Structural Determinants for the Non-Canonical Substrate Specificity of the ω-Transaminase from Paracoccus denitrificans

Substrate binding pockets of -transaminase (-TA) consist of a large (L) pocket capable of dual recognition of hydrophobic and carboxyl substituents, and a small (S) pocket displaying a strict steric constraint that permits entry of a substituent no larger than an ethyl group. Despite the unique catalytic utility of -TA enabling asymmetric reductive amination of carbonyl compounds, the severe size exclusion occurring in the S pocket has limited synthetic applications of -TA to access structurally diverse chiral amines and amino acids. Here we report the first example of an -TA whose S pocket shows a non-canonical steric constraint and readily accommodates up to an n-butyl substituent. The relaxed substrate specificity of the (S)-selective -TA, cloned from Paracoccus denitrificans (PDTA), afforded efficient asymmetric syntheses of unnatural amino acids carrying long alkyl side chains such as L-norvaline and L-norleucine. Molecular modeling using the recently released X-ray structure of PDTA could pinpoint an exact location of the S pocket which had remained dubious. Entry of a hydrophobic substituent in the L pocket was found to have the S pocket accept up to an ethyl substituent, reminiscent of the canonical steric constraint. In contrast, binding of a carboxyl group to the L pocket induced a slight movement of V153 away from the small-pocket-forming residues. The resulting structural change elicited excavation of the S pocket, leading to formation of a narrow tunnel-like structure allowing accommodation of linear alkyl groups of carboxylate-bearing substrates. To verify the active site model, we introduced site-directed mutagenesis to six active site residues and examined whether the point mutations alleviated the steric constraint in the S pocket. Consistent with the molecular modeling results, the V153A variant assumed an elongated S pocket and accepted even an n-hexyl substituent. Our findings provide precise structural information on substrate binding to the active site of -TA, which is expected to benefit rational redesign of substrate specificity of omega-TA.