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Determination of the structure of the GAP domain from p120GAP, first in isolation2 and then in a Ras-rasGAP complex3, showed that an arginine residue from the GAP domain plays a crucial role in catalysis1,3. GAPs for the Rho family have also been characterized and the structure of a GAP domain from p50rhoGAP has been determined in isolation4 and in a transition-state complex with RhoA5. The rhoGAP domain provides a crucial arginine residue to the active site of RhoA.

A domain homologous to rhoGAPs but lacking GAP activity is found in the regulatory p85 subunit of phosphatidylinositol-3-OH kinase. The structure of this rhoGAP-like domain from p85α, called p85 BH (where BH indicates a BCR-homology domain), has also been determined6. The release of the coordinates for the rhoGAP and rasGAP domains allowed us to compare their structures. We found that the rhoGAP and rasGAP domains are clearly related (my Fig. 1 and Fig. 1 in the letter below by Rittinger et al.) and must have derived from the same ancestral protein.

Figure 1: A structurally based sequence alignment of comparable regions of the rasGAP domain from p120-GAP (PDB code: 1wer), the rhoGAP domain of p50rhoGAP (PDB code: 1rgp) and the BH rhoGAP-like domain of the p85 subunit of phosphatidylinositol-3-OH kinase (PDB code: 1pbw).
figure 1

The computer program COMPARER7,8 provided the alignment. α-Helices are underlined and shown in red (rasGAP) or blue (rhoGAP, p85 BH); 310helices are not underlined. The nomenclature for helices is as originally defined2,6,4. Residues labelled in upper-case lettering are inaccessible to solvent. The position of Arg 789 (rasGAP)/Arg 85 (rhoGAP)/Arg 151(p85 BH) is indicated by the arrow. Residues between helix aF and αG are disordered in the rhoGAP structure (in italics).

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To see the equivalence of the structures more clearly (in Fig. 1 of Rittinger et al.), place your finger on the top of helix F (of rhoGAP) and imagine pushing it away from you and down so that it lies more nearly parallel to helix G and between helices G and E (helices E and A then move to the left). The rasGAP and rhoGAP sequences (in my Fig. 1) are only 6% identical, whereas rasGAP and p85 BH are 13% identical (the two rhoGAP-like domains, whose similarity was identified at the sequence level, have a 17% sequence identity).

In the transition-state-analogue complexes of both Ras-rasGAP3 and Rho-rhoGAP5, helix α6/αF interacts with the switch II loop on Ras/Rho. This interaction helps to stabilize the conformation of the switch II loop which provides residue Gln 61 (Gln 63 in Rho) for the active site. The large structural shift in the relative orientation of helix α6/αF of rasGAP/rhoGAP may have occurred to compensate for the different structures of the switch II loop in Ras and Rho.

This equivalence in structure points to a parallel evolution by Ras and Rho G proteins and their GAPs.