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Figure 3.
Figure 3. Comparison of the GDP-binding interactions in Ffh (G2)
with those in Ras (4q21). a, In Ffh, the 'closing loop' wraps
around Lys 117 and forms van der Waals contacts with the guanine
base. Lys 117 and Thr 114 are bridged by a buried water molecule
that forms the floor of the binding site and provides a hydrogen
bond to the guanine N7. Motifs I and IV are coupled by
interactions of Lys 246 and Thr 245 with carbonyl oxygens of the
motif I backbone. b, In Ras, Asn 116 bridges the binding site by
hydrogen-bonding the carbonyl oxygen of motif I Val 14 and the
hydroxyl of Thr 144 of the G-5 loop. The G-5 loop provides a
hydrogen bond from Ala 146 to the guanine O6; similar O6
hydrogen bonding is present in other GTPases, but is absent in
Ffh. The hydrophobic character of the floor of the binding site
is also typical of most other GTPases (but not the Rho subfamily
of GTPases, which includes buried water molecules^46, ^47). A
packing interaction structurally analogous to the 'closing loop'
in Ffh is provided by Phe 28 from the  1-helix
in Ras; in other GTPases, it is provided by elements of the  4
loop.
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