Structural model of a2-subunit N-terminus and its binding interface for Arf-GEF CTH2: Implication for regulation of V-ATPase, CTH2 function and rational drug design

We have previously identified the interaction between mammalian V-ATPase a2-subunit isoform and cytohesin-2 (CTH2) and studied molecular details of binding between these proteins. In particular, we found that six peptides derived from the N-terminal cytosolic domain of a2 subunit (a2N(1-402)) are involved in interaction with CTH2 (Merkulova, Bakulina, Thaker, Gruber, & Marshansky, 2010). However, the actual 3D binding interface was not determined in that study due to the lack of high-resolution structural information about a-subunits of V-ATPase. Here, using a combination of homology modeling and NMR analysis, we generated the structural model of complete a2N(1-402) and uncovered the CTH2-binding interface. First, using the crystal-structure of the bacterial M. rubber I-cyt-subunit of A-ATPase as a template (Srinivasan, Vyas, Baker, & Quiocho, 2011), we built a homology model of mammalian a2N(1-352) fragment. Next, we combined it with the determined NMR structures of peptides a2N(368-395) and a2N(386-402) of the C-terminal section of a2N(1-402). The complete molecular model of a2N(1-402) revealed that six CTH2 interacting peptides are clustered in the distal and proximal lobe sub-domains of a2N(1-402). Our data indicate that the proximal lobe sub-domain is the major interacting site with the Sec7 domain of first CTH2 protein, while the distal lobe sub-domain of a2N(1-402) interacts with the PH-domain of second CTH2. Indeed, using Sec7/Arf-GEF activity assay we experimentally confirmed our model. The interface formed by peptides a2N(1-17) and a2N(35-49) is involved in specific interaction with Sec7 domain and regulation of GEF activity. These data are critical for understanding of the cross-talk between V-ATPase and CTH2 as well as for the rational drug design to regulate their function.