The complete amino acid sequence of rat liver CoA-dependent methylmalonate semialdehyde dehydrogenase, the enzyme responsible for the oxidative decarboxylation of malonate- and methylmalonate semialdehydes to acetyl- and propionyl-CoA in the distal portions of the valine and pyrimidine catabolic pathways, has been deduced from overlapping cDNAs obtained by screening a λgt11 library with nondegenerate oligonucleotide probes synthesized according to PCR-amplified portions coding for the N-terminal amino acid sequence of the enzyme. Although unique because of its requirement for coenzyme A, the methylmalonate semialdehyde dehydrogenase clearly belongs to the aldehyde dehydrogenase superfamily of enzymes. Quantitation of mRNA and protein levels indicates tissue-specific expression of methylmalonate semialdehyde dehydrogenase. A large increase in expression of methylmalonate semialdehyde dehydrogenase occurs during 3T3-L1 preadipocyte differentiation into adipocytes. The complete amino acid sequence of rat liver branched-chain α-ketoacid dehydrogenase kinase, the enzyme responsible for phosphorylation and inactivation of the branched-chain α-ketoacid dehydrogenase complex, was deduced from a cDNA cloned by a procedure similar to that described above for the methylmalonate semialdehyde dehydrogenase. Expression of the cDNA in E. coli yielded a protein that phosphorylated and inactivated the branched-chain α-ketoacid dehydrogenase complex. Very little sequence similarity between branched-chain α-ketoacid dehydrogenase kinase and other eukaryotic protein kinases could be identified. However, a high degree of similarity within subdomains characteristic of prokaryotic histidine protein kinases was apparent. Thus, this first mitochondrial protein kinase to be cloned appears closer, evolutionarily, to the prokaryotic histidine protein kinases than eukaryotic ser/thr protein kinases. © 1993.