Examination of Key Intermediates in the Catalytic Cycle of Aspartate-β-semialdehyde Dehydrogenase from a Gram-positive Infectious Bacteria

Abstract

Aspartate-␤-semialdehyde dehydrogenase (ASADH) catalyzes a critical branch point transformation in amino acid biosynthesis. The products of the aspartate pathway are essential in microorganisms, and this entire pathway is absent in mammals, making this enzyme an attractive target for antibiotic development. The first structure of an ASADH from a Gram-positive bacterium, Streptococcus pneumoniae, has now been determined. The overall structure of the apoenzyme has a similar fold to those of the Gram-negative and archaeal ASADHs but contains some interesting structural variations that can be exploited for inhibitor design. Binding of the coenzyme NADP, as well as a truncated nucleotide analogue, into an alternative conformation from that observed in Gram-negative ASADHs causes an enzyme domain closure that precedes catalysis. The covalent acyl-enzyme intermediate was trapped by soaking the substrate into crystals of the coenzyme complex, and the structure of this elusive intermediate provides detailed insights into the catalytic mechanism.The dramatic increase in the number of multidrug-resistant microorganisms has provided greater urgency to the search for new antibiotics against novel drug targets. Essential gene products involved in bacterial metabolism represent attractive targets for such compounds; however, exploitation of these targets in drug development has not been achieved. Among the potential metabolic targets, several genes have been identified in the aspartate biosynthetic pathway that are essential for the survival of Salmonella during infection (1). The aspartate pathway present in plants, bacteria, and fungi leads to the formation of the following four essential amino acids: threonine, lysine, methionine, and isoleucine (2, 3). This pathway also produces several important non-protein metabolites that includes dihydrodipicolinate, a precursor of dipicolinate that is the major component of bacterial spores (4), and diaminopimelate, needed for cross-linking of the peptidoglycan polymers during bacterial cell wall synthesis (5). An additional product of this pathway, S-adenosylmethionine, is an essential methyl group donor that can serve, after decarboxylation, as a propylamine donor in the synthesis of the polyamines spermidine and spermine. S-Adenosylmethionine is also a precursor for two groups of quorum-sensing signaling molecules that have a critical role in the triggering of virulence factors in infectious organisms. Thus, proper functioning and regulation of this pathway is critical for the survival of all microorganisms. Because this pathway is completely absent in mammals, inhibitors that are designed to selectively block key enzymes in this pathway should show minimal reactivity with other human proteins.Among the genes that belong to this pathway, the asd gene that encodes for aspartate-␤-semialdehyde dehydrogenase (ASADH) 2 has been identified as essential in both Gram-negative and Gram-positive bacteria such as Salmonella enterica (1), Legionella pneumophila (6), Mycobacterium bovis (7), B...

Structural Basis for a Bispecific NADP+ and CoA Binding Site in an Archaeal Malonyl-Coenzyme A Reductase

“…In complete agreement with the structure of the ASD-aspartyl thioacyl adduct (22,31), the malonyl group is mainly anchored to the polypeptide via its carboxylate group by forming hydrogen bonds with the strictly conserved residues Gln 180 , Arg 241 , and His 248 (Fig. 4).…”

“…3A), which resembles that found in the ASD-NADP ϩ and GAPDH-NADP ϩ -structures (22,23). NADP ϩ is positioned along the C-terminal side of the central ␤-sheet of the dinucleotide binding domain partly capped by the protruding cover loop that bridges strand 171:180 and 199:202 of the dimerization domain (Fig.…”

Crystal Structure of Escherichia coli Ketopantoate Reductase in a Ternary Complex with NADP+ and Pantoate Bound

“…Hinge Bending; Comparison with Apo-and HoloKPR-Cofactor-induced hinge bending domain closure has been observed for several dehydrogenases, including alcohol dehydrogenase (34), formate dehydrogenase (35), glutamate dehydrogenase (36), diaminopimelate dehydrogenase (37), and aspartate-␤-semialdehyde dehydrogenase (38). It was, therefore, surprising that the crystal structure of the KPR⅐NADP ϩ complex compared with apoKPR revealed no evidence of a hinge bending induced by the cofactor (18).…”

Crystal Structure of the LysY·LysW Complex from Thermus thermophilus

“…5A). Interdomain movement upon the binding of NADP ϩ was reported in aspartate-␤-semialdehyde dehydrogenases (28,29); however, this was not the case for TtLysY. A comparison of the present TtLysY structure with the apo-TtLysYHB8 structure revealed that both structures were essentially the same (root mean square deviation ϭ 0.4 Å).…”