Publications

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 ...	2011	21296881
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 ...	2011	21285351
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. ...	2011	21282615
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 ...	2011	21282428
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 ...	2011	21278279
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.	2011	21266052
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 ...	2011	21264299
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 ...	2011	21257750
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 ...	2011	21257746
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.	2011	21255416
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 ...	2011	21255213
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 ...	2011	21253384
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 ...	2011	21250660
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 ...	2011	21246636
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 ...	2011	21245352
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 ...	2011	21241053
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 ...	2011	21233089
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 ...	2011	21232525
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 ...	2011	21224389
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 ...	2011	21222438
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 ...	2009	21218180
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 ...	2011	21209330
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 ...	2010	21206036
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 ...	2010	21206036
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 ...	2010	21206021
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 ...	2010	21206021
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. ...	2010	21206019
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. ...	2010	21206019
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 ...	2010	21206014
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 ...	2011	21205901
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 ...	2007	21200504
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 ...	2007	21200504
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 ...	2011	21196577
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 ...	2010	21195716
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 ...	2010	21195716
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 ...	2010	21193640
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 ...	2010	21193640
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 ...	2010	21190941
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 ...	2010	21187417
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 ...	2010	21187417
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 ...	2010	21185305
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 ...	2010	21185305
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.	2010	21184843
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.	2010	21184843
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 ...	2010	21183704
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. ...	2010	21177858
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. ...	2010	21177858
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 ...	2011	21173199
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 ...	2010	21169681
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 ...	2010	21169565
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 ...	2010	21169565
lateral transfer of the denitrification pathway genes among thermus thermophilus strains.	nitrate respiration is a common and strain-specific property in thermus thermophilus encoded by the nitrate respiration conjugative element (nce) that can be laterally transferred by conjugation. in contrast, nitrite respiration and further denitrification steps are restricted to a few isolates of this species. these later steps of the denitrification pathway are under the regulatory control of an nce-encoded transcription factor, but nothing is known about their coding sequences or its putative ...	2010	21169443
metagenomic analyses: past and future trends.	metagenomics has revolutionized microbiology by paving the way for a cultivation-independent assessment and exploitation of microbial communities present in complex ecosystems. metagenomics comprising construction and screening of metagenomic dna libraries has proven to be a powerful tool to isolate new enzymes and drugs of industrial importance. so far, the majority of the metagenomically exploited habitats comprised temperate environments, such as soil and marine environments. recently, metage ...	2010	21169428
metagenomic analyses: past and future trends.	metagenomics has revolutionized microbiology by paving the way for a cultivation-independent assessment and exploitation of microbial communities present in complex ecosystems. metagenomics comprising construction and screening of metagenomic dna libraries has proven to be a powerful tool to isolate new enzymes and drugs of industrial importance. so far, the majority of the metagenomically exploited habitats comprised temperate environments, such as soil and marine environments. recently, metage ...	2010	21169428
a mechanism for single-stranded dna-binding protein (ssb) displacement from single-stranded dna upon ssb-reco interaction.	displacement of single-stranded dna (ssdna)-binding protein (ssb) from ssdna is necessary for filament formation of reca on ssdna to initiate homologous recombination. the interaction between reco and ssb is considered to be important for ssb displacement; however, the interaction has not been characterized at the atomic level. in this study, to clarify the mechanism underlying ssb displacement from ssdna upon reco binding, we examined the interaction between thermus thermophilus reco and cognat ...	2010	21169364
methylthioadenosine/s-adenosylhomocysteine nucleosidase, a critical enzyme for bacterial metabolism.	the importance of methylthioadenosine/s-adenosylhomocysteine (mta/sah) nucleosidase in bacteria has started to be appreciated only in the past decade. a comprehensive analysis of its various roles here demonstrates that it is an integral component of the activated methyl cycle, which recycles adenine and methionine through s-adenosylmethionine (sam)-mediated methylation reactions, and also produces the universal quorum-sensing signal, autoinducer-2 (ai-2). sam is also essential for synthesis of ...	2010	21166890
methylthioadenosine/s-adenosylhomocysteine nucleosidase, a critical enzyme for bacterial metabolism.	the importance of methylthioadenosine/s-adenosylhomocysteine (mta/sah) nucleosidase in bacteria has started to be appreciated only in the past decade. a comprehensive analysis of its various roles here demonstrates that it is an integral component of the activated methyl cycle, which recycles adenine and methionine through s-adenosylmethionine (sam)-mediated methylation reactions, and also produces the universal quorum-sensing signal, autoinducer-2 (ai-2). sam is also essential for synthesis of ...	2010	21166890
biochemistry. catalyzing no to n2o in the nitrogen cycle.		2010	21164002
intrinsic resistance to aminoglycosides in enterococcus faecium is conferred by the 16s rrna m5c1404-specific methyltransferase efmm.	aminoglycosides are ribosome-targeting antibiotics and a major drug group of choice in the treatment of serious enterococcal infections. here we show that aminoglycoside resistance in enterococcus faecium strain cip 54-32 is conferred by the chromosomal gene efmm, encoding the e. faecium methyltransferase, as well as by the previously characterized aac(6')-ii that encodes a 6'-n-aminoglycoside acetyltransferase. inactivation of efmm in e. faecium increases susceptibility to the aminoglycosides k ...	2010	21159796
interdependencies govern multidomain architecture in ribosomal small subunit assembly.	the 30s subunit is composed of four structural domains, the body, platform, head, and penultimate/ultimate stems. the functional integrity of the 30s subunit is dependent upon appropriate assembly and precise orientation of all four domains. we examined 16s rrna conformational changes during in vitro assembly using directed hydroxyl radical probing mediated by fe(ii)-derivatized ribosomal protein (r-protein) s8. r-protein s8 binds the central domain of 16s rrna directly and independently and its ...	2011	21156960
functional role of ribosomal signatures.	although structure and sequence signatures in ribosomal rna and proteins are defining characteristics of the three domains of life and instrumental in constructing the modern phylogeny, little is known about their functional roles in the ribosome. in this work, the largest coevolving rna/protein signatures in the bacterial 30s ribosome are investigated both experimentally and computationally through all-atom molecular-dynamics simulations. the complex includes the n-terminal fragment of the ribo ...	2010	21156135
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 ...	2011	21154411
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 ...	2011	21154411
molecular dynamics of ribosomal elongation factors g and tu.	translation on the ribosome is controlled by external factors. during polypeptide lengthening, elongation factors ef-tu and ef-g consecutively interact with the bacterial ribosome. ef-tu binds and delivers an aminoacyl-trna to the ribosomal a site and ef-g helps translocate the trnas between their binding sites after the peptide bond is formed. these processes occur at the expense of gtp. ef-tu:trna and ef-g are of similar shape, share a common binding site, and undergo large conformational chan ...	2010	21152913
molecular dynamics of ribosomal elongation factors g and tu.	translation on the ribosome is controlled by external factors. during polypeptide lengthening, elongation factors ef-tu and ef-g consecutively interact with the bacterial ribosome. ef-tu binds and delivers an aminoacyl-trna to the ribosomal a site and ef-g helps translocate the trnas between their binding sites after the peptide bond is formed. these processes occur at the expense of gtp. ef-tu:trna and ef-g are of similar shape, share a common binding site, and undergo large conformational chan ...	2010	21152913
phenotypic characterization of transgenic mice overexpressing neuregulin-1.	neuregulin-1 (nrg1) is one of the susceptibility genes for schizophrenia and implicated in the neurotrophic regulation of gabaergic and dopaminergic neurons, myelination, and nmda receptor function. postmortem studies often indicate a pathologic association of increased nrg1 expression or signaling with this illness. however, the psychobehavioral implication of nrg1 signaling has mainly been investigated using hypomorphic mutant mice for individual nrg1 splice variants.	2010	21151609
electron cryomicroscopy structure of a membrane-anchored mitochondrial aaa protease.	ftsh-related aaa proteases are conserved membrane-anchored, atp-dependent molecular machines, which mediate the processing and turnover of soluble and membrane-embedded proteins in eubacteria, mitochondria, and chloroplasts. homo- and hetero-oligomeric proteolytic complexes exist, which are composed of homologous subunits harboring an atpase domain of the aaa family and an h41 metallopeptidase domain. mutations in subunits of mitochondrial m-aaa proteases have been associated with different neur ...	2010	21147776
electron cryomicroscopy structure of a membrane-anchored mitochondrial aaa protease.	ftsh-related aaa proteases are conserved membrane-anchored, atp-dependent molecular machines, which mediate the processing and turnover of soluble and membrane-embedded proteins in eubacteria, mitochondria, and chloroplasts. homo- and hetero-oligomeric proteolytic complexes exist, which are composed of homologous subunits harboring an atpase domain of the aaa family and an h41 metallopeptidase domain. mutations in subunits of mitochondrial m-aaa proteases have been associated with different neur ...	2010	21147776
structure of leishmania major methionyl-trna synthetase in complex with intermediate products methionyladenylate and pyrophosphate.	leishmania parasites cause two million new cases of leishmaniasis each year with several hundreds of millions of people at risk. due to the paucity and shortcomings of available drugs, we have undertaken the crystal structure determination of a key enzyme from leishmania major in hopes of creating a platform for the rational design of new therapeutics. crystals of the catalytic core of methionyl-trna synthetase from l. major (lmmetrs) were obtained with the substrates mgatp and methionine presen ...	2010	21144880
structure of leishmania major methionyl-trna synthetase in complex with intermediate products methionyladenylate and pyrophosphate.	leishmania parasites cause two million new cases of leishmaniasis each year with several hundreds of millions of people at risk. due to the paucity and shortcomings of available drugs, we have undertaken the crystal structure determination of a key enzyme from leishmania major in hopes of creating a platform for the rational design of new therapeutics. crystals of the catalytic core of methionyl-trna synthetase from l. major (lmmetrs) were obtained with the substrates mgatp and methionine presen ...	2010	21144880
the folding of single domain proteins--have we reached a consensus?	rather than stressing the most recent advances in the field, this review highlights the fundamental topics where disagreement remains and where adequate experimental data are lacking. these topics include properties of the denatured state and the role of residual structure, the nature of the fundamental steps and barriers, the extent of pathway heterogeneity and non-native interactions, recent comparisons between theory and experiment, and finally, dynamical properties of the folding reaction.	2010	21144739
the folding of single domain proteins--have we reached a consensus?	rather than stressing the most recent advances in the field, this review highlights the fundamental topics where disagreement remains and where adequate experimental data are lacking. these topics include properties of the denatured state and the role of residual structure, the nature of the fundamental steps and barriers, the extent of pathway heterogeneity and non-native interactions, recent comparisons between theory and experiment, and finally, dynamical properties of the folding reaction.	2010	21144739
ribonucleotide reduction - horizontal transfer of a required function spans all three domains.	ribonucleotide reduction is the only de novo pathway for synthesis of deoxyribonucleotides, the building blocks of dna. the reaction is catalysed by ribonucleotide reductases (rnrs), an ancient enzyme family comprised of three classes. each class has distinct operational constraints, and are broadly distributed across organisms from all three domains, though few class i rnrs have been identified in archaeal genomes, and classes ii and iii likewise appear rare across eukaryotes. in this study, we ...	2010	21143941
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 ...	2011	21142182
cloning, purification, crystallization and preliminary x-ray crystallographic analysis of the n-terminal domain of dead-box rna helicase from staphylococcus aureus strain mu50.	dead-box helicases are enzymes with an atp-dependent rna-unwinding function that are involved in a variety of cellular processes including rna splicing, ribosome biogenesis and rna degradation. in this study, the n-terminal domain of dead-box rna helicase from staphylococcus aureus strain mu50 was overexpressed in escherichia coli, purified and crystallized. diffraction data were collected to 2.60 å resolution using a synchrotron-radiation source. the crystal belonged to space group p1, with uni ...	2010	21139222
structure of a crispr-associated protein cas2 from desulfovibrio vulgaris.	crisprs (clustered regularly interspaced short palindromic repeats) provide bacteria and archaea with rna-guided acquired immunity to invasive dnas. crispr-associated (cas) proteins carry out the immune effector functions. cas2 is a universal component of the crispr system. here, a 1.35 å resolution crystal structure of cas2 from the bacterium desulfovibrio vulgaris (dvucas2) is reported. dvucas2 is a homodimer, with each protomer consisting of an n-terminal βαββαβ ferredoxin fold (amino acids 1 ...	2010	21139194
mutations in the intersubunit bridge regions of 16s rrna affect decoding and subunit-subunit interactions on the 70s ribosome.	the small and large subunits of the ribosome are held together by a series of bridges, involving rna-rna, rna-protein and protein-protein interactions. some 12 bridges have been described for the escherichia coli 70s ribosome. in this work, we have targeted for mutagenesis, some of the 16s rrna residues involved in the formation of intersubunit bridges b3, b5, b6, b7b and b8. in addition to effects on subunit association, the mutant ribosomes also affect the fidelity of translation; bridges b5, ...	2010	21138965
mutations in the intersubunit bridge regions of 16s rrna affect decoding and subunit-subunit interactions on the 70s ribosome.	the small and large subunits of the ribosome are held together by a series of bridges, involving rna-rna, rna-protein and protein-protein interactions. some 12 bridges have been described for the escherichia coli 70s ribosome. in this work, we have targeted for mutagenesis, some of the 16s rrna residues involved in the formation of intersubunit bridges b3, b5, b6, b7b and b8. in addition to effects on subunit association, the mutant ribosomes also affect the fidelity of translation; bridges b5, ...	2010	21138965
phylogenomic analysis of the uracil-dna glycosylase superfamily.	the spontaneous deamination of cytosine produces uracil mispaired with guanine in dna, which will produce a mutation, unless repaired. in all domains of life, uracil-dna glycosylases (udgs) are responsible for the elimination of uracil from dna. thus, udgs contribute to the integrity of the genetic information and their loss results in mutator phenotypes. we are interested in understanding the role of udg genes in the evolutionary variation of the rate and the spectrum of spontaneous mutations. ...	2010	21135150
phylogenomic analysis of the uracil-dna glycosylase superfamily.	the spontaneous deamination of cytosine produces uracil mispaired with guanine in dna, which will produce a mutation, unless repaired. in all domains of life, uracil-dna glycosylases (udgs) are responsible for the elimination of uracil from dna. thus, udgs contribute to the integrity of the genetic information and their loss results in mutator phenotypes. we are interested in understanding the role of udg genes in the evolutionary variation of the rate and the spectrum of spontaneous mutations. ...	2010	21135150
nanometer propagation of millisecond motions in v-type allostery.	imidazole glycerol phosphate synthase (igps) is a v-type allosteric enzyme, which is catalytically inactive for glutamine hydrolysis until the allosteric effector, n'-[(5'-phosphoribulosyl)formimino]-5-aminoimidazole-4-carboxamide-ribonucleotide (prfar) binds 30 å away. in the apo state, nmr relaxation dispersion experiments indicate the absence of millisecond (ms) timescale motions. binding of the prfar to form the active ternary complex is endothermic with a large positive entropy change. in a ...	2010	21134639
construction and analyses of tetrameric forms of yeast nad(+)-specific isocitrate dehydrogenase.	yeast nad(+)-specific isocitrate dehydrogenase (idh) is an octameric enzyme composed of four heterodimers of regulatory idh1 and catalytic idh2 subunits. the crystal structure suggested that the interactions between tetramers in the octamer are restricted to defined regions in idh1 subunits from each tetramer. using truncation and mutagenesis, we constructed three tetrameric forms of idh. truncation of five residues from the amino terminus of idh1 did not alter the octameric form of the enzyme, ...	2010	21133413
construction and analyses of tetrameric forms of yeast nad(+)-specific isocitrate dehydrogenase.	yeast nad(+)-specific isocitrate dehydrogenase (idh) is an octameric enzyme composed of four heterodimers of regulatory idh1 and catalytic idh2 subunits. the crystal structure suggested that the interactions between tetramers in the octamer are restricted to defined regions in idh1 subunits from each tetramer. using truncation and mutagenesis, we constructed three tetrameric forms of idh. truncation of five residues from the amino terminus of idh1 did not alter the octameric form of the enzyme, ...	2010	21133413
an rna molecular switch: intrinsic flexibility of 23s rrna helices 40 and 68 5'-uaa/5'-gan internal loops studied by molecular dynamics methods.	functional rna molecules such as ribosomal rnas frequently contain highly conserved internal loops with a 5'-uaa/5'-gan (uaa/gan) consensus sequence. the uaa/gan internal loops adopt distinctive structure inconsistent with secondary structure predictions. the structure has a narrow major groove and forms a trans hoogsteen/sugar edge (ths) a/g base pair followed by an unpaired stacked adenine, a trans watson-crick/hoogsteen (twh) u/a base pair and finally by a bulged nucleotide (n). the structure ...	2010	21132104
head swivel on the ribosome facilitates translocation by means of intra-subunit trna hybrid sites.	the elongation cycle of protein synthesis involves the delivery of aminoacyl-transfer rnas to the aminoacyl-trna-binding site (a site) of the ribosome, followed by peptide-bond formation and translocation of the trnas through the ribosome to reopen the a site. the translocation reaction is catalysed by elongation factor g (ef-g) in a gtp-dependent manner. despite the availability of structures of various ef-g-ribosome complexes, the precise mechanism by which trnas move through the ribosome stil ...	2010	21124459
breps: a flexible and automatic protocol to compute enzyme-specific sequence profiles for functional annotation.	models for the simulation of metabolic networks require the accurate prediction of enzyme function. based on a genomic sequence, enzymatic functions of gene products are today mainly predicted by sequence database searching and operon analysis. other methods can support these techniques: we have developed an automatic method "breps" that creates highly specific sequence patterns for the functional annotation of enzymes.	2010	21122127
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 ...	2011	21121048
biocrystallography: past, present, future.	the evolution of biocrystallography from the pioneers' time to the present era of global biology is presented in relation to the development of methodological and instrumental advances for molecular sample preparation and structure elucidation over the last 6 decades. the interdisciplinarity of the field that generated cross-fertilization between physics- and biology-focused themes is emphasized. in particular, strategies to circumvent the main bottlenecks of biocrystallography are discussed. th ...	2010	21119764
mutation in subdomain g' of mitochondrial elongation factor g1 is associated with combined oxphos deficiency in fibroblasts but not in muscle.	the mitochondrial translation system is responsible for the synthesis of 13 proteins required for oxidative phosphorylation (oxphos), the major energy-generating process of our cells. mitochondrial translation is controlled by various nuclear encoded proteins. in 27 patients with combined oxphos deficiencies, in whom complex ii (the only complex that is entirely encoded by the nuclear dna) showed normal activities, and mutations in the mitochondrial genome as well as polymerase gamma were exclud ...	2010	21119709
mutation in subdomain g' of mitochondrial elongation factor g1 is associated with combined oxphos deficiency in fibroblasts but not in muscle.	the mitochondrial translation system is responsible for the synthesis of 13 proteins required for oxidative phosphorylation (oxphos), the major energy-generating process of our cells. mitochondrial translation is controlled by various nuclear encoded proteins. in 27 patients with combined oxphos deficiencies, in whom complex ii (the only complex that is entirely encoded by the nuclear dna) showed normal activities, and mutations in the mitochondrial genome as well as polymerase gamma were exclud ...	2010	21119709
n-acetyl-d-glucosaminylphosphatidylinositol de-n-acetylase from entamoeba histolytica: metal alters catalytic rates but not substrate affinity.	pig-l/gpi12 proteins are endoplasmic reticulum-resident membrane proteins involved in the second step of glycosylphosphatidylinositol anchor biosynthesis in eukaryotes. we show that the entamoeba histolytica pig-l protein is optimally active in the acidic ph range. the enzyme has an intrinsic low level of de-n-acetylase activity in the absence of metal and is significantly stimulated by divalent cations. metal binding induces a large conformational change in the protein that appears to improve c ...	2010	21118807
n-acetyl-d-glucosaminylphosphatidylinositol de-n-acetylase from entamoeba histolytica: metal alters catalytic rates but not substrate affinity.	pig-l/gpi12 proteins are endoplasmic reticulum-resident membrane proteins involved in the second step of glycosylphosphatidylinositol anchor biosynthesis in eukaryotes. we show that the entamoeba histolytica pig-l protein is optimally active in the acidic ph range. the enzyme has an intrinsic low level of de-n-acetylase activity in the absence of metal and is significantly stimulated by divalent cations. metal binding induces a large conformational change in the protein that appears to improve c ...	2010	21118807
small rna sorting: matchmaking for argonautes.	small rnas directly or indirectly impact nearly every biological process in eukaryotic cells. to perform their myriad roles, not only must precise small rna species be generated, but they must also be loaded into specific effector complexes called rna-induced silencing complexes (riscs). argonaute proteins form the core of riscs and different members of this large family have specific expression patterns, protein binding partners and biochemical capabilities. in this review, we explore the mecha ...	2010	21116305
small rna sorting: matchmaking for argonautes.	small rnas directly or indirectly impact nearly every biological process in eukaryotic cells. to perform their myriad roles, not only must precise small rna species be generated, but they must also be loaded into specific effector complexes called rna-induced silencing complexes (riscs). argonaute proteins form the core of riscs and different members of this large family have specific expression patterns, protein binding partners and biochemical capabilities. in this review, we explore the mecha ...	2010	21116305
characterization of a mannose-6-phosphate isomerase from thermus thermophilus and increased l-ribose production by its r142n mutant.	an uncharacterized gene from thermus thermophilus, thought to encode a mannose-6-phosphate isomerase, was cloned and expressed in escherichia coli. the maximal activity of the recombinant enzyme for l-ribulose isomerization was observed at ph 7.0 and 75°c in the presence of 0.5 mm cu(2+). among all of the pentoses and hexoses evaluated, the enzyme exhibited the highest activity for the conversion of l-ribulose to l-ribose, a potential starting material for many l-nucleoside-based pharmaceutical ...	2010	21115698
identification of an rnase j ortholog in sulfolobus solfataricus: implications for 5'-to-3' directional decay and 5'-end protection of mrna in crenarchaeota.	in both bacteria and eukaryotes, degradation is known to start at the 5' and at the 3' extremities of mrnas. until the recent discovery of 5'-to-3' exoribonucleases in hyperthermophilic euryarchaeota, the exosome was assumed to be the key enzyme in mrna degradation in archaea. by means of zymogram assays and bioinformatics, we have identified a 5'-to-3' exoribonuclease activity in the crenarchaeum sulfolobus solfataricus (sso), which is affected by the phosphorylation state of the 5'-end of the ...	2010	21115637
evolution of respiratory complex i: "supernumerary" subunits are present in the alpha-proteobacterial enzyme.	modern α-proteobacteria are thought to be closely related to the ancient symbiont of eukaryotes, an ancestor of mitochondria. respiratory complex i from α-proteobacteria and mitochondria is well conserved at the level of the 14 "core" subunits, consistent with that notion. mitochondrial complex i contains the core subunits, present in all species, and up to 31 "supernumerary" subunits, generally thought to have originated only within eukaryotic lineages. however, the full protein composition of ...	2010	21115482
evolution of respiratory complex i: "supernumerary" subunits are present in the alpha-proteobacterial enzyme.	modern α-proteobacteria are thought to be closely related to the ancient symbiont of eukaryotes, an ancestor of mitochondria. respiratory complex i from α-proteobacteria and mitochondria is well conserved at the level of the 14 "core" subunits, consistent with that notion. mitochondrial complex i contains the core subunits, present in all species, and up to 31 "supernumerary" subunits, generally thought to have originated only within eukaryotic lineages. however, the full protein composition of ...	2010	21115482
an assessment of mechanisms underlying peripheral axonal degeneration caused by aminoacyl-trna synthetase mutations.	mutations in glycyl-, tyrosyl-, and alanyl-trna synthetases (gars, yars and aars respectively) cause autosomal dominant charcot-marie-tooth disease, and mutations in gars cause a similar peripheral neuropathy in mice. aminoacyl-trna synthetases (arss) charge amino acids onto their cognate trnas during translation; however, the pathological mechanism(s) of ars mutations remains unclear. to address this, we tested possible mechanisms using mouse models. first, amino acid mischarging was discounted ...	2010	21115117
an assessment of mechanisms underlying peripheral axonal degeneration caused by aminoacyl-trna synthetase mutations.	mutations in glycyl-, tyrosyl-, and alanyl-trna synthetases (gars, yars and aars respectively) cause autosomal dominant charcot-marie-tooth disease, and mutations in gars cause a similar peripheral neuropathy in mice. aminoacyl-trna synthetases (arss) charge amino acids onto their cognate trnas during translation; however, the pathological mechanism(s) of ars mutations remains unclear. to address this, we tested possible mechanisms using mouse models. first, amino acid mischarging was discounted ...	2010	21115117