The enzyme aspartate carbamoyltransferase (ATCase) catalyzes the first step in the pyrimidine biosynthetic pathway. Crystal structure of a catalytic (C) subunit of the Yersinia pestis CO92 ATCase was solved by molecular replacement using the structure of the unregulated, N-phosphonacetyl-L-aspartate (PALA)-bound C subunit of ATCase from Escherichia coli (PDB ID 1EKX) as a model. Both proteins share 84 % sequence identity, are trimeric in the crystal and have 1.6 Å root-mean-square deviation (rmsd) of the C-alpha atoms. The structural discrepancy between two proteins is due to the greater overall flexibility and disorder in loops containing active-site residues of the ligand-free Y. pestis C trimer. In contrast, the E.coli PALA-free C trimer (PDB ID 3CSU) has 0.5 Å rmsd of the C-alpha atoms with its Y. pestis homolog. This indicates that binding of a substrate (substrate analog) alters structural perturbations. In order to understand the regulation mechanism of the Y. pestis ATCase, conformational states that account for allosteric structural changes in catalytic activity should be defined.