Homocysteine is a key junction metabolite that can be converted to cystathionine in a reaction catalyzed by the heme and pyridoxal phosphate-dependent cystathionine beta-synthase. The heme has unusual spectroscopic properties and the axial ligands have been assigned as histidine and cysteine, respectively. Its role in the protein is not obvious from the chemistry of the beta-replacement reaction that is catalyzed. We have characterized the binding of the gaseous signaling molecule, NO, to cystathionine beta-synthase and examined its effect on the reactions catalyzed by the truncated dimeric form of the enzyme, W409X, which is a natural variant. Binding of NO appears to result in the formation of a five-coordinate ferrous nitrosyl species in which both endogenous ligands have been lost. This is in contrast to CO binding which is reported to displace the thiolate ligand and form a six-coordinate species. NO binds to the full-length enzyme with a K(d) of 281+/-50 microM and to the truncated enzyme with a K(d) of 350+/-44 microM. Binding of NO to the full-length enzyme inhibits activity with a K(i) of 320+/-60 microM. These studies demonstrate that as with CO, perturbation of the heme environment by NO is communicated to the active site with concomitant inhibition of enzyme activity, and suggests a regulatory role for heme in cystathionine beta-synthase.