Crystal Structure of D-Serine Dehydratase from Escherichia coli

Darya V. Urusova^$, Thomas D. Mueller ^& and Klaus D. Schnackerz*

^$Institute of Crystallography, Russian Academy of Sciences, Moscow, Russia, ^&Lehrstuhl fuer Pflanzenphysiologie und Biophysik, Julius-von-Sachs-Institut, Universitaet Wuerzburg, 97082 Wuerzburg und *Physiologische Chemie I, Theodor-Boveri-Institut fuer Biowissenschaften, Universitaet Wuezburg, 97074 Wuerzburg, Germany

D-Serine dehydratase (DSD) (EC 4.2.1.18) from Escherichia coli is a member of the pyridoxal 5'-phosphate (PLP)-dependent enzymes, catalyzing the conversion of D-serine to pyruvate and ammonia [1].

The crystal structure of monomeric DSD has been solved for an orthorhombic and a monoclinic data set to 1.97 and 1.55 Å, respectively, by molecular replacement. The monomer is divided into two domains, a larger PLP-binding domain and a smaller domain. The active site of DSD is very similar to those of other members of the b family. Lysine-118 forms a Schiff base with PLP, the cofactor phosphate group is liganded to a tetraglycine cluster (G279-G283), the 3-hydroxyl group of PLP is coordinated to N170 and N1 of PLP to T424, respectively.

In the closed conformation, the movement of the small domain blocks the entrance to the active site of DSD. The domain movement plays an important role in the formation of the substrate recognition site and the catalysis of the enzyme. Modeling of D-serine into the active site of DSD reveals that the hydroxyl group of D-serine is coordinated to the carboxyl group of D238. The carboxyl oxygens of D-serine are liganded to the hydroxyl group of S167 and the amide group of L171 (O1) and in addition, to the hydroxyl group of S167 and the amide group of T168 via hydrogen bonding. The catalytic reaction mechanism of DSD very similar to that proposed for L-serine dehydratase from rat liver [2] and serine racemase from Schistosaccharomyces pombe [3] is discussed.