Peptidoglycan monomer, GlcNAc-beta-(1----4)-MurNAc-L-Ala-D-iGln[ (L)-meso-A2pm-(D)-amide-(L)-D-Ala-D-Ala] (PGM), from Brevibacterium divaricatum is composed of the disaccharide pentapeptide containing muramic acid with a reducing end (ca. 90-95%) and of the anhydromuramyl analogue (anhydromuranyl-PGM; ca. 5-10%), according to analysis by high-performance liquid chromatography (HPLC) and fast atom bombardment mass spectrometry (FAB-MS). The two peptidoglycan analogues cannot be separated by simple physico-chemical procedures. The enzyme N-acetylmuramyl-L-alanine amidase (mucopeptide amidohydrolase, E.C. 3.5.1.28) cleaves the bond between N-acetylmuramic acid and L-alanine in the PGM molecule. It is shown that anhydromuramyl-PGM is also a substrate for the amidase. In a preparation containing both analogues, the amidase hydrolyses preferentially PGM rather than anhydromuramyl-PGM. The experimental conditions for treatment with the amidase were adjusted with respect to time and enzyme concentration to allow hydrolysis to proceed for several hours. The course of hydrolysis was followed by analysis of the unhydrolyzed substrate by HPLC, and FAB-MS at predetermined time intervals; after 6 h, the amount of anhydromuramyl-PGM in the unhydrolyzed substrate increased to 25% as compared to the starting material containing only 6%. Such a mixture was suitable for separation of components by preparative thin-layer chromatography and for isolation of completely purified PGM and the corresponding anhydromuramyl analogue containing an intramolecular 1,6-anhydromuramyl end. The separated purified compounds were characterized by HPLC and their structure confirmed by FAB-MS-MS.