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a proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of escherichia coli ribosomal protein s12.β-methylthiolation is a novel post-translational modification mapping to a universally conserved asp 88 of the bacterial ribosomal protein s12. this s12 specific modification has been identified on orthologs from multiple bacterial species. the origin and functional significance was investigated with both a proteomic strategy to identify candidate s12 interactors and expression microarrays to search for phenotypes that result from targeted gene knockouts of select candidates. utilizing an endoge ...201021169565
a proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of escherichia coli ribosomal protein s12.β-methylthiolation is a novel post-translational modification mapping to a universally conserved asp 88 of the bacterial ribosomal protein s12. this s12 specific modification has been identified on orthologs from multiple bacterial species. the origin and functional significance was investigated with both a proteomic strategy to identify candidate s12 interactors and expression microarrays to search for phenotypes that result from targeted gene knockouts of select candidates. utilizing an endoge ...201021169565
crystal structure of stable protein cuta1 from psychrotrophic bacterium shewanella sp. sib1.cuta1 is widely found in bacteria, plants and animals, including humans. the functions of cuta1, however, have not been well clarified. it is known that cuta1s from pyrococcus horikoshii, thermus thermophilus and oryza sativa unfold at temperatures remarkably higher than the growth temperatures of the host organisms. in this work the crystal structure of cuta1 from the psychrotrophic bacterium shewanella sp. sib1 (sib1-cuta1) in a trimeric form was determined at 2.7 å resolution. this is the fir ...201021169681
bidentate rna-magnesium clamps: on the origin of the special role of magnesium in rna folding.magnesium plays a special role in rna function and folding. although water is magnesium's most common first-shell ligand, the oxyanions of rna have significant affinity for magnesium. here we provide a quantum mechanical description of first-shell rna-magnesium and dna-magnesium interactions, demonstrating the unique features that characterize the energetics and geometry of magnesium complexes within large folded rnas. our work focuses on bidentate chelation of magnesium by rna or dna, where mul ...201121173199
the structural and biochemical characterization of human rnase h2 complex reveals the molecular basis for substrate recognition and aicardi-goutières syndrome defects.rnase h2 cleaves rna sequences that are part of rna/dna hybrids or that are incorporated into dna, thus, preventing genomic instability and the accumulation of aberrant nucleic acid, which in humans induces aicardi-goutières syndrome, a severe autoimmune disorder. the 3.1 å crystal structure of human rnase h2 presented here allowed us to map the positions of all 29 mutations found in aicardi-goutières syndrome patients, several of which were not visible in the previously reported mouse rnase h2. ...201021177858
the structural and biochemical characterization of human rnase h2 complex reveals the molecular basis for substrate recognition and aicardi-goutières syndrome defects.rnase h2 cleaves rna sequences that are part of rna/dna hybrids or that are incorporated into dna, thus, preventing genomic instability and the accumulation of aberrant nucleic acid, which in humans induces aicardi-goutières syndrome, a severe autoimmune disorder. the 3.1 å crystal structure of human rnase h2 presented here allowed us to map the positions of all 29 mutations found in aicardi-goutières syndrome patients, several of which were not visible in the previously reported mouse rnase h2. ...201021177858
form, function, and regulation of argonaute proteins.both transcriptional (tgs) and posttranscriptional gene silencing (ptgs) are conserved eukaryotic gene regulatory mechanisms, integral for taming exogenous (viruses and bacteria) or endogenous (repetitive elements and transposons) invasive nucleic acids to minimize their impact on genome integrity and function. tgs and ptgs also are essential for controlling the expression of protein coding genes throughout development or in response to environmental stimuli. in plants and animals, at least one ...201021183704
valproate uncompetitively inhibits arachidonic acid acylation by rat acyl-coa synthetase 4: relevance to valproate's efficacy against bipolar disorder.the ability of chronic valproate (vpa) to reduce arachidonic acid (aa) turnover in brain phospholipids of unanesthetized rats has been ascribed to its inhibition of acyl-coa synthetase (acsl)-mediated activation of aa to aa-coa. our aim was to identify a rat acsl isoenzyme that could be inhibited by vpa in vitro.201021184843
valproate uncompetitively inhibits arachidonic acid acylation by rat acyl-coa synthetase 4: relevance to valproate's efficacy against bipolar disorder.the ability of chronic valproate (vpa) to reduce arachidonic acid (aa) turnover in brain phospholipids of unanesthetized rats has been ascribed to its inhibition of acyl-coa synthetase (acsl)-mediated activation of aa to aa-coa. our aim was to identify a rat acsl isoenzyme that could be inhibited by vpa in vitro.201021184843
structural and functional studies of fatty acyl adenylate ligases from e. coli and l. pneumophila.fatty acyl-amp ligase (faal) is a new member of a family of adenylate-forming enzymes that were recently discovered in mycobacterium tuberculosis. they are similar in sequence to fatty acyl-coenzyme a (coa) ligases (facls). however, while facls perform a two-step catalytic reaction, amp ligation followed by coa ligation using atp and coa as cofactors, faals produce only the acyl adenylate and are unable to perform the second step. we report x-ray crystal structures of full-length faal from esche ...201021185305
structural and functional studies of fatty acyl adenylate ligases from e. coli and l. pneumophila.fatty acyl-amp ligase (faal) is a new member of a family of adenylate-forming enzymes that were recently discovered in mycobacterium tuberculosis. they are similar in sequence to fatty acyl-coenzyme a (coa) ligases (facls). however, while facls perform a two-step catalytic reaction, amp ligation followed by coa ligation using atp and coa as cofactors, faals produce only the acyl adenylate and are unable to perform the second step. we report x-ray crystal structures of full-length faal from esche ...201021185305
rna polymerase and transcription elongation factor spt4/5 complex structure.spt4/5 in archaea and eukaryote and its bacterial homolog nusg is the only elongation factor conserved in all three domains of life and plays many key roles in cotranscriptional regulation and in recruiting other factors to the elongating rna polymerase. here, we present the crystal structure of spt4/5 as well as the structure of rna polymerase-spt4/5 complex using cryoelectron microscopy reconstruction and single particle analysis. the spt4/5 binds in the middle of rna polymerase claw and enclo ...201021187417
rna polymerase and transcription elongation factor spt4/5 complex structure.spt4/5 in archaea and eukaryote and its bacterial homolog nusg is the only elongation factor conserved in all three domains of life and plays many key roles in cotranscriptional regulation and in recruiting other factors to the elongating rna polymerase. here, we present the crystal structure of spt4/5 as well as the structure of rna polymerase-spt4/5 complex using cryoelectron microscopy reconstruction and single particle analysis. the spt4/5 binds in the middle of rna polymerase claw and enclo ...201021187417
asymmetric atp hydrolysis cycle of the heterodimeric multidrug abc transport complex tmrab from thermus thermophilus.atp-binding cassette (abc) systems translocate a wide range of solutes across cellular membranes. the thermophilic gram-negative eubacterium thermus thermophilus, a model organism for structural genomics and systems biology, discloses ∼46 abc proteins, which are largely uncharacterized. here, we functionally analyzed the first two and only abc half-transporters of the hyperthermophilic bacterium, tmra and tmrb. the abc system mediates uptake of the drug hoechst 33342 in inside-out oriented vesic ...201021190941
structural basis for pirna 2'-o-methylated 3'-end recognition by piwi paz (piwi/argonaute/zwille) domains.argonaute and piwi proteins are key players in the rna silencing pathway, with the former interacting with micro-rnas (mirnas) and sirnas, whereas the latter targets piwi-interacting rnas (pirnas) that are 2'-o-methylated (2(')-och(3)) at their 3' ends. germline-specific pirnas and piwi proteins play a critical role in genome defense against transposable elements, thereby protecting the genome against transposon-induced defects in gametogenesis and fertility. humans contain four piwi family prot ...201021193640
structural basis for pirna 2'-o-methylated 3'-end recognition by piwi paz (piwi/argonaute/zwille) domains.argonaute and piwi proteins are key players in the rna silencing pathway, with the former interacting with micro-rnas (mirnas) and sirnas, whereas the latter targets piwi-interacting rnas (pirnas) that are 2'-o-methylated (2(')-och(3)) at their 3' ends. germline-specific pirnas and piwi proteins play a critical role in genome defense against transposable elements, thereby protecting the genome against transposon-induced defects in gametogenesis and fertility. humans contain four piwi family prot ...201021193640
genetic evidence for a novel interaction between transcriptional activator soxs and region 4 of the σ(70) subunit of rna polymerase at class ii soxs-dependent promoters in escherichia coli.escherichia coli soxs activates transcription of the genes of the soxrs regulon, which provide the cell's defense against oxidative stress. in response to this stress, soxs is synthesized de novo. because the dna binding site of soxs is highly degenerate, soxs efficiently activates transcription by the mechanism of prerecruitment. in prerecruitment, newly synthesized soxs first forms binary complexes with rna polymerase. these complexes then scan the chromosome for class i and ii soxs-dependent ...201021195716
genetic evidence for a novel interaction between transcriptional activator soxs and region 4 of the σ(70) subunit of rna polymerase at class ii soxs-dependent promoters in escherichia coli.escherichia coli soxs activates transcription of the genes of the soxrs regulon, which provide the cell's defense against oxidative stress. in response to this stress, soxs is synthesized de novo. because the dna binding site of soxs is highly degenerate, soxs efficiently activates transcription by the mechanism of prerecruitment. in prerecruitment, newly synthesized soxs first forms binary complexes with rna polymerase. these complexes then scan the chromosome for class i and ii soxs-dependent ...201021195716
quantitative mapping of reversible mitochondrial complex i cysteine oxidation in a parkinson disease mouse model.differential cysteine oxidation within mitochondrial complex i has been quantified in an in vivo oxidative stress model of parkinson disease. we developed a strategy that incorporates rapid and efficient immunoaffinity purification of complex i followed by differential alkylation and quantitative detection using sensitive mass spectrometry techniques. this method allowed us to quantify the reversible cysteine oxidation status of 34 distinct cysteine residues out of a total 130 present in murine ...201121196577
bis{μ-2,2'-[1,1'-(ethane-1,2-diyldinitrilo)diethyl-idyne]diphenolato}bis-[(benzoato-κo)manganese(iii)] dihydrate.the title compound, [mn(2)(c(18)h(18)n(2)o(2))(2)(c(7)h(5)o(2))(2)]·2h(2)o, was synthesized by the reaction between manganese(ii) benzoate and the schiff base generated in situ by the condensation of ethane-1,2-diamine and o-hydroxy-aceto-phen-one. the jahn-teller-distorted manganese(iii) ions of the centrosymmetric dimer are connected through phen-oxy bridges. hydrogen-bonding inter-actions between the uncoord-in-ated c=o of the benzoate and uncoordinated water mol-ecules link the dimers into a ...200721200504
bis{μ-2,2'-[1,1'-(ethane-1,2-diyldinitrilo)diethyl-idyne]diphenolato}bis-[(benzoato-κo)manganese(iii)] dihydrate.the title compound, [mn(2)(c(18)h(18)n(2)o(2))(2)(c(7)h(5)o(2))(2)]·2h(2)o, was synthesized by the reaction between manganese(ii) benzoate and the schiff base generated in situ by the condensation of ethane-1,2-diamine and o-hydroxy-aceto-phen-one. the jahn-teller-distorted manganese(iii) ions of the centrosymmetric dimer are connected through phen-oxy bridges. hydrogen-bonding inter-actions between the uncoord-in-ated c=o of the benzoate and uncoordinated water mol-ecules link the dimers into a ...200721200504
stress-induced evolution of escherichia coli points to original concepts in respiratory cofactor selectivity.bacterial metabolism is characterized by a remarkable capacity to rapidly adapt to environmental changes. we restructured the central metabolic network in escherichia coli to force a higher production of nadph, and then grew this strain in conditions favoring adaptive evolution. a six-fold increase in growth capacity was attained that could be attributed in multiple clones, after whole genome mutation mapping, to a specific single mutation. each clone had an evolved nuof*(e183a) enzyme in the re ...201121205901
crystal structures, dynamics and functional implications of molybdenum-cofactor biosynthesis protein moga from two thermophilic organisms.molybdenum-cofactor (moco) biosynthesis is an evolutionarily conserved pathway in almost all kingdoms of life, including humans. two proteins, moga and moea, catalyze the last step of this pathway in bacteria, whereas a single two-domain protein carries out catalysis in eukaryotes. here, three crystal structures of the moco-biosynthesis protein moga from the two thermophilic organisms thermus thermophilus (ttmoga; 1.64 å resolution, space group p2(1)) and aquifex aeolicus (aamoga; 1.70 å resolut ...201021206014
crystallization and preliminary x-ray crystallographic analysis of human quinolinate phosphoribosyltransferase.quinolinate phosphoribosyltransferase (qprtase) is a key nad-biosynthetic enzyme which catalyzes the transfer of quinolinic acid to 5-phosphoribosyl-1-pyrophosphate, yielding nicotinic acid mononucleotide. homo sapiens qprtase (hs-qprtase) appeared as a hexamer during purification and the protein was crystallized. diffraction data were collected and processed at 2.8 å resolution. native hs-qprtase crystals belonged to space group p2(1), with unit-cell parameters a=76.2, b=137.1, c=92.7 å, β=103. ...201021206019
crystallization and preliminary x-ray crystallographic analysis of human quinolinate phosphoribosyltransferase.quinolinate phosphoribosyltransferase (qprtase) is a key nad-biosynthetic enzyme which catalyzes the transfer of quinolinic acid to 5-phosphoribosyl-1-pyrophosphate, yielding nicotinic acid mononucleotide. homo sapiens qprtase (hs-qprtase) appeared as a hexamer during purification and the protein was crystallized. diffraction data were collected and processed at 2.8 å resolution. native hs-qprtase crystals belonged to space group p2(1), with unit-cell parameters a=76.2, b=137.1, c=92.7 å, β=103. ...201021206019
cloning, expression, crystallization and preliminary x-ray crystallographic analysis of the co-chaperonin xogroes from xanthomonas oryzae pv. oryzae.bacterial blight (bb), a devastating disease caused by xanthomonas oryzae pv. oryzae (xoo), causes serious production losses of rice in asian countries. protein misfolding may interfere with the function of proteins in all living cells and must be prevented to avoid cellular disaster. all cells naturally contain molecular chaperones that assist the unfolded proteins in folding into the native structure. one of the well characterized chaperone complexes is groel-groes. groel, which consists of tw ...201021206021
cloning, expression, crystallization and preliminary x-ray crystallographic analysis of the co-chaperonin xogroes from xanthomonas oryzae pv. oryzae.bacterial blight (bb), a devastating disease caused by xanthomonas oryzae pv. oryzae (xoo), causes serious production losses of rice in asian countries. protein misfolding may interfere with the function of proteins in all living cells and must be prevented to avoid cellular disaster. all cells naturally contain molecular chaperones that assist the unfolded proteins in folding into the native structure. one of the well characterized chaperone complexes is groel-groes. groel, which consists of tw ...201021206021
crystallization and preliminary x-ray analysis of isopentenyl diphosphate isomerase from methanocaldococcus jannaschii.type 2 isopentenyl diphosphate isomerase (idi-2) is a flavoprotein. recently, flavin has been proposed to play a role as a general acid-base catalyst with no redox role during the enzyme reaction. to clarify the detailed enzyme reaction mechanism of idi-2 and the unusual role of flavin, structural analysis of idi-2 from methanocaldococcus jannaschii (mjidi) was performed. recombinant mjidi was crystallized at 293 k using calcium acetate as a precipitant. the diffraction of the crystal extended t ...201021206036
crystallization and preliminary x-ray analysis of isopentenyl diphosphate isomerase from methanocaldococcus jannaschii.type 2 isopentenyl diphosphate isomerase (idi-2) is a flavoprotein. recently, flavin has been proposed to play a role as a general acid-base catalyst with no redox role during the enzyme reaction. to clarify the detailed enzyme reaction mechanism of idi-2 and the unusual role of flavin, structural analysis of idi-2 from methanocaldococcus jannaschii (mjidi) was performed. recombinant mjidi was crystallized at 293 k using calcium acetate as a precipitant. the diffraction of the crystal extended t ...201021206036
archaeal 3'-phosphate rna splicing ligase characterization identifies the missing component in trna maturation.intron removal from trna precursors involves cleavage by a trna splicing endonuclease to yield trna 3'-halves beginning with a 5'-hydroxyl, and 5'-halves ending in a 2',3'-cyclic phosphate. a trna ligase then incorporates this phosphate into the internucleotide bond that joins the two halves. although this 3'-p rna splicing ligase activity was detected almost three decades ago in extracts from animal and later archaeal cells, the protein responsible was not yet identified. here we report the pur ...201121209330
properties of the nucleic-acid bases in free and watson-crick hydrogen-bonded states: computational insights into the sequence-dependent features of double-helical dna.the nucleic-acid bases carry structural and energetic signatures that contribute to the unique features of genetic sequences. here we review the connection between the chemical structure of the constituent nucleotides and the polymeric properties of dna. the sequence-dependent accumulation of charge on the major- and minor-groove edges of the watson-crick base pairs, obtained from ab initio calculations, presents unique motifs for direct sequence recognition. the optimization of base interaction ...200921218180
fidelity escape by the unnatural amino acid β-hydroxynorvaline: an efficient substrate for escherichia coli threonyl-trna synthetase with toxic effects on growth.in all living systems, the fidelity of translation is maintained in part by the editing mechanisms of aminoacyl-trna synthetases (arss). some nonproteogenic amino acids, including β-hydroxynorvaline (hnv) are nevertheless efficiently aminoacylated and become incorporated into proteins. to investigate the basis of hnv's ability to function in protein synthesis, the utilization of hnv by escherichia coli threonyl-trna synthetase (thrrs) was investigated through both in vitro functional experiments ...201121222438
rtcb is the rna ligase component of an escherichia coli rna repair operon.rna 2',3'-cyclic phosphate ends play important roles in rna metabolism as substrates for rna ligases during trna restriction-repair and trna splicing. diverse bacteria from multiple phyla encode a two-component rna repair cassette, comprising pnkp (polynucleotide kinase-phosphatase-ligase) and hen1 (rna 3'-terminal ribose 2'-o-methyltransferase), that heals and then seals broken trnas with 2',3'-cyclic phosphate and 5'-oh ends. the pnkp-hen1 repair operon is absent in the majority of bacterial s ...201121224389
exploration of the cytochrome c oxidase pathway puzzle and examination of the origin of elusive mutational effects.gaining detailed understanding of the energetics of the proton-pumping process in cytochrome c oxidase (cco) is a problem of great current interest. despite promising mechanistic proposals, so far, a physically consistent model that would reproduce all the relevant barriers needed to create a working pump has not been presented. in addition, there are major problems in elucidating the origin of key mutational effects and in understanding the nature of the apparent pk(a) values associated with th ...201121232525
the biomolecular interaction network database in psi-mi 2.5.the biomolecular interaction network database (bind) is a major source of curated biomolecular interactions, which has been unmaintained for the last few years, a trend which will eventually result in the loss of a significant amount of unique biomolecular interaction information, mostly as database identifiers become out of date. to help reverse this trend, we converted bind to a standard format, proteomics standard initiative-molecular interaction 2.5, starting from the last curated data relea ...201121233089
biochemical and structural characterization of wlba from bordetella pertussis and chromobacterium violaceum: enzymes required for the biosynthesis of 2,3-diacetamido-2,3-dideoxy-d-mannuronic acid.the unusual sugar 2,3-diacetamido-2,3-dideoxy-d-mannuronic acid, or mannac3naca, has been observed in the lipopolysaccharides of both pathogenic and nonpathogenic gram-negative bacteria. it is added to the lipopolysaccharides of these organisms by glycosyltransferases that use as substrates udp-mannac3naca. five enzymes are ultimately required for the biosynthesis of udp-mannac3naca starting from udp-n-acetylglucosamine. the second enzyme in the pathway, encoded by the wlba gene and referred to ...201121241053
crystal structures of complexes containing domains from two viral internal ribosome entry site (ires) rnas bound to the 70s ribosome.internal ribosome entry site (ires) rnas are elements of viral or cellular mrnas that bypass steps of canonical eukaryotic cap-dependent translation initiation. understanding of the structural basis of ires mechanisms is limited, partially due to a lack of high-resolution structures of ires rnas bound to their cellular targets. prompted by the universal phylogenetic conservation of the ribosomal p site, we solved the crystal structures of proposed p site binding domains from two intergenic regio ...201121245352
crystal structure of a bacterial phosphoglucomutase, an enzyme involved in the virulence of multiple human pathogens.the crystal structure of the enzyme phosphoglucomutase from salmonella typhimurium (stpgm) is reported at 1.7 a resolution. this is the first high-resolution structural characterization of a bacterial protein from this large enzyme family, which has a central role in metabolism and is also important to bacterial virulence and infectivity. a comparison of the active site of stpgm with that of other phosphoglucomutases reveals conserved residues that are likely involved in catalysis and ligand bin ...201121246636
escherichia coli class ib ribonucleotide reductase contains a dimanganese(iii)-tyrosyl radical cofactor in vivo.escherichia coli class ib ribonucleotide reductase (rnr) converts nucleoside 5'-diphosphates to deoxynucleoside 5'-diphosphates in iron-limited and oxidative stress conditions. we have recently demonstrated in vitro that this rnr is active with both diferric-tyrosyl radical (fe(iii)(2)-y(•)) and dimanganese(iii)-y(•) (mn(iii)(2)-y(•)) cofactors in the β2 subunit, nrdf [cotruvo, j. a., jr., and stubbe, j. (2010) biochemistry 49, 1297-1309]. here we demonstrate, by purification of this protein fro ...201121250660
trna/mrna mimicry by tmrna and smpb in trans-translation.since accurate translation from mrna to protein is critical to survival, cells have developed translational quality control systems. bacterial ribosomes stalled on truncated mrna are rescued by a system involving tmrna and smpb referred to as trans-translation. here, we review current understanding of the mechanism of trans-translation. based on results obtained by using directed hydroxyl radical probing, we propose a new type of molecular mimicry during trans-translation. besides such chemical ...201121253384
superfolder gfp is fluorescent in oxidizing environments when targeted via the sec translocon.the ability to study proteins in live cells using genetically encoded fluorescent proteins (fps) has revolutionized cell biology (1-3). researchers have created numerous fp biosensors and optimized fps for specific organisms and subcellular environments in a rainbow of colors (4,5). however, expressing fps in oxidizing environments such as the eukaryotic endoplasmic reticulum (er) or the bacterial periplasm can impair folding, thereby preventing fluorescence (6,7). a substantial fraction of enha ...201121255213
modeling rna polymerase competition: the effect of σ-subunit knockout and heat shock on gene transcription level.modeling of a complex biological process can explain the results of experimental studies and help predict its characteristics. among such processes is transcription in the presence of competing rna polymerases. this process involves rna polymerases collision followed by transcription termination.201121255416
identification of macrodomain proteins as novel o-acetyl-adp-ribose deacetylases.sirtuins are a family of protein lysine deacetylases, which regulate gene silencing, metabolism, life span, and chromatin structure. sirtuins utilize nad(+) to deacetylate proteins, yielding o-acetyl-adp-ribose (oaadpr) as a reaction product. the macrodomain is a ubiquitous protein module known to bind adp-ribose derivatives, which diverged through evolution to support many different protein functions and pathways. the observation that some sirtuins and macrodomains are physically linked as fusi ...201121257746
manipulations in the peripheral stalk of the saccharomyces cerevisiae f1f0-atp synthase.the saccharomyces cerevisiae f(1)f(0)-atp synthase peripheral stalk is composed of the oscp, h, d, and b subunits. the b subunit has two membrane-spanning domains and a large hydrophilic domain that extends along one side of the enzyme to the top of f(1). in contrast, the escherichia coli peripheral stalk has two identical b subunits, and subunits with substantially altered lengths can be incorporated into a functional f(1)f(0)-atp synthase. the differences in subunit structure between the eukar ...201121257750
identification of critical residues of the mycobacterial dephosphocoenzyme a kinase by site-directed mutagenesis.dephosphocoenzyme a kinase performs the transfer of the ?-phosphate of atp to dephosphocoenzyme a, catalyzing the last step of coenzyme a biosynthesis. this enzyme belongs to the p-loop-containing ntp hydrolase superfamily, all members of which posses a three domain topology consisting of a coa domain that binds the acceptor substrate, the nucleotide binding domain and the lid domain. differences in the enzymatic organization and regulation between the human and mycobacterial counterparts, have ...201121264299
bacillus pumilus laccase: a heat stable enzyme with a wide substrate spectrum.laccases are multi-copper oxidases that catalyze the one electron oxidation of a broad range of compounds. laccase substrates include substituted phenols, arylamines and aromatic thiols. such compounds are activated by the enzyme to the corresponding radicals. owing to their broad substrate range laccases are considered to be versatile biocatalysts which are capable of oxidizing natural and non-natural industrial compounds, with water as sole by-product.201121266052
poly-alpha-glutamic acid synthesis using a novel catalytic activity of rimk from escherichia coli k-12.poly-l-a-amino acids have various applications because of their biodegradable properties and biocompatibility. microorganisms contain several enzymes that catalyze the polymerization of l-amino acids in an atp-dependent manner, but the products from these reactions contain amide linkages at the side residues of amino acids: e.g., poly-?-glutamic acid, poly-e-lysine, and cyanophycin. in this study, we found a novel catalytic activity of rimk, a ribosomal protein s6-modifying enzyme derived from e ...201121278279
selective inhibitors of methionyl-trna synthetase have potent activity against trypanosoma brucei infection in mice.human african trypanosomiasis continues to be an important public health threat in extensive regions of sub-saharan africa. treatment options for infected patients are unsatisfactory due to toxicity, difficult administration regimes, and poor efficacy of available drugs. the aminoacyl-trna synthetases were selected as attractive drug targets due to their essential roles in protein synthesis and cell survival. comparative sequence analysis disclosed differences between the trypanosome and mammali ...201121282428
crystal structure of the synergistic antibiotic pair, lankamycin and lankacidin, in complex with the large ribosomal subunit.the structures of the large ribosomal subunit of deinococcus radiodurans (d50s) in complex with the antibiotic lankamycin (3.2 å) and a double antibiotic complex of lankamycin and lankacidin c (3.45 å) have been determined, in continuation of previous crystallographic studies on lankacidin-d50s complex. these two drugs have been previously reported to inhibit ribosomal function with mild synergistic effect. lankamycin, a member of the macrolide family, binds in a similar manner to erythromycin. ...201121282615
structure and function of pilq, a secretin of the dna transporter from the thermophilic bacterium thermus thermophilus hb27.secretins are a family of large bacterial outer membrane protein complexes mediating the transport of complex structures, such as type iv pili, dna and filamentous phage, or various proteins, such as extracellular enzymes and pathogenicity determinants. pilq of the thermophilic bacterium thermus thermophilus hb27 is a member of the secretin family required for natural transformation. here we report the isolation, structural, and functional analyses of a unique pilq from t. thermophilus. native p ...201121285351
two novel classes of enzymes are required for the biosynthesis of aurofusarin in fusarium graminearum.previous studies have reported the functional characterization of 9 out of 11 genes found in the gene cluster responsible for biosynthesis of the polyketide pigment aurofusarin in fusarium graminearum. here we reanalyze the function of a putative aurofusarin pump (aurt) and the two remaining orphan genes, aurz and aurs. targeted gene replacement of aurz resulted in the discovery that the compound ywa1, rather than nor-rubrofusarin, is the primary product of f. graminearum polyketide synthase 12 ...201121296881
molecular breeding of polymerases for resistance to environmental inhibitors.potent inhibitors limit the use of pcr assays in a wide spectrum of specimens. here, we describe the engineering of polymerases with a broad resistance to complex environmental inhibitors using molecular breeding of eight different polymerase orthologues from the genus thermus and directed evolution by csr in the presence of inhibitors. selecting for resistance to the inhibitory effects of neomylodon bone powder, we isolated 2d9, a chimeric polymerase comprising sequence elements derived from dn ...201121297114
dead-box proteins as rna helicases and chaperones.dead-box proteins are ubiquitous in rna-mediated processes and function by coupling cycles of atp binding and hydrolysis to changes in affinity for single-stranded rna. many dead-box proteins use this basic mechanism as the foundation for a version of rna helicase activity, efficiently separating the strands of short rna duplexes in a process that involves little or no translocation. this activity, coupled with mechanisms to direct different dead-box proteins to their physiological substrates, a ...201121297876
moderna: a tool for comparative modeling of rna 3d structure.rna is a large group of functionally important biomacromolecules. in striking analogy to proteins, the function of rna depends on its structure and dynamics, which in turn is encoded in the linear sequence. however, while there are numerous methods for computational prediction of protein three-dimensional (3d) structure from sequence, with comparative modeling being the most reliable approach, there are very few such methods for rna. here, we present moderna, a software tool for comparative mode ...201121300639
structure of the dimeric form of ctp synthase from sulfolobus solfataricus.ctp synthase catalyzes the last committed step in de novo pyrimidine-nucleotide biosynthesis. active ctp synthase is a tetrameric enzyme composed of a dimer of dimers. the tetramer is favoured in the presence of the substrate nucleotides atp and utp; when saturated with nucleotide, the tetramer completely dominates the oligomeric state of the enzyme. furthermore, phosphorylation has been shown to regulate the oligomeric states of the enzymes from yeast and human. the crystal structure of a dimer ...201121301086
crystallization and preliminary x-ray crystallographic studies of ß-transaminase from mesorhizobium sp. strain luk.ß-transaminase (ß-ta) catalyzes the transamination reaction between ß-aminocarboxylic acids and keto acids. this enzyme is a particularly suitable candidate for use as a biocatalyst for the asymmetric synthesis of enantiochemically pure ß-amino acids for pharmaceutical purposes. the ß-ta from mesorhizobium sp. strain luk (ß-tams) belongs to a novel class in that it shows ß-transaminase activity with a broad and unique substrate specificity. in this study, ß-tams was overexpressed in escherichia ...201121301093
understanding ribosome assembly: the structure of in vivo assembled immature 30s subunits revealed by cryo-electron microscopy.four decades after early in vitro assembly studies demonstrated that ribosome assembly is a controlled process, our understanding of ribosome assembly is still incomplete. just as structure determination has been so important to understanding ribosome function, so too will it be critical to sorting out the assembly process. here, we used a viable deletion in the yjeq gene, a recognized ribosome assembly factor, to isolate and structurally characterize immature 30s subunits assembled in vivo. the ...201121303937
complete genome sequence of meiothermus ruber type strain (21).meiothermus ruber (loginova et al. 1984) nobre et al. 1996 is the type species of the genus meiothermus. this thermophilic genus is of special interest, as its members share relatively low degrees of 16s rrna gene sequence similarity and constitute a separate evolutionary lineage from members of the genus thermus, from which they can generally be distinguished by their slightly lower temperature optima. the temperature related split is in accordance with the chemotaxonomic feature of the polar l ...201021304689
complete genome sequence of meiothermus silvanus type strain (vi-r2).meiothermus silvanus (tenreiro et al. 1995) nobre et al. 1996 belongs to a thermophilic genus whose members share relatively low degrees of 16s rrna gene sequence similarity. meiothermus constitutes an evolutionary lineage separate from members of the genus thermus, from which they can generally be distinguished by their slightly lower temperature optima. m. silvanus is of special interest as it causes colored biofilms in the paper making industry and may thus be of economic importance as a biof ...201021304690
complete genome sequence of archaeoglobus profundus type strain (av18).archaeoglobus profundus (burggraf et al. 1990) is a hyperthermophilic archaeon in the euryarchaeal class archaeoglobi, which is currently represented by the single family archaeoglobaceae, containing six validly named species and two strains ascribed to the genus 'geoglobus' which is taxonomically challenged as the corresponding type species has no validly published name. all members were isolated from marine hydrothermal habitats and are obligate anaerobes. here we describe the features of the ...201021304717
comparative metagenomics of microbial traits within oceanic viral communities.viral genomes often contain genes recently acquired from microbes. in some cases (for example, psba) the proteins encoded by these genes have been shown to be important for viral replication. in this study, using a unique search strategy on the global ocean survey (gos) metagenomes in combination with marine virome and microbiome pyrosequencing-based datasets, we characterize previously undetected microbial metabolic capabilities concealed within the genomes of uncultured marine viral communitie ...201121307954
genetic tool development underpins recent advances in thermophilic whole-cell biocatalysts.the environmental value of sustainably producing bioproducts from biomass is now widely appreciated, with a primary target being the economic production of fuels such as bioethanol from lignocellulose. the application of thermophilic prokaryotes is a rapidly developing niche in this field, driven by their known catabolic versatility with lignocellulose-derived carbohydrates. fundamental to the success of this work has been the development of reliable genetic and molecular systems. these technica ...201121310009
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
x-ray crystal structures elucidate the nucleotidyl transfer reaction of transcript initiation using two nucleotides.we have determined the x-ray crystal structures of the pre- and postcatalytic forms of the initiation complex of bacteriophage n4 rna polymerase that provide the complete set of atomic images depicting the process of transcript initiation by a single-subunit rna polymerase. as observed during t7 rna polymerase transcript elongation, substrate loading for the initiation process also drives a conformational change of the o-helix, but only the correct base pairing between the +2 substrate and dna b ...201121321236
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
modulation of rna polymerase activity through the trigger loop folding.folding of the trigger loop of rna polymerase promotes nucleotide addition through creating a closed, catalytically competent conformation of the active center. here, we discuss the impact of adjacent rna polymerase elements, including the f loop and the jaw domain, as well as external regulatory factors on the trigger loop folding and catalysis.201021326898
card: a new rna polymerase modulator in mycobacteria.mycobacteria card is an essential rnap binding protein that regulates many transcripts including rrna. this article will review our present state of knowledge regarding card and compare the known functions of card with other rnap binding proteins in e. coli, emphasizing how this information can guide future investigations.201021326904
card: a new rna polymerase modulator in mycobacteria.mycobacteria card is an essential rnap binding protein that regulates many transcripts including rrna. this article will review our present state of knowledge regarding card and compare the known functions of card with other rnap binding proteins in e. coli, emphasizing how this information can guide future investigations.201021326904
heterologous laccase production and its role in industrial applications.laccases are blue multicopper oxidases, catalyzing the oxidation of an array of aromatic substrates concomitantly with the reduction of molecular oxygen to water. these enzymes are implicated in a variety of biological activities. most of the laccases studied thus far are of fungal origin. the large range of substrates oxidized by laccases has raised interest in using them within different industrial fields, such as pulp delignification, textile dye bleaching, and bioremediation. laccases secret ...201021327057
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
the conformation of microrna seed regions in native micrornps is prearranged for presentation to mrna targets.micrornas control gene expression by post-transcriptional down-regulation of their target mrnas. complementarity between the seed region (nucleotides 2-8) of a microrna and the 3'-utr of its target mrna is the key determinant in recognition. however, the structural basis of the ability of the seed region to dominate target recognition in eukaryotic argonaute complexes has not been directly demonstrated. to better understand this problem, we performed chemical probing of micrornas held in native ...201121335607
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
the origin of a derived superkingdom: how a gram-positive bacterium crossed the desert to become an archaeon.the tree of life is usually rooted between archaea and bacteria. we have previously presented three arguments that support placing the root of the tree of life in bacteria. the data have been dismissed because those who support the canonical rooting between the prokaryotic superkingdoms cannot imagine how the vast divide between the prokaryotic superkingdoms could be crossed.201121356104
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
mechanism of bacterial transcription initiation: rna polymerase - promoter binding, isomerization to initiation-competent open complexes, and initiation of rna synthesis.initiation of rna synthesis from dna templates by rna polymerase (rnap) is a multi-step process, in which initial recognition of promoter dna by rnap triggers a series of conformational changes in both rnap and promoter dna. the bacterial rnap functions as a molecular isomerization machine, using binding free energy to remodel the initial recognition complex, placing downstream duplex dna in the active site cleft and then separating the nontemplate and template strands in the region surrounding ...201121371479
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
eukaryote-like serine/threonine kinases and phosphatases in bacteria.genomic studies have revealed the presence of ser/thr kinases and phosphatases in many bacterial species, although their physiological roles have largely been unclear. here we review bacterial ser/thr kinases (estks) that show homology in their catalytic domains to eukaryotic ser/thr kinases and their partner phosphatases (estps) that are homologous to eukaryotic phosphatases. we first discuss insights into the enzymatic mechanism of estk activation derived from structural studies on both the li ...201121372323
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
how mutations in trna distant from the anticodon affect the fidelity of decoding.the ribosome converts genetic information into protein by selecting aminoacyl trnas whose anticodons base-pair to an mrna codon. mutations in the trna body can perturb this process and affect fidelity. the hirsh suppressor is a well-studied trna(trp) harboring a g24a mutation that allows readthrough of uga stop codons. here we present crystal structures of the 70s ribosome complexed with ef-tu and aminoacyl trna (native trna(trp), g24a trna(trp) or the miscoding a9c trna(trp)) bound to cognate u ...201121378964
evolution of introns in the archaeal world.the self-splicing group i introns are removed by an autocatalytic mechanism that involves a series of transesterification reactions. they require rna binding proteins to act as chaperones to correctly fold the rna into an active intermediate structure in vivo. pre-trna introns in bacteria and in higher eukaryote plastids are typical examples of self-splicing group i introns. by contrast, two striking features characterize rna splicing in the archaeal world. first, self-splicing group i introns c ...201121383132
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
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