Proton, carbon-13, and nitrogen-15 sequence-specific backbone assignments have been obtained for the periplasmic cyclophilin type cis-trans peptidyl-prolyl isomerase from Escherichia coli (167 residues, M(r) = 18,244). Assignments were obtained using both 1H, 13C, and 15N triple-resonance and 1H and 15N double-resonance three-dimensional (3D) NMR spectroscopy at pH 6.2, 25 degrees C. Complete or partial residue-specific assignments have been obtained for 165 of the 167 residues. The secondary structure has been characterized using long- and medium-range NOEs. The protein consists of an eight-stranded anti-parallel beta-sheet and two helices. The overall topology of E. coli cyclophilin is similar to that of human T-cell cyclophilin. Sequence alignment with human T-cell cyclophilin based on secondary structure homology implicates several residues in E. coli cyclophilin that may be crucial for binding the peptide substrate AC-A-A-P-A-AMC and the immunosuppressive drug cyclosporin A.