There are two proteases commonly used for cleavage at Lys residues.
Wako sells Lysyl Endopeptidase from Achromobacter lyticus E.C.
3.4.21.50. The enzyme from Boehringer is Endoproteinase Lys-C from
Lysobacter enzymogenes E.C.3.4.99.30. Unfortunately, for convenience,
both of these proteinases are often called Lys-C. When looking for
autolytic fragments it is obviously important to make sure you are
trying to match masses to the correct sequence.
I know the general consensus has been that the Wako enzyme gives more
reproducible results but we have not found that to be true for the
proteins we have digested. We switched from the Wako enzyme to the
Boehringer sequencing grade enzyme many years ago due to a high
background of autolytic fragments and incomplete digestion products
obtained with the Wako enzyme. Obviously there is a significant cost
difference between the Boehringer sequencing grade enzyme and the Wako
enzyme and our observations may not hold up for the Boehringer bulk
Lys-C.
Tim
Tim Edmunds
Director
Structural Protein Chemistry
Genzyme Corporation
P.O Box 9322
Framingham
MA 01701-9322
Tel (508) 270 2260
Fax (508)872 9080
EMail tedmunds@genzyme.com