Structural Consideration of the Working Mechanism of Fold Type I Transaminases From Eubacteria: Overt and Covert Movement

Abstract

Transaminases (TAs) reversibly catalyze the transfer reaction of an amino group between an amino group donor and an amino group acceptor, using pyridoxal 5′-phosphate (PLP) as a cofactor. TAs are categorized according to the amino group position of the donor substrate and respective TAs recognize their own specific substrates. Over the past decade, a number of TA structures have been determined by X-ray crystallography. On the basis of the structural information, the detailed mechanism of substrate recognition by TAs has also been elucidated. In this review, fold type I TAs are addressed intensively. Comparative studies on structural differences between the apo and holo forms of fold type I TAs have demonstrated that regions containing the active site exhibit structural plasticity in the apo form, facilitating PLP insertion into the active site. In addition, given that TAs recognize two different kinds of substrates, they possess dual substrate specificity. It is known that spatial rearrangements of active site residues occur upon binding of the substrates. Intriguingly, positively charged residues are predominantly distributed at the active site cavity. The electric field generated by such charge distributions may attract negatively charged molecules, such as PLP and amino group acceptors, into the active site. Indeed, TAs show remarkable dynamics in diverse aspects. In this review, we describe the comprehensive working mechanism of fold type I TAs, with a focus on conformational changes.

Metabolism of Cysteine Conjugates and Production of Flavor Sulfur Compounds by a Carbon–Sulfur Lyase from the Oral Anaerobe Fusobacterium nucleatum

“…Indeed, we observed a population peak at 6.93 nm (Figure S3), which corresponds to the average hydrodynamic diameter of the FnaPatB1 dimer estimated from its crystal structure (approximately 6.5 nm). FnaPatB1 adopted the typical type-I aminotransferase fold composed of a large domain and a small domain. , Careful examination of electron density maps allowed identification of ligands bound to the FnaPatB1 active site (Figure B). The substrate allyl-cysteine was observed at the entrance of the active site pocket, near an extended loop present in FnaPatB1 only (in red in Figure A).…”

Structural and Preliminary Biochemical Characterization of MppQ, a PLP-Dependent Aminotransferase from Streptomyces hygroscopicus

“…The two chains in the asymmetric unit form a homodimer (Figure 2-3; 2,974 Å 2 buried surface area) that matches the quaternary structures observed for known fold type I aminotransferases. 23, 24 Superposition of the ShMppQ dimer onto the E. coli aspartate aminotransferase dimer (PDB ID 1ARS 25 ) gives and RMSD of 2.85 Å for 620 of the 775 Cα atoms in the ShMppQ·PLP model.…”

Structure and Cooperativity in Substrate–Enzyme Interactions: Perspectives on Enzyme Engineering and Inhibitor Design

“…The active site of the PLP-TAs is dominant with positively charged residues and sparsely distributed negatively charged residues. Therefore, it is reasonable to assume that amine group acceptors are usually negatively charged and attracted to the catalytic site through electrostatic steering, whereas the amine group donors are usually zwitter ions that get into the catalytic site through simple diffusion. ,− On the other hand, the substrate-binding pocket is complementary to the substrates in shape and physicochemical properties and also provides specific interactions to the given substrates of the enzyme. Another important feature of these unique catalytic pockets is that they are evolutionarily tailored to control enantioselectivity without changing the mode or position of the cofactor binding.…”

“…Another important feature of these unique catalytic pockets is that they are evolutionarily tailored to control enantioselectivity without changing the mode or position of the cofactor binding. Binary and ternary complexes of PLP-TAs revealed the geometry and shape of the catalytic pocket required for catalyzing the two halves of the ping-pong reactions through a common cofactor and also disclose how each enzyme of the families is highly evolved to accept a specific acceptor substrate to form a specific product with a set of catalytic residues, PLP, and the donor substrate commonly given to the family of the PLP-TAs. ,− …”

“…Transaminases are extensively engineered and characterized for their applications in the biosynthesis of chiral amines. As indicated by their names, PLP-TAs not only are stereoselective but also synthesize diverse compounds with chiral amine functionality, such as β- and ω-amino acids, α-amino acids (both d - and l -), and branched and aromatic amino acids, as well as produce polyamines, etc. − Both engineered and wild-type are extensively used in the multienzyme or one-pot synthesis of chiral compounds, useful for the production of APIs, agrochemicals, and fine chemicals, through strategies such as asymmetric synthesis from prochiral carbonyl precursors and kinetic resolution of racemates. ,− Therefore, the structural and mechanistic understanding of the functioning of PLP-TAs is highly useful for the prediction of substrate scope and stereoselectivity of newly discovered TAs and for structure guided engineering of several biocatalysts for wider substrates specificity and for enhanced or inverted stereoselectivity without interfering with cofactor or donor substrate binding.…”