GTP-binding Motifs

Only 1 GTP molecule is bound per GTPase domain, but the sequences that contribute to the interactions (G1 to G4) are spread over the domain. The key residues are shown in bold in the table below. The G1 motif (on the P-loop) of ras coordinates the phosphates while the T in the G2 motif is involved in catalysis. The G4 motif is involved in guanine and ribose coordination. The G2 motif (a single Threonine residue) is hard to predict by sequence comparisons but has been confirmed experimentally for dynamin (see Marks et al 2001). As the names imply, Switch1 and Switch2 regions in ras are the loops that move (switch) on GTP hydrolysis. Ras effectors can also interact with these sequences. Switch 2 overlaps with G3.

G1 (P-Loop)
Switch1....G2
G3 (Switch2)
G4
hDynamin 1
38 GGQSAGKS 45
56 FLPRGSGIVT 65
136 DLPGMTKVPVGDQPPDIE 153
205 TKLD 208
Dicty-DymA
32 GSQSSGKS 39
50 FLPRGSGIVT 59
138 DLPGITKVPVGDQPTDIE 155
207 TKLD 210
hRas
10 GAGGVGKS 17
29 VDEYDPT 35
57 DTAGQ E 62
116 NKCD 119
hGBP 1
45 GLYRTGKS 52
65 FSLGSTVQSHT*75

97 DTEGLGDVEKGDNQN D 112
181 TLRD 184
All these residues are highlighted in red in the structures below

Comparisons of G1 to G4 in ras, DymA and GBP structures
These structures demonstrate the homology of the binding pocket for GTP/GDP. They also show that the additional sequences in the GTPase domains of GBP and DymA are quite different and are likely implicated in oligomerisation.

Endocytosis, Dynamin, Dynamic dynamin, Shibire, Vesicle scission, Harvey McMahon, Dlp, OPA, Dmn, DymA, GBP, GTPase, Poppase, Pinchase, GTP, PIP2, PtdIns(4,5)P2, phosphatidylinositol phosphates, synaptic vesicle endocytosis Endocytosis, Dynamin, Dynamic dynamin, Shibire, Vesicle scission, Harvey McMahon, Dlp, OPA, Dmn, DymA, GBP, GTPase, Poppase, Pinchase, GTP, PIP2, PtdIns(4,5)P2, phosphatidylinositol phosphates, synaptic vesicle endocytosis Endocytosis, Dynamin, Dynamic dynamin, Shibire, Vesicle scission, Harvey McMahon, Dlp, OPA, Dmn, DymA, GBP, GTPase, Poppase, Pinchase, GTP, PIP2, PtdIns(4,5)P2, phosphatidylinositol phosphates, synaptic vesicle endocytosis

The above structures give an overview of the major features of the GTP binding region. For more detail of the individual residues involved in coordination and the effects of mutations please see 'residues important for GTP binding'.

*In GBP the Threonine 75 in G2 is structurally in the same position as T35 in Ras. T35 in Ras contacts the water molecules involved in catalysis and also makes a direct coordination of the Mg ion. The sidechain of T75 contacts the oxygen of the gamma-phosphate and also contacts a water molecule which in turn contacts the catalytic Mg. We do not know the coordination of T65 in dynamin (and in DymA this region is not resolved in the structure), but the predominant effect of mutations in all these threonine residues are catalytically severely imparied GTPase activities.

The reduction of the third GTP-binding motif N/TKxD to RD in the GBPs leads to an unusual orientation of the guanine base (see pictures above). This sequence is also found in several other large GTP-binding proteins e.g. Atlastin (SP3A) that are likely to interact with the nucleotide in the same way.

Further information on G1-G4 motifs in superfamily members
Back to GTPase domain
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