3DAA

CRYSTALLOGRAPHIC STRUCTURE OF D-AMINO ACID AMINOTRANSFERASE INACTIVATED BY PYRIDOXYL-D-ALANINE

Summary for 3DAA

• Entry DOI: 10.2210/pdb3daa/pdb
• Descriptor: D-AMINO ACID AMINOTRANSFERASE, N-(5'-PHOSPHOPYRIDOXYL)-D-ALANINE (3 entities in total)
• Functional Keywords: aminotransferase, pyridoxal phosphate, transaminase
• Biological source: Bacillus sp.
• Total number of polymer chains: 2
• Total formula weight: 64082.78

Authors

Peisach, D.,Chipman, D.M.,Ringe, D. (deposition date: 1998-01-20, release date: 1998-04-29, Last modification date: 2024-05-22)

Primary citation

Peisach, D.,Chipman, D.M.,Van Ophem, P.W.,Manning, J.M.,Ringe, D.
Crystallographic study of steps along the reaction pathway of D-amino acid aminotransferase.
Biochemistry, 37:4958-4967, 1998

PubMed Abstract: 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.

PubMed: 9538014
DOI: 10.1021/bi972884d

Experimental method

X-RAY DIFFRACTION (1.9 Å)