Biotin synthase: insights into radical-mediated carbon-sulfur bond formation

The enzyme cofactor and essential vitamin biotin is biosynthesized in bacteria, fungi, and plants through a pathway that culminates with the addition of a sulfur atom to generate the five-membered thiophane ring. The immediate precursor, dethiobiotin, has methylene and methyl groups at the C6 and C9 positions, respectively, and formation of a thioether bridging these carbon atoms requires cleavage of unactivated CH bonds. Biotin synthase is an S-adenosyl-l-methionine (SAM or AdoMet) radical enzyme that catalyzes reduction of the AdoMet sulfonium to produce 5'-deoxyadenosyl radicals, high-energy carbon radicals that can directly abstract hydrogen atoms from dethiobiotin. The available experimental and structural data suggest that a [2Fe-2S](2+) cluster bound deep within biotin synthase provides a sulfur atom that is added to dethiobiotin in a stepwise reaction, first at the C9 position to generate 9-mercaptodethiobiotin, and then at the C6 position to close the thiophane ring. The formation of sulfur-containing biomolecules through a radical reaction involving an iron-sulfur cluster is an unprecedented reaction in biochemistry; however, recent enzyme discoveries suggest that radical sulfur insertion reactions may be a distinct subgroup within the burgeoning Radical SAM superfamily. This article is part of a Special Issue entitled: Radical SAM enzymes and Radical Enzymology.     

Photochemical carbon-sulfur bond cleavage in some alkyl and benzyl sulfides

Irradiation (254 nm) of five alkyl and benzyl ethyl sulfides causes efficient (Φ_r 0.27-0.90) homolytic cleavage of the C-S bond. Of the resulting fragments, thiyl radicals mainly couple, while alkyl radicals abstract hydrogen, disproportionate or couple when stabilized (benzyl). Selective trapping of either of the two types of radicals occurs in the presence of nucleophilic (methyl vinyl ether and 1-hexene) and, respectively, electrophilic (acrylonitrile) alkenes. When an easily oxidized radical is formed, e.g. cumyl, secondary electron transfer leads to the corresponding cation.     

Enzymology of butyrate formation by Butyrivibrio fibrisolvens.

Butyrivibrio fibrisolvens is a major butyrate-forming species in the bovine and ovine rumen. The enzymology of butyrate formation from pyruvate was investigated in cell-free extracts of B. fibrisolvens D1. Pyruvate owas oxidized to acetylcoenzyme A (CoA) in the presence of CoA.SH and benzyl viologen or flavin nucleotides. The bacterium uses thiolase, beta-hydroxybutyryl-CoA dehydrogenase, crotonase, and crotonyl-CoA reductase to form butyryl-CoA from acetyl-CoA. Reduction of acetoacetyl-CoA to beta-hydroxybutyryl-CoA was faster with NADH than with NADPH. Crotonyl-CoA was reduced to butyryl-CoA by NADH, but not by NADPH, only in the presence of flavin nucleotides. Reduction of flavin nucleotides by NADH was much slower than the flavin-dependent reduction of crotonyl-CoA. This indicates that flavoproteins rather than free flavin participated in the reduction of crotonyl-CoA. Butyryl-CoA was converted to butyrate by phosphate butyryl transferase and butyrate kinase.     

Use of a novel fluorinated organosulfur compound to isolate bacteria capable of carbon-sulfur bond cleavage

The vacuum residue fraction of heavy crudes contributes to the viscosity of these oils. Specific microbial cleavage of C-S bonds in alkylsulfide bridges that form linkages in this fraction may result in dramatic viscosity reduction. To date, no bacterial strains have been shown conclusively to cleave C-S bonds within alkyl chains. Screening for microbes that can perform this activity was greatly facilitated by the use of a newly synthesized compound, bis-(3-pentafluorophenylpropyl)-sulfide (PFPS), as a novel sulfur source. The terminal pentafluorinated aromatic rings of PFPS preclude growth of aromatic ring-degrading bacteria but allow for selective enrichment of strains capable of cleaving C-S bonds. A unique bacterial strain, Rhodococcus sp. strain JVH1, that used PFPS as a sole sulfur source was isolated from an oil-contaminated environment. Gas chromatography-mass spectrometry analysis revealed that JVH1 oxidized PFPS to a sulfoxide and then a sulfone prior to cleaving the C-S bond to form an alcohol and, presumably, a sulfinate from which sulfur could be extracted for growth. Four known dibenzothiophene-desulfurizing strains, including Rhodococcus sp. strain IGTS8, were all unable to cleave the C-S bond in PFPS but could oxidize PFPS to the sulfone via the sulfoxide. Conversely, JVH1 was unable to oxidize dibenzothiophene but was able to use a variety of alkyl sulfides, in addition to PFPS, as sole sulfur sources. Overall, PFPS is an excellent tool for isolating bacteria capable of cleaving subterminal C-S bonds within alkyl chains. The type of desulfurization displayed by JVH1 differs significantly from previously described reaction results.     

Enzyme-catalysed siloxane bond formation

Biosilicification occurs on a globally vast scale under mild conditions. Although research has progressed in the area of silica biosynthesis, the molecular mechanisms of these interactions are effectively unknown. The natural production of silica in the Tethya aurantia marine sponge, Cylindrotheca fusiformis diatom, and Equisetum telmateia plant appear to be similar. However, the studies were complicated mechanistic queries due to the use of silicic acid analogues. Given these complications, a carefully chosen model study was carried out to test the ability of enzymes to catalyse the formation of molecules with a single siloxane bond during the in vitro hydrolysis and condensation of alkoxysilanes. Our data suggest that homologous lipase and protease enzymes catalyse the formation of siloxane bonds under mild conditions. Non-specific interactions with trypsin promoted the in vitro hydrolysis of alkoxysilanes, while the active site was determined to selectively catalyse the condensation of silanols.     

Isopeptide bond formation in epidermis

Summary Proteins which are major substrates of epidermal transglutaminases can be identified in cultured keratinocytes of human, cow, and new-born rat.Cow and human keratinocytes both contain substrate proteins which are 30000 to 50000 daltons in size but dissociable in SDS to 12000 daltons or less. In both species these proteins correspond to in vivo synthesized proteins which are probable precursors of cornified envelope. Human keratinocytes synthesize a 125000 dalton protein which is also a precursor of cornified envelope both in cells and tissue. By SDS electrophoresis two 100000 dalton substrate proteins are seen in cow keratinocyte extracts and a 23000 dalton substrate protein is seen in rat keratinocyte extracts. Minor substrates of transglutaminase are seen in human keratinocytes, and one has been isolated by preparative electrophoresis. Major structural proteins of epidermis which are in vitro substrates of epidermal transglutaminase include the keratins and the stratum corneum basic protein.     

RNA-catalyzed carbon-carbon bond formation.

RNA molecules with catalytic properties have been isolated by in vitro selection from combinatorial libraries. A broad range of chemical reactions can be catalyzed, and nucleic acids can accelerate bond formation between small organic substrates. The catalytic performance of nucleic acids can be enhanced by incorporation of additional functional groups. This minireview focuses on carbon-carbon bond formation accelerated by in vitro selected ribozymes.     

Optimization of enzyme-mediated peptide bond formation

Enzyme-catalyzed peptide bond formation requires thorough examination and optimization of each coupling step. In order to identify factors influencing the selectivity between aminolysis and hydrolysis, a systematic study was carried out for the kinetically controlled peptide synthesis. The reaction temperature, the type of C-terminal protecting group, and different organic cosolvents showed little influence on the selectivity. The enzyme, excess nucleophile, pH, N-terminal protecting group, and ionic strength of the solution were identified as major factors controlling the selectivity and, therefore, the yield of the dipeptide synthesis. Under optimized conditions, the selectivity of the chymotrypsin-catalyzed synthesis of PheSer could be increased from 35 to 100%.     

Oxynitrilases for asymmetric C-C bond formation

Oxynitrilases for the preparation of (R)- or (S)-cyanohydrins are now readily available. The research efforts of a number of groups have established these enzymes as catalysts with significant potential for application to asymmetric synthesis. Advances made in molecular cloning and genetics have delivered information on the oxynitrilase mechanism of action and sufficient quantities of enzyme to satisfy industrial requirements.     

Pathways for protein disulphide bond formation

The folding of many secretory proteins depends upon the formation of disulphide bonds. Recent advances in genetics and cell biology have outlined a core pathway for disulphide bond formation in the endoplasmic reticulum (ER) of eukaryotic cells. In this pathway, oxidizing equivalents flow from the recently identified ER membrane protein Ero1p to secretory proteins via protein disulphide isomerase (PDI). Contrary to prior expectations, oxidation of glutathione in the ER competes with oxidation of protein thiols. Contributions of PDI homologues to the catalysis of oxidative folding will be discussed, as will similarities between eukaryotic and prokaryotic disulphide-bond-forming systems.     

Native disulfide bond formation in proteins

Native disulfide bond formation is critical for the proper folding of many proteins. Recent studies using newly identified protein oxidants, folding catalysts, and mutant cells provide insight into the mechanism of oxidative protein folding in vivo. This insight promises new strategies for more efficient protein production.     

Ribosomal tolerance and peptide bond formation

In the ribosome, the decoding and peptide bond formation sites are composed entirely of ribosomal RNA, thus confirming that the ribosome is a ribozyme. Precise alignment of the aminoacylated and peptidyl tRNA 3'-ends, which is the major enzymatic contribution of the ribosome, is dominated by remote interactions of the tRNA double helical acceptor stem with the distant rims of the peptidyl transferase center. An elaborate architecture and a sizable symmetry-related region within the otherwise asymmetric ribosome guide the A --> P passage of the tRNA 3'-end by a spiral rotatory motion, and ensures its outcome: stereochemistry suitable for peptide bond formation and geometry facilitating the entrance of newly formed proteins into their exit tunnel.     

Statistics of disulfide bond formation in proteins

A new set of statistical expressions describing the reformation of disulfide bonds from SH groups is proposed. The results of the statistical calculations of disulfide bond reformation are discussed in terms of protein folding.     

Enzymology of cellulose degradation

In the last few years there has been a considerable improvement in the understanding of the mechanisms involved in the microbial degradation of cellulose, but there are still many uncertainties. As presently understood, it would appear that different mechanisms may operate in the various types of microorganism. Thus degradation of crystalline cellulose is effected by anaerobic bacteria by large Ca-dependent and thiol-dependent multicomponent endoglucanase-containing complexes (cellulosomes) located on concerted action of endo- and exo-glucanases which act some distance from the cell which renders cellulose soluble. All of the endo- and exo-glucanases possess a bifunctional domain structure: one contains the catalytic site, the other is involved in binding the enzyme to crystalline cellulose.