RSS

PDB:1DAA

Protein Name

D-amino acid aminotransferase

Species

Thermophilic bacterium PS3

Biological Context

The aminotransferases catalyze an exchange reaction in which the amino group of an amino acid (R-CH(NH2)-COOH) is transferred to 2-oxo acid (R'-CO-COOH), resulting in the 2-oxo acid (R-CO-COOH) and the amino acid (R'-CH(NH2)-COOH). These enzymes require pyridoxal phosphates (PLP) as their coenzymes. They are specific for particular types of amino acid substrates, for instance there is D-amino acid aminotransferase (D-AAT) which is active for D-amino acids only. D-amino acids are the enantiomers of the corresponding L-amino acids usually found in proteins. D-amino acids are an essential constituent of the bacterial cell wall. D-AAT is thus important for bacteria because this enzyme catalyzes the synthesis of D-amino acids. Because of this function D-AAT possibly provides a suitable target for the development of novel antimicrobial agents. The catalytic mechanism and in addition the mechanism through which D-AAT recognizes D-amino acids but not L-amino acids has been revealed by the three-dimensional structure of the complex of D-AAT with PLP.

Structure Description

1daa1daa_x1daa_y

D-AAT is a homodimer. Each monomer requires one molecule of PLP. D-AAT is active for all kinds of D-amino acids. The comparison with the well studied L-Asp-aminotransferase (L-Asp-AT) which specifically recognizes L-Asp has shown that D-AAT is smaller than L-Asp-AT and that the protein fold of D-AAT is different from that of L-Asp-AT. The catalytic mechanism comprises two half-reactions, each involving three steps, and strongly resembles that of L-Asp-AT. The substrate binds in the active site of D-AAT by interacting with the C-alpha atom of arginine residue in D-AAT. When the substrate first interacts with PLP attached to the amino group of Lys145 in D-AAT, PLP detaches Lys145 and forms an intermediate complex with the substrate. Then this intermediate undergoes hydrolysis producing the keto-form RCOCOOH. The second half-reaction is the reversal of these steps. The catalytic site Lys145 is crucial in the determination of the stereospecificity in these reactions. Lys145 in L-Asp-AT is facing towards the substrate but in D-AAT is facing away from the substrate. Because the orientation of the substrate binding to the active site in D-AAT is opposite to that found in L-Asp-AT, this leads to the enzyme being active only for D-amino acids.

Protein Data Bank (PDB)

References

Source

  • Sugio, S. Petsko, G.A. Manning, J.M. Soda, K. Ringe, D.; "Crystal structure of a D-amino acid aminotransferase: how the protein controls stereoselectivity."; Biochemistry; (1995) 34:9661-9669 PubMed:7626635.

Others

author: Yuko Tsuchiya


Japanese version:PDB:1DAA