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Strictosidine synthase (STR), the gate enzyme for monoterpenoid indole alkaloid biosynthesis, catalyzes the Pictet–Spengler reaction (PSR) of various tryptamine derivatives with secologanin assisted by “indole sandwich” stabilization. Continuous exploration with β-methyltryptamine (IPA) stereoselectively delivered the C6-methylstrictosidines and C6-methylvincosides by enzymatic and nonenzymatic PSR, respectively. Unexpectedly, the first “nonindole sandwich” binding mode was witnessed by the X-ray structures of STR1-ligand complexes. Site-directed mutagenesis revealed the critical cryptic role of the hydroxyl group of Tyr151 in IPA biotransformation. Further computational calculations demonstrated the adjustable IPA position in STR1 upon the binding of secologanin, and Tyr151-OH facilitates the productive PSR binding mode via an advantageous hydrogen-bond network. Further chemo-enzymatic manipulation of C6-methylvincosides successfully resulted in the discovered antimalarial framework (IC50= 0.92 μM).

Helicobacter pylori(Hp) is a human pathogen that lives in the gastric mucosa of approximately 50% of the world’s population causing gastritis, peptic ulcers, and gastric cancer. An increase in resistance to current drugs has sparked the search for new Hp drug targets and therapeutics. One target is the disruption of nucleic acid production, which can be achieved by impeding the synthesis of 6-oxopurine nucleoside monophosphates, the precursors of DNA and RNA. These metabolites are synthesized by Hp xanthine–guanine–hypoxanthine phosphoribosyltransferase (XGHPRT). Here, nucleoside phosphonates have been evaluated, which inhibit the activity of this enzyme with Kivalues as low as 200 nM. The prodrugs of these compounds arrest the growth of Hp at a concentration of 50 μM in cell-based assays. The kinetic properties of HpXGHPRT have been determined together with its X-ray crystal structure in the absence and presence of 9-[(N-3-phosphonopropyl)-aminomethyl-9-deazahypoxanthine, providing a basis for new antibiotic development.

Lanthanoid heteroleptic complexes with cucurbit[5]uril {Q[5]} and two dicarboxylate ligands, e.g., diglycolic acid (H2DGC) and glutaric acid (H2GT), have been investigated with six new compounds featuring a tetrametallic and dimetallic discrete structures, a one-dimensional (1D) polymer, and three two-dimensional (2D) polymers with a unique honeycomb-type topology being synthesized and structurally characterized. [La4(Q[5])3(DGC)2(NO3)2(H2O)12][La(DGC)(H2O)6]·7NO3·nH2O (1) has a tetrametallic structure constructed with three bis-bidentate Q[5] ligands linking two [La(DGC)(H2O)2]+species in the middle and two [La(H2O)4(NO3)]2+species at both ends. [Ce2(Q[5])(DGC)(NO3)(H2O)10]·3NO3·4H2O (2) has a dimetallic structure built up with a bis-bidentate Q[5] ligand linking [Ce(DGC)(H2O)3(NO3)] and [Ce(H2O)7]3+on each side of the Q[5] portals. [Ce3(Q[5])3(DGC)2(H2O)9][Ce(DGC)(H2O)6]2·7NO3·nH2O (3) has a 1D polymeric structure built up with bis-bidentate Q[5] ligands in-turn linking one [Ce(H2O)6]3+and two [Ce(DGC)(H2O)6]1+cationic species. [Ln2(Q[5])2(GT)(H2O)6]·4NO3·nH2O [Ln = La (4), Ce (5) and Nd (6)] have similar 2D polymeric structures built up with two types of 9-fold coordinated Ln polyhedra linked by Q[5] via bis-bidentate carbonyl groups on both sides forming 1D chains which are further connected by bridging GT2–ligands to form 2D polymers with a unique honeycomb-type topology. Their vibrational modes and electronic structures have also been investigated.

Phenol and its derivatives are common pollutants that are present in industrial discharge and are major xenobiotics that lead to water pollution. To monitor as well as improve water quality, attempts have been made in the past to engineer bacterial in vivobiosensors. However, due to the paucity of structural information, there is insufficiency in gauging the factors that lead to high sensitivity and selectivity, thereby impeding development. Here, we present the crystal structure of the sensor domain of MopR (MopRAB) from Acinetobacter calcoaceticusin complex with phenol and its derivatives to a maximum resolution of 2.5 Å. The structure reveals that the N-terminal residues 21–47 possess a unique fold, which are involved in stabilization of the biological dimer, and the central ligand binding domain belongs to the “nitric oxide signaling and golgi transport” fold, commonly present in eukaryotic proteins that bind long-chain fatty acids. In addition, MopRABnests a zinc atom within a novel zinc binding motif, crucial for maintaining structural integrity. We propose that this motif is crucial for orchestrated motions associated with the formation of the effector binding pocket. Our studies reveal that residues W134 and H106 play an important role in ligand binding and are the key selectivity determinants. Furthermore, comparative analysis of MopR with XylR and DmpR sensor domains enabled the design of a MopR binding pocket that is competent in binding DmpR-specific ligands. Collectively, these findings pave way towards development of specific/broad based biosensors, which can act as useful tools for detection of this class of pollutants.

A broad working definition of structural proteomics (SP) is that it is the process of the high-throughput characterization of the three-dimensional structures of biological macromolecules. Recently, the process for protein structure determination has become highly automated and SP platforms have been established around the globe, utilizing X-ray crystallography as a tool. Although protein structures often provide clues about the biological function of a target, once the three-dimensional structures have been determined, bioinformatics and proteomics-driven strategies can be employed to derive their biological activities and physiological roles. This article reviews the current status of SP methods for the structure determination pipeline, including target selection, isolation, expression, purification, crystallization, diffraction data collection, structure solution, refinement and functional annotation.

Two similar enzymes with different biosynthetic function in one species have evolved to catalyze two distinct reactions. X-ray structures of both enzymes help reveal their most important differences. The Rauvolfiaalkaloid biosynthetic network harbors two O-glucosidases: raucaffricine glucosidase (RG), which hydrolyses raucaffricine to an intermediate downstream in the ajmaline pathway, and strictosidine glucosidase (SG), which operates upstream. RG converts strictosidine, the substrate of SG, but SG does not accept raucaffricine. Now elucidation of crystal structures of RG, inactive RG-E186Q mutant, and its complexes with ligands dihydro-raucaffricine and secologanin reveals that it is the “wider gate” of RG that allows strictosidine to enter the catalytic site, whereas the “slot-like” entrance of SG prohibits access by raucaffricine. Trp392 in RG and Trp388 in SG control the gate shape and acceptance of substrates. Ser390 directs the conformation of Trp392. 3D structures, supported by site-directed mutations and kinetic data of RG and SG, provide a structural and catalytic explanation of substrate specificity and deeper insights into O-glucosidase chemistry.

AbstractStructural proteomics (SP) projects are capable of producing thousands of protein structures per year by employing semi-automated technologies. It is too early to assess and evaluate the scientific impact of these protein structures, although SP initiatives have substantially changed the traditional way of protein characterization. Many of the methodologies and technologies developed by SP have been adapted by structural biology laboratories and pharmaceutical companies to lower the costs, increase the speed and productivity of structure determination pipelines and to enhance drug discovery programs. The advent of genomic and proteomic technologies have facilitated rapid advances in our understanding of the molecular details of cellular function. The purpose of this review is to consider the impact of these technologies on protein structure analysis and to illustrate how it’s directing the focus of research relevant to biotechnology.

Cutting carbons: The threedimensional structure of polyneuridine aldehyde esterase PNAE gives insight into the enzymatic mechanism of the biosynthesis of C9 from C10monoterpenoid indole alkaloids see scheme. PNAE is a very substratespecific serine esterase. It harbors the catalytic triad S87D216H244, and is a new member of the αβfold hydrolase superfamily. Its novel function leads to the diversification of alkaloid structures.

Alle Neune: Die dreidimensionale Struktur der PolyneuridinaldehydEsterase PNAE gibt einen Einblick in den Enzymmechanismus der Biosynthese von C9 aus C10monoterpenoiden IndolAlkaloiden siehe Schema. PNAE ist eine sehr substratspezifische SerinEsterase. Sie enthält die katalytische Triade S87D216H244 und ist ein neues Mitglied der Superfamilie der αβHydrolasen, allerdings mit einer neuartigen Funktion: der Diversifizierung von Alkaloidstrukturen.

The cholesterol-dependent cytolysins (CDCs) are the archetype for the superfamily of oligomeric pore-forming proteins that includes the membrane attack complex/perforin (MACPF) family of immune defense proteins and the stonefish venom toxins (SNTX). The CDC/MACPF/SNTX family exhibits a common protein fold, which forms a membrane-spanning β-barrel pore. We show that changing the relative stability of an extensive intramolecular interface within this fold, which is necessarily disrupted to form the large β-barrel pore, dramatically alters the kinetic and temperature-dependent properties of CDC pore formation. These studies show that the CDCs and other members of the CDC/MACPF/SNTX superfamily have the capacity to significantly alter their pore-forming properties to function under widely different environmental conditions encountered by these species.

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