Crystal Structure of the Ancient Domain of Chicken IMPACT Reveals an Evolutionarily Conserved Candidate Functional Surface in the IMPACT/YigZ Family

IMPACT (Imprinted and Ancient domain protein) is a stress-responsive regulator that antagonizes the eIF2α kinase GCN2 and contains an N-terminal RWD domain and a C-terminal Ancient domain conserved across eukaryotes, bacteria and archaea. Here, we determined the crystal structure of the Ancient domain of chicken (Gallus gallus) IMPACT (GgIMPACTAncient) at 2.0 Å resolution. The domain adopts the canonical Ancient-domain fold, comprising four α-helices packed against a five-stranded antiparallel β-sheet. Comparison with experimentally determined budding-yeast and bacterial Ancient-domain structures and a representative archaeal AlphaFold model is consistent with conservation of the overall architecture despite modest pairwise sequence identities of 23.4–41.6% relative to GgIMPACTAncient. Surface analysis identifies a conserved acidic DDGE motif (D238–E241) and a spatially clustered polar quartet (S184, H217, E241 and R266). The corresponding residues are conserved in representative Ancient/YigZ homologues and overlap with candidate functional residues proposed for Escherichia coli YigZ and Leishmania donovani IMPACT. A chloride ion bound near R266 in GgIMPACTAncient and a crystallization-derived tartrate at the homologous site in Thermus thermophilus YigZ further show that this surface can accommodate small anions under crystallization conditions. These results provide the first crystallographic view of a metazoan IMPACT Ancient domain and a structural framework for testing the biochemical function of this evolutionarily conserved module.