Crystal structure of diaminopelargonic acid synthase: Evolutionary relationships between pyridoxal-5 '-phosphate-dependent enzymes

The three-dimensional structure of diaminopelargonic acid synthase, a vitam in B-6-dependent enzyme in the pathway of the biosynthesis of biotin, has b een determined to 1.8 Angstrom resolution by X-ray crystallography. The str ucture was solved by multi-wavelength anomalous diffraction techniques usin g a crystal derivatized with mercury ions. The protein model has been refin ed to a crystallographic X-value of 17.5% (X-free 22.6%). Each enzyme subun it consists of two domains, a large domain (residues 50-329) containing a s even-stranded predominantly parallel beta-sheet, surrounded by alpha-helice s, and a small domain comprising residues 1-49 and 330-429. Two subunits, r elated by a non-crystallographic dyad in the crystals, form the homodimeric molecule, which contains two equal active sites. Pyridoxal-5'-phosphate is bound in a cleft formed by both domains of one subunit and the large domai n of the second subunit. The cofactor is anchored to the enzyme by a covale nt linkage to the sidechain of the invariant residue Lys274. The phosphate group interacts with main-chain nitrogen atoms and the side-chain of Ser113 , located at the N terminus of an alpha-helix. The pyridine nitrogen forms a hydrogen bond to the side-chain of the invariant residue Asp245. Electron density corresponding to a metal ion, most likely Na+, was found in a tigh t turn at the surface of the enzyme. Structure analysis reveals that diamin opelargonic acid synthase belongs to the family of vitamin B-6-dependent am inotransferases with the same fold as originally observed in aspartate amin otransferase. A multiple structure alignment of enzymes in this family indi cated that they form at least six different subclasses. Striking difference s in the fold of the N-terminal part of the polypeptide chain are one of th e hallmarks of these subclasses. Diaminopelargonic acid synthase is a membe r of the aminotransferase subclass III. From the structure of the non-produ ctive complex of the holoenzyme with the substrate 7-keto-8-aminopelargonic acid the location of the active site and residues involved in substrate bi nding have been identified. (C) 1999 Academic Press.