Tandem duplications and fusions of single genes led to magnificent expansions of the divergence of protein structures and functions over evolutionary timescales.One of the possible results is poly-domain enzymes with inter-domain cooperativities, however, few examples have been structurally characterized at a full-length level to explore their innate synergism mechanisms.This work reports the crystal structures of a double-domain phosphagen kinase in both apo-and ligand-bound states, revealing a novel asymmetric L-shape arrangement of two domains.