The diffusive transport and mixing times of regulatory molecules in micrometer and submicrometer reaction volumes can be shorter than characteristic times of conformational transformations in single enzyme molecules. Under these conditions, synchronization of individual molecular turnover cycles takes place when a fraction of the reaction products is converted through a second chemical reaction into the substrate molecules. Using a stochastic model which explicitly describes the internal dynamics of the catalytic process, we analyze the properties of the synchronization transition and the role of statistical fluctuations in the synchronization phenomena.