Publications
| Title | Abstract | Year Filter | PMID(sorted ascending) Filter |
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| conserved lipid-binding sites in membrane proteins: a focus on cytochrome c oxidase. | specific interactions between lipids and membrane proteins have been observed in recent high-resolution crystal structures of membrane proteins. a number of cytochrome oxidase structures were analyzed, along with many amino acid sequences of membrane-spanning regions aligned according to their location in the membrane. the results reveal conservation of lipid-binding sites and of the residues that form them. these studies imply that bound lipids have important roles that are crucial to the assem ... | 2007 | 17719219 |
| messenger rna conformations in the ribosomal e site revealed by x-ray crystallography. | a comparison of messenger rna in x-ray crystal structures of 70s ribosomal complexes in the initiation, post-initiation and elongation states of translation shows distinct conformational differences in the exit (e) codon. here, we present structural evidence indicating that, after the initiation event, the e codon nucleotides relax and form a classical a-helical conformation. this conformation is similar to that of the p and a codons, and is favourable for establishing watson-crick interactions ... | 2007 | 17721443 |
| human tryptophanyl-trna synthetase is switched to a trna-dependent mode for tryptophan activation by mutations at v85 and i311. | for most aminoacyl-trna synthetases (aars), their cognate trna is not obligatory to catalyze amino acid activation, with the exception of four class i (aars): arginyl-trna synthetase, glutamyl-trna synthetase, glutaminyl-trna synthetase and class i lysyl-trna synthetase. furthermore, for arginyl-, glutamyl- and glutaminyl-trna synthetase, the integrated 3' end of the trna is necessary to activate the atp-ppi exchange reaction. tryptophanyl-trna synthetase is a class i aars that catalyzes tryptop ... | 2007 | 17726052 |
| anticodon recognition and discrimination by the alpha-helix cage domain of class i lysyl-trna synthetase. | aminoacyl-trna synthetases are normally found in one of two mutually exclusive structural classes, the only known exception being lysyl-trna synthetase which exists in both classes i (lysrs1) and ii (lysrs2). differences in trna acceptor stem recognition between lysrs1 and lysrs2 do not drastically impact cellular aminoacylation levels, focusing attention on the mechanism of trna anticodon recognition by lysrs1. on the basis of structure-based sequence alignments, seven trnalys anticodon variant ... | 2007 | 17760422 |
| redox-dependent change of nucleotide affinity to the active site of the mammalian complex i. | a very potent and specific inhibitor of mitochondrial nadh:ubiquinone oxidoreductase (complex i), a derivative of nadh (nadh-oh) has recently been discovered (kotlyar, a. b., karliner, j. s., and cecchini, g. (2005) febs lett. 579, 4861-4866). here we present a quantitative analysis of the interaction of nadh-oh and other nucleotides with oxidized and reduced complex i in tightly coupled submitochondrial particles. both the rate of the nadh-oh binding and its affinity to complex i are strongly d ... | 2007 | 17760425 |
| structure-based design of robust glucose biosensors using a thermotoga maritima periplasmic glucose-binding protein. | we report the design and engineering of a robust, reagentless fluorescent glucose biosensor based on the periplasmic glucose-binding protein obtained from thermotoga maritima (tmgbp). the gene for this protein was cloned from genomic dna and overexpressed in escherichia coli, the identity of its cognate sugar was confirmed, ligand binding was studied, and the structure of its glucose complex was solved to 1.7 angstrom resolution by x-ray crystallography. tmgbp is specific for glucose and exhibit ... | 2007 | 17766373 |
| analysis of promoter targets for escherichia coli transcription elongation factor grea in vivo and in vitro. | transcription elongation factor grea induces nucleolytic activity of bacterial rna polymerase (rnap). in vitro, transcript cleavage by grea contributes to transcription efficiency by (i) suppressing pauses and arrests, (ii) stimulating rnap promoter escape, and (iii) enhancing transcription fidelity. however, it is unclear which of these functions is (are) most relevant in vivo. by comparing global gene expression profiles of escherichia coli strains lacking gre factors and strains expressing ei ... | 2007 | 17766423 |
| an aminoacyl-trna synthetase:elongation factor complex for substrate channeling in archaeal translation. | translation requires the specific attachment of amino acids to trnas by aminoacyl-trna synthetases (aarss) and the subsequent delivery of aminoacyl-trnas to the ribosome by elongation factor 1 alpha (ef-1alpha). interactions between ef-1alpha and various aarss have been described in eukaryotes, but the role of these complexes remains unclear. to investigate possible interactions between ef-1alpha and other cellular components, a yeast two-hybrid screen was performed for the archaeon methanotherm ... | 2007 | 17766929 |
| the primordial metabolism: an ancestral interconnection between leucine, arginine, and lysine biosynthesis. | it is generally assumed that primordial cells had small genomes with simple genes coding for enzymes able to react with a wide range of chemically related substrates, interconnecting different metabolic routes. new genes coding for enzymes with a narrowed substrate specificity arose by paralogous duplication(s) of ancestral ones and evolutionary divergence. in this way new metabolic pathways were built up by primordial cells. useful hints to disclose the origin and evolution of ancestral metabol ... | 2007 | 17767731 |
| purification, crystallization and preliminary x-ray characterization of a human mitochondrial phenylalanyl-trna synthetase. | human monomeric mitochondrial phenylalanyl-trna synthetase (mitphers) is an enzyme that catalyzes the charging of trna with the cognate amino acid phenylalanine. human mitphers is a chimera of the bacterial alpha-subunit of phers and the b8 domain of its beta-subunit. together, the alpha-subunit and the 'rnp-domain' (b8 domain) at the c-terminus form the minimal structural set to construct an enzyme with phenylalanylation activity. the recombinant human mitphers was purified to homogeneity and c ... | 2007 | 17768348 |
| crystallization and preliminary x-ray crystallographic analysis of a 40 kda n-terminal fragment of the yeast prion-remodeling factor hsp104. | a 40 kda n-terminal fragment of saccharomyces cerevisiae hsp104 was crystallized in two different crystal forms. native 1 diffracted to 2.6 a resolution and belonged to space group p2(1)2(1)2(1), with unit-cell parameters a = 66.6, b = 75.8, c = 235.7 a. native 2 diffracted to 2.9 a resolution and belonged to space group p6(1)22 or p6(5)22, with unit-cell parameters a = 179.1, b = 179.1, c = 69.7 a. this is the first report of the crystallization of a eukaryotic member of the hsp100 family of mo ... | 2007 | 17768355 |
| purification, crystallization and preliminary x-ray analysis of the fumarylacetoacetase family member ttha0809 from thermus thermophilus hb8. | fumarylacetoacetase catalyzes the final step of tyrosine and phenylalanine catabolism. a recombinant form of the fumarylacetoacetase family member ttha0809 from thermus thermophilus hb8 has been crystallized by the oil-microbatch method using sodium chloride as a precipitating agent. the crystals belong to the monoclinic space group p2(1), with unit-cell parameters a = 93.3, b = 73.4, c = 122.6 a, beta = 111.8 degrees. the crystals are most likely to contain two dimers in the asymmetric unit, wi ... | 2007 | 17768357 |
| phenylalanyl-trna synthetase editing defects result in efficient mistranslation of phenylalanine codons as tyrosine. | translational quality control is monitored at several steps, including substrate selection by aminoacyl-trna synthetases (aarss), and discrimination of aminoacyl-trnas by elongation factor tu (ef-tu) and the ribosome. phenylalanyl-trna synthetase (phers) misactivates tyr but is able to correct the mistake using a proofreading activity named editing. previously we found that overproduction of editing-defective phers resulted in tyr incorporation at phe-encoded positions in vivo, although the misr ... | 2007 | 17804641 |
| first experimental evidence for the preferential stabilization of the natural d- over the nonnatural l-configuration in nucleic acids. | the homochirality of biomolecules is a prerequisite for the origin and evolution of terrestrial life. the unique selection of d-monosaccharides, in particular, d-ribose in rna and d-deoxyribose in dna, leads to the construction of proteins by l-amino acids. this points to the exclusive role of stereoselectivity in the most important physiological processes. so far, there is no experimental confirmation for the theoretical calculations of the energy differences between enantiomers used for the ex ... | 2007 | 17804644 |
| ribosome biogenesis and the translation process in escherichia coli. | translation, the decoding of mrna into protein, is the third and final element of the central dogma. the ribosome, a nucleoprotein particle, is responsible and essential for this process. the bacterial ribosome consists of three rrna molecules and approximately 55 proteins, components that are put together in an intricate and tightly regulated way. when finally matured, the quality of the particle, as well as the amount of active ribosomes, must be checked. the focus of this review is ribosome b ... | 2007 | 17804668 |
| nmr analysis of [methyl-13c]methionine uvrb from bacillus caldotenax reveals uvrb-domain 4 heterodimer formation in solution. | uvrb is a central dna damage recognition protein involved in bacterial nucleotide excision repair. structural information has been limited by the apparent disorder of the c-terminal domain 4 in crystal structures of intact uvrb; in solution, the isolated domain 4 is found to form a helix-loop-helix dimer. in order to gain insight into the behavior of uvrb in solution, we have performed nmr studies on [methyl-13c]methionine-labeled uvrb from bacillus caldotenax (molecular mass=75 kda). the 13 met ... | 2007 | 17822711 |
| elongation factor 1a mediates the specificity of mitochondrial trna import in t. brucei. | mitochondrial trna import is widespread in eukaryotes. yet, the mechanism that determines its specificity is unknown. previous in vivo experiments using the trnas(met), trna(ile) and trna(lys) have suggested that the t-stem nucleotide pair 51:63 is the main localization determinant of trnas in trypanosoma brucei. in the cytosol-specific initiator trna(met), this nucleotide pair is identical to the main antideterminant that prevents interaction with cytosolic elongation factor (eef1a). here we sh ... | 2007 | 17853889 |
| virus-encoded aminoacyl-trna synthetases: structural and functional characterization of mimivirus tyrrs and metrs. | aminoacyl-trna synthetases are pivotal in determining how the genetic code is translated in amino acids and in providing the substrate for protein synthesis. as such, they fulfill a key role in a process universally conserved in all cellular organisms from their most complex to their most reduced parasitic forms. in contrast, even complex viruses were not found to encode much translation machinery, with the exception of isolated components such as trnas. in this context, the discovery of four am ... | 2007 | 17855524 |
| a quantitative kinetic scheme for 70 s translation initiation complex formation. | association of the 30 s initiation complex (30sic) and the 50 s ribosomal subunit, leading to formation of the 70 s initiation complex (70sic), is a critical step of the translation initiation pathway. the 70sic contains initiator trna, fmet-trna(fmet), bound in the p (peptidyl)-site in response to the aug start codon. we have formulated a quantitative kinetic scheme for the formation of an active 70sic from 30sic and 50 s subunits on the basis of parallel rapid kinetics measurements of gtp hydr ... | 2007 | 17868692 |
| structural and kinetic characterization of quinolinate phosphoribosyltransferase (hqprtase) from homo sapiens. | human quinolinate phosphoribosyltransferase (ec 2.4.2.19) (hqprtase) is a member of the type ii phosphoribosyltransferase family involved in the catabolism of quinolinic acid (qa). it catalyses the formation of nicotinic acid mononucleotide from quinolinic acid, which involves a phosphoribosyl transfer reaction followed by decarboxylation. hqprtase has been implicated in a number of neurological conditions and in order to study it further, we have carried out structural and kinetic studies on re ... | 2007 | 17868694 |
| substrate specificity and properties of the escherichia coli 16s rrna methyltransferase, rsme. | the small ribosome subunit of escherichia coli contains 10 base-methylated sites distributed in important functional regions. at present, seven enzymes responsible for methylation of eight bases are known, but most of them have not been well characterized. one of these enzymes, rsme, was recently identified and shown to specifically methylate u1498. here we describe the enzymatic properties and substrate specificity of rsme. the enzyme forms dimers in solution and is most active in the presence ... | 2007 | 17872509 |
| conformational energy and structure in canonical and noncanonical forms of trna determined by temperature analysis of the rate of s(4)u8-c13 photocrosslinking. | bacterial trnas frequently have 4-thiouridine (s(4)u) modification at position 8, which is adjacent to the c13-g22-m(7)g46 base triple in the elbow region of the trna tertiary structure. irradiation with light in the uva range induces an efficient photocrosslink between s(4)u8 and c13. the temperature dependence of the rate constants for photocrosslinking between the s(4)u8 and c13 has been used to investigate the trna conformational energy and structure in escherichia coli trna(val), trna(phe), ... | 2007 | 17872510 |
| phosphopantetheine adenylyltransferase from escherichia coli: investigation of the kinetic mechanism and role in regulation of coenzyme a biosynthesis. | phosphopantetheine adenylyltransferase (ppat) from escherichia coli is an essential hexameric enzyme that catalyzes the penultimate step in coenzyme a (coa) biosynthesis and is a target for antibacterial drug discovery. the enzyme utilizes mg-atp and phosphopantetheine (php) to generate dephospho-coa (dpcoa) and pyrophosphate. when overexpressed in e. coli, ppat copurifies with tightly bound coa, suggesting a feedback inhibitory role for this cofactor. using an enzyme-coupled assay for the forwa ... | 2007 | 17873050 |
| pathogenic mechanism of a human mitochondrial trnaphe mutation associated with myoclonic epilepsy with ragged red fibers syndrome. | human mitochondrial trna (hmt-trna) mutations are associated with a variety of diseases including mitochondrial myopathies, diabetes, encephalopathies, and deafness. because the current understanding of the precise molecular mechanisms of these mutations is limited, there is no efficient method to treat their associated mitochondrial diseases. here, we use a variety of known mutations in hmt-trna(phe) to investigate the mechanisms that lead to malfunctions. we tested the impact of hmt-trna(phe) ... | 2007 | 17878308 |
| human ribosomal protein s13 regulates expression of its own gene at the splicing step by a feedback mechanism. | the expression of ribosomal protein (rp) genes is regulated at multiple levels. in yeast, two genes are autoregulated by feedback effects of the protein on pre-mrna splicing. here, we have investigated whether similar mechanisms occur in eukaryotes with more complicated and highly regulated splicing patterns. comparisons of the sequences of ribosomal protein s13 gene (rps13) among mammals and birds revealed that intron 1 is more conserved than the other introns. transfection of hek 293 cells wit ... | 2007 | 17881366 |
| role of hsp104 in the propagation and inheritance of the [het-s] prion. | the chaperones of the clpb/hsp100 family play a central role in thermotolerance in bacteria, plants, and fungi by ensuring solubilization of heat-induced protein aggregates. in addition in yeast, hsp104 was found to be required for prion propagation. herein, we analyze the role of podospora anserina hsp104 (pahsp104) in the formation and propagation of the [het-s] prion. we show that deltapahsp104 strains propagate [het-s], making [het-s] the first native fungal prion to be propagated in the abs ... | 2007 | 17881723 |
| saturation mutagenesis of a +1 programmed frameshift-inducing mrna sequence derived from a yeast retrotransposon. | errors during the process of translating mrna information into protein products occur infrequently. frameshift errors occur less frequently than other types of errors, suggesting that the translational machinery has more robust mechanisms for precluding that kind of error. despite these mechanisms, mrna sequences have evolved that increase the frequency up to 10,000-fold. these sequences, termed programmed frameshift sites, usually consist of a heptameric nucleotide sequence, at which the change ... | 2007 | 17881742 |
| dissection of 16s rrna methyltransferase (ksga) function in escherichia coli. | a 16s rrna methyltransferase, ksga, identified originally in escherichia coli is highly conserved in all living cells, from bacteria to humans. ksga orthologs in eukaryotes possess functions in addition to their rrna methyltransferase activity. e. coli era is an essential gtp-binding protein. we recently observed that ksga functions as a multicopy suppressor for the cold-sensitive cell growth of an era mutant [era(e200k)] strain (q. lu and m. inouye, j. bacteriol. 180:5243-5246, 1998). here we o ... | 2007 | 17890303 |
| flavin-dependent thymidylate synthase thyx activity: implications for the folate cycle in bacteria. | although flavin-dependent thyx proteins show thymidylate synthase activity in vitro and functionally complement thya defects in heterologous systems, direct proof of their cellular functions is missing. using insertional mutagenesis of rhodobacter capsulatus thyx, we constructed the first defined thyx inactivation mutant. phenotypic analyses of the obtained mutant strain confirmed that r. capsulatus thyx is required for de novo thymidylate synthesis. full complementation of the r. capsulatus thy ... | 2007 | 17890305 |
| molecular architecture of strictosidine glucosidase: the gateway to the biosynthesis of the monoterpenoid indole alkaloid family. | strictosidine beta-d-glucosidase (sg) follows strictosidine synthase (str1) in the production of the reactive intermediate required for the formation of the large family of monoterpenoid indole alkaloids in plants. this family is composed of approximately 2000 structurally diverse compounds. sg plays an important role in the plant cell by activating the glucoside strictosidine and allowing it to enter the multiple indole alkaloid pathways. here, we report detailed three-dimensional information d ... | 2007 | 17890378 |
| deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks. | bacteria of the genus deinococcus are extremely resistant to ionizing radiation (ir), ultraviolet light (uv) and desiccation. the mesophile deinococcus radiodurans was the first member of this group whose genome was completely sequenced. analysis of the genome sequence of d. radiodurans, however, failed to identify unique dna repair systems. to further delineate the genes underlying the resistance phenotypes, we report the whole-genome sequence of a second deinococcus species, the thermophile de ... | 2007 | 17895995 |
| functional analysis of the gtpases enga and yhbz encoded by salmonella typhimurium. | the s. typhimurium genome encodes proteins, designated enga and yhbz, which have a high sequence identity with the gtpases enga/der and obge/cgtae of escherichia coli. the wild-type activity of the e. coli proteins is essential for normal ribosome maturation and cell viability. in order to characterize the potential involvement of the salmonella typhimurium enga and yhbz proteins in ribosome biology, we used high stringency affinity chromatography experiments to identify strongly binding ribosom ... | 2007 | 17905831 |
| evaluation of the staphylococcus aureus class c nonspecific acid phosphatase (saps) as a reporter for gene expression and protein secretion in gram-negative and gram-positive bacteria. | a phosphatase secreted by staphylococcus aureus strain 154 has previously been characterized and classified as a new member of the bacterial class c family of nonspecific acid phosphatases. as the acid phosphatase activity can be easily detected with a cost-effective plate screen assay, quantitatively measured by a simple enzyme assay, and detected by zymography, its potential use as a reporter system was investigated. the s. aureus acid phosphatase (saps) gene has been cloned and expressed from ... | 2007 | 17905879 |
| identification of promoters recognized by rna polymerase-sigmae holoenzyme from thermus thermophilus hb8. | thermus thermophilus sigma(e), an extracytoplasmic function sigma factor from the extremely thermophilic bacterium thermus thermophilus hb8, bound to the rna polymerase core enzyme and showed transcriptional activity. with the combination of in vitro transcription assay and genechip technology, we identified three promoters recognized by sigma(e). the predicted consensus promoter sequence for sigma(e) is 5'-ca(a/t)(a/c)c(a/c)-n(15)-ccgta-3'. | 2007 | 17905996 |
| electron transport chain of saccharomyces cerevisiae mitochondria is inhibited by h2o2 at succinate-cytochrome c oxidoreductase level without lipid peroxidation involvement. | the deleterious effects of h202 on the electron transport chain of yeast mitochondria and on mitochondrial lipid peroxidation were evaluated. exposure to h2o2 resulted in inhibition of the oxygen consumption in the uncoupled and phosphorylating states to 69% and 65%, respectively. the effect of h2o2 on the respiratory rate was associated with an inhibition of succinate-ubiquinone and succinate-dcip oxidoreductase activities. inhibitory effect of h2o2 on respiratory complexes was almost completel ... | 2007 | 17907001 |
| x-ray structures of two proteins belonging to pfam duf178 revealed unexpected structural similarity to the duf191 pfam family. | pfam is a comprehensive collection of protein domains and families, with a range of well-established information including genome annotation. pfam has two large series of functionally uncharacterized families, known as domains of unknown function (dufs) and uncharacterized protein families (upfs). | 2007 | 17908300 |
| cocrystallizing natural rna with its unnatural mirror image: biochemical and preliminary x-ray diffraction analysis of a 5s rrna a-helix racemate. | chemically synthesized rnas with the unnatural l-configuration possess enhanced in vivo stability and nuclease resistance, which is a highly desirable property for pharmacological applications. for a structural comparison, both l- and d-rna oligonucleotides of a shortened thermus flavus 5s rrna a-helix were chemically synthesized. the enantiomeric rna duplexes were stochiometrically cocrystallized as a racemate, which enabled analysis of the d- and l-rna enantiomers in the same crystals. in addi ... | 2007 | 17909284 |
| human trna(gly) acceptor-stem microhelix: crystallization and preliminary x-ray diffraction analysis at 1.2 a resolution. | the major dissimilarities between the eukaryotic/archaebacterial-type and eubacterial-type glycyl-trna synthetase systems (glyrs; class ii aminoacyl-trna synthetases) represent an intriguing example of evolutionarily divergent solutions to similar biological functions. the differences in the identity elements of the respective trna(gly) systems are located within the acceptor stem and include the discriminator base u73. in the present work, the human trna(gly) acceptor-stem microhelix was crysta ... | 2007 | 17909289 |
| functional smpb-ribosome interactions require tmrna. | small protein b (smpb) is a requisite component of the transfer messenger rna (tmrna)-mediated bacterial translational quality control system known as trans-translation. the initial binding of tmrna and its subsequent accommodation into the ribosomal a-site are activities intimately linked to smpb protein function. from a mechanistic perspective, two key unanswered questions that require further investigation are: 1) what constitutes a stalled ribosome recognition complex and 2) does smpb pre-bi ... | 2007 | 17911096 |
| an expanded set of amino acid analogs for the ribosomal translation of unnatural peptides. | the application of in vitro translation to the synthesis of unnatural peptides may allow the production of extremely large libraries of highly modified peptides, which are a potential source of lead compounds in the search for new pharmaceutical agents. the specificity of the translation apparatus, however, limits the diversity of unnatural amino acids that can be incorporated into peptides by ribosomal translation. we have previously shown that over 90 unnatural amino acids can be enzymatically ... | 2007 | 17912351 |
| analysis of gene order data supports vertical inheritance of the leukotoxin operon and genome rearrangements in the 5' flanking region in genus mannheimia. | the mannheimia subclades belong to the same bacterial genus, but have taken divergent paths toward their distinct lifestyles. for example, m. haemolytica + m. glucosida are potential pathogens of the respiratory tract in the mammalian suborder ruminantia, whereas m. ruminalis, the supposed sister group, lives as a commensal in the ovine rumen. we have tested the hypothesis that vertical inheritance of the leukotoxin (lktcabd) operon has occurred from the last common ancestor of genus mannheimia ... | 2007 | 17915007 |
| the carboxy-terminal coiled-coil of the rna polymerase beta'-subunit is the main binding site for gre factors. | bacterial gre transcript cleavage factors stimulate the intrinsic endonucleolytic activity of rna polymerase (rnap) to rescue stalled transcription complexes. they bind to rnap and extend their coiled-coil (cc) domains to the catalytic centre through the secondary channel. three existing models for the gre-rnap complex postulate congruent mechanisms of gre-assisted catalysis, while offering conflicting views of the gre-rnap interactions. here, we report the greb structure of escherichia coli. th ... | 2007 | 17917675 |
| evolution and functional characterization of the rh50 gene from the ammonia-oxidizing bacterium nitrosomonas europaea. | the family of ammonia and ammonium channel proteins comprises the amt proteins, which are present in all three domains of life with the notable exception of vertebrates, and the homologous rh proteins (rh50 and rh30) that have been described thus far only in eukaryotes. the existence of an rh50 gene in bacteria was first revealed by the genome sequencing of the ammonia-oxidizing bacterium nitrosomonas europaea. here we have used a phylogenetic approach to study the evolution of the n. europaea r ... | 2007 | 17921289 |
| orotate phosphoribosyltransferase from corynebacterium ammoniagenes lacking a conserved lysine. | the pyre gene, encoding orotate phosphoribosyltransferase (oprtase), was cloned by nested pcr and colony blotting from corynebacterium ammoniagenes atcc 6872, which is widely used in nucleotide production. sequence analysis shows that there is a lack of an important conserved lysine (lys 73 in salmonella enterica serovar typhimurium oprtase) in the c. ammoniagenes oprtase. this lysine has been considered to contribute to the initiation of catalysis. the enzyme was overexpressed and purified from ... | 2007 | 17921291 |
| insights into hsp70 chaperone activity from a crystal structure of the yeast hsp110 sse1. | classic hsp70 chaperones assist in diverse processes of protein folding and translocation, and hsp110s had seemed by sequence to be distant relatives within an hsp70 superfamily. the 2.4 a resolution structure of sse1 with atp shows that hsp110s are indeed hsp70 relatives, and it provides insight into allosteric coupling between sites for atp and polypeptide-substrate binding in hsp70s. subdomain structures are similar in intact sse1(atp) and in the separate hsp70 domains, but conformational dis ... | 2007 | 17923091 |
| genetic and phenotypic identification of fusidic acid-resistant mutants with the small-colony-variant phenotype in staphylococcus aureus. | small-colony variants (scvs) of staphylococcus aureus are a slow-growing subpopulation whose phenotypes can include resistance to aminoglycosides, defects in electron transport, and enhanced persistence in mammalian cells. here we show that a subset of mutants selected as scvs by reduced susceptibility to aminoglycosides are resistant to the antibiotic fusidic acid (fa) and conversely that a subset of mutants selected for resistance to fa are scvs. mutation analysis reveals different genetic cla ... | 2007 | 17923494 |
| transfer rna in the hybrid p/e state: correlating molecular dynamics simulations with cryo-em data. | transfer rna (trna) transiently occupies the hybrid p/e state (p/e-trna) when mrna-trna are translocated in the ribosome. in this study, we characterize the structure of p/e-trna and its interactions with the ribosome by correlating the results from molecular dynamics simulations on free trna with the cryo-em map of p/e-trna. in our approach, we show that the cryo-em map may be interpreted as a conformational average. along the molecular dynamics trajectories (44 ns, 18 ns, and 18 ns), some of t ... | 2007 | 17925437 |
| a cysteine-rich ccg domain contains a novel [4fe-4s] cluster binding motif as deduced from studies with subunit b of heterodisulfide reductase from methanothermobacter marburgensis. | heterodisulfide reductase (hdr) of methanogenic archaea with its active-site [4fe-4s] cluster catalyzes the reversible reduction of the heterodisulfide (com-s-s-cob) of the methanogenic coenzyme m (com-sh) and coenzyme b (cob-sh). com-hdr, a mechanistic-based paramagnetic intermediate generated upon half-reaction of the oxidized enzyme with com-sh, is a novel type of [4fe-4s]3+ cluster with com-sh as a ligand. subunit hdrb of the methanothermobacter marburgensis hdrabc holoenzyme contains two cy ... | 2007 | 17929940 |
| separating the effects of mutation and selection in producing dna skew in bacterial chromosomes. | many bacterial chromosomes display nucleotide asymmetry, or skew, between the leading and lagging strands of replication. mutational differences between these strands result in an overall pattern of skew that is centered about the origin of replication. such a pattern could also arise from selection coupled with a bias for genes coded on the leading strand. the relative contributions of selection and mutation in producing compositional skew are largely unknown. | 2007 | 17935620 |
| interactions and dynamics of the shine dalgarno helix in the 70s ribosome. | the crystal structure of an initiation-like 70s ribosome complex containing an 8-bp shine-dalgarno (sd) helix was determined at 3.8-a resolution. translation-libration-screw analysis showed that the inherent anisotropic motions of the sd helix were biased along its helical axis, suggesting that during the first step of translocation, the sd helix moves along its helical screw axis. contacts between the sd helix and the ribosome were primarily through interactions with helices 23a, 26, and 28 of ... | 2007 | 17940016 |
| the wobble hypothesis revisited: uridine-5-oxyacetic acid is critical for reading of g-ending codons. | according to crick's wobble hypothesis, trnas with uridine at the wobble position (position 34) recognize a- and g-, but not u- or c-ending codons. however, u in the wobble position is almost always modified, and salmonella enterica trnas containing the modified nucleoside uridine-5-oxyacetic acid (cmo(5)u34) at this position are predicted to recognize u- (but not c-) ending codons, in addition to a- and g-ending codons. we have constructed a set of s. enterica mutants with only the cmo(5)u-cont ... | 2007 | 17942742 |
| the 3d rrna modification maps database: with interactive tools for ribosome analysis. | the 3d rrna modification maps database is the first general resource of information about the locations of modified nucleotides within the 3d structure of the full ribosome, with mrna and trnas in the a-, p- and e-sites. the database supports analyses for several model organisms, including higher eukaryotes, and enables users to construct 3d maps for other organisms. data are provided for human and plant (arabidopsis) ribosomes, and for other representative organisms from eubacteria, archaea and ... | 2008 | 17947322 |
| the 3d rrna modification maps database: with interactive tools for ribosome analysis. | the 3d rrna modification maps database is the first general resource of information about the locations of modified nucleotides within the 3d structure of the full ribosome, with mrna and trnas in the a-, p- and e-sites. the database supports analyses for several model organisms, including higher eukaryotes, and enables users to construct 3d maps for other organisms. data are provided for human and plant (arabidopsis) ribosomes, and for other representative organisms from eubacteria, archaea and ... | 2008 | 17947322 |
| thiostrepton inhibition of trna delivery to the ribosome. | ribosome-stimulated hydrolysis of guanosine-5'-triphosphate (gtp) by guanosine triphosphatase (gtpase) translation factors drives protein synthesis by the ribosome. allosteric coupling of gtp hydrolysis by elongation factor tu (ef-tu) at the ribosomal gtpase center to messenger rna (mrna) codon:aminoacyl-transfer rna (aa-trna) anticodon recognition at the ribosomal decoding site is essential for accurate and rapid aa-trna selection. here we use single-molecule methods to investigate the mechanis ... | 2007 | 17951333 |
| the structure of mycobacteria 2c-methyl-d-erythritol-2,4-cyclodiphosphate synthase, an essential enzyme, provides a platform for drug discovery. | the prevalence of tuberculosis, the prolonged and expensive treatment that this disease requires and an increase in drug resistance indicate an urgent need for new treatments. the 1-deoxy-d-xylulose 5-phosphate pathway of isoprenoid precursor biosynthesis is an attractive chemotherapeutic target because it occurs in many pathogens, including mycobacterium tuberculosis, and is absent from humans. to underpin future drug development it is important to assess which enzymes in this biosynthetic path ... | 2007 | 17956607 |
| interaction of smpb with ribosome from directed hydroxyl radical probing. | to add a tag-peptide for degradation to the nascent polypeptide in a stalled ribosome, an unusual translation called trans-translation is facilitated by transfer-messenger rna (tmrna) having an upper half of the trna structure and the sequence encoding the tag-peptide except the first alanine. during this event, tmrna enters the vacant a-site of the stalled ribosome without a codon-anticodon interaction, but with a protein factor smpb. here, we studied the sites and modes of binding of smpb to t ... | 2007 | 17959652 |
| domain i of ribosomal protein l1 is sufficient for specific rna binding. | ribosomal protein l1 has a dual function as a ribosomal protein binding 23s rrna and as a translational repressor binding its mrna. l1 is a two-domain protein with n- and c-termini located in domain i. earlier it was shown that l1 interacts with the same targets on both rrna and mrna mainly through domain i. we have suggested that domain i is necessary and sufficient for specific rna-binding by l1. to test this hypothesis, a truncation mutant of l1 from thermus thermophilus, representing domain ... | 2007 | 17962298 |
| the activities and function of molecular chaperones in the endoplasmic reticulum. | most proteins in the secretory pathway are translated, folded, and subjected to quality control at the endoplasmic reticulum (er). these processes must be flexible enough to process diverse protein conformations, yet specific enough to recognize when a protein should be degraded. molecular chaperones are responsible for this decision making process. er associated chaperones assist in polypeptide translocation, protein folding, and er associated degradation (erad). nevertheless, we are only begin ... | 2007 | 17964199 |
| knotted and topologically complex proteins as models for studying folding and stability. | among proteins of known three-dimensional structure, only a few possess complex topological features such as knotted or interlinked (catenated) protein backbones. such unusual proteins offer potentially unique insights into folding pathways and stabilization mechanisms. they also present special challenges for both theorists and computational scientists interested in understanding and predicting protein-folding behavior. here, we review complex topological features in proteins with a focus on re ... | 2007 | 17967433 |
| mutational analysis of s12 protein and implications for the accuracy of decoding by the ribosome. | the fidelity of aminoacyl-trna selection by the ribosome depends on a conformational switch in the decoding center of the small ribosomal subunit induced by cognate but not by near-cognate aminoacyl-trna. the aminoglycosides paromomycin and streptomycin bind to the decoding center and induce related structural rearrangements that explain their observed effects on miscoding. structural and biochemical studies have identified ribosomal protein s12 (as well as specific nucleotides in 16s ribosomal ... | 2007 | 17967466 |
| novel hexamerization motif is discovered in a conserved cytoplasmic protein from salmonella typhimurium. | the cytoplasmic protein stm3548 of unknown function obtained from a strain of salmonella typhimurium was determined by x-ray crystallography at a resolution of 2.25 a. the asymmetric unit contains a hexamer of structurally identical monomers. the monomer is a globular domain with a long beta-hairpin protrusion that distinguishes this structure. this beta-hairpin occupies a central position in the hexamer, and its residues participate in the majority of interactions between subunits of the hexame ... | 2007 | 17968677 |
| translation initiation region sequence preferences in escherichia coli. | the mrna translation initiation region (tir) comprises the initiator codon, shine-dalgarno (sd) sequence and translational enhancers. probably the most abundant class of enhancers contains a/u-rich sequences. we have tested the influence of sd sequence length and the presence of enhancers on the efficiency of translation initiation. | 2007 | 17973990 |
| development of a novel one-tube isothermal reverse transcription thermophilic helicase-dependent amplification platform for rapid rna detection. | the high complexity and cost of polymerase chain reaction-based molecular diagnostics sometimes limits their use in the clinical diagnostics setting. a new helicase-based isothermal amplification method offers an alternative to standard polymerase chain reaction, allowing amplification and detection of specific dna sequences at a constant reaction temperature without thermocycling equipment. herein, we describe the development of a novel one-tube isothermal reverse transcription-thermophilic hel ... | 2007 | 17975029 |
| zinc is the metal cofactor of borrelia burgdorferi peptide deformylase. | peptide deformylase (pdf, e.c. 3.5.1.88) catalyzes the removal of n-terminal formyl groups from nascent ribosome-synthesized polypeptides. pdf contains a catalytically essential divalent metal ion, which is tetrahedrally coordinated by three protein ligands (his, his, and cys) and a water molecule. previous studies revealed that the metal cofactor is a fe2+ ion in escherichia coli and many other bacterial pdfs. in this work, we found that pdfs from two iron-deficient bacteria, borrelia burgdorfe ... | 2007 | 17977509 |
| rna catalysis: ribozymes, ribosomes, and riboswitches. | the catalytic mechanisms employed by rna are chemically more diverse than initially suspected. divalent metal ions, nucleobases, ribosyl hydroxyl groups, and even functional groups on metabolic cofactors all contribute to the various strategies employed by rna enzymes. this catalytic breadth raises intriguing evolutionary questions about how rna lost its biological role in some cases, but not in others, and what catalytic roles rna might still be playing in biology. | 2007 | 17981494 |
| the role of the mitochondrial glycine cleavage complex in the metabolism and virulence of the protozoan parasite leishmania major. | for the human pathogen leishmania major, a key metabolic function is the synthesis of thymidylate, which requires 5,10-methylenetetrahydrofolate (5,10-ch(2)-thf). 5,10-ch(2)-thf can be synthesized from glycine by the mitochondrial glycine cleavage complex (gcc). bioinformatic analysis revealed the four subunits of the gcc in the l. major genome, and the role of the gcc in parasite metabolism and virulence was assessed through studies of the p subunit (glycine decarboxylase (gcvp)). first, a tagg ... | 2008 | 17981801 |
| the role of the mitochondrial glycine cleavage complex in the metabolism and virulence of the protozoan parasite leishmania major. | for the human pathogen leishmania major, a key metabolic function is the synthesis of thymidylate, which requires 5,10-methylenetetrahydrofolate (5,10-ch(2)-thf). 5,10-ch(2)-thf can be synthesized from glycine by the mitochondrial glycine cleavage complex (gcc). bioinformatic analysis revealed the four subunits of the gcc in the l. major genome, and the role of the gcc in parasite metabolism and virulence was assessed through studies of the p subunit (glycine decarboxylase (gcvp)). first, a tagg ... | 2008 | 17981801 |
| detecting coevolution in and among protein domains. | correlated changes of nucleic or amino acids have provided strong information about the structures and interactions of molecules. despite the rich literature in coevolutionary sequence analysis, previous methods often have to trade off between generality, simplicity, phylogenetic information, and specific knowledge about interactions. furthermore, despite the evidence of coevolution in selected protein families, a comprehensive screening of coevolution among all protein domains is still lacking. ... | 2007 | 17983264 |
| specific interaction between ef-g and rrf and its implication for gtp-dependent ribosome splitting into subunits. | after termination of protein synthesis, the bacterial ribosome is split into its 30s and 50s subunits by the action of ribosome recycling factor (rrf) and elongation factor g (ef-g) in a guanosine 5'-triphosphate (gtp)-hydrolysis-dependent manner. based on a previous cryo-electron microscopy study of ribosomal complexes, we have proposed that the binding of ef-g to an rrf-containing posttermination ribosome triggers an interdomain rotation of rrf, which destabilizes two strong intersubunit bridg ... | 2007 | 17996252 |
| structural basis of j cochaperone binding and regulation of hsp70. | the many protein processing reactions of the atp-hydrolyzing hsp70s are regulated by j cochaperones, which contain j domains that stimulate hsp70 atpase activity and accessory domains that present protein substrates to hsp70s. we report the structure of a j domain complexed with a j responsive portion of a mammalian hsp70. the j domain activates atpase activity by directing the linker that connects the hsp70 nucleotide binding domain (nbd) and substrate binding domain (sbd) toward a hydrophobic ... | 2007 | 17996706 |
| structural aspects of rbfa action during small ribosomal subunit assembly. | ribosome binding factor a (rbfa) is a bacterial cold shock response protein, required for an efficient processing of the 5' end of the 16s ribosomal rna (rrna) during assembly of the small (30s) ribosomal subunit. here we present a crystal structure of thermus thermophilus (tth) rbfa and a three-dimensional cryo-electron microscopic (em) map of the tth 30s*rbfa complex. rbfa binds to the 30s subunit in a position overlapping the binding sites of the a and p site trnas, and rbfa's functionally im ... | 2007 | 17996707 |
| two distinct components of release factor function uncovered by nucleophile partitioning analysis. | during translation termination, release factor (rf) protein catalyzes a hydrolytic reaction in the large subunit peptidyl transferase center to release the finished polypeptide chain. while the mechanism of catalysis of peptide release remains obscure, important contributing factors have been identified, including conserved active-site nucleotides and a ggq tripeptide motif in the rf. here we describe pre-steady-state kinetic and nucleophile competition experiments to examine rf contributions to ... | 2007 | 17996709 |
| fourier transform infrared characterization of a cub-nitrosyl complex in cytochrome ba3 from thermus thermophilus: relevance to no reductase activity in heme-copper terminal oxidases. | the two heme-copper terminal oxidases of thermus thermophilus have been shown to catalyze the two-electron reduction of nitric oxide (no) to nitrous oxide (n2o) [giuffre, a.; stubauer, g.; sarti, p.; brunori, m.; zumft, w. g.; buse, g.; soulimane, t. proc. natl. acad. sci. u.s.a. 1999, 96, 14718-14723]. while it is well-established that no binds to the reduced heme a3 to form a low-spin heme {feno}7 species, the role cub plays in the binding of the second no remains unclear. here we present low- ... | 2007 | 17997553 |
| structural basis of a ribozyme's thermostability: p1-l9 interdomain interaction in rnase p rna. | for stability, many catalytic rnas rely on long-range tertiary interactions, the precise role of each often being unclear. here we demonstrate that one of the three interdomain architectural struts of rnase p rna (p rna) is the key to activity at higher temperatures: disrupting the p1-l9 helix-tetraloop interaction in p rna of the thermophile thermus thermophilus decreased activity at high temperatures in the rna-alone reaction and at low mg2+ concentrations in the holoenzyme reaction. conversel ... | 2008 | 17998289 |
| a novel chromatography system to isolate active ribosomes from pathogenic bacteria. | we have developed a novel chromatography for the rapid isolation of active ribosomes from bacteria without the use of harsh conditions or lengthy procedures that damage ribosomes. ribosomes interact with an alkyl linker attached to the resin, apparently through their rna component. examples are given with ribosomes from escherichia coli, deinococcus radiodurans, and with clinical isolates of streptococcus pneumoniae and methicillin-resistant staphylococcus aureus (mrsa). the ribosomes obtained b ... | 2008 | 17998293 |
| the process of displacing the single-stranded dna-binding protein from single-stranded dna by reco and recr proteins. | the regions of single-stranded (ss) dna that result from dna damage are immediately coated by the ssdna-binding protein (ssb). recf pathway proteins facilitate the displacement of ssb from ssdna, allowing the reca protein to form protein filaments on the ssdna region, which facilitates the process of recombinational dna repair. in this study, we examined the mechanism of ssb displacement from ssdna using purified thermus thermophilus recf pathway proteins. to date, reco and recr are thought to a ... | 2008 | 18000001 |
| the process of mrna-trna translocation. | in the elongation cycle of translation, translocation is the process that advances the mrna-trna moiety on the ribosome, to allow the next codon to move into the decoding center. new results obtained by cryoelectron microscopy, interpreted in the light of x-ray structures and kinetic data, allow us to develop a model of the molecular events during translocation. | 2007 | 18003906 |
| eukaryotic ribosomal rna determinants of aminoglycoside resistance and their role in translational fidelity. | recent studies of prokaryotic ribosomes have dramatically increased our knowledge of ribosomal rna (rrna) structure, functional centers, and their interactions with antibiotics. however, much less is known about how rrna function differs between prokaryotic and eukaryotic ribosomes. the core decoding sites are identical in yeast and human 18s rrnas, suggesting that insights obtained in studies with yeast rrna mutants can provide information about ribosome function in both species. in this study, ... | 2008 | 18003936 |
| a comprehensive analysis of non-sequential alignments between all protein structures. | the majority of relations between proteins can be represented as a conventional sequential alignment. nevertheless, unusual non-sequential alignments with different connectivity of the aligned fragments in compared proteins have been reported by many researchers. it is interesting to understand those non-sequential alignments; are they unique, sporadic cases or they occur frequently; do they belong to a few specific folds or spread among many different folds, as a common feature of protein struc ... | 2007 | 18005453 |
| cloning, expression, purification, crystallization and preliminary x-ray diffraction analysis of universal stress protein f (ynaf) from salmonella typhimurium. | the universal stress protein uspf (ynaf) is a small cytoplasmic bacterial protein. the expression of stress proteins is enhanced when cells are exposed to heat shock, nutrition starvation and certain other stress-inducing agents. ynaf promotes cell survival during prolonged exposure to stress and may activate a general mechanism for stress endurance. this manuscript reports preliminary crystallographic studies on ynaf from salmonella typhimurium. the gene coding for ynaf was cloned and overexpre ... | 2007 | 18007050 |
| crystallization and preliminary x-ray diffraction studies of tetrameric malate dehydrogenase from the novel antarctic psychrophile flavobacterium frigidimaris kuc-1. | flavobacterium frigidimaris kuc-1 is a novel psychrotolerant bacterium isolated from antarctic seawater. malate dehydrogenase (mdh) is an essential metabolic enzyme in the citric acid cycle and has been cloned, overexpressed and purified from f. frigidimaris kuc-1. in contrast to the already known dimeric form of mdh from the psychrophile aquaspirillium arcticum, f. frigidimaris mdh exists as a tetramer. it was crystallized at 288 k by the hanging-drop vapour-diffusion method using ammonium sulf ... | 2007 | 18007057 |
| the [fefe] hydrogenase of nyctotherus ovalis has a chimeric origin. | the hydrogenosomes of the anaerobic ciliate nyctotherus ovalis show how mitochondria can evolve into hydrogenosomes because they possess a mitochondrial genome and parts of an electron-transport chain on the one hand, and a hydrogenase on the other hand. the hydrogenase permits direct reoxidation of nadh because it consists of a [fefe] hydrogenase module that is fused to two modules, which are homologous to the 24 kda and the 51 kda subunits of a mitochondrial complex i. | 2007 | 18021395 |
| structural basis for signal-sequence recognition by the translocase motor seca as determined by nmr. | recognition of signal sequences by cognate receptors controls the entry of virtually all proteins to export pathways. despite its importance, this process remains poorly understood. here, we present the solution structure of a signal peptide bound to seca, the 204 kda atpase motor of the sec translocase. upon encounter, the signal peptide forms an alpha-helix that inserts into a flexible and elongated groove in seca. the mode of binding is bimodal, with both hydrophobic and electrostatic interac ... | 2007 | 18022369 |
| the methyltransferase yfgb/rlmn is responsible for modification of adenosine 2503 in 23s rrna. | a2503 in 23s rrna of the gram-negative bacterium escherichia coli is located in a functionally important region of the ribosome, at the entrance to the nascent peptide exit tunnel. in e. coli, and likely in other species, this adenosine residue is post-transcriptionally modified to m2a. the enzyme responsible for this modification was previously unknown. we identified e. coli protein yfgb, which belongs to the radical sam enzyme superfamily, as the methyltransferase that modifies a2503 of 23s rr ... | 2008 | 18025251 |
| simple fluorescent sensors engineered with catalytic dna 'mgz' based on a non-classic allosteric design. | most nae (nucleic acid enzyme) sensors are composed of an rna-cleaving catalytic motif and an aptameric receptor. they operate by activating or repressing the catalytic activity of a relevant nae through the conformational change in the aptamer upon target binding. to transduce a molecular recognition event to a fluorescence signal, a fluorophore-quencher pair is attached to opposite ends of the rna substrate such that when the nae cleaves the substrate, an increased level of fluorescence can be ... | 2007 | 18030352 |
| pseudouridylation of helix 69 of 23s rrna is necessary for an effective translation termination. | escherichia coli strains with inactivated rlud genes were previously found to lack the conserved pseudouridines in helix 69 of 23s ribosomal rna and to grow slowly. a suppressor mutant was isolated with a near normal growth rate that had changed the conserved glu-172 codon to a lys codon in prfb, encoding translation termination factor rf2. when nonsense suppression in strains with all combinations of prfb(+)/prfb(e172k) and rlud(+)/rlud::cat was analyzed, misreading of all three stop codons as ... | 2007 | 18032607 |
| protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures. | the number of macromolecular structures deposited in the protein data bank now exceeds 45,000, with the vast majority determined using crystallographic methods. thousands of studies describing such structures have been published in the scientific literature, and 14 nobel prizes in chemistry or medicine have been awarded to protein crystallographers. as important as these structures are for understanding the processes that take place in living organisms and also for practical applications such as ... | 2007 | 18034855 |
| protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures. | the number of macromolecular structures deposited in the protein data bank now exceeds 45,000, with the vast majority determined using crystallographic methods. thousands of studies describing such structures have been published in the scientific literature, and 14 nobel prizes in chemistry or medicine have been awarded to protein crystallographers. as important as these structures are for understanding the processes that take place in living organisms and also for practical applications such as ... | 2007 | 18034855 |
| proline modulates the intracellular redox environment and protects mammalian cells against oxidative stress. | the potential of proline to suppress reactive oxygen species (ros) and apoptosis in mammalian cells was tested by manipulating intracellular proline levels exogenously and endogenously by overexpression of proline metabolic enzymes. proline was observed to protect cells against h(2)o(2), tert-butyl hydroperoxide, and a carcinogenic oxidative stress inducer but was not effective against superoxide generators such as menadione. oxidative stress protection by proline requires the secondary amine of ... | 2007 | 18036351 |
| proline modulates the intracellular redox environment and protects mammalian cells against oxidative stress. | the potential of proline to suppress reactive oxygen species (ros) and apoptosis in mammalian cells was tested by manipulating intracellular proline levels exogenously and endogenously by overexpression of proline metabolic enzymes. proline was observed to protect cells against h(2)o(2), tert-butyl hydroperoxide, and a carcinogenic oxidative stress inducer but was not effective against superoxide generators such as menadione. oxidative stress protection by proline requires the secondary amine of ... | 2007 | 18036351 |
| the stator complex of the a1a0-atp synthase--structural characterization of the e and h subunits. | archaeal atp synthase (a-atpase) is the functional homolog to the atp synthase found in bacteria, mitochondria and chloroplasts, but the enzyme is structurally more related to the proton-pumping vacuolar atpase found in the endomembrane system of eukaryotes. we have cloned, overexpressed and characterized the stator-forming subunits e and h of the a-atpase from the thermoacidophilic archaeon, thermoplasma acidophilum. size exclusion chromatography, cd, matrix-assisted laser desorption ionization ... | 2008 | 18036615 |
| the stator complex of the a1a0-atp synthase--structural characterization of the e and h subunits. | archaeal atp synthase (a-atpase) is the functional homolog to the atp synthase found in bacteria, mitochondria and chloroplasts, but the enzyme is structurally more related to the proton-pumping vacuolar atpase found in the endomembrane system of eukaryotes. we have cloned, overexpressed and characterized the stator-forming subunits e and h of the a-atpase from the thermoacidophilic archaeon, thermoplasma acidophilum. size exclusion chromatography, cd, matrix-assisted laser desorption ionization ... | 2008 | 18036615 |
| reversible dissociation of flavin mononucleotide from the mammalian membrane-bound nadh: ubiquinone oxidoreductase (complex i). | conditions for the reversible dissociation of flavin mononucleotide (fmn) from the membrane-bound mitochondrial nadh:ubiquinone oxidoreductase (complex i) are described. the catalytic activities of the enzyme, i.e. rotenone-insensitive nadh:hexaammineruthenium iii reductase and rotenone-sensitive nadh:quinone reductase decline when bovine heart submitochondrial particles are incubated with nadh in the presence of rotenone or cyanide at alkaline ph. fmn protects and fully restores the nadh-induce ... | 2007 | 18037377 |
| structural basis for different substrate specificities of two adp-ribose pyrophosphatases from thermus thermophilus hb8. | adp-ribose (adpr) is one of the main substrates of nudix proteins. among the eight nudix proteins of thermus thermophilus hb8, we previously determined the crystal structure of ndx4, an adpr pyrophosphatase (adprase). in this study we show that ndx2 of t. thermophilus also preferentially hydrolyzes adpr and flavin adenine dinucleotide and have determined its crystal structure. we have determined the structures of ndx2 alone and in complex with mg2+, with mg2+ and amp, and with mg2+ and a nonhydr ... | 2008 | 18039767 |
| clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea. | an evolutionary classification of genes from sequenced genomes that distinguishes between orthologs and paralogs is indispensable for genome annotation and evolutionary reconstruction. shortly after multiple genome sequences of bacteria, archaea, and unicellular eukaryotes became available, an attempt on such a classification was implemented in clusters of orthologous groups of proteins (cogs). rapid accumulation of genome sequences creates opportunities for refining cogs but also represents a c ... | 2007 | 18042280 |
| cryo-em study of the spinach chloroplast ribosome reveals the structural and functional roles of plastid-specific ribosomal proteins. | protein synthesis in the chloroplast is carried out by chloroplast ribosomes (chloro-ribosome) and regulated in a light-dependent manner. chloroplast or plastid ribosomal proteins (prps) generally are larger than their bacterial counterparts, and chloro-ribosomes contain additional plastid-specific ribosomal proteins (psrps); however, it is unclear to what extent these proteins play structural or regulatory roles during translation. we have obtained a three-dimensional cryo-em map of the spinach ... | 2007 | 18042701 |
| assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data. | comparison of completely sequenced microbial genomes has revealed how fluid these genomes are. detecting synteny blocks requires reliable methods to determining the orthologs among the whole set of homologs detected by exhaustive comparisons between each pair of completely sequenced genomes. this is a complex and difficult problem in the field of comparative genomics but will help to better understand the way prokaryotic genomes are evolving. | 2007 | 18047665 |
| discrimination of class i cyclobutane pyrimidine dimer photolyase from blue light photoreceptors by single methionine residue. | dna photolyase recognizes ultraviolet-damaged dna and breaks improperly formed covalent bonds within the cyclobutane pyrimidine dimer by a light-activated electron transfer reaction between the flavin adenine dinucleotide, the electron donor, and cyclobutane pyrimidine dimer, the electron acceptor. theoretical analysis of the electron-tunneling pathways of the dna photolyase derived from anacystis nidulans can reveal the active role of the protein environment in the electron transfer reaction. h ... | 2008 | 18055535 |
| discrimination of class i cyclobutane pyrimidine dimer photolyase from blue light photoreceptors by single methionine residue. | dna photolyase recognizes ultraviolet-damaged dna and breaks improperly formed covalent bonds within the cyclobutane pyrimidine dimer by a light-activated electron transfer reaction between the flavin adenine dinucleotide, the electron donor, and cyclobutane pyrimidine dimer, the electron acceptor. theoretical analysis of the electron-tunneling pathways of the dna photolyase derived from anacystis nidulans can reveal the active role of the protein environment in the electron transfer reaction. h ... | 2008 | 18055535 |
| redox properties of thermus thermophilus ba3: different electron-proton coupling in oxygen reductases? | a comprehensive study of the thermodynamic redox behavior of the hemes of the ba3 enzyme from thermus thermophilus, a b-type heme-copper oxygen reductase, is presented. this enzyme, in contrast to those having a single type of heme, allows the b- and a-type hemes to be monitored separately by visible spectroscopy and the reduction potential of each heme to be determined unequivocally. the relative order of the midpoint reduction potentials of each center changed in the ph range from 6 to 8.4, an ... | 2008 | 18065462 |