The three-dimensional structure of cystathionine beta-lyase from Arabidopsis and its substrate specificity

The pyridoxal 5 ' -phosphate-dependent enzyme cystathionine P-lyase (CBL) c atalyzes the penultimate step in the de novo biosynthesis of Met in microbe s and plants. Absence of CBL in higher organisms makes it an important targ et for the development of antibiotics and herbicides. The three-dimensional structure of cystathionine P-lyase from Arabidopsis was determined by Patt erson search techniques, using the structure of tobacco (Nicotiana tabacum) cystathionine gamma -synthase as starting point. At a resolution of 2.3 An gstrom, the model was refined to a final crystallographic R-factor of 24.9% . The overall structure is very similar to other pyridoxal 5 ' -phosphate-d ependent enzymes of the gamma -family. Exchange of a few critical residues within the active site causes the different substrate preferences between E scherichia coli and Arabidopsis CBL. Loss of interactions at the ol-carboxy l site is the reason for the poorer substrate binding of Arabidopsis CBI;. In addition, the binding pocket of Arabidopsis CBL is larger than that of E . coli CBL, explaining the similar binding of L-cystathionine and L-djenkol ate in Arabidopsis CBT, in contrast to E. coli CBL, where the substrate bin ding site is optimized for the natural substrate cystathionine.