Crystal structure of phosphoserine aminotransferase from Escherichia coli at 2.3 Å resolution:: Comparison of the unligated enzyme and a complex with α-methyl-L-glutamate

Phosphoserine aminotransferase (PSAT; EC 2.6.1.52), a member of subgroup IV of the aminotransferases, catalyses the conversion of 3-phosphohydroxypyruvate to L-phosphoserine. The crystal structure of PSAT from Escherichia coli has been solved in space group P2(1)2(1)2(1) using MIRAS phases in combination with density modification and was refined to an R-factor of 17.5% (R-free = 20.1%) at 2.3 Angstrom resolution in addition, the structure of PSAT in complex with alpha-methyl-L-glutamate (AMG) has been refined to an R-factor of 18.5% (R-free = 25.1%) at 2.8 Angstrom resolution. Each subunit (361 residues) of the PSAT homodimer is composed of a large pyridoxal-5'-phosphate binding domain (residues 16-268), consisting of a seven-stranded mainly parallel beta-sheet, two additional beta-strands and seven alpha-helices, and a small C-terminal domain, which incorporates a five-stranded beta-sheet and two alpha-helices. A three-dimensional structural comparison to four other vitamin B-6-dependent enzymes reveals that three alpha-helices of the large domain, as well as an N-terminal domain (subgroup II) or subdomain (subgroup I) are absent in PSAT. Its only 15 N-terminal residues form a single P-strand, which participates in the beta-sheet of the C-terminal domain. The cofactor is bound through an aldimine linkage to Lys198 in the active site. Ln the PSAT-AMG complex Ser9 and Arg335 bind the AMG alpha-carboxylate group while His41, Arg42 and His328 are involved in binding the AMG side-chain. Arg77 binds the AMG side-chain indirectly through a solvent molecule and is expected to position itself during catalysis between the PLP phosphate group and the substrate side-chain. Comparison of the active sites of PSAT and aspartate aminotransferase suggests a similar catalytic mechanism, except for the transaldimination step, since in PSAT the Schiff base is protonated. Correlation of the PSAT crystal structure to a published profile sequence analysis of all subgroup IV members allows active site modelling of nifs and the proposal of a likely molecular reaction mechanism. (C) 1999 Academic Press.