C-terminal motif within Sec7 domain regulates guanine nucleotide exchange activity via tuning protein conformation

•Loop>J motif is indispensible for the catalytic activity of Sec7 domain.•Existence of loop>J motif raises conformation changes of Sec7 domain.•Mutation of Ile1010 to Ala abolishes the catalytic activity of Sec7 domain.•Mutation of Ile1010 to Ala alters the conformational stability of Sec7 domain. ADP-ribosylation factors (Arfs) play key roles in controlling membrane traffic and organelle structures. The activation of Arfs from GDP to GTP binding form is triggered by the guanine exchange factors (GEFs). There are six families of Arf-GEFs with a common guanine exchange catalytic domain (Sec7 domain) and various mechanisms of guanine exchange activity regulation. A loop region (loop>J motif) just following the helix J of Sec7 domain was found conserved and important for the catalytic activity regulation of Arf-GEFs. However, the molecular detail of the role the loop>J motif plays has been yet unclear. Here, we studied the catalytic domain of Sec7p, a yeast trans-Golgi network membrane localized Arf-GEFs, and found that the loop>J motif is indispensible for its GEF catalytic activity. Crystallographic, NMR spectrum and mutagenesis studies suggested that the loop>J motif with a key conserved residue Ile1010 modulates the fine conformation of Sec7 domain and thereby regulates its guanine exchange activity.