Bacterial serine proteases, especially those from Bacillus, have been extensively studied. Intracellular serine protease 1 (Isp1) is responsible for most of the proteolytic activity in B. subtilis. To identify Isp1 substrates and study its physiological functions, a mutant of Isp1, which has lost the enzymatic activity, was constructed. Through a GST affinity chromatographic method, several Bacillus proteins that specifically interacted with S246A mutant Isp1 protein were isolated and then identified by MALDI-TOF analysis. ClpC and elongation factor Tu (EF-Tu) were among those proteins specifically bound to mutant Isp1. In addition, several proteins involved in stationary phase adaptive response (such as RNA polymerase sigma factor, spoIIIE) were also identified. These findings led us to suggest that the major function of this serine protease, whose expression is greatly increased during the stationary phase, is to mediate transition of the cell into the stationary phase in a proper and timely manner.