Protein histidine kinase was prepared from whole cell extracts of the yeast, Saccharomyces cerevisiae. The enzyme was assayed using either histone H4 or a synthetic peptide corresponding to residues 70 to 102 of histone H4 as an in vitro substrate. With either substrate, both genistein and its solvent, dimethyl sulfoxide (Me2SO), inhibited protein histidine kinase. Me2SO alone gave a cooperative dose-response curve, with inhibition changing from almost zero below 10% Me2SO to 80% at 20% Me2SO with either substrate. Genistein gave a simple dose-response curve with 50% inhibition of protein histidine kinase at 110 microM genistein. In experiments with protein histidine kinase, genistein was a noncompetitive inhibitor with respect to ATP, histone H4 or the synthetic peptide, although, in the case of the synthetic peptide, the data were also consistent with competitive inhibition. These data gave Km values for both ATP and histone H4 of 15 microM, in satisfactory agreement with previously reported values (Huang, J., Wei, Y., Kim, Y., Osterberg, L., and Matthews, H. R. (1991) J. Biol. Chem. 266, 9023-9031). The Km for the synthetic peptide was 80 microM. The KI values were 270 or 310 microM measured with histone H4 or the synthetic peptide as substrate, respectively. While these KI values are relatively high, relative to published KI values for genistein inhibition of protein tyrosine kinases, many reported experiments use genistein at concentrations where inhibition of protein histidine kinase occurs. It is possible that some of the observed effects of genistein in vivo may be due to inhibition of protein histidine kinase.