Phosphoester Bond Research Articles

From DNA to Nerve Agents – The Biomimetic Catalysts for the Hydrolysis of Phosphate Esters

AbstractThe phosphate ester bonds are widely present in living organisms and in the environment. From the nucleic acids to the sparingly dispersed pesticides and chemical warfare residues, the phosphoester bond's stability against hydrolysis can be extremely high or exceptionally low. Recently, the enzyme‐mimicking nanomaterials, namely ‘nanozyme’, have been explored for their activities in hydrolytically cleaving DNA, organophosphate and their analogues. Herein in a broad perspective these nanomaterials were summarized and compared with a view to reproducing the catalysis efficiency and selectivity of natural phosphatases and nucleases. The development of biomimetic inorganic materials would not only provide potential nanomedicine for future gene editing, but also offer alternative solutions to the environmentally friendly treatment of pesticide residues and chemical warfare stockpiles.

Crystal structures of SAMHD1 inhibitor complexes reveal the mechanism of water-mediated dNTP hydrolysis

SAMHD1 regulates cellular 2′-deoxynucleoside-5′-triphosphate (dNTP) homeostasis by catalysing the hydrolysis of dNTPs into 2′-deoxynucleosides and triphosphate. In CD4+ myeloid lineage and resting T-cells, SAMHD1 blocks HIV-1 and other viral infections by depletion of the dNTP pool to a level that cannot support replication. SAMHD1 mutations are associated with the autoimmune disease Aicardi–Goutières syndrome and hypermutated cancers. Furthermore, SAMHD1 sensitises cancer cells to nucleoside-analogue anti-cancer therapies and is linked with DNA repair and suppression of the interferon response to cytosolic nucleic acids. Nevertheless, despite its requirement in these processes, the fundamental mechanism of SAMHD1-catalysed dNTP hydrolysis remained unknown. Here, we present structural and enzymological data showing that SAMHD1 utilises an active site, bi-metallic iron-magnesium centre that positions a hydroxide nucleophile in-line with the Pα-O5′ bond to catalyse phosphoester bond hydrolysis. This precise molecular mechanism for SAMHD1 catalysis, reveals how SAMHD1 down-regulates cellular dNTP and modulates the efficacy of nucleoside-based anti-cancer and anti-viral therapies.

Quantum-Based Modeling of Dephosphorylation in the Catalytic Site of Serine/Threonine Protein Phosphatase-5 (PPP5C)

Serine/threonine protein phosphatase-5 (PP5; PPP5C) is a member of the phosphoprotein phosphatase (PPP) gene family. The PPP catalytic domains feature a bimetal system (M1/M2), an associated bridge hydroxide (W1(OH−)), an M1-bound water/hydroxide (W2), and a highly conserved core sequence. The PPPs are presumed to share a common mechanism: The seryl/threonyl phosphoryl group of the phosphoprotein coordinates the metal ions, W1(OH−) attacks the central phosphorous atom, rupturing the antipodal phosphoester bond and releasing the phosphate-free protein. Also, a histidine/aspartate tandem is responsible for protonating the exiting seryl/threonyl alkoxide. Here, we employed quantum-based computations on a large section of the PP5 catalytic site. A 33-residue, ONIOM(UB3LYP/6-31G(d):UPM7) model was built to perform computations using methylphosphate dianion as a stand-in substrate for phosphoserine/phosphothreonine. We present a concerted transition state (TS) in which W1(OH−) attacks the phosphate center at the same time that the exiting seryl/threonyl alkoxide is protonated directly by the His304/Asp274 tandem, with W2 assigned as a water molecule: W2(H2O). Arg275, proximal to M1, stabilizes the substrate and TS by binding both the ester oxygen (Oγ) and a phosphoryl oxygen (O1) in a bidentate fashion; in the product state, Tyr451 aids in decoupling Arg275 from O1 of the product phosphate ion. The reaction is exothermic (ΔH = −2.0 kcal/mol), occurs in a single step, and has a low activation barrier (ΔH‡ = +10.0 kcal/mol). Our work is an improvement over an earlier computational study that also found bond rupture and alkoxide protonation to be concerted, but concluded that Arg275 is deprotonated during the reactant and TS stages of the pathway. In that earlier study, the critical electron-withdrawal role that Arg275 plays during the hydroxide attack was not correctly accounted for.

Synthesis, crystal structure, phosphate hydrolysis activity and antibacterial activity of macrocyclic dinuclear Zn(II) complex with benzyl pendant-arms

A new macrocyclic dinuclear Zn(II) complex is synthesized by the cyclocondensation between 3,3’-(ethane-1,2-diylbis (benzylazanediyl))bis(methylene) bis (2-hydroxy-5-methyl-benzaldehyde) and 1,3-diaminopropane and the subsequent with zinc salts. The as-prepared complex is characterized by elemental analysis, FT-IR, ES-MS and single crystal X-ray diffraction. The complex consists of one independent molecular unit of [Zn2(μ-OAC)L]+ ClO4− and two water molecules with one on a symmetry element. Four of these units collectively form two pairs of dinuclear complex units of [Zn2(μ-OAc)L]+ with one unit sharing two perchlorate ions and one water molecule and the other unit sharing two perchlorate ions and one symmetry equivalent water molecule. Each zinc(II) ion exhibits a slightly distorted square pyramidal geometry. Two Zn atoms are bridged by two oxygen atoms of an acetate anion and two phenolic O atoms. The Zn–Zn distance is 2.951 Å. An ordered two-dimensional network is formed by weak intermolecular interactions in the crystal structure of the complex. The phosphate ester hydrolysis activity and the antibacterial activity of the complex are studied. The results showed that the synthesized complex has an efficient catalytic activity of phosphoester bond cleavage and the potential to inhibit the growth of E. coli. The optimum catalytic rate constant (kcat) at pH 7.8 for the hydrolysis of 4-nitrophenyl phosphate disodium salt hexahydrate (pNPP) by the synthesized complex is 2.98 × 10−4 s−1, and 105 times faster than that the spontaneous hydrolysis of the phosphate monoester.

Biotransformation of Tris(2-chloroethyl) Phosphate (TCEP) in Sediment Microcosms and the Adaptation of Microbial Communities to TCEP

Tris(2-chloroethyl) phosphate (TCEP), a typical chlorinated organophosphate ester (OPE), is an emerging contaminant of global concern because of its frequent occurrence, potential toxic effects, and persistence in the environment. In this study, we investigated the microbial TCEP biotransformation and the development of microbial communities in sediment microcosms with repeated TCEP amendments. The TCEP degradation fitted pseudo-zero-order kinetics, with reaction rates of 0.068 mg/(L h) after the first spike of 5 mg/L and 1.85 mg/(L h) after the second spike of 50 mg/L. TCEP was mainly degraded via phosphoester bond hydrolysis, evidenced by the production of bis(2-chloroethyl) phosphate (BCEP) and mono-chloroethyl phosphate (MCEP). Bis(2-chloroethyl) 2-hydroxyethyl phosphate (TCEP-OH), phosphoric bis(2-chloroethyl) (2-oxoethyl) ester (TCEP-CHO), phosphoric acid bis(2-chloroethyl)(carboxymethyl) ester (TCEP-COOH), and 2-chloroethyl 2-hydroxyethyl hydrogen phosphate (BCEP-OH) were also identified as microbial TCEP transformation products, indicating that TCEP degradation may follow hydrolytic dechlorination and oxidation pathways. Microbial community compositions in TCEP-amended microcosms shifted away from control microcosms after the second TCEP spike. Burkholderiales and Rhizobiales were two prevalent bacterial guilds enriched in TCEP-amended microcosms and were linked to the higher abundances of alkaline and acid phosphatase genes and genes involved in the metabolism of 2-chloroethanol, a side product of TCEP hydrolysis, indicating their importance in degrading TCEP and its metabolites.

A Potent Host Defense Peptide Triggers DNA Damage and Is Active against Multidrug-Resistant Gram-Negative Pathogens.

Gram-negative bacteria are some of the biggest threats to public health due to a large prevalence of antibiotic resistance. The difficulty in treating bacterial infections, stemming from their double membrane structure combined with efflux pumps in the outer membrane, has resulted in a much greater need for antimicrobials with activity against these pathogens. Tunicate host defense peptide (HDP), Clavanin A, is capable of not only inhibiting Gram-negative growth but also potentiating activity in the presence of Zn(II). Here, we provide evidence that the improvements of Clavanin A activity in the presence of Zn(II) are due to its novel mechanism of action. We employed E.coli TD172 (ΔrecA::kan) and the terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL) assay to show in cellulae that DNA damage occurs upon treatment with Clavanin A. In vitro assays demonstrated that Zn(II) ions are required for the nuclease activity of the peptide. The quantum mechanics/molecular mechanics (QM/MM) calculations were used to investigate the mechanism of DNA damage. In the rate-determining step of the proposed mechanism, due to its Lewis acidity, the Zn(II) ion activates the scissile P-O bond of DNA and creates a hydroxyl nucleophile from a water molecule. A subsequent attack by this group to the electrophilic phosphorus cleaves the scissile phosphoester bond. Additionally, we utilized bacterial cytological profiling (BCP), circular dichroism (CD) spectroscopy in the presence of lipid vesicles, and surface plasmon resonance combined with electrical impedance spectroscopy in order to address the apparent discrepancies between our results and the previous studies regarding the mechanism of action of Clavanin A. Finally, our approach may lead to the identification of additional Clavanin A like HDPs and promote the development of antimicrobial peptide based therapeutics.

Direct Damage of Deoxyadenosine Monophosphate by Low Energy Electrons Probed by X-Ray Photoelectron Spectroscopy

Low-energy (3-25 eV) electron interactions with multilayers of 2'-deoxyadenosine 5'-monophosphate (dAMP) were probed using X-ray photoelectron spectroscopy (XPS). Understanding how electrons damage the nucleotide dAMP, which is a building block of DNA, can give insight into how the DNA undergoes radiation damage. Chemical modifications to the constituent units of the nucleotide were revealed in situ through monitoring of the O 1s, C 1s, and N 1s elemental transitions. It is shown that direct electron irradiation causes decomposition of both the base and sugar subunits, as well as cleavage of glycosidic and phosphoester bonds. Incident electrons undergo inelastic energy losses, including creation of core-excited resonances above 3-4 eV. In the condensed phase, these resonances decay via autoionization, producing electronically excited targets and <3 eV electrons. The excited states dissociate and the slow (<3 eV) electrons are captured by neighboring molecules, forming molecular shape resonances that can lead to bond rupture. Since the observed chemical changes were similar at all incident electron energies studied, they can be primarily attributed to formation and decay of transient negative ions. Damage enhancements in the energy ranges typical of all scattering resonances are expected, with the damage probability dominated by the low-energy shape resonances.

Mechanisms of peptide and phosphoester hydrolysis catalyzed by two promiscuous metalloenzymes (insulin degrading enzyme and glycerophosphodiesterase) and their synthetic analogues

AbstractThe hydrolysis of extremely stable peptide and phosphoester bonds by metalloenzymes is of great interest in biotechnology and industry. However, due to various shortcomings only a handful of these enzymes have been used for industrial applications. Therefore, in the last two decades intensive scientific efforts have been made in rational development of small molecules to imitate the activities of natural enzymes. Despite these efforts, their currently available synthetic analogues are inferior in terms of selectivity, catalytic rate, and turnover and the designing of efficient artificial metalloenzymes remains a distant goal. This is a challenging area of research that necessitates a rigorous integration between experiments and theory. The realization of this goal requires knowledge of the catalytic activities of both enzymes and their existing analogues and an effective fusion of that knowledge. This article reviews several studies in which a plethora of computational techniques have been successfully employed to investigate the functioning of two chemically promiscuous mono‐ and binuclear metalloenzymes (insulin degrading enzyme and glycerophosphodiesterase) and two synthetic analogues. These studies will help us derive fundamental principles of peptide and phosphoester hydrolysis and pave the way to design efficient small molecule catalysts for these reactions.This article is categorized under: Structure and Mechanism &gt; Reaction Mechanisms and Catalysis

Mutational analysis of the flavinylation and binding motifs in two protein targets of the flavin transferase ApbE.

Many flavoproteins belonging to three domain types contain an FMN residue linked through a phosphoester bond to a threonine or serine residue found in a conserved seven-residue motif. The flavinylation reaction is catalyzed by a specific enzyme, ApbE, which uses FAD as a substrate. To determine the structural requirements of the flavinylation reaction, we examined the effects of single substitutions in the flavinylation motif of Klebsiella pneumoniae cytoplasmic fumarate reductase on its modification by its own ApbE in recombinant Escherichia coli cells. The replacement of the flavin acceptor threonine with alanine completely abolished the modification reaction, whereas the replacements of conserved aspartate and serine had only minor effects. Effects of other substitutions, including replacing the acceptor threonine with serine, (a 10-55% decrease in the flavinylation degree) pinpointed important glycine and alanine residues and suggested an excessive capacity of the ApbE-based flavinylation system in vivo. Consistent with this deduction, drastic replacements of conserved leucine and threonine residues in the binding pocket that accommodates FMN residue still allowed appreciable flavinylation of the NqrC subunit of Vibrio harveyi Na+-translocating NADH:quinone oxidoreductase, despite a profound weakening of the isoalloxazine ring binding and an increase in its exposure to solvent.

Zinc(II) complexes of a versatile heptadentate ligand as phosphohydrolase structural and functional mimics

A mono-nuclear [Zn(H2O)6][1] and a di-nuclear zinc (NMe4)2[2] complexes of a carboxylate-rich ligand, N,N′-Bis[2-carboxybenzomethyl]-N,N′ -Bis[carboxymethyl]-1,3-diaminopropan-2-ol (H5ccdp) have shown catalytic activity towards hydrolysis of the phosphoester bonds in bis(4-nitrophenyl) phenylphosphonate, BNPPP. Kinetic measurements for the zinc(II) complexes, using spectrophotometric techniques in DMSO, were performed in order to investigate the metal-metal cooperativity vs metal-hydrogen bonding effect on the phosphoester bond cleavage rate in BNPP. The results showed that, compared to un-catalyzed hydrolysis of BNPPP, (NMe4)2[2] complex showed 103-fold rate enhancement, whereas ([Zn(H2O)6][1]) shows only 450-fold rate enhancement under the same reaction conditions. Based on the structural and activity information obtained in this study, reaction mechanisms for the hydrolysis of BNPPP have been proposed.

Critical Sites of DNA Backbone Integrity for Damaged Base Removal by Formamidopyrimidine-DNA Glycosylase.

DNA glycosylases, the enzymes that initiate base excision DNA repair, recognize damaged bases through a series of precisely orchestrated movements. Most glycosylases sharply kink the DNA axis at the lesion site and extrude the target base from the DNA double helix into the enzyme's active site. Little attention has been paid so far to the role of the physical continuity of the DNA backbone in allowing the required conformational distortion. Here, we analyze base excision by formamidopyrimidine-DNA glycosylase (Fpg) from substrates keeping all phosphates but containing a nick within three nucleotides of the lesion in either DNA strand. Four phosphoester linkages at the damaged nucleotide and two nucleotides 3' to it were essential for Fpg activity, while the breakage of the others, even at the same critical phosphates, had no effect or even stimulated the reaction. Reduction of the likelihood of hydrogen bonding at the nicks by using dideoxynucleotides as their 3'-terminal groups was more detrimental for the activity. All phosphoester bonds in the complementary strand were dispensable for base excision, but nicks close to the orphaned nucleotide caused early termination of damaged strand cleavage. Elastic network analysis of Fpg-DNA structures showed that the vibrational motions of the critical phosphates are strongly correlated, in part due to the presence of the protein. Overall, our results suggest that mechanical forces propagating along the DNA backbone play a critical role in the correct conformational distortion of DNA by Fpg and possibly by other target base-everting DNA glycosylases.

A new macrocyclic heterobinuclear Cu(II)-Zn(II) complex: synthesis, crystal structure, phosphate hydrolysis, and DNA binding studies

A new macrocyclic heterobinuclear Cu(II)-Zn(II) complex was synthesized and characterized by elemental analysis, FT-IR, ES-MS, and single-crystal X-ray diffraction. Five-coordinate geometry for the new complex is proposed. The copper…zinc distance bridged by two phenolic oxygens and a acetate ligand is 2.9508 Å. The phosphate ester hydrolysis activity and the DNA binding ability of the complex were studied. The results showed that the present complex has an efficient catalytic activity of phosphoester bond cleavage. The catalytic rate constant kcat for the hydrolysis of 4-nitrophenyl phosphate disodium salt hexahydrate (pNPP) by the synthesized complex is 2.69 × 10−4 s−1 and 105 times faster than the spontaneous hydrolysis of the phosphate monoester. The complex shows a good binding ability to calf thymus (CT-DNA) and the corresponding binding constant is 1.9 × 105 M−1. The linear Stern-Volmer quenching constant obtained by the fluorescent spectroscopic is 6.3 × 104 M−1.

Biodegradable Antibacterial Polymeric Nanosystems: A New Hope to Cope with Multidrug-Resistant Bacteria.

The human society is faced with daunting threats from bacterial infections. Over decades, a variety of antibacterial polymeric nanosystems have exhibited great promise for the eradication of multidrug-resistant bacteria and persistent biofilms by enhancing bacterial recognition and binding capabilities. In this Review, the "state-of-the-art" biodegradable antibacterial polymeric nanosystems, which could respond to bacteria environments (e.g., acidity or bacterial enzymes) for controlled antibiotic release or multimodal antibacterial treatment, are summarized. The current antibacterial polymeric nanosystems can be categorized into antibiotic-containing and intrinsic antibacterial nanosystems. The antibiotic-containing polymeric nanosystems include antibiotic-encapsulated nanocarriers (e.g., polymeric micelles, vesicles, nanogels) and antibiotic-conjugated polymer nanosystems for the delivery of antibiotic drugs. On the other hand, the intrinsic antibacterial polymer nanosystems containing bactericidal moieties such as quaternary ammonium groups, phosphonium groups, polycations, antimicrobial peptides (AMPs), and their synthetic mimics, are also described. The biodegradability of the nanosystems can be rendered by the incorporation of labile chemical linkages, such as carbonate, ester, amide, and phosphoester bonds. The design and synthesis of the degradable polymeric building blocks and their fabrications into nanosystems are also explicated, together with their plausible action mechanisms and potential biomedical applications. The perspectives of the current research in this field are also described.

Effects of the Metal Ion on the Mechanism of Phosphodiester Hydrolysis Catalyzed by Metal-Cyclen Complexes.

In this study, mechanisms of phosphodiester hydrolysis catalyzed by six di- and tetravalent metal-cyclen (M-C) complexes (Zn-C, Cu-C, Co-C, Ce-C, Zr-C and Ti-C) have been investigated using DFT calculations. The activities of these complexes were studied using three distinct mechanisms: (1) direct attack (DA), (2) catalyst-assisted (CA), and (3) water-assisted (WA). All divalent metal complexes (Zn-C, Cu-C and Co-C) coordinated to the BNPP substrate in a monodentate fashion and activated its scissile phosphoester bond. However, all tetravalent metal complexes (Ce-C, Zr-C, and Ti-C) interacted with BNPP in a bidentate manner and strengthened this bond. The DAmechanism was energetically the most feasible for all divalent M-C complexes, while the WAmechanism was favored by the tetravalent complexes, except Ce-C. The divalent complexes were found to be more reactive than their tetravalent counterparts. Zn-C catalyzed the hydrolysis with the lowest barrier among all M-C complexes, while Ti-C was the most reactive tetravalent complex. The activities of Ce-C and Zr-C, except Ti-C, were improved with an increase in the coordination number of the metal ion. The structural and mechanistic information provided in this study will be very helpful in the development of more efficient metal complexes for this critical reaction.

The acid phosphatase Pho5 of Saccharomyces cerevisiae is not involved in polyphosphate breakdown.

Inorganic polyphosphate is involved in architecture and functioning of yeast cell wall. The strain of Saccharomyces cerevisiae constitutively overexpressing acid phosphatase Pho5 was constructed for studying the Pho5 properties and its possible participation in polyphosphate metabolism. The parent strain was transformed by the vector carrying the PHO5 gene under a strong constitutive promoter of glyceraldehyde-3-phosphate dehydrogenase of S. cerevisiae. The culture liquid and biomass of transformant strain contained approximately equal total acid phosphatase activity. The levels of acid phosphatase activity associated with the cell wall and culture liquid increased in the transformant strain compared to the parent strain ~ 10- and 20-fold, respectively. The Pho5 preparation (specific activity of 46U/mg protein and yield of 95U/L) was obtained from culture liquid of overproducing strain. The overproducing strain had no changes in polyphosphate level. The activity of Pho5 with long-chained polyP was negligible. We concluded that Pho5 is not involved in polyphosphate metabolism. Purified Pho5 showed a similar activity with p-nitrophenylphosphate, ATP, ADP, glycerophosphate, and glucose-6-phosphate. The substrate specificity of Pho5 and its extracellular localization suggest its function: the hydrolysis of organic compounds with phosphoester bonds at phosphate limitation.

Pyrophosphate Prompted Aggregation‐Induced Emission: Chemosensor Studies, Cell Imaging, Cytotoxicity, and Hydrolysis of the Phosphoester Bond with Alkaline Phosphatase

Two benzimidazole‐based zinc complexes [(Zn)2(L2)2Cl2(DMSO)2] (R1) and [Zn(L2)2(NO3)2(H2O)2] (R2) were synthesized and characterized with various spectroscopic data. The single X‐ray structure determination reveals that complex R1 is dinuclear and tetrahedral in geometry, while complex R2 is mononuclear and octahedral in geometry. Further, both zinc complexes were investigated for pyrophosphate sensing in an aqueous medium. Complex R1 is found to be selective towards pyrophosphate; it leads to 5.5‐fold enhancement in the emission intensity due to aggregation‐induced emission. However, complex R2 has shown binding with all, ATP, AMP, ADP, and pyrophosphate, which is attributed to the chelate effect. Consequently, complex R1 was utilized for the intracellular detection of pyrophosphate in HeLa cells. Furthermore, the PPi based zinc complex R1 is also used as a bio‐analytical tool to construct a real‐time fluorescence assay for the enzymatic activity of alkaline phosphatases (ALP).

Divalent Cations Alter the Rate-Limiting Step of PrimPol-Catalyzed DNA Elongation

PrimPol is the most recently discovered human DNA polymerase/primase and plays an emerging role in nuclear and mitochondrial genomic maintenance. As a member of archaeo-eukaryotic primase superfamily enzymes, PrimPol possesses DNA polymerase and primase activities that are important for replication fork progression in vitro and in cellulo. The enzymatic activities of PrimPol are critically dependent on the nucleotidyl-transfer reaction to incorporate deoxyribonucleotides successively; however, our knowledge concerning the kinetic mechanism of the reaction remains incomplete. Using enzyme kinetic analyses and computer simulations, we dissected the mechanism by which PrimPol transfers a nucleotide to a primer-template DNA, which comprises DNA binding, conformational transition, nucleotide binding, phosphoester bond formation, and dissociation steps. We obtained the rate constants of the steps by steady-state and pre-steady-state kinetic analyses and simulations. Our data demonstrate that the rate-limiting step of PrimPol-catalyzed DNA elongation depends on the metal cofactor involved. In the presence of Mn2+, a conformational transition step from non-productive to productive PrimPol:DNA complexes limits the enzymatic turnover, whereas in the presence of Mg2+, the chemical step becomes rate limiting. As evidenced from our kinetic and simulation data, PrimPol maintains the same kinetic mechanism under either millimolar or physiological micromolar Mn2+ concentration. Our study revealed the underlying mechanism by which PrimPol catalyzes nucleotide incorporation with two common metal cofactors and provides a kinetic basis for further understanding the regulatory mechanism of this functionally diverse primase-polymerase.

Flavin transferase: the maturation factor of flavin-containing oxidoreductases.

Flavins, cofactors of many enzymes, are often covalently linked to these enzymes; for instance, flavin adenine mononucleotide (FMN) can form a covalent bond through either its phosphate or isoalloxazine group. The prevailing view had long been that all types of covalent attachment of flavins occur as autocatalytic reactions; however, in 2013, the first flavin transferase was identified, which catalyzes phosphoester bond formation between FMN and Na+-translocating NADH:quinone oxidoreductase in certain bacteria. Later studies have indicated that this post-translational modification is widespread in prokaryotes and is even found in some eukaryotes. Flavin transferase can occur as a separate ∼40 kDa protein or as a domain within the target protein and recognizes a degenerate DgxtsAT/S motif in various target proteins. The purpose of this review was to summarize the progress already achieved by studies of the structure, mechanism, and specificity of flavin transferase and to encourage future research on this topic. Interestingly, the flavin transferase gene (apbE) is found in many bacteria that have no known target protein, suggesting the presence of yet unknown flavinylation targets.

Electron Attachment to Microhydrated Deoxycytidine Monophosphate.

DNA constituents are effectively decomposed via dissociative electron attachment (DEA). However, the DEA contribution to radiation damage in living tissues is a subject of ongoing discussion. We address an essential question, how aqueous environment influences the DEA to DNA. In particular, we report experimental fragmentation patterns for DEA to microhydrated 2-deoxycytidine 5-monophosphate (dCMP). Isolated dCMP was previously set as a model to describe mechanisms of DNA-strand breaks induced by secondary electrons and decomposes primarily by dissociation of the C-O phosphoester bond. We show that hydrated molecules decompose via dissociation of the C-N glycosidic bond followed by dissociation of the P-O bond. This significant change of the proposed mechanism can be interpreted by a reactive role of water in the postattachment dynamics. Comparison of the fragmentation with previous macroscopic irradiation studies suggests that the actual contribution of DEA to DNA radiation damage in living tissue is rather small.

Catalytically important flavin linked through a phosphoester bond in a eukaryotic fumarate reductase

One of the three domains of kinetoplastid NADH:fumarate oxidoreductase (FRD) is homologous to bacterial flavin transferase that catalyzes transfer of FMN residue from FAD to threonine in flavoproteins. Leptomonas pyrrhocoris FRD produced in yeast cells, which lack flavin transferase gene in their proteome, reduces fumarate in the presence of NADH and contains an FMN residue covalently linked to a Ser9 residue. The conserved flavinylation motif of FRD, D3(g/s)x(s/t)(s/g)AS9, is similar to the Dxx(s/t)gAT motif recognized by flavin transferase in prokaryotic proteins. Ser9 replacement abolished the flavinylation and fumarate reductase activity of FRD. These findings suggest that the flavinylation is important for the activity of FRD and that this post-translational modification is carried out by the own flavin transferase domain.