Crystallographic study of steps along the reaction pathway of D-amino acid aminotransferase.
The three-dimensional structures of two forms of the D-amino acid aminotransferase (D-aAT) from Bacillus sp. YM-1 have been determined crystallographically: the pyridoxal phosphate (PLP) form and a complex with the reduced analogue of the external aldimine, N-(5'-phosphopyridoxyl)-d-alanine (PPDA). Together with the previously reported pyridoxamine phosphate form of the enzyme [Sugio et al. (1995) Biochemistry 34, 9661], these structures allow us to describe the pathway of the enzymatic reaction in structural terms. A major determinant of the enzyme's stereospecificity for D-amino acids is a group of three residues (Tyr30, Arg98, and His100, with the latter two contributed by the neighboring subunit) forming four hydrogen bonds to the substrate alpha-carboxyl group. The replacement by hydrophobic groups of the homologous residues of the branched chain L-amino acid aminotransferase (which has a similar fold) could explain its opposite stereospecificity. As in L-aspartate aminotransferase (L-AspAT), the cofactor in D-aAT tilts (around its phosphate group and N1 as pivots) away from the catalytic lysine 145 and the protein face in the course of the reaction. Unlike L-AspAT, D-aAT shows no other significant conformational changes during the reaction.
Peisach
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Program in Bioorganic Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02254-9110, USA.
Chipman
D M
DM
Van Ophem
P W
PW
Manning
J M
JM
Ringe
D
D
D000410:Alanine Transaminase / Q000737:chemistry / Q000378:metabolism*; D001407:Bacillus / Q000201:enzymology; D001665:Binding Sites; D002384:Catalysis; D018360:Crystallography, X-Ray; D051263:D-Alanine Transaminase; D003979:Diazonium Compounds / Q000737:chemistry / Q000378:metabolism; D015394:Molecular Structure; D011725:Pyridines / Q000737:chemistry / Q000378:metabolism; D011732:Pyridoxal Phosphate / Q000737:chemistry / Q000378:metabolism; D011733:Pyridoxamine / Q000031:analogs & derivatives / Q000737:chemistry / Q000378:metabolism; D013379:Substrate Specificity
D003979:Diazonium Compounds; D011725:Pyridines; C056729:4-(2'-pyridyldithio)benzyldiazoacetate; D011732:Pyridoxal Phosphate; D011733:Pyridoxamine; D000410:Alanine Transaminase; D051263:D-Alanine Transaminase; C010627:pyridoxamine phosphate