, a nitrogen-fixing bacterium, metabolizes l
-arabinose through a hypothetical pathway via
nonphosphorylated intermediates, which differs from the well known bacterial and fungal pathways. We are in the process of characterizing this alternative l
-arabinose pathway enzymatically and genetically and have recently identified a set of five metabolic genes (Watanabe, Kodaki et al.
; Watanabe, Shimada et al.
; Watanabe et al.
-KDA) dehydratase (EC 22.214.171.124; encoded by the AraD
gene; GenBank accession No. BAE94270) catalyzes the fourth reaction step in this pathway, converting l
-KDA to α-ketoglutaric semialdehyde (Fig. 1). This enzyme consists of 309 amino-acid residues and belongs to the dihydrodipicolinate synthase (DHDPS)/N
-acetylneuraminate lyase (NAL) protein family, which includes the archetypal DHDPS and NAL and also d
-5-keto-4-deoxyglucarate dehydratase, d
-2-keto-deoxygluconate aldolase, trans
-hydroxybenzylidenepyruvate hydrolase-aldolase and trans
-2′-carboxybenzalpyruvate hydratase-aldolase (Watanabe, Shimada et al.
). Although these enzymes form single clusters in the phylogenetic tree, l
-KDA dehydratase shows a poor relationship to all of the subclasses. Many crystallographic analyses of DHDPS/NAL proteins, including DHDPS (Blagova et al.
; Blickling et al.
; Mirwaldt et al.
; Pearce et al.
; Tam et al.
), NAL (Barbosa et al.
; Izard et al.
) and d
-2-keto-deoxygluconate aldolase (Theodossis et al.
), have revealed a common (β/α)8
-barrel fold and a common reaction step in their reactions, namely the formation of a Schiff-base intermediate between a strictly conserved lysine residue and the C2
carbon of a common α-keto acid moiety of the substrate. In the case of l
-KDA dehydratase, the structurally equivalent lysine residue has been assigned in the amino-acid sequence (Lys171), but the enzyme reaction does not include cleavage of the C—C or C=C bond of the substrate, in contrast to the reactions catalyzed by other DHDPS/NAL enzymes; therefore, three-dimensional structure analysis should provide a novel insight into the catalytic mechanism of this unique enzyme. Here, we describe the crystallization and preliminary X-ray crystallographic analysis of l
The enzyme reaction catalyzed by l-KDA dehydratase.