The structure of arginyltransferase 1 (ATE1)

Abstract

Eukaryotic post-translational arginylation, mediated by the family of enzymes known as the arginyltransferases (ATE1s), is an important post-translational modification that can alter protein function and even dictate cellular protein half-life. Multiple major biological pathways are linked to the fidelity of this process, including neural and cardiovascular developments, cell division, and even the stress response. Despite this significance, the structural, mechanistic, and regulatory mechanisms that govern ATE1 function remain enigmatic. To that end, we have used X-ray crystallography to solve the first crystal structure of ATE1 from Saccharomyces cerevisiae ATE1 (ScATE1) to 2.85 Å resolution. The three-dimensional structure of ScATE1 reveals a bilobed protein containing a GCN5-related N-acetyltransferase (GNAT) fold, and this crystalline behavior is faithfully recapitulated in solution based on size-exclusion chromatography-coupled small angle X-ray scattering (SEC-SAXS) analyses and cryo-EM 2D class averaging. Structural superpositions and electrostatic analyses indicate this domain as the location of catalytic activity and tRNA binding, and these comparisons strongly suggest a mechanism for post-translational arginylation. Additionally, our structure reveals the spatial connectivity of the N-terminal domain, which we have previously shown to bind a regulatory [Fe-S] cluster, and the enzymatic active site, hinting at the atomic-level details of the cluster’s regulatory influence. When taken together, these insights into the first structure of ATE1 bring us closer to answering pressing questions regarding the molecular-level mechanism of eukaryotic post-translational arginylation.