RESUMEN
Dihydrodipicolinate synthase is a tetrameric enzyme of the diaminopimelate pathway in bacteria and plants. The protein catalyzes the condensation of pyruvate (Pyr) and aspartate semialdehyde en route to the end product lysine (Lys). Dihydrodipicolinate synthase from Campylobacter jejuni (CjDHDPS) is allosterically inhibited by Lys. CjDHDPS is a promising antibiotic target, as highlighted by the recent development of a potent bis-lysine (bisLys) inhibitor. The mechanism whereby Lys and bisLys allosterically inhibit CjDHDPS remains poorly understood. In contrast to the case for other allosteric enzymes, crystallographically detectable conformational changes in CjDHDPS upon inhibitor binding are very minor. Also, it is difficult to envision how Pyr can access the active site; the available X-ray data seemingly imply that each turnover step requires diffusion-based mass transfer through a narrow access channel. This study employs hydrogen/deuterium exchange mass spectrometry for probing the structure and dynamics of CjDHDPS in a native solution environment. The deuteration kinetics reveal that the most dynamic protein regions are in the direct vicinity of the substrate access channel. This finding is consistent with the view that transient opening/closing fluctuations facilitate access of the substrate to the active site. Under saturating conditions, both Lys and bisLys cause dramatically reduced dynamics in the inhibitor binding region. In addition, rigidification extends to regions close to the substrate access channel. This finding strongly suggests that allosteric inhibitors interfere with conformational fluctuations that are required for CjDHDPS substrate turnover. In particular, our data imply that Lys and bisLys suppress opening/closing events of the access channel, thereby impeding diffusion of the substrate into the active site. Overall, this work illustrates why allosteric control does not have to be associated with crystallographically detectable large-scale transitions. Our experiments provide evidence that in CjDHDPS allostery is mediated by changes in the extent of thermally activated conformational fluctuations.
Asunto(s)
Hidroliasas/química , Regulación Alostérica , Cristalografía por Rayos X , Deuterio/química , Hidrógeno/química , Conformación ProteicaRESUMEN
Dihydrodipicolinate synthase (DHDPS), an enzyme required for bacterial peptidoglycan biosynthesis, catalyzes the condensation of pyruvate and ß-aspartate semialdehyde (ASA) to form a cyclic product which dehydrates to form dihydrodipicolinate. DHDPS has, for several years, been considered a putative target for novel antibiotics. We have designed the first potent inhibitor of this enzyme by mimicking its natural allosteric regulation by lysine, and obtained a crystal structure of the protein-inhibitor complex at 2.2 Å resolution. This novel inhibitor, which we named "bislysine", resembles two lysine molecules linked by an ethylene bridge between the α-carbon atoms. Bislysine is a mixed partial inhibitor with respect to the first substrate, pyruvate, and a noncompetitive partial inhibitor with respect to ASA, and binds to all forms of the enzyme with a Ki near 200 nM, more than 300 times more tightly than lysine. Hill plots show that the inhibition is cooperative, indicating that the allosteric sites are not independent despite being located on opposite sides of the protein tetramer, separated by approximately 50 Å. A mutant enzyme resistant to lysine inhibition, Y110F, is strongly inhibited by this novel inhibitor, suggesting this may be a promising strategy for antibiotic development.
Asunto(s)
Biomimética , Campylobacter jejuni/enzimología , Inhibidores Enzimáticos/farmacología , Hidroliasas/antagonistas & inhibidores , Regulación Alostérica , Cristalografía por Rayos X , Inhibidores Enzimáticos/químicaRESUMEN
Dihydrodipicolinate synthase (DHDPS), an enzyme found in most bacteria and plants, controls a critical step in the biosynthesis of l-lysine and meso-diaminopimelate, necessary components for bacterial cell wall biosynthesis. DHDPS catalyzes the condensation of pyruvate and (S)-aspartate-ß-semialdehyde, forming an unstable product that is dehydrated to dihydrodipicolinate. The tetrameric enzyme is allosterically inhibited by l-lysine, and a better understanding of the allosteric inhibition mechanism is necessary for the design of potent antibacterial therapeutics. Here we describe the high-resolution crystal structures of DHDPS from Campylobacter jejuni with and without its inhibitor bound to the allosteric sites. These structures reveal a role for Y110 in the regulation of the allosteric inhibition by lysine. Mutation of Y110 to phenylalanine results in insensitivity to lysine inhibition, although the mutant crystal structure reveals that lysine does bind in the allosteric site. Comparison of the lysine-bound Y110F structure with wild-type structures reveals that key structural changes due to lysine binding are absent in this mutant.
Asunto(s)
Campylobacter jejuni/enzimología , Inhibidores Enzimáticos/farmacología , Hidroliasas/química , Hidroliasas/metabolismo , Lisina/farmacología , Tirosina/metabolismo , Regulación Alostérica/efectos de los fármacos , Dominio Catalítico/efectos de los fármacos , Inhibidores Enzimáticos/metabolismo , Hidroliasas/antagonistas & inhibidores , Hidroliasas/genética , Ligandos , Lisina/metabolismo , Modelos Moleculares , Movimiento , Mutagénesis Sitio-Dirigida , MutaciónRESUMEN
Dihydrodipicolinate synthase (DHDPS), an enzyme of the meso-diaminopimelate pathway of lysine biosynthesis, is essential for bacterial growth and is considered a target for novel antibiotics. We have studied DHDPS from Campylobacter jejuni for the first time, determining the kinetic mechanism of catalysis and inhibition with its natural allosteric feedback inhibitor (S)-lysine. The tetrameric enzyme is known to have two allosteric sites, each of which binds two molecules of lysine. The results suggest that lysine binds highly cooperatively, and primarily to the F form of the enzyme during the ping-pong mechanism. By applying graphical methods and nonlinear regression, we have discriminated between the possible kinetic models and determined the kinetic and inhibition constants and Hill coefficients. We conclude that (S)-lysine is an uncompetitive partial inhibitor with respect to its first substrate, pyruvate, and a mixed partial inhibitor with respect to its second substrate, (S)-aspartate-ß-semialdehyde (ASA), which differs from the kinetic models for inhibition reported for DHDPS from other sources. The Hill coefficients for the binding of lysine to different forms of the enzyme are all greater than 2, suggesting that the two allosteric sites are not independent. It has been found that ASA binds cooperatively in the presence of (S)-lysine, and the cooperativity of binding increases at near-KM concentrations of pyruvate. The incorporation of Hill coefficients into the kinetic equations was crucial for determining the kinetic model for this enzyme.