| spectral identification of intermediates generated during the reaction of dioxygen with the wild-type and eq(i-286) mutant of rhodobacter sphaeroides cytochrome c oxidase. | cytochrome c oxidase from rhodobacter sphaeroides is frequently used to model the more complex mitochondrial enzyme. the o(2) reduction in both enzymes is generally described by a unidirectional mechanism involving the sequential formation of the ferrous-oxy complex (compound a), the p(r) state, the oxyferryl f form, and the oxidized state. in this study we investigated the reaction of dioxygen with the wild-type reduced r. sphaeroides cytochrome oxidase and the eq(i-286) mutant using the co flo ... | 2012 | 23057757 |
| effects of the loss of the axial tyrosine ligand of the low-spin heme of maug on its physical properties and reactivity. | maug catalyzes posttranslational modifications of methylamine dehydrogenase to complete the biosynthesis of its protein-derived tryptophan tryptophylquinone (ttq) cofactor. maug possesses a five-coordinate high-spin and a six-coordinate low-spin ferric heme, the latter with his-tyr ligation. replacement of this tyrosine with lysine generates a maug variant with only high-spin ferric heme and altered spectroscopic and redox properties. y294k maug cannot stabilize the bis-fe(iv) redox state requir ... | 2012 | 23127557 |
| bacterial iron-sulfur regulatory proteins as biological sensor-switches. | in recent years, bacterial iron-sulfur cluster proteins that function as regulators of gene transcription have emerged as a major new group. in all cases, the cluster acts as a sensor of the environment and enables the organism to adapt to the prevailing conditions. this can range from mounting a response to oxidative or nitrosative stress to switching between anaerobic and aerobic respiratory pathways. the sensitivity of these ancient cofactors to small molecule reactive oxygen and nitrogen spe ... | 2012 | 22239203 |
| roles of subunit nuok (nd4l) in the energy-transducing mechanism of escherichia coli ndh-1 (nadh:quinone oxidoreductase). | the bacterial h(+)-translocating nadh:quinone oxidoreductase (ndh-1) catalyzes electron transfer from nadh to quinone coupled with proton pumping across the cytoplasmic membrane. the nuok subunit (counterpart of the mitochondrial nd4l subunit) is one of the seven hydrophobic subunits in the membrane domain and bears three transmembrane segments (tm1-3). two glutamic residues located in the adjacent transmembrane helices of nuok are important for the energy coupled activity of ndh-1. in particula ... | 2012 | 23105119 |
| nitric oxide and nitrous oxide turnover in natural and engineered microbial communities: biological pathways, chemical reactions, and novel technologies. | nitrous oxide (n(2)o) is an environmentally important atmospheric trace gas because it is an effective greenhouse gas and it leads to ozone depletion through photo-chemical nitric oxide (no) production in the stratosphere. mitigating its steady increase in atmospheric concentration requires an understanding of the mechanisms that lead to its formation in natural and engineered microbial communities. n(2)o is formed biologically from the oxidation of hydroxylamine (nh(2)oh) or the reduction of ni ... | 2012 | 23109930 |
| maug: a di-heme enzyme required for methylamine dehydrogenase maturation. | methylamine dehydrogenase (madh) requires the cofactor tryptophan tryptophylquinone (ttq) for activity. ttq is a posttranslational modification that results from an 8-electron oxidation of two specific tryptophans in the madh β-subunit. the final 6-electron oxidation is catalyzed by an unusual c-type di-heme enzyme, maug. the di-ferric enzyme can react with h(2)o(2), but atypically for c-type hemes the di-ferrous enzyme can react with o(2) as well. in both cases, an unprecedented bis-fe(iv) redo ... | 2012 | 23086017 |
| maug: a di-heme enzyme required for methylamine dehydrogenase maturation. | methylamine dehydrogenase (madh) requires the cofactor tryptophan tryptophylquinone (ttq) for activity. ttq is a posttranslational modification that results from an 8-electron oxidation of two specific tryptophans in the madh β-subunit. the final 6-electron oxidation is catalyzed by an unusual c-type di-heme enzyme, maug. the di-ferric enzyme can react with h(2)o(2), but atypically for c-type hemes the di-ferrous enzyme can react with o(2) as well. in both cases, an unprecedented bis-fe(iv) redo ... | 2012 | 23086017 |
| cell-free protein synthesis: the state of the art. | cell-free protein synthesis harnesses the synthetic power of biology, programming the ribosomal translational machinery of the cell to create macromolecular products. like pcr, which uses cellular replication machinery to create a dna amplifier, cell-free protein synthesis is emerging as a transformative technology with broad applications in protein engineering, biopharmaceutical development, and post-genomic research. by breaking free from the constraints of cell-based systems, it takes the nex ... | 2012 | 23086573 |
| cell-free protein synthesis: the state of the art. | cell-free protein synthesis harnesses the synthetic power of biology, programming the ribosomal translational machinery of the cell to create macromolecular products. like pcr, which uses cellular replication machinery to create a dna amplifier, cell-free protein synthesis is emerging as a transformative technology with broad applications in protein engineering, biopharmaceutical development, and post-genomic research. by breaking free from the constraints of cell-based systems, it takes the nex ... | 2012 | 23086573 |
| metabolic modeling of denitrification in agrobacterium tumefaciens: a tool to study inhibiting and activating compounds for the denitrification pathway. | a metabolic network model for facultative denitrification was developed based on experimental data obtained with agrobacterium tumefaciens. the model includes kinetic regulation at the enzyme level and transcription regulation at the enzyme synthesis level. the objective of this work was to study the key factors regulating the metabolic response of the denitrification pathway to transition from oxic to anoxic respiration and to find parameter values for the biological processes that were modeled ... | 2012 | 23087683 |
| accurate simulation and detection of coevolution signals in multiple sequence alignments. | while the conserved positions of a multiple sequence alignment (msa) are clearly of interest, non-conserved positions can also be important because, for example, destabilizing effects at one position can be compensated by stabilizing effects at another position. different methods have been developed to recognize the evolutionary relationship between amino acid sites, and to disentangle functional/structural dependencies from historical/phylogenetic ones. | 2012 | 23091608 |
| co-operation between different targeting pathways during integration of a membrane protein. | membrane protein assembly is a fundamental process in all cells. the membrane-bound rieske iron-sulfur protein is an essential component of the cytochrome bc(1) and cytochrome b(6)f complexes, and it is exported across the energy-coupling membranes of bacteria and plants in a folded conformation by the twin arginine protein transport pathway (tat) transport pathway. although the rieske protein in most organisms is a monotopic membrane protein, in actinobacteria, it is a polytopic protein with th ... | 2012 | 23045547 |
| an l-glucose catabolic pathway in paracoccus species 43p. | l-glucose, the enantiomer of d-glucose, was believed not to be utilized by any organisms. | 2012 | 23038265 |
| geometric and electronic structures of the his-fe(iv)=o and his-fe(iv)-tyr hemes of maug. | biosynthesis of the tryptophan tryptophylquinone (ttq) cofactor activates the enzyme methylamine dehydrogenase. the diheme enzyme maug catalyzes o-atom insertion and cross-linking of two trp residues to complete ttq synthesis. solution optical and mössbauer spectroscopic studies have indicated that the reactive form of maug during turnover is an unusual bisfe(iv) intermediate, which has been formulated as a his-ligated ferryl heme [fe(iv)=o] (heme a), and an fe(iv) heme with an atypical his/tyr ... | 2012 | 23053529 |
| copper starvation-inducible protein for cytochrome oxidase biogenesis in bradyrhizobium japonicum. | microarray analysis of bradyrhizobium japonicum grown under copper limitation uncovered five genes named pcuabcde, which are co-transcribed and co-regulated as an operon. the predicted gene products are periplasmic proteins (pcua, pcuc, and pcud), a tonb-dependent outer membrane receptor (pcub), and a cytoplasmic membrane-integral protein (pcue). homologs of pcuc and pcue had been discovered in other bacteria, namely pcu(a)c and ycnj, where they play a role in cytochrome oxidase biogenesis and c ... | 2012 | 23012364 |
| mutational analysis of the respiratory nitrate transporter nark2 of mycobacterium tuberculosis. | mycobacterium tuberculosis induces nitrate reductase activity in response to decreasing oxygen levels. this is due to regulation of both the transcription and the activity of the nitrate transporter nark2. a model of nark2 structure is proposed containing 12 membrane spanning regions consistent with other members of the major facilitator superfamily. the role of the proton gradient was determined by exposing m. tuberculosis to uncouplers. nitrite production decreased indicating that the importat ... | 2012 | 23029022 |
| design and use of photoactive ruthenium complexes to study electron transfer within cytochrome bc1 and from cytochrome bc1 to cytochrome c. | the cytochrome bc1 complex (ubiquinone:cytochrome c oxidoreductase) is the central integral membrane protein in the mitochondrial respiratory chain as well as the electron-transfer chains of many respiratory and photosynthetic prokaryotes. based on x-ray crystallographic studies of cytochrome bc1, a mechanism has been proposed in which the extrinsic domain of the iron-sulfur protein first binds to cytochrome b where it accepts an electron from ubiquinol in the qo site, and then rotates by 57° to ... | 2012 | 22985600 |
| design and use of photoactive ruthenium complexes to study electron transfer within cytochrome bc1 and from cytochrome bc1 to cytochrome c. | the cytochrome bc1 complex (ubiquinone:cytochrome c oxidoreductase) is the central integral membrane protein in the mitochondrial respiratory chain as well as the electron-transfer chains of many respiratory and photosynthetic prokaryotes. based on x-ray crystallographic studies of cytochrome bc1, a mechanism has been proposed in which the extrinsic domain of the iron-sulfur protein first binds to cytochrome b where it accepts an electron from ubiquinol in the qo site, and then rotates by 57° to ... | 2012 | 22985600 |
| functional importance of a pair of conserved glutamic acid residues and of ca(2+) binding in the cbb(3)-type oxygen reductases from rhodobacter sphaeroides and vibrio cholerae. | the cbb(3)-type cytochrome c oxidases are members of the family of heme-copper proton pumping respiratory oxygen reductases. the structure of the cbb(3)-type oxidase from pseudomonas stutzeri reveals that, in addition to the six redox-active metal centers (two b-type hemes, three c-type hemes, and cu(b)), the enzyme also contains at least one ca(2+). the calcium bridges two propionate carboxyls at the interface between the low-spin heme b and the active-site heme b(3) and, in addition, is ligate ... | 2012 | 22913716 |
| the periplasmic nitrate reductase nap is required for anaerobic growth and involved in redox control of magnetite biomineralization in magnetospirillum gryphiswaldense. | the magnetosomes of many magnetotactic bacteria consist of membrane-enveloped magnetite crystals, whose synthesis is favored by a low redox potential. however, the cellular redox processes governing the biomineralization of the mixed-valence iron oxide have remained unknown. here, we show that in the alphaproteobacterium magnetospirillum gryphiswaldense, magnetite biomineralization is linked to dissimilatory nitrate reduction. a complete denitrification pathway, including gene functions for nitr ... | 2012 | 22730130 |
| mitochondrial evolution. | viewed through the lens of the genome it contains, the mitochondrion is of unquestioned bacterial ancestry, originating from within the bacterial phylum α-proteobacteria (alphaproteobacteria). accordingly, the endosymbiont hypothesis--the idea that the mitochondrion evolved from a bacterial progenitor via symbiosis within an essentially eukaryotic host cell--has assumed the status of a theory. yet mitochondrial genome evolution has taken radically different pathways in diverse eukaryotic lineage ... | 2012 | 22952398 |
| spectroscopic and kinetic investigation of the fully reduced and mixed valence states of ba3-cytochrome c oxidase from thermus thermophilus: a fourier transform infrared (ftir) and time-resolved step-scan ftir study. | the complete understanding of a molecular mechanism of action requires the thermodynamic and kinetic characterization of different states and intermediates. cytochrome c oxidase reduces o(2) to h(2)o, a reaction coupled to proton translocation across the membrane. therefore, it is necessary to undertake a thorough characterization of the reduced form of the enzyme and the determination of the electron transfer processes and pathways between the redox-active centers. in this study fourier transfo ... | 2012 | 22927441 |
| insights into the evolution of sorbitol metabolism: phylogenetic analysis of sdr196c family. | short chain dehydrogenases/reductases (sdr) are nad(p)(h)-dependent oxidoreductases with a highly conserved 3d structure and of an early origin, which has allowed them to diverge into several families and enzymatic activities. the sdr196c family (http://www.sdr-enzymes.org) groups bacterial sorbitol dehydrogenases (sdh), which are of great industrial interest. in this study, we examine the phylogenetic relationship between the members of this family, and based on the findings and some sequence c ... | 2012 | 22899811 |
| revelation of the ability of burkholderia sp. usm (jcm 15050) pha synthase to polymerize 4-hydroxybutyrate monomer. | the nutrition-versatility of burkholderia sp. strain usm (jcm 15050) has initiated the studies on the use of this bacterium for polyhydroxyalkanoate (pha) production. to date, the burkholderia sp. has been reported to synthesize 3-hydroxybutyrate, 3-hydroxyvalerate and 3-hydroxy-4-methylvalerate monomers. in this study, the pha biosynthetic genes of this strain were successfully cloned and characterized. the pha biosynthetic cluster of this strain consisted of a pha synthase (phac), β-ketothiola ... | 2012 | 22877240 |
| a three-dimensional topology of complex i inferred from evolutionary correlations. | the quaternary structure of eukaryotic nadh:ubiquinone oxidoreductase (complex i), the largest complex of the oxidative phosphorylation, is still mostly unresolved. furthermore, it is unknown where transiently bound assembly factors interact with complex i. we therefore asked whether the evolution of complex i contains information about its 3d topology and the binding positions of its assembly factors. we approached these questions by correlating the evolutionary rates of eukaryotic complex i su ... | 2012 | 22857522 |
| link between microbial composition and carbon substrate-uptake preferences in a pha-storing community. | the microbial community of a fermented molasses-fed sequencing batch reactor (sbr) operated under feast and famine conditions for production of polyhydroxyalkanoates (phas) was identified and quantified through a 16 s rrna gene clone library and fluorescence in situ hybridization (fish). the microbial enrichment was found to be composed of pha-storing populations (84% of the microbial community), comprising members of the genera azoarcus, thauera and paracoccus. the dominant pha-storing populati ... | 2012 | 22810062 |
| link between microbial composition and carbon substrate-uptake preferences in a pha-storing community. | the microbial community of a fermented molasses-fed sequencing batch reactor (sbr) operated under feast and famine conditions for production of polyhydroxyalkanoates (phas) was identified and quantified through a 16 s rrna gene clone library and fluorescence in situ hybridization (fish). the microbial enrichment was found to be composed of pha-storing populations (84% of the microbial community), comprising members of the genera azoarcus, thauera and paracoccus. the dominant pha-storing populati ... | 2012 | 22810062 |
| recovering from a bad start: rapid adaptation and tradeoffs to growth below a threshold density. | bacterial growth in well-mixed culture is often assumed to be an autonomous process only depending upon the external conditions under control of the investigator. however, increasingly there is awareness that interactions between cells in culture can lead to surprising phenomena such as density-dependence in the initiation of growth. | 2012 | 22762241 |
| sealing the mitochondrial respirasome. | the mitochondrial respiratory chain is organized within an array of supercomplexes that function to minimize the generation of reactive oxygen species (ros) during electron transfer reactions. structural models of supercomplexes are now known. another recent advance is the discovery of non-oxphos complex proteins that appear to adhere to and seal the individual respiratory complexes to form stable assemblages that prevent electron leakage. this review highlights recent advances in our understand ... | 2012 | 22586278 |
| the chemical interplay between nitric oxide and mitochondrial cytochrome c oxidase: reactions, effectors and pathophysiology. | nitric oxide (no) reacts with complex i and cytochrome c oxidase (ccox, complex iv), inducing detrimental or cytoprotective effects. two alternative reaction pathways (pws) have been described whereby no reacts with ccox, producing either a relatively labile nitrite-bound derivative (ccox-no(2) (-), pw1) or a more stable nitrosyl-derivative (ccox-no, pw2). the two derivatives are both inhibited, displaying different persistency and o(2) competitiveness. in the mitochondrion, during turnover with ... | 2012 | 22811713 |
| rmtf, a new member of the aminoglycoside resistance 16s rrna n7 g1405 methyltransferase family. | multidrug-resistant clinical isolate klebsiella pneumoniae bm4686 was highly resistant to 4,6-disubstituted 2-deoxystreptamines and to fortimicin. resistance was due to the presence, on the 40-kb non-self-transferable plasmid pip849, of the rmtf gene which was cotranscribed with the upstream aac(6')-ib gene. the deduced rmtf protein had 25 to 46% identity with members of the n7 g1405 family of aminoglycoside resistance 16s rrna methyltransferases. | 2012 | 22547620 |
| lipidomics of intact mitochondria by maldi-tof/ms. | a simple and fast method of lipid analysis of isolated intact mitochondria by means of maldi-tof mass spectrometry is described. mitochondria isolated from bovine heart and yeast have been employed to set up and validate the new method of lipid analysis. the mitochondrial suspension is directly applied over the target and, after drying, covered by a thin layer of the 9-aminoacridine matrix solution. the lipid profiles acquired with this procedure contain all peaks previously obtained by analyzin ... | 2012 | 22556215 |
| structural determinants of the β-selectivity of a bacterial aminotransferase. | chiral β-amino acids occur as constituents of various natural and synthetic compounds with potentially useful bioactivities. the pyridoxal 5'-phosphate (plp)-dependent s-selective transaminase from mesorhizobium sp. strain luk (mesat) is a fold type i aminotransferase that can be used for the preparation of enantiopure β-phe and derivatives thereof. using x-ray crystallography, we solved structures of mesat in complex with (s)-β-phe, (r)-3-amino-5-methylhexanoic acid, 2-oxoglutarate, and the inh ... | 2012 | 22745123 |
| purification and properties of s-hydroxymethylglutathione dehydrogenase of paecilomyces variotii no. 5, a formaldehyde-degrading fungus. | s-hydroxymethylglutathione dehydrogenase from paecilomyces variotii no. 5 strain (nbrc 109023), isolated as a formaldehyde-degrading fungus, was purified by a procedure that included ammonium sulfate precipitation, deae-sepharose and hydroxyapatite chromatography and isoelectrofocusing. approximately 122-fold purification was achieved with a yield of 10.5%. the enzyme preparation was homogeneous as judged by sodium dodecyl polyacrylamide gel electrophoresis (sds-page). the molecular mass of the ... | 2012 | 22731626 |
| engineering a prokaryotic apocytochrome c as an efficient substrate for saccharomyces cerevisiae cytochrome c heme lyase. | cytochromes c are heme proteins that require multiple maturation components, such as heme lyases, for cofactor incorporation. saccharomyces cerevisiae has two heme lyases that are specific for apocytochromes c (cchl) or c(1) (cc(1)hl). cchl can covalently attach heme b groups to apocytochrome c substrates of eukaryotic but not prokaryotic origin. besides their conserved cys-xxx-xxx-cys-his heme-binding motifs, the amino-terminal regions of apocytochrome c substrates appear to be important for cc ... | 2012 | 22732413 |
| the interplay between the disulfide bond formation pathway and cytochrome c maturation in escherichia coli. | heme attachment to c-type cytochromes in bacteria requires cysteine thiols in the cxxch motif of the protein. the involvement of the periplasmic disulfide generation system in this process remains unclear. we undertake a systematic evaluation of the role of dsba and dsbd in cytochrome c biogenesis in escherichia coli and show unequivocally that dsba is not essential for holocytochrome production under aerobic or anaerobic conditions. we also prove that dsbd is important but not essential for mat ... | 2012 | 22569094 |
| biological sources and sinks of nitrous oxide and strategies to mitigate emissions. | nitrous oxide (n(2)o) is a powerful atmospheric greenhouse gas and cause of ozone layer depletion. global emissions continue to rise. more than two-thirds of these emissions arise from bacterial and fungal denitrification and nitrification processes in soils, largely as a result of the application of nitrogenous fertilizers. this article summarizes the outcomes of an interdisciplinary meeting, 'nitrous oxide (n(2)o) the forgotten greenhouse gas', held at the kavli royal society international cen ... | 2012 | 22451101 |
| regulation of denitrification at the cellular level: a clue to the understanding of n2o emissions from soils. | denitrifying prokaryotes use no(x) as terminal electron acceptors in response to oxygen depletion. the process emits a mixture of no, n(2)o and n(2), depending on the relative activity of the enzymes catalysing the stepwise reduction of no(3)(-) to n(2)o and finally to n(2). cultured denitrifying prokaryotes show characteristic transient accumulation of no(2)(-), no and n(2)o during transition from oxic to anoxic respiration, when tested under standardized conditions, but this character appears ... | 2012 | 22451108 |
| impacts of nitrogen application rates on the activity and diversity of denitrifying bacteria in the broadbalk wheat experiment. | bacterial denitrification results in the loss of fertilizer nitrogen and greenhouse gas emissions as nitrous oxides, but ecological factors in soil influencing denitrifier communities are not well understood, impeding the potential for mitigation by land management. communities vary in the relative abundance of the alternative dissimilatory nitrite reductase genes nirk and nirs, and the nitrous oxide reductase gene nosz; however, the significance for nitrous oxide emissions is unclear. we assess ... | 2012 | 22451109 |
| biochemical characterization of the purple form of marinobacter hydrocarbonoclasticus nitrous oxide reductase. | nitrous oxide reductase (n(2)or) catalyses the final step of the denitrification pathway-the reduction of nitrous oxide to nitrogen. the catalytic centre (cuz) is a unique tetranuclear copper centre bridged by inorganic sulphur in a tetrahedron arrangement that can have different oxidation states. previously, marinobacter hydrocarbonoclasticus n(2)or was isolated with the cuz centre as cuz*, in the [1cu(2+) : 3cu(+)] redox state, which is redox inert and requires prolonged incubation under reduc ... | 2012 | 22451106 |
| structural basis for nitrous oxide generation by bacterial nitric oxide reductases. | the crystal structure of the bacterial nitric oxide reductase (cnor) from pseudomonas aeruginosa is reported. its overall structure is similar to those of the main subunit of aerobic and micro-aerobic cytochrome oxidases (coxs), in agreement with the hypothesis that all these enzymes are members of the haem-copper oxidase superfamily. however, substantial structural differences between cnor and cox are observed in the catalytic centre and the delivery pathway of the catalytic protons, which shou ... | 2012 | 22451105 |
| nitrous oxide production and consumption: regulation of gene expression by gas-sensitive transcription factors. | several biochemical mechanisms contribute to the biological generation of nitrous oxide (n(2)o). n(2)o generating enzymes include the respiratory nitric oxide (no) reductase, an enzyme from the flavo-diiron family, and flavohaemoglobin. on the other hand, there is only one enzyme that is known to use n(2)o as a substrate, which is the respiratory n(2)o reductase typically found in bacteria capable of denitrification (the respiratory reduction of nitrate and nitrite to dinitrogen). this article w ... | 2012 | 22451107 |
| from static structure to living protein: computational analysis of cytochrome c oxidase main-chain flexibility. | crystallographic structure and deuterium accessibility comparisons of cco in different redox states have suggested conformational changes of mechanistic significance. to predict the intrinsic flexibility and low energy motions in cco, this work has analyzed available high-resolution crystallographic structures with proflex and elnémo computational methods. the results identify flexible regions and potential conformational changes in cco that correlate well with published structural and biochemic ... | 2012 | 22824280 |
| structure, function, and assembly of heme centers in mitochondrial respiratory complexes. | the sequential flow of electrons in the respiratory chain, from a low reduction potential substrate to o(2), is mediated by protein-bound redox cofactors. in mitochondria, hemes-together with flavin, iron-sulfur, and copper cofactors-mediate this multi-electron transfer. hemes, in three different forms, are used as a protein-bound prosthetic group in succinate dehydrogenase (complex ii), in bc(1) complex (complex iii) and in cytochrome c oxidase (complex iv). the exact function of heme b in comp ... | 2012 | 22554985 |
| mechanistic stoichiometry of proton translocation by cytochrome cbb3. | cytochrome cbb(3) belongs to the superfamily of respiratory heme-copper oxidases that couple the reduction of molecular oxygen to proton translocation across the bacterial or mitochondrial membrane. the cbb(3)-type enzymes are found only in bacteria, and are both structurally and functionally the most distant from their mitochondrial counterparts. the mechanistic h(+)/e(-) stoichiometry of proton translocation in these cbb(3)-type cytochrome c oxidases has remained controversial. a stoichiometri ... | 2012 | 22529361 |
| structural changes caused by radiation-induced reduction and radiolysis: the effect of x-ray absorbed dose in a fungal multicopper oxidase. | x-ray radiation induces two main effects at metal centres contained in protein crystals: radiation-induced reduction and radiolysis and a resulting decrease in metal occupancy. in blue multicopper oxidases (bmcos), the geometry of the active centres and the metal-to-ligand distances change depending on the oxidation states of the cu atoms, suggesting that these alterations are catalytically relevant to the binding, activation and reduction of o(2). in this work, the x-ray-determined three-dimens ... | 2012 | 22525754 |
| the influence of extracellular superoxide on iron redox chemistry and bioavailability to aquatic microorganisms. | superoxide, the one-electron reduced form of dioxygen, is produced in the extracellular milieu of aquatic microbes through a range of abiotic chemical processes and also by microbes themselves. due to its ability to promote both oxidative and reductive reactions, superoxide may have a profound impact on the redox state of iron, potentially influencing iron solubility, complex speciation, and bioavailability. the interplay between iron, superoxide, and oxygen may also produce a cascade of other h ... | 2012 | 22514548 |
| product-controlled steady-state kinetics between cytochrome aa(3) from rhodobacter sphaeroides and equine ferrocytochrome c analyzed by a novel spectrophotometric approach. | cytochrome c oxidase (cco) catalyzes the reduction of molecular oxygen to water using ferrocytochrome c (cyt c(2+)) as the electron donor. in this study, the oxidation of horse cyt c(2+) by cco from rhodobacter sphaeroides, was monitored using stopped-flow spectrophotometry. a novel analytic procedure was applied in which the spectra were deconvoluted into the reduced and oxidized forms of cyt c by a least-squares fitting method, yielding the reaction rates at various concentrations of cyt c(2+) ... | 2012 | 22516686 |
| electron transfer in subunit nuoi (tyky) of escherichia coli nadh:quinone oxidoreductase (ndh-1). | bacterial proton-translocating nadh:quinone oxidoreductase (ndh-1) consists of a peripheral and a membrane domain. the peripheral domain catalyzes the electron transfer from nadh to quinone through a chain of seven iron-sulfur (fe/s) clusters. subunit nuoi in the peripheral domain contains two [4fe-4s] clusters (n6a and n6b) and plays a role in bridging the electron transfer from cluster n5 to the terminal cluster n2. we constructed mutants for eight individual cys-coordinating fe/s clusters. wi ... | 2012 | 22474289 |
| evaluations of the effects of extremely low-frequency electromagnetic fields on growth and antibiotic susceptibility of escherichia coli and pseudomonas aeruginosa. | we aimed to investigate the effects of exposure to extremely low-frequency electromagnetic fields (2 mt; 50 hz) on the growth rate and antibiotic sensitivity of e. coli atcc 25922 and p. aeruginosa atcc 27853. the electromagnetic field treatment significantly influenced the growth rate of both strains when incubated in the presence of subinhibitory concentrations of kanamycin (1 μg/ml) and amikacin (0.5 μg/ml), respectively. in particular, at 4, 6, and 8 h of incubation the number of cells was s ... | 2012 | 22577384 |
| structural insights into tir domain specificity of the bridging adaptor mal in tlr4 signaling. | myd88 adaptor-like protein (mal) is a crucial adaptor that acts as a bridge to recruit the myd88 molecule to activated tlr4 receptors in response to invading pathogens. the specific assembly of the toll/interleukin-1 receptor (tir) domains of tlr4, mal and myd88 is responsible for proper signal transduction in the tlr4 signaling pathway. however, the molecular mechanism for the specificity of these tir domains remains unclear. here, we present the crystal structure of the tir domain of the human ... | 2012 | 22485159 |
| the multifaceted roles of neutrophil gelatinase associated lipocalin (ngal) in inflammation and cancer. | neutrophil gelatinase associated lipocalin (ngal), also known as oncogene 24p3, uterocalin, siderocalin or lipocalin 2, is a 24kda secreted glycoprotein originally purified from a culture of mouse kidney cells infected with simian virus 40 (sv-40). subsequent investigations have revealed that it is a member of the lipocalin family of proteins that transport small, hydrophobic ligands. since then, ngal expression has been reported in several normal tissues where it serves to provide protection ag ... | 2012 | 22513004 |
| abiotic and microbial interactions during anaerobic transformations of fe(ii) and [formula: see text]. | microbial fe(ii) oxidation using [formula: see text] as the terminal electron acceptor [nitrate-dependent fe(ii) oxidation, ndfo] has been studied for over 15 years. although there are reports of autotrophic isolates and stable enrichments, many of the bacteria capable of ndfo are known organotrophic [formula: see text]-reducers that require the presence of an organic, primary substrate, e.g., acetate, for significant amounts of fe(ii) oxidation. although the thermodynamics of fe(ii) oxidation a ... | 2012 | 22479259 |
| exploring the proton pump and exit pathway for pumped protons in cytochrome ba3 from thermus thermophilus. | the heme-copper oxygen reductases are redox-driven proton pumps. in the current work, the effects of mutations in a proposed exit pathway for pumped protons are examined in the ba(3)-type oxygen reductase from thermus thermophilus, leading from the propionates of heme a(3) to the interface between subunits i and ii. recent studies have proposed important roles for his376 and asp372, both of which are hydrogen-bonded to propionate-a of heme a(3), and for glu126(ii) (subunit ii), which is hydrogen ... | 2012 | 22431640 |
| inter-monomer electron transfer is too slow to compete with monomeric turnover in bc(1) complex. | the homodimeric bc(1) complexes are membrane proteins essential in respiration and photosynthesis. the ~11å distance between the two b(l)-hemes of the dimer opens the possibility of electron transfer between them, but contradictory reports make such inter-monomer electron transfer controversial. we have constructed in rhodobacter sphaeroides a heterodimeric expression system similar to those used before, in which the bc(1) complex can be mutated differentially in the two copies of cyt b to test ... | 2012 | 22465023 |
| value-added uses for crude glycerol--a byproduct of biodiesel production. | biodiesel is a promising alternative, and renewable, fuel. as its production increases, so does production of the principle co-product, crude glycerol. the effective utilization of crude glycerol will contribute to the viability of biodiesel. in this review, composition and quality factors of crude glycerol are discussed. the value-added utilization opportunities of crude glycerol are reviewed. the majority of crude glycerol is used as feedstock for production of other value-added chemicals, fol ... | 2012 | 22413907 |
| two tyrosyl radicals stabilize high oxidation states in cytochrome c oxidase for efficient energy conservation and proton translocation. | the reaction of oxidized bovine cytochrome c oxidase (bcco) with hydrogen peroxide (h(2)o(2)) was studied by electron paramagnetic resonance (epr) to determine the properties of radical intermediates. two distinct radicals with widths of 12 and 46 g are directly observed by x-band epr in the reaction of bcco with h(2)o(2) at ph 6 and ph 8. high-frequency epr (d-band) provides assignments to tyrosine for both radicals based on well-resolved g-tensors. the wide radical (46 g) exhibits g-values sim ... | 2012 | 22296274 |
| cofactor biosynthesis through protein post-translational modification. | post-translational modifications of amino acids can be used to generate novel cofactors capable of chemistries inaccessible to conventional amino acid side chains. the biosynthesis of these sites often requires one or more enzyme or protein accessory factors, the functions of which are quite diverse and often difficult to isolate in cases where multiple enzymes are involved. herein is described the current knowledge of the biosynthesis of urease and nitrile hydratase metal centers, pyrroloquinol ... | 2012 | 22387133 |
| group x aldehyde dehydrogenases of pseudomonas aeruginosa pao1 degrade hydrazones. | hydrazones are natural and synthetic compounds containing a c=n-n moiety. here we found that the opportunistic pathogen pseudomonas aeruginosa pao1 produced nad(+)- or nadp(+)-dependent hydrazone dehydrogenase (hdh), which converts hydrazones to the corresponding hydrazides and acids rather than to the simple hydrolytic product aldehydes. gene cloning indicated that the hdh is part of the group x aldehyde dehydrogenase (aldh) family, which is distributed among bacteria, although the physiologica ... | 2012 | 22267508 |
| out of plane distortions of the heme b of escherichia coli succinate dehydrogenase. | the role of the heme b in escherichia coli succinate dehydrogenase is highly ambiguous and its role in catalysis is questionable. to examine whether heme reduction is an essential step of the catalytic mechanism, we generated a series of site-directed mutations around the heme binding pocket, creating a library of variants with a stepwise decrease in the midpoint potential of the heme from the wild-type value of +20 mv down to -80 mv. this difference in midpoint potential is enough to alter the ... | 2012 | 22393428 |
| trace metal requirements for microbial enzymes involved in the production and consumption of methane and nitrous oxide. | fluxes of greenhouse gases to the atmosphere are heavily influenced by microbiological activity. microbial enzymes involved in the production and consumption of greenhouse gases often contain metal cofactors. while extensive research has examined the influence of fe bioavailability on microbial co(2) cycling, fewer studies have explored metal requirements for microbial production and consumption of the second- and third-most abundant greenhouse gases, methane (ch(4)), and nitrous oxide (n(2)o). ... | 2012 | 22363333 |
| role of calcium in metalloenzymes: effects of calcium removal on the axial ligation geometry and magnetic properties of the catalytic diheme center in maug. | maug is a diheme enzyme possessing a five-coordinate high-spin heme with an axial his ligand and a six-coordinate low-spin heme with his-tyr axial ligation. a ca(2+) ion is linked to the two hemes via hydrogen bond networks, and the enzyme activity depends on its presence. removal of ca(2+) altered the electron paramagnetic resonance (epr) signals of each ferric heme such that the intensity of the high-spin heme was decreased and the low-spin heme was significantly broadened. addition of ca(2+) ... | 2012 | 22320333 |
| the genome sequence of polymorphum gilvum sl003b-26a1(t) reveals its genetic basis for crude oil degradation and adaptation to the saline soil. | polymorphum gilvum sl003b-26a1(t) is the type strain of a novel species in the recently published novel genus polymorphum isolated from saline soil contaminated with crude oil. it is capable of using crude oil as the sole carbon and energy source and can adapt to saline soil at a temperature of 45°c. the polymorphum gilvum genome provides a genetic basis for understanding how the strain could degrade crude oil and adapt to a saline environment. genome analysis revealed the versatility of the str ... | 2012 | 22359583 |
| proline 107 is a major determinant in maintaining the structure of the distal pocket and reactivity of the high-spin heme of maug. | the diheme enzyme maug catalyzes a six-electron oxidation required for posttranslational modification of a precursor of methylamine dehydrogenase (premadh) to complete the biosynthesis of its protein-derived tryptophan tryptophylquinone (ttq) cofactor. crystallographic studies had shown that pro107, which resides in the distal pocket of the high-spin heme of maug, changes conformation upon binding of co or no to the heme iron. in this study, pro107 was converted to cys, val, and ser by site-dire ... | 2012 | 22299652 |
| optimization of gene expression through divergent mutational paths. | adaptation under similar selective pressure often leads to comparable phenotypes. a longstanding question is whether such phenotypic repeatability entails similar (parallelism) or different genotypic changes (convergence). to better understand this, we characterized mutations that optimized expression of a plasmid-borne metabolic pathway during laboratory evolution of a bacterium. expressing these pathway genes was essential for growth but came with substantial costs. starting from overexpressio ... | 2012 | 22832162 |
| tryptophan tryptophylquinone biosynthesis: a radical approach to posttranslational modification. | protein-derived cofactors are formed by irreversible covalent posttranslational modification of amino acid residues. an example is tryptophan tryptophylquinone (ttq) found in the enzyme methylamine dehydrogenase (madh). ttq biosynthesis requires the cross-linking of the indole rings of two trp residues and the insertion of two oxygen atoms onto adjacent carbons of one of the indole rings. the diheme enzyme maug catalyzes the completion of ttq within a precursor protein of madh. the premadh subst ... | 2012 | 22314272 |
| oxoferryl-porphyrin radical catalytic intermediate in cytochrome bd oxidases protects cells from formation of reactive oxygen species. | the quinol-linked cytochrome bd oxidases are terminal oxidases in respiration. these oxidases harbor a low spin heme b(558) that donates electrons to a binuclear heme b(595)/heme d center. the reaction with o(2) and subsequent catalytic steps of the escherichia coli cytochrome bd-i oxidase were investigated by means of ultra-fast freeze-quench trapping followed by epr and uv-visible spectroscopy. after the initial binding of o(2), the o-o bond is heterolytically cleaved to yield a kinetically co ... | 2012 | 22287551 |
| the diheme cytochrome c peroxidase from shewanella oneidensis requires reductive activation. | we report the characterization of the diheme cytochrome c peroxidase (ccp) from shewanella oneidensis (so) using uv-visible absorbance, electron paramagnetic resonance spectroscopy, and michaelis-menten kinetics. while sequence alignment with other bacterial diheme cytochrome c peroxidases suggests that so ccp may be active in the as-isolated state, we find that so ccp requires reductive activation for full activity, similar to the case for the canonical pseudomonas type of bacterial ccp enzyme. ... | 2012 | 22239664 |
| the gtar protein negatively regulates transcription of the gtari operon and modulates gene transfer agent (rcgta) expression in rhodobacter capsulatus. | the gtai gene of rhodobacter capsulatus encodes an n-acyl-homoserine lactone (acyl-hsl) synthase. immediately 5' of the gtai gene is orf rcc00328 that encodes a potential acyl-hsl receptor protein. a combination of genetic and biochemical approaches showed that rcc00328 (renamed gtar) modulates the production of a genetic exchange element called the gene transfer agent (rcgta), and regulates the transcription of gtai. although gtai mutants exhibited decreased levels of rcgta production, mutagene ... | 2012 | 22211723 |
| net proton uptake is preceded by multiple proton transfer steps upon electron injection into cytochrome c oxidase. | cytochrome c oxidase (cox), the last enzyme of the respiratory chain of aerobic organisms, catalyzes the reduction of molecular oxygen to water. it is a redox-linked proton pump, whose mechanism of proton pumping has been controversially discussed, and the coupling of proton and electron transfer is still not understood. here, we investigated the kinetics of proton transfer reactions following the injection of a single electron into the fully oxidized enzyme and its transfer to the hemes using t ... | 2012 | 22238345 |
| an unusual subtilisin-like serine protease is essential for biogenesis of quinohemoprotein amine dehydrogenase. | quinohemoprotein amine dehydrogenase (qhndh), an αβγ heterotrimer present in the periplasm of several gram-negative bacteria, catalyzes the oxidative deamination of various aliphatic amines such as n-butylamine for assimilation as carbon and energy sources. the γ subunit of mature qhndh contains a protein-derived quinone cofactor, cysteine tryptophylquinone, and three intrapeptidyl thioether cross-links between cys and asp or glu residues. in its cytoplasmic nascent form, the γ subunit has a 28- ... | 2012 | 22235135 |
| enzymatic activities of isolated cytochrome bc₁-like complexes containing fused cytochrome b subunits with asymmetrically inactivated segments of electron transfer chains. | homodimeric structure of cytochrome bc₁, a common component of biological energy conversion systems, builds in four catalytic quinone oxidation/reduction sites and four chains of cofactors (branches) that, connected by a centrally located bridge, form a symmetric h-shaped electron transfer system. the mechanism of operation of this complex system is under constant debate. here, we report on isolation and enzymatic examination of cytochrome bc₁-like complexes containing fused cytochrome b subunit ... | 2012 | 22233445 |
| microbial alkyl- and aryl-sulfatases: mechanism, occurrence, screening and stereoselectivities. | this review gives an overview on the occurrence of sulfatases in prokaryota, eukaryota and archaea. the mechanism of enzymes acting with retention or inversion of configuration during sulfate ester hydrolysis is discussed taking two complementary examples. methods for the discovery of novel alkyl sulfatases are described by way of sequence-based search and enzyme induction. a comprehensive list of organisms with their respective substrate scope regarding prim- and sec-alkyl sulfate esters allows ... | 2013 | 24352732 |
| microbial alkyl- and aryl-sulfatases: mechanism, occurrence, screening and stereoselectivities. | this review gives an overview on the occurrence of sulfatases in prokaryota, eukaryota and archaea. the mechanism of enzymes acting with retention or inversion of configuration during sulfate ester hydrolysis is discussed taking two complementary examples. methods for the discovery of novel alkyl sulfatases are described by way of sequence-based search and enzyme induction. a comprehensive list of organisms with their respective substrate scope regarding prim- and sec-alkyl sulfate esters allows ... | 2013 | 24352732 |
| intrigues and intricacies of the biosynthetic pathways for the enzymatic quinocofactors: pqq, ttq, ctq, tpq, and ltq. | | 2013 | 24350630 |
| intrigues and intricacies of the biosynthetic pathways for the enzymatic quinocofactors: pqq, ttq, ctq, tpq, and ltq. | | 2013 | 24350630 |
| oxidative damage in maug: implications for the control of high-valent iron species and radical propagation pathways. | the di-heme enzyme maug catalyzes the oxidative biosynthesis of a tryptophan tryptophylquinone cofactor on a precursor of the enzyme methylamine dehydrogenase (premadh). reaction of h2o2 with the diferric form of maug, or reaction of o2 with diferrous maug, forms the catalytic intermediate known as bis-fe(iv), which acts as the key oxidant during turnover. the site of substrate oxidation is more than 40 å from the high-spin heme iron where h2o2 initially reacts, and catalysis relies on radical h ... | 2013 | 24320950 |
| density functional study for the bridged dinuclear center based on a high-resolution x-ray crystal structure of ba3 cytochrome c oxidase from thermus thermophilus. | strong electron density for a peroxide type dioxygen species bridging the fea3 and cub dinuclear center (dnc) was observed in the high-resolution (1.8 å) x-ray crystal structures (pdb entries 3s8g and 3s8f) of ba3 cytochrome c oxidase (cco) from thermus thermophilus. the crystals represent the as-isolated x-ray photoreduced cco structures. the bridging peroxide was proposed to arise from the recombination of two radiation-produced ho(•) radicals formed either very near to or even in the space be ... | 2013 | 24262070 |
| mechanism of bacterial interference with tlr4 signaling by brucella toll/interleukin-1 receptor domain-containing protein tcpb. | upon activation of toll-like receptors (tlrs), cytoplasmic toll/interleukin-1 receptor (tir) domains of the receptors undergo homo- or heterodimerization. this in turn leads to the recruitment of adaptor proteins, activation of transcription factors, and the secretion of pro-inflammatory cytokines. recent studies have described the tir domain-containing protein from brucella melitensis, tcpb (btpa/btp1), to be involved in virulence and suppression of host innate immune responses. tcpb interferes ... | 2013 | 24265315 |
| mechanism of bacterial interference with tlr4 signaling by brucella toll/interleukin-1 receptor domain-containing protein tcpb. | upon activation of toll-like receptors (tlrs), cytoplasmic toll/interleukin-1 receptor (tir) domains of the receptors undergo homo- or heterodimerization. this in turn leads to the recruitment of adaptor proteins, activation of transcription factors, and the secretion of pro-inflammatory cytokines. recent studies have described the tir domain-containing protein from brucella melitensis, tcpb (btpa/btp1), to be involved in virulence and suppression of host innate immune responses. tcpb interferes ... | 2013 | 24265315 |
| copper control of bacterial nitrous oxide emission and its impact on vitamin b12-dependent metabolism. | global agricultural emissions of the greenhouse gas nitrous oxide (n2o) have increased by around 20% over the last 100 y, but regulation of these emissions and their impact on bacterial cellular metabolism are poorly understood. denitrifying bacteria convert nitrate in soils to inert di-nitrogen gas (n2) via n2o and the biochemistry of this process has been studied extensively in paracoccus denitrificans. here we demonstrate that expression of the gene encoding the nitrous oxide reductase (nosz) ... | 2013 | 24248380 |
| detrimental effect of the 6 his c-terminal tag on yedy enzymatic activity and influence of the tat signal sequence on yedy synthesis. | yedy, a molybdoenzyme belonging to the sulfite oxidase family, is found in most gram-negative bacteria. it contains a twin-arginine signal sequence that is cleaved after its translocation into the periplasm. despite a weak reductase activity with substrates such as dimethyl sulfoxide or trimethylamine n-oxide, its natural substrate and its role in the cell remain unknown. although sequence conservation of the yedy family displays a strictly conserved hydrophobic c-terminal residue, all known stu ... | 2013 | 24180491 |
| cumate-inducible gene expression system for sphingomonads and other alphaproteobacteria. | tunable promoters represent a pivotal genetic tool for a wide range of applications. here we present such a system for sphingomonads, a phylogenetically diverse group of bacteria that have gained much interest for their potential in bioremediation and their use in industry and for which no dedicated inducible gene expression system has been described so far. a strong, constitutive synthetic promoter was first identified through a genetic screen and subsequently combined with the repressor and th ... | 2013 | 23995928 |
| diversity and ecophysiology of new isolates of extremely acidophilic cs2-converting acidithiobacillus strains. | biofiltration of industrial carbon disulfide (cs2)-contaminated waste air streams results in the acidification of biofilters and therefore reduced performance, high water use, and increased costs. to address these issues, we isolated 16 extremely acidophilic cs2-converting acidithiobacillus thiooxidans strains that tolerated up to 6% (vol/vol) sulfuric acid. the ecophysiological properties of five selected strains (2bp, sts 4-3, s1p, g8, and bbw1) were compared. these five strains had ph optima ... | 2013 | 23995926 |
| investigating the function of [2fe-2s] cluster n1a, the off-pathway cluster in complex i, by manipulating its reduction potential. | nadh:quinone oxidoreductase (complex i) couples nadh oxidation and quinone reduction to proton translocation across an energy-transducing membrane. all complexes i contain a flavin to oxidize nadh, seven iron-sulfur clusters to transfer electrons from the flavin to quinone and an eighth cluster (n1a) on the opposite side of the flavin. the role of cluster n1a is unknown, but escherichia coli complex i has an unusually high-potential cluster n1a and its reduced flavin produces h2o2, not superoxid ... | 2013 | 23980528 |
| a robust genetic system for producing heterodimeric native and mutant cytochrome bc(1). | the ubihydroquinone:cytochrome c oxidoreductase, or cytochrome bc1, is central to the production of atp by oxidative phosphorylation and photophosphorylation in many organisms. its three-dimensional structure depicts it as a homodimer with each monomer composed of the fe-s protein, cytochrome b, and cytochrome c1 subunits. recent genetic approaches successfully produced heterodimeric variants of this enzyme, providing insights into its mechanism of function. however, these experimental setups ar ... | 2013 | 24028512 |
| the heme a synthase cox15 associates with cytochrome c oxidase assembly intermediates during cox1 maturation. | cox1, the core subunit of the cytochrome c oxidase, receives two heme a cofactors during assembly of the 13-subunit enzyme complex. however, at which step of the assembly process and how heme is inserted into cox1 have remained an enigma. shy1, the yeast surf1 homolog, has been implicated in heme transfer to cox1, whereas the heme a synthase, cox15, catalyzes the final step of heme a synthesis. here we performed a comprehensive analysis of cytochrome c oxidase assembly intermediates containing s ... | 2013 | 23979592 |
| cloning, expression, purification, crystallization and preliminary x-ray crystallographic analysis of the tir domain from the brucella melitensis tir-domain-containing protein tcpb. | in mammals, toll-like receptors (tlrs) recognize conserved microbial molecular signatures and induce an early innate immune response in the host. tlr signalling is mediated by interactions between the cytosolic tir (toll/interleukin-1 receptor) domains of the receptor and the adaptor proteins. increasingly, it is apparent that pathogens target this interaction via pathogen-expressed tir-domain-containing proteins to modulate immune responses. a tir-domain-containing protein tcpb has been reporte ... | 2013 | 24100574 |
| molecular mechanism and physiological role of active-deactive transition of mitochondrial complex i. | the unique feature of mitochondrial complex i is the so-called a/d transition (active-deactive transition). the a-form catalyses rapid oxidation of nadh by ubiquinone (k ~104 min-1) and spontaneously converts into the d-form if the enzyme is idle at physiological temperatures. such deactivation occurs in vitro in the absence of substrates or in vivo during ischaemia, when the ubiquinone pool is reduced. the d-form can undergo reactivation given both nadh and ubiquinone availability during slow ( ... | 2013 | 24059527 |
| discovery of new enzymes and metabolic pathways by using structure and genome context. | assigning valid functions to proteins identified in genome projects is challenging: overprediction and database annotation errors are the principal concerns. we and others are developing computation-guided strategies for functional discovery with 'metabolite docking' to experimentally derived or homology-based three-dimensional structures. bacterial metabolic pathways often are encoded by 'genome neighbourhoods' (gene clusters and/or operons), which can provide important clues for functional ass ... | 2013 | 24056934 |
| probing heme delivery processes in cytochrome c biogenesis system i. | cytochromes c comprise a diverse and widespread family of proteins containing covalently bound heme that are central to the life of most organisms. in many bacteria and in certain mitochondria, the synthesis of cytochromes c is performed by a complex post-translational modification apparatus called system i (or cytochrome c maturation, ccm, system). in escherichia coli , there are eight maturation proteins, several of which are involved in heme handling, but the mechanism of heme transfer from o ... | 2013 | 24044352 |
| the nitric-oxide reductase from paracoccus denitrificans uses a single specific proton pathway. | the no reductase from paracoccus denitrificans reduces no to n2o (2no + 2h(+) + 2e(-) → n2o + h2o) with electrons donated by periplasmic cytochrome c (cytochrome c-dependent no reductase; cnor). cnors are members of the heme-copper oxidase superfamily of integral membrane proteins, comprising the o2-reducing, proton-pumping respiratory enzymes. in contrast, although no reduction is as exergonic as o2 reduction, there are no protons pumped in cnor, and in addition, protons needed for no reduction ... | 2013 | 24014024 |
| functions of the hydrophilic channels in protonmotive cytochrome c oxidase. | the structures and functions of hydrophilic channels in electron-transferring membrane proteins are discussed. a distinction is made between proton channels that can conduct protons and dielectric channels that are non-conducting but can dielectrically polarize in response to the introduction of charge changes in buried functional centres. functions of the k, d and h channels found in a1-type cytochrome c oxidases are reviewed in relation to these ideas. possible control of function by dielectri ... | 2013 | 23864498 |
| nitrogen oxyanion-dependent dissociation of a two-component complex that regulates bacterial nitrate assimilation. | nitrogen is an essential nutrient for growth and is readily available to microbes in many environments in the form of ammonium and nitrate. both ions are of environmental significance due to sustained use of inorganic fertilizers on agricultural soils. diverse species of bacteria that have an assimilatory nitrate/nitrite reductase system (nas) can use nitrate or nitrite as the sole nitrogen source for growth when ammonium is limited. in paracoccus denitrificans, the pathway-specific two-componen ... | 2013 | 24005668 |
| haloarchaeal-type β-ketothiolases involved in poly(3-hydroxybutyrate-co-3-hydroxyvalerate) synthesis in haloferax mediterranei. | the key enzymes for poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (phbv) biosynthesis in haloarchaea have been identified except the β-ketothiolase(s), which condense two acetyl coenzyme a (acetyl-coa) molecules to acetoacetyl-coa, or one acetyl-coa and one propionyl-coa to 3-ketovaleryl-coa. whole-genome analysis has revealed eight potential β-ketothiolase genes in the haloarchaeon haloferax mediterranei, among which the phbv-specific bktb and phaa were identified by gene knockout and complement ... | 2013 | 23793631 |
| carboxyl group of glu113 is required for stabilization of the diferrous and bis-fe(iv) states of maug. | the diheme enzyme maug catalyzes a six-electron oxidation required for post-translational modification of a precursor of methylamine dehydrogenase (premadh) to complete the biosynthesis of its protein-derived tryptophan tryptophylquinone (ttq) cofactor. crystallographic studies have implicated glu113 in the formation of the bis-fe(iv) state of maug, in which one heme is fe(iv)═o and the other is fe(iv) with his-tyr axial ligation. an e113q mutation had no effect on the structure of maug but sign ... | 2013 | 23952537 |
| iron binding at specific sites within the octameric hbps protects streptomycetes from iron-mediated oxidative stress. | the soil bacterium streptomyces reticuli secretes the octameric protein hbps that acts as a sensory component of the redox-signalling pathway hbps-sens-senr. this system modulates a genetic response on iron- and haem-mediated oxidative stress. moreover, hbps alone provides this bacterium with a defence mechanism to the presence of high concentrations of iron ions and haem. while the protection against haem has been related to its haem-binding and haem-degrading activity, the interaction with iro ... | 2013 | 24013686 |
| phasing statistics for alpha helical membrane protein structures. | in this report we highlight the latest trends in phasing methods used to solve alpha helical membrane protein structures and analyze the use of heavy atom metals for the purpose of experimental phasing. our results reveal that molecular replacement is emerging as the most successful method for phasing alpha helical membrane proteins, with the notable exception of the transporter family, where experimentally derived phase information still remains the most effective method. to facilitate selectio ... | 2013 | 23963889 |
| axial interactions in the mixed-valent cua active site and role of the axial methionine in electron transfer. | within cu-containing electron transfer active sites, the role of the axial ligand in type 1 sites is well defined, yet its role in the binuclear mixed-valent cua sites is less clear. recently, the mutation of the axial met to leu in a cua site engineered into azurin (cua az) was found to have a limited effect on e(0) relative to this mutation in blue copper (bc). detailed low-temperature absorption and magnetic circular dichroism, resonance raman, and electron paramagnetic resonance studies on c ... | 2013 | 23964128 |
| genome sequence of the phage-gene rich marine phaeobacter arcticus type strain dsm 23566(t.). | phaeobacter arcticus zhang et al. 2008 belongs to the marine roseobacter clade whose members are phylogenetically and physiologically diverse. in contrast to the type species of this genus, phaeobacter gallaeciensis, which is well characterized, relatively little is known about the characteristics of p. arcticus. here, we describe the features of this organism including the annotated high-quality draft genome sequence and highlight some particular traits. the 5,049,232 bp long genome with its 4, ... | 2013 | 24501630 |