, and can explain the low nucleotide affinity
of the SRP GTPase.