Crystal structure at 2.4 angstrom resolution of E-coli serine hydroxymethyltransferase in complex with glycine substrate and 5-formyl tetrahydrofolate

Serine hydroxymethyltransferase (EC 2.1.2.1), a member of the a-class of py ridoxal phosphate enzymes, catalyzes the reversible interconversion of seri ne and glycine, changing the chemical bonding at the C-alpha-C-beta bond of the serine side-chain mediated by the pyridoxal phosphate cofactor. Scissi on of the C-alpha-C-beta bond of serine substrate produces a glycine produc t and most likely formaldehyde, which reacts without dissociation with tetr ahydropteroylglutamate cofactor. Crystal structures of the human and rabbit cytosolic serine hydroxymethyltransferases (SHMT) confirmed their close si milarity in tertiary and dimeric subunit structure to each other and to asp artate aminotransferase, the archetypal alpha-class pyridoxal 5'-phosphate enzyme. We describe here the structure at 2.4 Angstrom resolution of Escher ichia coli serine hydroxymethyltransferase in ternary complex with glycine and 5-formyl tetrahydropteroylglutamate, refined to an R-factor value of 17 .4 % and R-free value of 19.6 %. This structure reveals the interactions of both cofactors and glycine substrate with the enzyme. Comparison with the E. coil aspartate aminotransferase structure shows the distinctions in sequ ence and structure which define the folate cofactor binding site in serine hydroxymethyltransferase and the differences in orientation of the amino te rminal arm, the evolution of which was necessary for elaboration of the fol ate binding site. Comparison with the unliganded rabbit cytosolic serine hy droxymethyltransferase structure identifies changes in the conformation of the enzyme, similar to those observed in aspartate aminotransferase, that p robably accompany the binding of substrate. The tetrameric quaternary struc ture of Liganded E. coil serine hydroxymethyltransferase also differs in sy mmetry and relative disposition of the functional tight dimers from that of the unliganded eukaryotic enzymes. SHMT tetramers have surface charge dist ributions which suggest distinctions in folate binding between eukaryotic a nd E. coli enzymes. The structure of the E. coli ternary complex provides t he basis for a thorough investigation of its mechanism through characteriza tion and structure determination of site mutants. (C) 2000 Academic Press.