Structure features of novel D-amino acid transaminase from Aminobacterium colombiense

by Shilova S., Nikolaeva A., Rakitina T., Matuta I., Boyko K. , Bezsudnova E. | Bach Institute
of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow, Russia |
Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow, Russia

D-amino acid transaminases (DAATs) are pyridoxal-5′-phosphate-(PLP)-dependent enzymes
that catalyze reversible and stereoselective transfer of the amino group between D-amino
acids and α-keto acids. DAATs belong to fold type IV of the PLP-dependent enzymes in
which the PLP forms a covalent bond with the catalytic Lys residue as well as a number of
noncovalent conservative interactions among TAs of fold type IV. In the active site of known
DAATs, two modes of the organization of residues responsible for the substrate binding are
observed. The first type is observed in the DAAT from Bacillus suptilis (bsDAAT, PDB ID:
3DAA), in which α-carboxylic group is bound by a “carboxylate trap” formed by three
residues – Y31 from the βX-strand and R98*, H100* from the O-loop. The second type is
observed in TAs from Curtobacterium pusillum (CpuTA, PDB ID: 5K3W) and
Haliscomenobacter hydrossis (Halhy, PDB ID: 7P7X): here the α-carboxylic group of
substrate is bound by two residues, R51*, K117 in CpuTA and R28*, R90 in Halhy. The R51*
and R28* residues are directed to the active site from the adjacent subunit, and the K117
and R90 residues are located on the βY-strand. DAAT from Aminobacterium colombiense
(Amico) in the active site possesses residues similar to the bsDAAT (K99* and H101* on the
O-loop) and both CpuTA and Halhy (R27* and R88). To understand the Amico’s active site
organization, structure of holo-form and the R88L variant were determined by the RSA.