Structure of a NifS Homologue: X-ray Structure Analysis of CsdB, an Escherichia coli Counterpart of Mammalian Selenocysteine Lyase,

Abstract

Escherichia coli CsdB, a NifS homologue with a high specificity for l-selenocysteine, is a pyridoxal 5‘-phosphate (PLP)-dependent dimeric enzyme that belongs to aminotransferases class V in fold-type I of PLP enzymes and catalyzes the decomposition of l-selenocysteine into selenium and l-alanine. The crystal structure of the enzyme has been determined by the X-ray crystallographic method of multiple isomorphous replacement and refined to an R-factor of 18.7% at 2.8 Å resolution. The subunit structure consists of three parts: a large domain of an α/β-fold containing a seven-stranded β-sheet flanked by seven helices, a small domain containing a four-stranded antiparallel β-sheet flanked by three α-helices, and an N-terminal segment containing two α-helices. The overall fold of the subunit is similar to those of the enzymes belonging to the fold-type I family represented by aspartate aminotransferase. However, CsdB has several structural features that are not observed in other families of the enzymes. A remarkable feature is that an α-helix in the lobe extending from the small domain to the large domain in one subunit of the dimer interacts with a β-hairpin loop protruding from the large domain of the other subunit. The extended lobe and the protruded β-hairpin loop form one side of a limb of each active site in the enzyme. The most striking structural feature of CsdB lies in the location of a putative catalytic residue; the side chain of Cys364 on the extended lobe of one subunit is close enough to interact with the γ-atom of a modeled substrate in the active site of the subunit. Moreover, His55 from the other subunit is positioned so that it interacts with the γ- or β-atom of the substrate and may be involved in the catalytic reaction. This is the first report on three-dimensional structures of NifS homologues.