Electronic chemical potentials of porous metal-organic frameworks

The binding energy of an electron in a material is a fundamental characteristic, which determines a wealth of important chemical and physical properties. For metal-organic frameworks this quantity is hitherto unknown. We present a general approach for determining the vacuum level of porous metal-organic frameworks and apply it to obtain the first ionisation energy for six prototype materials including zeolitic, covalent and ionic frameworks. This approach for valence band alignment can explain observations relating to the electrochemical, optical and electrical properties of porous frameworks

An Enzymatic Cyclopentyl[b]indole Formation Involved in Scytonemin Biosynthesis

Previous studies of the biosynthetic enzymes involved in the assembly of scytonemin (1), a cyanobacterial sunscreen, have identified β-ketoacid 2 as an important intermediate that is produced by ThDP-dependent enzyme ScyA. We now report that ScyC, previously annotated as a hypothetical protein, catalyzes cyclization and decarboxylation of 2 to generate ketone 5. Assembly of the cyclopentyl[b]indole structure in this manner has little precedent in the chemical literature. Additional mechanistic experiments have revealed that cyclization likely precedes decarboxylation and that the latter event may provide a driving force for cyclopentane formation.Chemistry and Chemical Biolog

Investigating the Initial Steps in the Biosynthesis of Cyanobacterial Sunscreen Scytonemin

The cyanobacterial natural product scytonemin (1) functions as a sunscreen, absorbing harmful UV-A radiation. Using information from a recently identified gene cluster, we propose a biosynthetic route to this pigment. We also report the characterization of two enzymes, NpR1275 and NpR1276, which are involved in the initial stages of this pathway. A regioselective acyloin reaction between indole-3-pyruvic acid (4) and p-hydroxyphenylpyruvic acid (5) is a key step in assembling the carbon framework of a proposed monomeric scytonemin precursor (2).Chemistry and Chemical Biolog

The biosynthesis of cyanobacterial sunscreen scytonemin in intertidal microbial mat communities

We have examined the biosynthesis and accumulation of cyanobacterial sunscreening pigment scytonemin within intertidal microbial mat communities using a combination of chemical, molecular, and phylogenetic approaches. Both laminated (layered) and nonlaminated mats contained scytonemin, with morphologically distinct mats having different cyanobacterial community compositions. Within laminated microbial mats, regions with and without scytonemin had different dominant oxygenic phototrophs, with scytonemin-producing areas consisting primarily of Lyngbya aestuarii and scytonemin-deficient areas dominated by a eukaryotic alga. The nonlaminated mat was populated by a diverse group of cyanobacteria and did not contain algae. The amplification and phylogenetic assignment of scytonemin biosynthetic gene scyC from laminated mat samples confirmed that the dominant cyanobacterium in these areas, L. aestuarii, is likely responsible for sunscreen production. This study is the first to utilize an understanding of the molecular basis of scytonemin assembly to explore its synthesis and function within natural microbial communities.Chemistry and Chemical Biolog

The structure of the substrate-free form of MurB, an essential enzyme for the synthesis of bacterial cell walls

AbstractBackground: The repeating disaccharide and pentapeptide units of the bacterial peptidoglycan layer are connected by a lactyl ether bridge biosynthesized from UDP-N-acetylglucosamine and phosphoenolpyruvate in sequential enol ether transfer and reduction steps catalyzed by MurA and MurB respectively. Knowledge of the structure and mechanism of the MurB enzyme will permit analysis of this unusual enol ether reduction reaction and may facilitate the design of inhibitors as candidate next-generation antimicrobial agents.Results The crystal structure of UDP-N-acetylenolpyruvylglucosamine reductase, MurB, has been solved at 3.0 å and compared with our previously reported structure of MurB complexed with its substrate enolpyruvyl-UDP-N-acetylglucosamine. Comparison of the liganded structure of MurB with this unliganded form reveals that the binding of substrate induces a substantial movement of domain 3 (residues 219–319) of the enzyme and a significant rearrangement of a loop within this domain. These ligand induced changes disrupt a stacking interaction between two tyrosines (Tyr190 and Tyr254) which lie at the side of the channel leading to the active site of the free enzyme.Conclusion The conformational change induced by enolpyruvyl-UDP-N-acetylglucosamine binding to MurB results in the closure of the substrate-binding channel over the substrate. Tyr190 swings over the channel opening and establishes a hydrogen bond with an oxygen of the α-phosphate of the sugar nucleotide substrate which is critical to substrate binding

Nature\u27s Assembly Line Logic for Natural Products

Nature fashions a very large number of diverse products (molecular weights ranging from ca. 200 to 2000 daltons) from simple monomeric metabolites used in primary metabolism. These include polyketide scaffolds generated from the simple C₃ malonyl CoA and C₄ methylmalonyl CoA monomers and nonribosomal peptides made from both the 20 proteinogenic amino acids and dozens of nonpoteinogenic amino acids.¹ A large family of terpenoid skeletons are built from the Δ²- and Δ³-alkene isomers of the biological isoprene monomer, isoprenyl-pyrophosphate.

Macrolactamization of Glycosylated Peptide Thioesters by the Thioesterase Domain of Tyrocidine Synthetase

SummaryThe 35 kDa thioesterase (TE) domain excised from the megadalton tyrocidine synthetase (Tyc Syn) retains autonomous capacity to macrocyclize peptidyl thioesters to D-Phe1-L-Leu10-macrolactams. Since a number of nonribosomal peptides undergo O-glycosylation events during tailoring to gain biological activity, the Tyc Syn TE domain was evaluated for cyclization capacity with glycosylated peptidyl-S-NAC substrates. First, Tyr7 was replaced with Tyr(β-D-Gal) and Tyr(β-D-Glc) as well as with Ser-containing β-linked D-Gal, D-Glc, D-GlcNAc, and D-GlcNH2, and these new analogs were shown to be cyclized with comparable kcat/Km catalytic efficiency. Similarly, Gal- or tetra-O-acetyl-Gal-Ser could also be substituted at residues 5, 6, and 8 in the linear decapeptidyl-S-NAC sequences and cyclized without substantial loss in catalytic efficiency by Tyc Syn TE. The cyclic glycopeptides retained antibiotic activity as membrane perturbants in MIC assays, opening the possibility for library construction of cyclic glycopeptides by enzymatic macrocyclization

Crystal Structure of \u3cem\u3eO\u3c/em\u3e-Methyltransferase CalO6 from the Calicheamicin Biosynthetic Pathway: A Case of Challenging Structure Determination at Low Resolution

BACKGROUND: Calicheamicins (CAL) are enedyine natural products with potent antibiotic and cytotoxic activity, used in anticancer therapy. The O-methyltransferase CalO6 is proposed to catalyze methylation of the hydroxyl moiety at the C2 position of the orsellinic acid group of CAL. RESULTS: Crystals of CalO6 diffracted non-isotropically, with the usable data extending to 3.4 Å. While no single method of crystal structure determination yielded a structure of CalO6, we were able to determine its structure by using molecular replacement-guided single wavelength anomalous dispersion by using diffraction data from native crystals of CalO6 and a highly non-isomorphous mercury derivative. The structure of CalO6 reveals the methyltransferase fold and dimeric organization characteristic of small molecule O-methyltransferases involved in secondary metabolism in bacteria and plants. Uncommonly, CalO6 was crystallized in the absence of S-adenosylmethionine (SAM; the methyl donor) or S-adenosylhomocysteine (SAH; its product). CONCLUSIONS: Likely as a consequence of the dynamic nature of CalO6 in the absence of its cofactor, the central region of CalO6, which forms a helical lid-like structure near the active site in CalO6 and similar enzymes, is not observed in the electron density. We propose that this region controls the entry of SAM into and the exit of SAH from the active site of CalO6 and shapes the active site for substrate binding and catalysis

The Genetic and Molecular Basis for Sunscreen Biosynthesis in Cyanobacteria

Ultraviolet UV-A and UV-B radiation is harmful to living systems, causing damage to biological macromolecules. An important strategy for dealing with UV exposure is the biosynthesis of small-molecule sunscreens. Among such metabolites, the mycosporine and mycosporine-like amino acids (MAAs) are remarkable for their wide phylogenetic distribution and their unique chemical structures. Here, we report the identification of a MAA biosynthetic gene cluster in a cyanobacterium and the discovery of analogous pathways in other sequenced organisms. We have expressed the cluster in a heterologous bacterial host and characterized all four biosynthetic enzymes in vitro. In addition to clarifying the origin of the MAAs, these efforts have revealed two unprecedented enzymatic strategies for imine formation.Chemistry and Chemical Biolog

Electronic structure design for nanoporous, electrically conductive zeolitic imidazolate frameworks

Electronic structure calculations are used to develop design rules for enhanced electrical conductivity in zeolitic imidazolate frameworks. The electrical resistivity of Co2+ based zeolitic imidazolate frameworks has previously been found to be ∼1000 times lower than that of Zn2+ based materials. The electrical conductivity of the frameworks can also be tuned by ligand molecule selection. Using density functional theory calculations, this controllable electrical conductivity is explained in terms of tuneable conduction band edge character, with calculations revealing the improved hybridisation and extended band character of the Co2+ frameworks. The improvements in the methylimidazolate frameworks are understood in terms of improved frontier orbital matching between metal and ligand. The modular tuneability and previously demonstrated facile synthesis provides a route to rational design of stable framework materials for electronic applications. By outlining these design principles we provide a route to the future development of stable, electrically conductive zeolitic imidazolate frameworks