Publications

TitleAbstractYear(sorted descending)
Filter
PMID
Filter
in silico analysis of a therapeutic target in leishmania infantum: the guanosine-diphospho-d-mannose pyrophosphorylase.leishmaniases are tropical and sub-tropical diseases for which classical drugs (i.e. antimonials) exhibit toxicity and drug resistance. such a situation requires to find new chemical series with antileishmanial activity. this work consists in analyzing the structure of a validated target in leishmania: the gdp-mannose pyrophosphorylase (gdp-mp), an enzyme involved in glycosylation and essential for amastigote survival. by comparing both human and l. infantum gdp-mp 3d homology models, we identif ...201222314241
characterization of the genome, proteome, and structure of yersiniophage ϕr1-37.the bacteriophage vb_yecm-ϕr1-37 (ϕr1-37) is a lytic yersiniophage that can propagate naturally in different yersinia species carrying the correct lipopolysaccharide receptor. this large-tailed phage has deoxyuridine (du) instead of thymidine in its dna. in this study, we determined the genomic sequence of phage ϕr1-37, mapped parts of the phage transcriptome, characterized the phage particle proteome, and characterized the virion structure by cryo-electron microscopy and image reconstruction. t ...201222973030
mathematical modeling and comparison of protein size distribution in different plant, animal, fungal and microbial species reveals a negative correlation between protein size and protein number, thus providing insight into the evolution of proteomes.the sizes of proteins are relevant to their biochemical structure and for their biological function. the statistical distribution of protein lengths across a diverse set of taxa can provide hints about the evolution of proteomes.201222296664
diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system.the yeast two-hybrid system pioneered the field of in vivo protein-protein interaction methods and undisputedly gave rise to a palette of ingenious techniques that are constantly pushing further the limits of the original method. sensitivity and selectivity have improved because of various technical tricks and experimental designs. here we present an exhaustive overview of the genetic approaches available to study in vivo binary protein interactions, based on two-hybrid and protein fragment comp ...201222688816
cellular function and molecular structure of ecto-nucleotidases.ecto-nucleotidases play a pivotal role in purinergic signal transmission. they hydrolyze extracellular nucleotides and thus can control their availability at purinergic p2 receptors. they generate extracellular nucleosides for cellular reuptake and salvage via nucleoside transporters of the plasma membrane. the extracellular adenosine formed acts as an agonist of purinergic p1 receptors. they also can produce and hydrolyze extracellular inorganic pyrophosphate that is of major relevance in the c ...201222555564
on the molecular mechanism of gc content variation among eubacterial genomes.as a key parameter of genome sequence variation, the gc content of bacterial genomes has been investigated for over half a century, and many hypotheses have been put forward to explain this gc content variation and its relationship to other fundamental processes. previously, we classified eubacteria into dnae-based groups (the dimeric combination of dna polymerase iii alpha subunits), according to a hypothesis where gc content variation is essentially governed by genome replication and dna repai ...201222230424
accommodation of profound sequence differences at the interfaces of eubacterial rna polymerase multi-protein assembly.evolutionarily divergent proteins have been shown to change their interacting partners. rna polymerase assembly is one of the rare cases which retain its component proteins in the course of evolution. this ubiquitous molecular assembly, involved in transcription, consists of four core subunits (alpha, beta, betaprime, and omega), which assemble to form the core enzyme. remarkably, the orientation of the four subunits in the complex is conserved from prokaryotes to eukaryotes although their seque ...201222359428
learning from bacteriophages - advantages and limitations of phage and phage-encoded protein applications.the emergence of bacteria resistance to most of the currently available antibiotics has become a critical therapeutic problem. the bacteria causing both hospital and community-acquired infections are most often multidrug resistant. in view of the alarming level of antibiotic resistance between bacterial species and difficulties with treatment, alternative or supportive antibacterial cure has to be developed. the presented review focuses on the major characteristics of bacteriophages and phage-en ...201223305359
characterization and structure of the aquifex aeolicus protein duf752: a bacterial trna-methyltransferase (mnmc2) functioning without the usually fused oxidase domain (mnmc1).post-transcriptional modifications of the wobble uridine (u34) of trnas play a critical role in reading nna/g codons belonging to split codon boxes. in a subset of escherichia coli trna, this wobble uridine is modified to 5-methylaminomethyluridine (mnm(5)u34) through sequential enzymatic reactions. uridine 34 is first converted to 5-carboxymethylaminomethyluridine (cmnm(5)u34) by the mnme-mnmg enzyme complex. the cmnm(5)u34 is further modified to mnm(5)u by the bifunctional mnmc protein. in the ...201223091054
redundancy and modularity in membrane-associated dissimilatory nitrate reduction in bacillus.the genomes of two phenotypically denitrifying type strains of the genus bacillus were sequenced and the pathways for dissimilatory nitrate reduction were reconstructed. results suggest that denitrification proceeds in the periplasmic space and in an analogous fashion as in gram-negative organisms, yet with the participation of proteins that tend to be membrane-bound or membrane-associated. a considerable degree of functional redundancy was observed with marked differences between b. azotoforman ...201223087684
the crystal structures of the α-subunit of the α(2)β (2) tetrameric glycyl-trna synthetase.aminoacyl-trna synthetases (aarss) are ligases (ec.6.1.1.-) that catalyze the acylation of amino acids to their cognate trnas in the process of translating genetic information from mrna to protein. their amino acid and trna specificity are crucial for correctly translating the genetic code. glycine is the smallest amino acid and the glycyl-trna synthetase (glyrs) belongs to class ii aarss. the enzyme is unusual because it can assume different quaternary structures. in eukaryotes, archaebacteria ...201223054484
specific metal recognition in nickel trafficking.nickel is an essential metal for a number of bacterial species that have developed systems for acquiring, delivering, and incorporating the metal into target enzymes and controlling the levels of nickel in cells to prevent toxic effects. as with other transition metals, these trafficking systems must be able to distinguish between the desired metal and other transition metal ions with similar physical and chemical properties. because there are few enzymes (targets) that require nickel for activi ...201222970729
the role of bacterial enhancer binding proteins as specialized activators of σ54-dependent transcription.bacterial enhancer binding proteins (bebps) are transcriptional activators that assemble as hexameric rings in their active forms and utilize atp hydrolysis to remodel the conformation of rna polymerase containing the alternative sigma factor σ(54). we present a comprehensive and detailed summary of recent advances in our understanding of how these specialized molecular machines function. the review is structured by introducing each of the three domains in turn: the central catalytic domain, the ...201222933558
double-stranded endonuclease activity in bacillus halodurans clustered regularly interspaced short palindromic repeats (crispr)-associated cas2 protein.the crispr (clustered regularly interspaced short palindromic repeats) system is a prokaryotic rna-based adaptive immune system against extrachromosomal genetic elements. cas2 is a universally conserved core crispr-associated protein required for the acquisition of new spacers for crispr adaptation. it was previously characterized as an endoribonuclease with preference for single-stranded (ss)rna. here, we show using crystallography, mutagenesis, and isothermal titration calorimetry that the bac ...201222942283
phylogenetic position of aquificales based on the whole genome sequences of six aquificales species.species belonging to the order aquificales are believed to be an early branching lineage within the bacteria. however, the branching order of this group in single-gene phylogenetic trees is highly variable; for example, it has also been proposed that the aquificales should be grouped with ε-proteobacteria. to investigate the phylogenetic position of aquificales at the whole-genome level, here we reconstructed the phylogenetic trees of 18 bacteria including six aquificales species based on the co ...201222844640
structural dynamics of the aminoacylation and proofreading functional cycle of bacterial leucyl-trna synthetase.leucyl-trna synthetase (leurs) produces error-free leucyl-trna(leu) by coordinating translocation of the 3' end of (mis-)charged trnas from its synthetic site to a separate proofreading site for editing. here we report cocrystal structures of the escherichia coli leurs-trna(leu) complex in the aminoacylation or editing conformations, showing that translocation involves correlated rotations of four flexibly linked leurs domains. this pivots the trna to guide its charged 3' end from the closed ami ...201222683997
rational design and directed evolution of a bacterial-type glutaminyl-trna synthetase precursor.protein biosynthesis requires aminoacyl-transfer rna (trna) synthetases to provide aminoacyl-trna substrates for the ribosome. most bacteria and all archaea lack a glutaminyl-trna synthetase (glnrs); instead, gln-trna(gln) is produced via an indirect pathway: a glutamyl-trna synthetase (glurs) first attaches glutamate (glu) to trna(gln), and an amidotransferase converts glu-trna(gln) to gln-trna(gln). the human pathogen helicobacter pylori encodes two glurs enzymes, with glurs2 specifically amin ...201222661575
structure of escherichia coli aspartate α-decarboxylase asn72ala: probing the role of asn72 in pyruvoyl cofactor formation.the crystal structure of the asn72ala site-directed mutant of escherichia coli aspartate α-decarboxylase (adc) has been determined at 1.7 å resolution. the refined structure is consistent with the presence of a hydrolysis product serine in the active site in place of the pyruvoyl group required for catalysis, which suggests that the role of asn72 is to protect the ester formed during adc activation from hydrolysis. in previously determined structures of activated adc, including the wild type and ...201222505409
chemoinformatic identification of novel inhibitors against mycobacterium tuberculosis l-aspartate α-decarboxylase.l-aspartate α-decarboxylase (adc) belongs to a class of pyruvoyl dependent enzymes and catalyzes the conversion of aspartate to β-alanine in the pantothenate pathway, which is critical for the growth of several micro-organisms, including mycobacterium tuberculosis (mtb). its presence only in micro-organisms, fungi and plants and its absence in animals, particularly human, make it a promising drug target. we have followed a chemoinformatics-based approach to identify potential drug-like inhibitor ...201222470451
genetic recombination in bacillus subtilis: a division of labor between two single-strand dna-binding proteins.we have investigated the structural, biochemical and cellular roles of the two single-stranded (ss) dna-binding proteins from bacillus subtilis, ssba and ssbb. during transformation, ssbb localizes at the dna entry pole where it binds and protects internalized ssdna. the 2.8-å resolution structure of ssbb bound to ssdna reveals a similar overall protein architecture and ssdna-binding surface to that of escherichia coli ssb. ssba, which binds ssdna with higher affinity than ssbb, co-assembles ont ...201222373918
new insight into the transcarbamylase family: the structure of putrescine transcarbamylase, a key catalyst for fermentative utilization of agmatine.transcarbamylases reversibly transfer a carbamyl group from carbamylphosphate (cp) to an amine. although aspartate transcarbamylase and ornithine transcarbamylase (otc) are well characterized, little was known about putrescine transcarbamylase (ptc), the enzyme that generates cp for atp production in the fermentative catabolism of agmatine. we demonstrate that ptc (from enterococcus faecalis), in addition to using putrescine, can utilize l-ornithine as a poor substrate. crystal structures at 2.5 ...201222363663
substrate channeling in proline metabolism.proline metabolism is an important pathway that has relevance in several cellular functions such as redox balance, apoptosis, and cell survival. results from different groups have indicated that substrate channeling of proline metabolic intermediates may be a critical mechanism. one intermediate is pyrroline-5-carboxylate (p5c), which upon hydrolysis opens to glutamic semialdehyde (gsa). recent structural and kinetic evidence indicate substrate channeling of p5c/gsa occurs in the proline catabol ...201222201749
the genome of pelobacter carbinolicus reveals surprising metabolic capabilities and physiological features.the bacterium pelobacter carbinolicus is able to grow by fermentation, syntrophic hydrogen/formate transfer, or electron transfer to sulfur from short-chain alcohols, hydrogen or formate; it does not oxidize acetate and is not known to ferment any sugars or grow autotrophically. the genome of p. carbinolicus was sequenced in order to understand its metabolic capabilities and physiological features in comparison with its relatives, acetate-oxidizing geobacter species.201223227809
oxygen and hydrogen peroxide in the early evolution of life on earth: in silico comparative analysis of biochemical pathways.in the universe, oxygen is the third most widespread element, while on earth it is the most abundant one. moreover, oxygen is a major constituent of all biopolymers fundamental to living organisms. besides o(2), reactive oxygen species (ros), among them hydrogen peroxide (h(2)o(2)), are also important reactants in the present aerobic metabolism. according to a widely accepted hypothesis, aerobic metabolism and many other reactions/pathways involving o(2) appeared after the evolution of oxygenic ...201222970865
frequency, spectrum, and nonzero fitness costs of resistance to myxopyronin in staphylococcus aureus.the antibiotic myxopyronin (myx) functions by inhibiting bacterial rna polymerase (rnap). the binding site on rnap for myx-the rnap "switch region sw1/sw2 subregion"-is different from the binding site on rnap for the rnap inhibitor currently used in broad-spectrum antibacterial therapy, rifampin (rif). here, we report the frequency, spectrum, and fitness costs of myx resistance in staphylococcus aureus. the resistance rate for myx is 4 × 10(-8) to 7 × 10(-8) per generation, which is equal within ...201223006749
crystal structure of rlmm, the 2'o-ribose methyltransferase for c2498 of escherichia coli 23s rrna.rlmm (ygde) catalyzes the s-adenosyl methionine (adomet)-dependent 2'o methylation of c2498 in 23s ribosomal rna (rrna) of escherichia coli. previous experiments have shown that rlmm is active on 23s rrna from an rlmm knockout strain but not on mature 50s subunits from the same strain. here, we demonstrate rlmm methyltransferase (mtase) activity on in vitro transcribed 23s rrna and its domain v. we have solved crystal structures of e. coli rlmm at 1.9 å resolution and of an rlmm-adomet complex a ...201222923526
the porphyrias: advances in diagnosis and treatment.the inborn errors of heme biosynthesis, the porphyrias, are 8 genetically distinct metabolic disorders that can be classified as "acute hepatic," "hepatic cutaneous," and "erythropoietic cutaneous" diseases. recent advances in understanding their pathogenesis and molecular genetic heterogeneity have led to improved diagnosis and treatment. these advances include dna-based diagnoses for all the porphyrias, new understanding of the pathogenesis of the acute hepatic porphyrias, identification of th ...201222791288
chemosensory signaling controls motility and subcellular polarity in myxococcus xanthus.myxococcus xanthus is a model system for the study of dynamic protein localization and cell polarity in bacteria. m. xanthus cells are motile on solid surfaces enabled by two forms of motility. motility is controlled by the che-like frz pathway, which is essential for fruiting body formation and differentiation. the frz signal is mediated by a gtpase/gap protein pair that establishes cell polarity and directs the motility systems. pilus driven motility at the leading pole of the cell requires dy ...201223142584
function and regulation of clustered regularly interspaced short palindromic repeats (crispr) / crispr associated (cas) systems.phages are the most abundant biological entities on earth and pose a constant challenge to their bacterial hosts. thus, bacteria have evolved numerous 'innate' mechanisms of defense against phage, such as abortive infection or restriction/modification systems. in contrast, the clustered regularly interspaced short palindromic repeats (crispr) systems provide acquired, yet heritable, sequence-specific 'adaptive' immunity against phage and other horizontally-acquired elements, such as plasmids. re ...201223202464
interaction of card with rna polymerase mediates mycobacterium tuberculosis viability, rifampin resistance, and pathogenesis.mycobacterium tuberculosis infection continues to cause substantial human suffering. new chemotherapeutic strategies, which require insight into the pathways essential for m. tuberculosis pathogenesis, are imperative. we previously reported that depletion of the card protein in mycobacteria compromises viability, resistance to oxidative stress and fluoroquinolones, and pathogenesis. card associates with the rna polymerase (rnap), but it has been unknown which of the diverse functions of card are ...201222904282
whole genome analysis of leptospira licerasiae provides insight into leptospiral evolution and pathogenicity.the whole genome analysis of two strains of the first intermediately pathogenic leptospiral species to be sequenced (leptospira licerasiae strains var010 and mmd0835) provides insight into their pathogenic potential and deepens our understanding of leptospiral evolution. comparative analysis of eight leptospiral genomes shows the existence of a core leptospiral genome comprising 1547 genes and 452 conserved genes restricted to infectious species (including l. licerasiae) that are likely to be pa ...201223145189
architecture and conservation of the bacterial dna replication machinery, an underexploited drug target.new antibiotics with novel modes of action are required to combat the growing threat posed by multi-drug resistant bacteria. over the last decade, genome sequencing and other high-throughput techniques have provided tremendous insight into the molecular processes underlying cellular functions in a wide range of bacterial species. we can now use these data to assess the degree of conservation of certain aspects of bacterial physiology, to help choose the best cellular targets for development of n ...201222206257
naxd is a deacetylase required for lipid a modification and francisella pathogenesis.modification of specific gram-negative bacterial cell envelope components, such as capsule, o-antigen and lipid a, are often essential for the successful establishment of infection. francisella species express lipid a molecules with unique characteristics involved in circumventing host defences, which significantly contribute to their virulence. in this study, we show that naxd, a member of the highly conserved ydjc superfamily, is a deacetylase required for an important modification of the oute ...201222966934
structure of ribose 5-phosphate isomerase from the probiotic bacterium lactobacillus salivarius ucc118.the structure of ribose 5-phosphate isomerase from the probiotic bacterium lactobacillus salivarius ucc188 has been determined at 1.72 å resolution. the structure was solved by molecular replacement, which identified the functional homodimer in the asymmetric unit. despite only showing 57% sequence identity to its closest homologue, the structure adopted the typical α and β d-ribose 5-phosphate isomerase fold. comparison to other related structures revealed high homology in the active site, allo ...201223192019
high-resolution structures of thermus thermophilus enoyl-acyl carrier protein reductase in the apo form, in complex with nad+ and in complex with nad+ and triclosan.enoyl-acyl carrier protein reductase (enr; the product of the fabi gene) is an important enzyme that is involved in the type ii fatty-acid-synthesis pathway of bacteria, plants, apicomplexan protozoa and mitochondria. harmful pathogens such as mycobacterium tuberculosis and plasmodium falciparum use the type ii fatty-acid-synthesis system, but not mammals or fungi, which contain a type i fatty-acid-synthesis pathway consisting of one or two multifunctional enzymes. for this reason, specific inhi ...201223027736
molecular evolution of hydrogen peroxide degrading enzymes.for efficient removal of intra- and/or extracellular hydrogen peroxide by dismutation to harmless dioxygen and water (2h(2)o(2) → o(2) + 2h(2)o), nature designed three metalloenzyme families that differ in oligomeric organization, monomer architecture as well as active site geometry and catalytic residues. here we report on the updated reconstruction of the molecular phylogeny of these three gene families. ubiquitous typical (monofunctional) heme catalases are found in all domains of life showin ...201222330759
glutamine versus ammonia utilization in the nad synthetase family.nad is a ubiquitous and essential metabolic redox cofactor which also functions as a substrate in certain regulatory pathways. the last step of nad synthesis is the atp-dependent amidation of deamido-nad by nad synthetase (nads). members of the nads family are present in nearly all species across the three kingdoms of life. in eukaryotic nads, the core synthetase domain is fused with a nitrilase-like glutaminase domain supplying ammonia for the reaction. this two-domain nads arrangement enabling ...201222720044
staphylococcus aureus fabi: inhibition, substrate recognition, and potential implications for in vivo essentiality.methicillin-resistant staphylococcus aureus (mrsa) infections constitute a serious health threat worldwide, and novel antibiotics are therefore urgently needed. the enoyl-acp reductase (safabi) is essential for the s. aureus fatty acid biosynthesis and, hence, serves as an attractive drug target. we have obtained a series of snapshots of this enzyme that provide a mechanistic picture of ligand and inhibitor binding, including a dimer-tetramer transition combined with extensive conformational cha ...201222579249
aggregate reactivation mediated by the hsp100 chaperones.hsp100 family of molecular chaperones shows a unique capability to resolubilize and reactivate aggregated proteins. the hsp100-mediated protein disaggregation is linked to the activity of other chaperones from the hsp70 and hsp40 families. the best-studied members of the hsp100 family are the bacterial clpb and hsp104 from yeast. hsp100 chaperones are members of a large super-family of energy-driven conformational "machines" known as aaa+ atpases. this review describes the current mechanistic mo ...201222306514
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 ...201223057757
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 ...201223105119
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 ...201223086573
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 ...201223086573
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 ...201223012364
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 ...201222927441
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 ...201222857522
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 ...201222745123
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 ...201222824280
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 ...201222554985
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 ...201222529361
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+) ...201222516686
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 ...201222474289
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 ...201222431640
structural biology of redox partner interactions in p450cam monooxygenase: a fresh look at an old system.the p450cam monooxygenase system consists of three separate proteins: the fad-containing, nadh-dependent oxidoreductase (putidaredoxin reductase or pdr), cytochrome p450cam and the 2fe2s ferredoxin (putidaredoxin or pdx), which transfers electrons from pdr to p450cam. over the past few years our lab has focused on the interaction between these redox components. it has been known for some time that pdx can serve as an effector in addition to its electron shuttle role. the binding of pdx to p450ca ...201120816746
structural biology of redox partner interactions in p450cam monooxygenase: a fresh look at an old system.the p450cam monooxygenase system consists of three separate proteins: the fad-containing, nadh-dependent oxidoreductase (putidaredoxin reductase or pdr), cytochrome p450cam and the 2fe2s ferredoxin (putidaredoxin or pdx), which transfers electrons from pdr to p450cam. over the past few years our lab has focused on the interaction between these redox components. it has been known for some time that pdx can serve as an effector in addition to its electron shuttle role. the binding of pdx to p450ca ...201120816746
biochemical and structural characterization of mouse mitochondrial aspartate aminotransferase, a newly identified kynurenine aminotransferase-iv.mammalian maspat (mitochondrial aspartate aminotransferase) is recently reported to have kat (kynurenine aminotransferase) activity and plays a role in the biosynthesis of kyna (kynurenic acid) in rat, mouse and human brains. this study concerns the biochemical and structural characterization of mouse maspat. in this study, mouse maspat cdna was amplified from mouse brain first stand cdna and its recombinant protein was expressed in an escherichia coli expression system. sixteen oxo acids were t ...201120977429
idiosyncrasy and identity in the prokaryotic phe-system: crystal structure of e. coli phenylalanyl-trna synthetase complexed with phenylalanine and amp.the crystal structure of phenylalanyl-trna synthetase from e. coli (ecphers), a class ii aminoacyl-trna synthetase, complexed with phenylalanine and amp was determined at 3.05 å resolution. ecphers is a (αβ)₂ heterotetramer: the αβ heterodimer of ecphers consists of 11 structural domains. three of them: the n-terminus, a1 and a2 belong to the α-subunit and b1-b8 domains to the β subunit. the structure of ecphers revealed that architecture of four helix-bundle interface, characteristic of class i ...201121082706
idiosyncrasy and identity in the prokaryotic phe-system: crystal structure of e. coli phenylalanyl-trna synthetase complexed with phenylalanine and amp.the crystal structure of phenylalanyl-trna synthetase from e. coli (ecphers), a class ii aminoacyl-trna synthetase, complexed with phenylalanine and amp was determined at 3.05 å resolution. ecphers is a (αβ)₂ heterotetramer: the αβ heterodimer of ecphers consists of 11 structural domains. three of them: the n-terminus, a1 and a2 belong to the α-subunit and b1-b8 domains to the β subunit. the structure of ecphers revealed that architecture of four helix-bundle interface, characteristic of class i ...201121082706
structural insights into pre-translocation ribosome motions.subsequent to the peptidyl transfer step of the translation elongation cycle, the initially formed pre-translocation ribosome, which we refer to here as r(1), undergoes a ratchet-like intersubunit rotation in order to sample a rotated conformation, referred to here as r(f), that is an obligatory intermediate in the translocation of trnas and mrna through the ribosome during the translocation step of the translation elongation cycle. r(f) and the r(1) to r(f) transition are currently the subject ...201121121048
a combined global and local approach to elucidate spatial organization of the mycobacterial parb-pars partition assembly.combining diverse sets of data at global (size, shape) and local (residue) scales is an emerging trend for elucidating the organization and function of the cellular assemblies. we used such a strategy, combining data from x-ray and neutron scattering with h/d-contrast variation and x-ray footprinting with mass spectrometry, to elucidate the spatial organization of the parb-pars assembly from mycobacterium tuberculosis. the parb-pars participates in plasmid and chromosome segregation and condensa ...201121142182
structures of domains i and iv from ybbr are representative of a widely distributed protein family.ybbr domains are widespread throughout eubacteria and are expressed as monomeric units, linked in tandem repeats or cotranslated with other domains. although the precise role of these domains remains undefined, the location of the multiple ybbr domain-encoding ybbr gene in the bacillus subtilis glmm operon and its previous identification as a substrate for a surfactin-type phosphopantetheinyl transferase suggests a role in cell growth, division, and virulence. to further characterize the ybbr do ...201121154411
structures of domains i and iv from ybbr are representative of a widely distributed protein family.ybbr domains are widespread throughout eubacteria and are expressed as monomeric units, linked in tandem repeats or cotranslated with other domains. although the precise role of these domains remains undefined, the location of the multiple ybbr domain-encoding ybbr gene in the bacillus subtilis glmm operon and its previous identification as a substrate for a surfactin-type phosphopantetheinyl transferase suggests a role in cell growth, division, and virulence. to further characterize the ybbr do ...201121154411
proline dehydrogenase contributes to pathogen defense in arabidopsis.l-proline (pro) catabolism is activated in plants recovering from abiotic stresses associated with water deprivation. in this catabolic pathway, pro is converted to glutamate by two reactions catalyzed by proline dehydrogenase (prodh) and ?(1)-pyrroline-5-carboxylate dehydrogenase (p5cdh), with ?(1)-pyrroline-5-carboxylate (p5c) as the intermediate. alternatively, under certain conditions, the p5c derived from pro is converted back to pro by p5c reductase, thus stimulating the pro-p5c cycle, whi ...201121311034
energetics of seca dimerization.transport of many proteins to extracytoplasmic locations occurs via the general secretion (sec) pathway. in escherichia coli, this pathway is composed of the secyeg protein-conducting channel and the seca atpase. seca plays a central role in binding the signal peptide region of preproteins, directing preproteins to membrane-bound secyeg and promoting translocation coupled with atp hydrolysis. although it is well established that seca is crucial for preprotein transport and thus cell viability, i ...201121315086
natural competence in the hyperthermophilic archaeon pyrococcus furiosus facilitates genetic manipulation: construction of markerless deletions of genes encoding the two cytoplasmic hydrogenases.in attempts to develop a method of introducing dna into pyrococcus furiosus, we discovered a variant within the wild-type population that is naturally and efficiently competent for dna uptake. a pyrf gene deletion mutant was constructed in the genome, and the combined transformation and recombination frequencies of this strain allowed marker replacement by direct selection using linear dna. we have demonstrated the use of this strain, designated com1, for genetic manipulation. using genetic sele ...201121317259
il-10 expression by primary tumor cells correlates with melanoma progression from radial to vertical growth phase and development of metastatic competence.downregulation of the immune system facilitates tumor progression at different stages of cutaneous melanoma. sentinel nodes, the first lymph nodes on lymphatics draining directly from a primary melanoma, are immune downregulated by tumor-generated immunosuppressive cytokines, including interleukin-10 (il-10). to better understand the kinetics of sentinel node suppression, we investigated il-10 expression by melanoma cells and tumor-associated macrophages and lymphocytes at different stages of pr ...201121317876
unusual outer membrane lipid composition of the gram-negative, lipopolysaccharide-lacking myxobacterium sorangium cellulosum so ce56.the gram-negative myxobacterium sorangium cellulosum so ce56 bears the largest bacterial genome published so far, coding for nearly 10,000 genes. careful analysis of this genome data revealed that part of the genes coding for the very well conserved biosynthesis of lipopolysaccharides (lps) are missing in this microbe. biochemical analysis gave no evidence for the presence of lps in the membranes of so ce56. by analyzing the lipid composition of its outer membrane sphingolipids were identified a ...201121321121
activity of and development of resistance to corallopyronin a, an inhibitor of rna polymerase.we explored the properties of corallopyronin a (cora), a poorly characterized inhibitor of bacterial rna polymerase (rnap). it displayed a 50% inhibitory concentration of 0.73 µm against rnap, compared with 11.5 nm for rifampin. the antibacterial activity of cora was also inferior to rifampin, and resistant mutants of staphylococcus aureus were easily selected. the mutations conferring resistance resided in the rpob and rpoc subunits of rnap. we conclude that cora is not a promising antibacteria ...201121321139
bacterial toxin rele mediates frequent codon-independent mrna cleavage from the 5' end of coding regions in vivo.the enzymatic activity of the rele bacterial toxin component of the escherichia coli relbe toxin-antitoxin system has been extensively studied in vitro and to a lesser extent in vivo. these earlier reports revealed that 1) rele alone does not exhibit mrna cleavage activity, 2) rele mediates mrna cleavage through its association with the ribosome, 3) rele-mediated mrna cleavage occurs at the ribosomal a site and, 4) cleavage of mrna by rele exhibits high codon specificity. more specifically, rele ...201121324908
a highly conserved protein of unknown function in sinorhizobium meliloti affects srna regulation similar to hfq.the smc01113/ybey protein, belonging to the upf0054 family, is highly conserved in nearly every bacterium. however, the function of these proteins still remains elusive. our results show that smc01113/ybey proteins share structural similarities with the mid domain of the argonaute (ago) proteins, and might similarly bind to a small-rna (srna) seed, making a special interaction with the phosphate on the 5'-side of the seed, suggesting they may form a component of the bacterial srna pathway. indee ...201121325267
avoiding premature oxidation during the binding of cu(ii) to a dithiolate site in bssco. a rapid freeze-quench epr study.the bacillus subtilis version of sco1 (bssco) is required for assembly of cu(a) in cytochrome c oxidase and may function in thiol-disulfide exchange and/or copper delivery. bssco binds cu(ii) with ligation by two cysteines, one histidine and one water. however, copper is a catalyst of cysteine oxidation and bssco must avoid this reaction to remain functional. time resolved, rapid freeze-quench (rfq) electron paramagnetic resonance of apo-bssco reacting with cu(ii) reveals an initial cu(ii) speci ...201121333651
organic hydroperoxide resistance protein and ergothioneine compensate for loss of mycothiol in mycobacterium smegmatis mutants.the msha::tn5 mutant of mycobacterium smegmatis does not produce mycothiol (msh) and was found to markedly overproduce both ergothioneine and an ~15-kda protein determined to be organic hydroperoxide resistance protein (ohr). an msha(g32d) mutant lacking msh overproduced ergothioneine but not ohr. comparison of the mutant phenotypes with those of the wild-type strain indicated the following: ohr protects against organic hydroperoxide toxicity, whereas ergothioneine does not; an additional msh-de ...201121335456
chlorite dismutases, dyps, and efeb: 3 microbial heme enzyme families comprise the cde structural superfamily.heme proteins are extremely diverse, widespread, and versatile biocatalysts, sensors, and molecular transporters. the chlorite dismutase family of hemoproteins received its name due to the ability of the first-isolated members to detoxify anthropogenic clo(2)(-), a function believed to have evolved only in the last few decades. family members have since been found in 15 bacterial and archaeal genera, suggesting ancient roots. a structure- and sequence-based examination of the family is presented ...201121354424
activity map of the escherichia coli rna polymerase bridge helix.transcription, the synthesis of rna from a dna template, is performed by multisubunit rna polymerases (rnaps) in all cellular organisms. the bridge helix (bh) is a distinct feature of all multisubunit rnaps and makes direct interactions with several active site-associated mobile features implicated in the nucleotide addition cycle and rna and dna binding. because the bh has been captured in both kinked and straight conformations in different crystals structures of rnap, recently supported by mol ...201121357417
correct assembly of iron-sulfur cluster fs0 into escherichia coli dimethyl sulfoxide reductase (dmsabc) is a prerequisite for molybdenum cofactor insertion.the fs0 [4fe-4s] cluster of the catalytic subunit (dmsa) of escherichia coli dimethyl sulfoxide reductase (dmsabc) plays a key role in the electron transfer relay. we have now established an additional role for the cluster in directing molybdenum cofactor assembly during enzyme maturation. epr spectroscopy indicates that fs0 has a high spin ground state (s = 3/2) in its reduced form, resulting in an epr spectrum with a peak at g ~ 5.0. the cluster is predicted to be in close proximity to the mol ...201121357619
an expanded collection and refined consensus model of glms ribozymes.self-cleaving glms ribozymes selectively bind glucosamine-6-phosphate (glcn6p) and use this metabolite as a cofactor to promote self-cleavage by internal phosphoester transfer. representatives of the glms ribozyme class are found in gram-positive bacteria where they reside in the 5' untranslated regions (utrs) of glms messenger rnas that code for the essential enzyme l-glutamine:d-fructose-6-phosphate aminotransferase. by using comparative sequence analyses, we have expanded the number of glms r ...201121367971
insertion domain within mammalian mitochondrial translation initiation factor 2 serves the role of eubacterial initiation factor 1.mitochondria have their own translational machineries for the synthesis of thirteen polypeptide chains that are components of the complexes that participate in the process of oxidative phosphorylation (or atp generation). translation initiation in mammalian mitochondria requires two initiation factors, if2(mt) and if3(mt), instead of the three that are present in eubacteria. the mammalian if2(mt) possesses a unique 37 amino acid insertion domain, which is known to be important for the formation ...201121368145
two rotary motors in f-atp synthase are elastically coupled by a flexible rotor and a stiff stator stalk.atp is synthesized by atp synthase (f(o)f(1)-atpase). its rotary electromotor (f(o)) translocates protons (in some organisms sodium cations) and generates torque to drive the rotary chemical generator (f(1)). elastic power transmission between f(o) and f(1) is essential for smoothing the cooperation of these stepping motors, thereby increasing their kinetic efficiency. a particularly compliant elastic domain is located on the central rotor (c(10-15)/e/?), right between the two sites of torque ge ...201121368147
e1- and ubiquitin-like proteins provide a direct link between protein conjugation and sulfur transfer in archaea.based on our recent work with haloferax volcanii, ubiquitin-like (ubl) proteins (samp1 and samp2) are known to be covalently attached to proteins in archaea. here, we investigated the enzymes required for the formation of these ubl-protein conjugates (sampylation) and whether this system is linked to sulfur transfer. markerless in-frame deletions were generated in h. volcanii target genes. the mutants were examined for: (i) the formation of ubl protein conjugates, (ii) growth under various condi ...201121368171
oxidative stress resistance in deinococcus radiodurans.deinococcus radiodurans is a robust bacterium best known for its capacity to repair massive dna damage efficiently and accurately. it is extremely resistant to many dna-damaging agents, including ionizing radiation and uv radiation (100 to 295 nm), desiccation, and mitomycin c, which induce oxidative damage not only to dna but also to all cellular macromolecules via the production of reactive oxygen species. the extreme resilience of d. radiodurans to oxidative stress is imparted synergistically ...201121372322
partial functional replacement of cyma by sircd in shewanella oneidensis mr-1.the gammaproteobacterium shewanella oneidensis mr-1 utilizes a complex electron transfer network composed primarily of c-type cytochromes to respire under anoxic conditions a variety of compounds, including fumarate, nitrate, and dimethyl sulfoxide (dmso), in addition to the minerals fe(iii) and mn(iv). central to several respiratory pathways is cyma, a cytoplasmic membrane-bound tetraheme c-type cytochrome that functions as the major hydroquinone dehydrogenase. to investigate functional redunda ...201121378180
structural insights into cognate versus near-cognate discrimination during decoding.the structural basis of the trna selection process is investigated by cryo-electron microscopy of ribosomes programmed with uga codons and incubated with ternary complex (tc) containing the near-cognate trp-trna(trp) in the presence of kirromycin. going through more than 350 000 images and employing image classification procedures, we find ~8% in which the tc is bound to the ribosome. the reconstructed 3d map provides a means to characterize the arrangement of the near-cognate aa-trna with respe ...201121378755
architecture of the rna polymerase-spt4/5 complex and basis of universal transcription processivity.related rna polymerases (rnaps) carry out cellular gene transcription in all three kingdoms of life. the universal conservation of the transcription machinery extends to a single rnap-associated factor, spt5 (or nusg in bacteria), which renders rnap processive and may have arisen early to permit evolution of long genes. spt5 associates with spt4 to form the spt4/5 heterodimer. here, we present the crystal structure of archaeal spt4/5 bound to the rnap clamp domain, which forms one side of the rn ...201121386817
mutagenesis of the l, m, and n subunits of complex i from escherichia coli indicates a common role in function.the membrane arm of complex i (nadh:ubiquinone oxidoreductase) contains three large, and closely related subunits, which are called l, m, and n in e. coli. these subunits are homologous to components of multi-subunit na(+)/h(+) antiporters, and so are implicated in proton translocation.201121387012
susceptibility and mode of binding of the mycobacterium tuberculosis cysteinyl transferase mycothiol ligase to trna synthetase inhibitors.the cysteinyl transferase mycothiol ligase, or mshc, catalyzes the fourth step in the biosynthesis of the small molecular weight thiol mycothiol. mshc is essential for growth of mycobacterium tuberculosis. two groups of known aminoacyl trna synthetase inhibitors were evaluated for inhibition of m. tuberculosis mshc including aminoacyl adenosine analogs and natural products. using enzyme assays, isothermal titration calorimetry and nmr, we show that mshc is selectively inhibited by cysteinyl sulf ...201121392992
cloning, expression, purification, crystallization and preliminary x-ray diffraction analysis of the regulatory domain of aspartokinase (rv3709c) from mycobacterium tuberculosis.the regulatory domain of mycobacterium tuberculosis aspartokinase (mtb-ak, mtb-ask, rv3709c) has been cloned, heterologously expressed in escherichia coli and purified using standard chromatographic techniques. screening for initial crystallization conditions using the regulatory domain (ak-+¦) in the presence of the potential feedback inhibitor threonine identified four conditions which yielded crystals suitable for x-ray diffraction analysis. from these four conditions five different crystal f ...201121393848
crystallization and preliminary x-ray analysis of mannosyl-3-phosphoglycerate phosphatase from thermus thermophilus hb27.mannosylglycerate (mg) is primarily known as an osmolyte and is widely distributed among (hyper)thermophilic marine microorganisms. the synthesis of mg via mannosyl-3-phosphoglycerate synthase (mpgs) and mannosyl-3-phosphoglycerate phosphatase (mpgp), the so-called two-step pathway, is the most prevalent route among these organisms. the phosphorylated intermediate mannosyl-3-phosphoglycerate is synthesized by the first enzyme and is subsequently dephosphorylated by the second. the structure of m ...201121393850
purification and biochemical properties of a cytochrome bc complex from the aerobic hyperthermophilic archaeon aeropyrum pernix.the bioenergetics of archaea with respect to the evolution of electron transfer systems is very interesting. in contrast to terminal oxidases, a canonical bc1 complex has not yet been isolated from archaea. in particular, c-type cytochromes have been reported only for a limited number of species.201121396131
the antibacterial threaded-lasso peptide capistruin inhibits bacterial rna polymerase.capistruin, a ribosomally synthesized, post-translationally modified peptide produced by burkholderia thailandensis e264, efficiently inhibits growth of burkholderia and closely related pseudomonas strains. the functional target of capistruin is not known. capistruin is a threaded-lasso peptide (lariat peptide) consisting of an n-terminal ring of nine amino acids and a c-terminal tail of 10 amino acids threaded through the ring. the structure of capistruin is similar to that of microcin j25 (mcc ...201121396375
biosynthesis of the rna polymerase inhibitor streptolydigin in streptomyces lydicus: tailoring modification of 3-methyl-aspartate.the asparaginyl-trna synthetase-like slgz and methyltransferase slgm enzymes are involved in the biosynthesis of the tetramic acid streptolydigin in streptomyces lydicus. inactivation of slgz led to a novel streptolydigin derivative. overexpression of slgz, slgm, or both in s. lydicus led to a considerable increase in streptolydigin production.201121398531
resolving stepping rotation in thermus thermophilus h(+)-atpase/synthase with an essentially drag-free probe.vacuole-type atpases (v(o)v1) and f(o)f1 atp synthases couple atp hydrolysis/synthesis in the soluble v(1) or f1 portion with proton (or na(+)) flow in the membrane-embedded v(o) or f(o) portion through rotation of one common shaft. here we show at submillisecond resolutions the atp-driven rotation of isolated v1 and the whole v(o)v1 from thermus thermophilus, by attaching a 40-nm gold bead for which viscous drag is almost negligible. v1 made 120° steps, commensurate with the presence of three c ...201121407199
genetic components of stringent response in vibrio cholerae.nutritional stress elicits stringent response in bacteria involving modulation of expression of several genes. this is mainly triggered by the intracellular accumulation of two small molecules, namely, guanosine 3'-diphosphate 5'-triphosphate and guanosine 3',5'-bis(diphosphate), collectively called (p)ppgpp. like in other gram-negative bacteria, the cellular level of (p)ppgpp is maintained in vibrio cholerae, the causative bacterial pathogen of the disease cholera, by the products of two genes ...201121415497
involvement of cara/litr and crp/fnr family transcriptional regulators in light-induced carotenoid production in thermus thermophilus.members of the cara/litr family are merr-type transcriptional regulators that contain a c-terminal cobalamin-binding domain. they are thought to be involved in light-induced transcriptional regulation in a wide variety of nonphototrophic bacteria. based on the distribution of this kind of regulator, the current study examined carotenoid production in thermus thermophilus, and it was found to occur in a light-induced manner. litr and carotenoid and cobalamin biosynthesis genes were all located on ...201121421762
substrate specificity of the bacillus licheniformis lyxose isomerase ydae and its application in in vitro catalysis for bioproduction of lyxose and glucose by two-step isomerization.enzymatic processes are useful for industrially important sugar production, and in vitro two-step isomerization has proven to be an efficient process in utilizing readily available sugar sources. a hypothetical uncharacterized protein encoded by ydae of bacillus licheniformis was found to have broad substrate specificities and has shown high catalytic efficiency on d-lyxose, suggesting that the enzyme is d-lyxose isomerase. escherichia coli bl21 expressing the recombinant protein, of 19.5 kda, s ...201121421786
insights into physiological and genetic mupirocin susceptibility in bifidobacteria.mupirocin is an antibiotic commonly used in selective media for the isolation of bifidobacteria. however, little is known about the genetic traits responsible for bifidobacterial resistance to mupirocin. our investigation demonstrates that all of the bifidobacteria tested exhibit a phenotype of generally high resistance to this antibiotic. the genotypic reason for bifidobacterial mupirocin resistance was further characterized by sequencing of the isoleucyl-trna synthetase gene (iles) coupled wit ...201121421794
a rigidifying salt-bridge favors the activity of thermophilic enzyme at high temperatures at the expense of low-temperature activity.thermophilic enzymes are often less active than their mesophilic homologues at low temperatures. one hypothesis to explain this observation is that the extra stabilizing interactions increase the rigidity of thermophilic enzymes and hence reduce their activity. here we employed a thermophilic acylphosphatase from pyrococcus horikoshii and its homologous mesophilic acylphosphatase from human as a model to study how local rigidity of an active-site residue affects the enzymatic activity.201121423654
phylogenetic distribution and evolutionary history of bacterial dead-box proteins.dead-box proteins are found in all domains of life and participate in almost all cellular processes that involve rna. the presence of dead and helicase_c conserved domains distinguish these proteins. dead-box proteins exhibit rna-dependent atpase activity in vitro, and several also show rna helicase activity. in this study, we analyzed the distribution and architecture of dead-box proteins among bacterial genomes to gain insight into the evolutionary pathways that have shaped their history. we i ...201121437710
nmr structure of the c-terminal domain of a tyrosyl-trna synthetase that functions in group i intron splicing.the mitochondrial tyrosyl-trna synthetases (mt tyrrss) of pezizomycotina fungi are bifunctional proteins that aminoacylate mitochondrial trna(tyr) and are structure-stabilizing splicing cofactors for group i introns. studies with the neurospora crassa synthetase (cyt-18 protein) showed that splicing activity is dependent upon pezizomycotina-specific structural adaptations that form a distinct group i intron-binding site in the n-terminal catalytic domain. although cyt-18's c-terminal domain also ...201121438536
unexpected diversity of chlorite dismutases: a catalytically efficient dimeric enzyme from nitrobacter winogradskyi.chlorite dismutase (cld) is a unique heme enzyme catalyzing the conversion of clo(2)(-) to cl(-) and o(2). cld is usually found in perchlorate- or chlorate-reducing bacteria but was also recently identified in a nitrite-oxidizing bacterium of the genus nitrospira. here we characterized a novel cld-like protein from the chemolithoautotrophic nitrite oxidizer nitrobacter winogradskyi which is significantly smaller than all previously known chlorite dismutases. its three-dimensional (3d) crystal st ...201121441524
solution structure of an alternate conformation of helix27 from escherichia coli16s rrna.helix (h)27 of 16s ribosomal (r)rna from escherichia coli was dubbed the "switch helix" when mutagenesis suggested that two alternative base pair registers may have distinct functional roles in the bacterial ribosome. although more recent genetic analyses suggest that h27 conformational switching is not required for translation, previous solution studies demonstrated that the isolated e. coli h27 can dynamically convert between the 885 and 888 conformations. here, we have solved the nuclear magn ...201121442607
Refresh
firstprev
...21222324252627282930...
nextlast
Displaying items 2001 - 2100 of 5451