Oligonucleotide-directed site-specific mutagenesis was carried out on pyruvate decarboxylase (EC 126.96.36.199) from Saccharomyces cerevisiae at W412, located on the putative substrate activation pathway and linking E91 on the α domain with W412 on the γ domain of the enzyme. While C221 on the β domain is the residue at which substrate activation is triggered [Baburina, I., et al. (1994) Biochemistry 33, 5630-5635; Baburina, I., et al. (1996) Biochemistry 35, 10249-10255], that information, via the substrate bound at C221, is transmitted to H92 on the α domain, across the domain divide from C221 [Baburina, I., et al. (1998) Biochemistry 37, 1235-1244; Baburina, I., et al. (1998) Biochemistry 37, 1245-1255], thence to E91 on the α domain [Li, H., and Jordan, F. (1999) Biochemistry 38, 999210003], and then on to W412 on the γ domain and to the active site thiamin diphosphate located at the interface of the α and γ domains [Arjunan, D., et al. (1996) J. Mol. Biol. 256, 590-600]. Substitution at W412 with F and A was carried out, resulting in active enzymes with specific activities about 4- and 10-fold lower than that of the wild-type enzyme. Even though W412 interacts with E91 and H115 via a main chain hydrogen bond donor and acceptor, respectively, there is clear evidence for the importance of the indole side chain of W412 from a variety of experiments: thermostability, fluorescence quenching, and the binding constants of the thiamin diphosphate, and circular dichroism spectroscopy, in addition to conventional steady-state kinetic measurements. While the substrate activation is still prominent in the W412F variant, its level is very much reduced in the W412A variant, signaling that the size of the side chain is also important in positioning the amino acids surrounding the active center to achieve substrate activation. The fluorescence studies demonstrate that W412 is a relatively minor contributor to the well- documented fluorescence of apopyruvate decarboxylase in its native state. The information about the W412 variants provides strong additional support for the putative substrate activation pathway from C221 H92 → E91 → W412 → G413 → thiamin diphosphate. The accumulating evidence for the central role of the β domain in stabilizing the overall structure is summarized.
All Science Journal Classification (ASJC) codes