Crystallographic study of steps along the reaction pathway of D-amino acid aminotransferase

Biochemistry. 1998 Apr 7;37(14):4958-67. doi: 10.1021/bi972884d.


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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Alanine Transaminase / chemistry
  • Alanine Transaminase / metabolism*
  • Bacillus / enzymology
  • Binding Sites
  • Catalysis
  • Crystallography, X-Ray
  • D-Alanine Transaminase
  • Diazonium Compounds / chemistry
  • Diazonium Compounds / metabolism
  • Molecular Structure
  • Pyridines / chemistry
  • Pyridines / metabolism
  • Pyridoxal Phosphate / chemistry
  • Pyridoxal Phosphate / metabolism
  • Pyridoxamine / analogs & derivatives
  • Pyridoxamine / chemistry
  • Pyridoxamine / metabolism
  • Substrate Specificity


  • Diazonium Compounds
  • Pyridines
  • 4-(2'-pyridyldithio)benzyldiazoacetate
  • Pyridoxal Phosphate
  • Pyridoxamine
  • Alanine Transaminase
  • D-Alanine Transaminase
  • pyridoxamine phosphate

Associated data

  • PDB/3DAA
  • PDB/4DAA