Browsing by Subject "membrane protein"

Nucleoside transport into the cell plays a key role in providing building blocks for DNA and RNA synthesis, terminating adenosine signaling, and delivering nucleoside-analog drugs to their targets. Concentrative nucleoside transporters (CNTs) constitute one of the classes of membrane transporters responsible for the cellular uptake of nucleosides and nucleoside-derived drugs. We solved the first structure of a member of the CNT family, vcCNT, by X-ray crystallography, revealing the overall architecture of the transporter, delineating the locations of the nucleoside- and sodium-binding sites, and providing insight into the mechanism of transport. Next we examined the molecular origins of nucleoside and nucleoside-drug selectivity by solving structures of the transporter bound to different nucleosides and drugs and measuring their binding affinities for vcCNT to determine energetically important interactions. We then used this information to design a compound that is better transported by and subtype-selective for human CNTs. Finally, we probed the role of sodium in the ion-coupled transport of nucleosides using binding and transport studies and developed a hypothesis for the structural basis of sodium coupling. Taken together, these studies helped to elucidate the molecular mechanism by which CNTs selectively recognize nucleosides and pump them into the cell and provided insight into drug uptake by these transporters, laying a framework for the improvement of targeted nucleoside-drug delivery by CNTs.

Lipopolysaccharide, the physical barrier that protects Gram-negative bacteria from various antibiotics and environmental stressors, is anchored to the outer membrane by the phosphorylated, acylated disaccharide of glucosamine known as lipid A. Besides being necessary for the viability of most Gram-negative bacteria, lipid A interacts directly with specific mammalian immune cell receptors, causing an inflammatory response that can result in septic shock. The lipid A biosynthetic pathway contains nine enzymatic steps, the sixth being the phosphorylation of the tetraacyldisaccharide-1-phosphate (DSMP) precursor to form lipid IV_A by the inner membrane-bound kinase LpxK, a divergent member of the P-loop containing nucleotide triphosphate hydrolase superfamily. LpxK is the only known P-loop kinase to act on a lipid at the membrane interface.

We report herein multiple crystal structures of Aquifex aeolicus LpxK in apo as well as ATP, ADP/Mg2+, AMP-PCP, and chloride-bound forms. LpxK consists of two α/β/α sandwich domains connected by a two-stranded β-sheet linker. The N-terminal domain, which has most structural homology to other P-loop kinase family members, is responsible for catalysis at the P-loop and positioning of the DSMP substrate for phosphoryl transfer on the inner membrane. The smaller C-terminal domain, a substructure unique to LpxK, helps bind the nucleotide substrate using a 25º hinge motion about its base which also assembles the necessary catalytic residues at the active site.

Using a thin-layer chromatography-based radioassay, we have performed extensive kinetic characterization of the enzyme and demonstrate that LpxK activity in vitro is dependent on the presence of detergent micelles, the use of divalent cations, and formation of a ternary LpxK-ATP/Mg2+-DSMP complex. Implementing steady-state kinetic analysis of multiple point mutants, we identify crucial active site residues. We propose that the interaction of D99 with H261 acts to increase the pK_a of the imidazole group, which in turn serves as the catalytic base to deprotonate the 4’-hydroxyl of DSMP. An analogous mechanism has not yet been reported for any member of the P-loop kinase family.

The membrane/lipid binding characteristics of LpxK have also been also investigated through a crystal structure of the LpxK-lipid IV_A product complex along with point mutagenesis of residues in the DSMP binding pocket. Critical contacts with the bound lipid include interactions along the glucosamine backbone and the 1-position phosphate group, especially through R171. Furthermore, analysis of truncation mutants of the N-terminal helix of LpxK demonstrates that this substructure is a critical hydrophobic contact point with the membrane, and that both charge-charge and hydrophobic interactions contribute to the localization of LpxK at the lipid bilayer.

Overall, this work has contributed significantly to the limited knowledge surrounding membrane-bound enzymes that act upon lipid substrates. It has also provided insight into the process of enzyme evolution as LpxK, while containing a similar core domain as other P-loop kinases, has developed multiple subdomains required for both cellular localization and recognition of novel substrates. Finally, the presence of multiple crystal structures and detailed understanding of the LpxK catalytic mechanism will improve the chances of successfully targeting this essential step in lipid A biosynthesis in the pursuit of novel antimicrobials.

The biosynthesis of many important polysaccharides (including peptidoglycan, lipopolysaccharide, and N-linked glycans) necessitates membrane transport of oligosaccharide precursors from their cytoplasmic site of synthesis to their site of assembly outside the cytoplasm. To address this problem, cells utilize transporters such as those of the multidrug/oligosaccharidyl-lipid/polysaccharide (MOP) superfamily to flip lipid-linked oligosaccharides across the cytoplasmic membrane. The MOP superfamily member MurJ has been shown to be the flippase that transports the lipid-linked peptidoglycan precursor lipid II, but the lack of structural information has limited our mechanistic understanding of the MurJ transport cycle. We determined the first crystal structure of MurJ (MurJTA from Thermosipho africanus) to 2.0-Å resolution, which assumed an inward-facing conformation unlike all other outward-facing structures of MOP transporters. Our structural and mutagenesis studies provide insight into a putative model of lipid II binding and an alternating-access mechanism of transport.