Publications

scaffolding as an organizing principle in trans-translation. the roles of small protein b and ribosomal protein s1.	a eubacterial ribosome stalled on a defective mrna can be released through a quality control mechanism referred to as trans-translation, which depends on the coordinating binding actions of transfer-messenger rna, small protein b, and ribosome protein s1. by means of cryo-electron microscopy, we obtained a map of the complex composed of a stalled ribosome and small protein b, which appears near the decoding center. this result suggests that, when lacking a codon, the a-site on the small subunit ...	2007	17179154
functional organization of the rpb5 subunit shared by the three yeast rna polymerases.	rpb5, a subunit shared by the three yeast rna polymerases, combines a eukaryotic n-terminal module with a globular c-end conserved in all non-bacterial enzymes. conditional and lethal mutants of the moderately conserved eukaryotic module showed that its large n-terminal helix and a short motif at the end of the module are critical in vivo. lethal or conditional mutants of the c-terminal globe altered the binding of rpb5 to rpb1-beta25/26 (prolonging the bridge helix) and rpb1-alpha44/47 (ahead o ...	2007	17179178
functional organization of the rpb5 subunit shared by the three yeast rna polymerases.	rpb5, a subunit shared by the three yeast rna polymerases, combines a eukaryotic n-terminal module with a globular c-end conserved in all non-bacterial enzymes. conditional and lethal mutants of the moderately conserved eukaryotic module showed that its large n-terminal helix and a short motif at the end of the module are critical in vivo. lethal or conditional mutants of the c-terminal globe altered the binding of rpb5 to rpb1-beta25/26 (prolonging the bridge helix) and rpb1-alpha44/47 (ahead o ...	2007	17179178
crystallization and preliminary crystallographic analysis of molybdenum-cofactor biosynthesis protein c from thermus thermophilus.	the gram-negative aerobic eubacterium thermus thermophilus is an extremely important thermophilic microorganism that was originally isolated from a thermal vent environment in japan. the molybdenum cofactor in this organism is considered to be an essential component required by enzymes that catalyze diverse key reactions in the global metabolism of carbon, nitrogen and sulfur. the molybdenum-cofactor biosynthesis protein c derived from t. thermophilus was crystallized in two different space grou ...	2007	17183168
crystallization and preliminary x-ray diffraction analysis of an escherichia coli trna(gly) acceptor-stem microhelix.	the trna(gly) and glycyl-trna synthetase (glyrs) system is an evolutionary special case within the class ii aminoacyl-trna synthetases because two divergent types of glyrs exist: an archaebacterial/human type and an eubacterial type. the trna identity elements which determine the correct aminoacylation process are located in the aminoacyl domain of trna(gly). to obtain further insight concerning structural investigation of the identity elements, the escherichia coli seven-base-pair trna(gly) acc ...	2007	17183173
crystallization and preliminary x-ray diffraction analysis of an escherichia coli trna(gly) acceptor-stem microhelix.	the trna(gly) and glycyl-trna synthetase (glyrs) system is an evolutionary special case within the class ii aminoacyl-trna synthetases because two divergent types of glyrs exist: an archaebacterial/human type and an eubacterial type. the trna identity elements which determine the correct aminoacylation process are located in the aminoacyl domain of trna(gly). to obtain further insight concerning structural investigation of the identity elements, the escherichia coli seven-base-pair trna(gly) acc ...	2007	17183173
catalases are nad(p)h-dependent tellurite reductases.	reactive oxygen species damage intracellular targets and are implicated in cancer, genetic disease, mutagenesis, and aging. catalases are among the key enzymatic defenses against one of the most physiologically abundant reactive oxygen species, hydrogen peroxide. the well-studied, heme-dependent catalases accelerate the rate of the dismutation of peroxide to molecular oxygen and water with near kinetic perfection. many catalases also bind the cofactors nadph and nadh tenaciously, but, surprising ...	2006	17183702
experimental rugged fitness landscape in protein sequence space.	the fitness landscape in sequence space determines the process of biomolecular evolution. to plot the fitness landscape of protein function, we carried out in vitro molecular evolution beginning with a defective fd phage carrying a random polypeptide of 139 amino acids in place of the g3p minor coat protein d2 domain, which is essential for phage infection. after 20 cycles of random substitution at sites 12-130 of the initial random polypeptide and selection for infectivity, the selected phage s ...	2006	17183728
mechanism of trna-dependent editing in translational quality control.	protein synthesis requires the pairing of amino acids with trnas catalyzed by the aminoacyl-trna synthetases. the synthetases are highly specific, but errors in amino acid selection are occasionally made, opening the door to inaccurate translation of the genetic code. the fidelity of protein synthesis is maintained by the editing activities of synthetases, which remove noncognate amino acids from trnas before they are delivered to the ribosome. although editing has been described in numerous syn ...	2006	17185419
mechanism of trna-dependent editing in translational quality control.	protein synthesis requires the pairing of amino acids with trnas catalyzed by the aminoacyl-trna synthetases. the synthetases are highly specific, but errors in amino acid selection are occasionally made, opening the door to inaccurate translation of the genetic code. the fidelity of protein synthesis is maintained by the editing activities of synthetases, which remove noncognate amino acids from trnas before they are delivered to the ribosome. although editing has been described in numerous syn ...	2006	17185419
temporal regulation of viral transcription during development of thermus thermophilus bacteriophage phiys40.	regulation of gene expression of lytic bacteriophage varphiys40 that infects the thermophilic bacterium thermus thermophilus was investigated and three temporal classes of phage genes, early, middle, and late, were revealed. varphiys40 does not encode a (rnap) and must rely on host rnap for transcription of its genes. bioinformatic analysis using a model of thermus promoters predicted 43 putative sigma(a)-dependent -10/-35 class phage promoters. a randomly chosen subset of those promoters was sh ...	2007	17187825
high performance computing in biology: multimillion atom simulations of nanoscale systems.	computational methods have been used in biology for sequence analysis (bioinformatics), all-atom simulation (molecular dynamics and quantum calculations), and more recently for modeling biological networks (systems biology). of these three techniques, all-atom simulation is currently the most computationally demanding, in terms of compute load, communication speed, and memory load. breakthroughs in electrostatic force calculation and dynamic load balancing have enabled molecular dynamics simulat ...	2007	17187988
high performance computing in biology: multimillion atom simulations of nanoscale systems.	computational methods have been used in biology for sequence analysis (bioinformatics), all-atom simulation (molecular dynamics and quantum calculations), and more recently for modeling biological networks (systems biology). of these three techniques, all-atom simulation is currently the most computationally demanding, in terms of compute load, communication speed, and memory load. breakthroughs in electrostatic force calculation and dynamic load balancing have enabled molecular dynamics simulat ...	2007	17187988
glucosylglycerate biosynthesis in the deepest lineage of the bacteria: characterization of the thermophilic proteins gpgs and gpgp from persephonella marina.	the pathway for the synthesis of glucosylglycerate (gg) in the thermophilic bacterium persephonella marina is proposed based on the activities of recombinant glucosyl-3-phosphoglycerate (gpg) synthase (gpgs) and glucosyl-3-phosphoglycerate phosphatase (gpgp). the sequences of gpgs and gpgp from the cold-adapted bacterium methanococcoides burtonii were used to identify the homologues in the genome of p. marina, which were separately cloned and overexpressed as his-tagged proteins in escherichia c ...	2007	17189358
glucosylglycerate biosynthesis in the deepest lineage of the bacteria: characterization of the thermophilic proteins gpgs and gpgp from persephonella marina.	the pathway for the synthesis of glucosylglycerate (gg) in the thermophilic bacterium persephonella marina is proposed based on the activities of recombinant glucosyl-3-phosphoglycerate (gpg) synthase (gpgs) and glucosyl-3-phosphoglycerate phosphatase (gpgp). the sequences of gpgs and gpgp from the cold-adapted bacterium methanococcoides burtonii were used to identify the homologues in the genome of p. marina, which were separately cloned and overexpressed as his-tagged proteins in escherichia c ...	2007	17189358
mass spectrometry-based detection of transfer rnas by their signature endonuclease digestion products.	the separation of biologically active, pure, and specific trnas is difficult due to the overall similarity in secondary and tertiary structures of different trnas. because prior methods do not facilitate high-resolution separations of the extremely complex mixture represented by a cellular trna population, global studies of trna identity and/or abundance are difficult. we have discovered that the enzymatic digestion of an individual trna by a ribonuclease (e.g., rnase t1) will generate digestion ...	2007	17194720
escherichia coli as a platform for functional expression of plant p450 carotene hydroxylases.	carotenoids and their derivatives are essential for growth, development, and signaling in plants and have an added benefit as nutraceuticals in food crops. despite the importance of the biosynthetic pathway, there remain open questions regarding some of the later enzymes in the pathway. the cyp97 family of p450 enzymes was predicted to function in carotene ring hydroxylation, to convert provitamin a carotenes to non-provitamin a xanthophylls. however, substrate specificity was difficult to inves ...	2007	17196929
escherichia coli as a platform for functional expression of plant p450 carotene hydroxylases.	carotenoids and their derivatives are essential for growth, development, and signaling in plants and have an added benefit as nutraceuticals in food crops. despite the importance of the biosynthetic pathway, there remain open questions regarding some of the later enzymes in the pathway. the cyp97 family of p450 enzymes was predicted to function in carotene ring hydroxylation, to convert provitamin a carotenes to non-provitamin a xanthophylls. however, substrate specificity was difficult to inves ...	2007	17196929
importance of the 5 s rrna-binding ribosomal proteins for cell viability and translation in escherichia coli.	a specific complex of 5 s rrna and several ribosomal proteins is an integral part of ribosomes in all living organisms. here we studied the importance of escherichia coli genes rple, rplr and rply, encoding 5 s rrna-binding ribosomal proteins l5, l18 and l25, respectively, for cell growth, viability and translation. using recombineering to create gene replacements in the e. coli chromosome, it was shown that rple and rplr are essential for cell viability, whereas cells deleted for rply are viabl ...	2007	17198710
importance of the 5 s rrna-binding ribosomal proteins for cell viability and translation in escherichia coli.	a specific complex of 5 s rrna and several ribosomal proteins is an integral part of ribosomes in all living organisms. here we studied the importance of escherichia coli genes rple, rplr and rply, encoding 5 s rrna-binding ribosomal proteins l5, l18 and l25, respectively, for cell growth, viability and translation. using recombineering to create gene replacements in the e. coli chromosome, it was shown that rple and rplr are essential for cell viability, whereas cells deleted for rply are viabl ...	2007	17198710
structure of glnk1 with bound effectors indicates regulatory mechanism for ammonia uptake.	a binary complex of the ammonia channel amt1 from methanococcus jannaschii and its cognate p(ii) signalling protein glnk1 has been produced and characterized. complex formation is prevented specifically by the effector molecules mg-atp and 2-ketoglutarate. single-particle electron microscopy of the complex shows that glnk1 binds on the cytoplasmic side of amt1. three high-resolution x-ray structures of glnk1 indicate that the functionally important t-loop has an extended, flexible conformation i ...	2007	17203075
a top-down/bottom-up study of the ribosomal proteins of caulobacter crescentus.	ribosomes from the gram-negative alpha-proteobacterium caulobacter crescentus were isolated using standard methods. proteins were separated using a two-dimensional liquid chromatographic system that allowed the analysis of whole proteins by direct coupling to an esi-qtof mass spectrometer and of proteolytic digests by a number of mass spectrometric methods. the masses of 53 of 54 ribosomal proteins were directly measured. protein identifications and proposed post-translational modifications were ...	2007	17203977
deinococcus radiodurans rna ligase exemplifies a novel ligase clade with a distinctive n-terminal module that is important for 5'-po4 nick sealing and ligase adenylylation but dispensable for phosphodiester formation at an adenylylated nick.	deinococcus radiodurans rna ligase (drarnl) is a template-directed ligase that seals nicked duplexes in which the 3'-oh strand is rna. drarnl is a 342 amino acid polypeptide composed of a c-terminal adenylyltransferase domain fused to a distinctive 126 amino acid n-terminal module (a putative ob-fold). an alanine scan of the c domain identified 9 amino acids essential for nick ligation, which are located within nucleotidyltransferase motifs i, ia, iii, iiia, iv and v. seven mutants were dysfunct ...	2007	17204483
effects of dksa, grea, and greb on transcription initiation: insights into the mechanisms of factors that bind in the secondary channel of rna polymerase.	escherichia coli dksa, grea, and greb have similar structures and bind to the same location on rna polymerase (rnap), the secondary channel. we show that greb can fulfil some roles of dksa in vitro, including shifting the promoter-open complex equilibrium in the dissociation direction, thus allowing rrna promoters to respond to changes in the concentration of ppgpp and ntps. however, unlike deletion of the dksa gene, deletion of greb had no effect on rrna promoters in vivo. we show that the appa ...	2007	17207814
effects of dksa, grea, and greb on transcription initiation: insights into the mechanisms of factors that bind in the secondary channel of rna polymerase.	escherichia coli dksa, grea, and greb have similar structures and bind to the same location on rna polymerase (rnap), the secondary channel. we show that greb can fulfil some roles of dksa in vitro, including shifting the promoter-open complex equilibrium in the dissociation direction, thus allowing rrna promoters to respond to changes in the concentration of ppgpp and ntps. however, unlike deletion of the dksa gene, deletion of greb had no effect on rrna promoters in vivo. we show that the appa ...	2007	17207814
phylogenetic distribution of translational gtpases in bacteria.	translational gtpases are a family of proteins in which gtpase activity is stimulated by the large ribosomal subunit. conserved sequence features allow members of this family to be identified.	2007	17214893
co-evolution of the archaeal trna-dependent amidotransferase gatcab with trna(asn).	the important identity elements in trna(gln) and trna(asn) for bacterial gatcab and in trna(gln) for archaeal gatde are the d-loop and the first base pair of the acceptor stem. here we show that methanothermobacter thermautotrophicus gatcab, the archaeal enzyme, is different as it discriminates asp-trna(asp) and asp-trna(asn) by use of u49, the d-loop and to a lesser extent the variable loop. since archaea possess the trna(gln)-specific amidotransferase gatde, the archaeal gatcab enzyme evolved ...	2007	17214986
nuclease activity of the muts homologue muts2 from thermus thermophilus is confined to the smr domain.	muts homologues are highly conserved enzymes engaged in dna mismatch repair (mmr), meiotic recombination and other dna modifications. genome sequencing projects have revealed that bacteria and plants possess a muts homologue, muts2. muts2 lacks the mismatch-recognition domain of muts, but contains an extra c-terminal region called the small muts-related (smr) domain. sequences homologous to the smr domain are annotated as 'proteins of unknown function' in various organisms ranging from bacteria ...	2007	17215294
recognition of ribosomal protein l11 by the protein trimethyltransferase prma.	bacterial ribosomal protein l11 is post-translationally trimethylated at multiple residues by a single methyltransferase, prma. here, we describe four structures of prma from the extreme thermophile thermus thermophilus. two apo-prma structures at 1.59 and 2.3 a resolution and a third with bound cofactor s-adenosyl-l-methionine at 1.75 a each exhibit distinct relative positions of the substrate recognition and catalytic domains, revealing how prma can position the l11 substrate for multiple, con ...	2007	17215866
the crystal structure of the escherichia coli amtb-glnk complex reveals how glnk regulates the ammonia channel.	amt proteins are ubiquitous channels for the conduction of ammonia in archaea, eubacteria, fungi, and plants. in escherichia coli, previous studies have indicated that binding of the pii signal transduction protein glnk to the ammonia channel amtb regulates the channel thereby controlling ammonium influx in response to the intracellular nitrogen status. here, we describe the crystal structure of the complex between amtb and glnk at a resolution of 2.5 a. this structure of pii in a complex with o ...	2007	17220269
atomic resolution structures of rieske iron-sulfur protein: role of hydrogen bonds in tuning the redox potential of iron-sulfur clusters.	the rieske [2fe-2s] iron-sulfur protein of cytochrome bc(1) functions as the initial electron acceptor in the rate-limiting step of the catalytic reaction. prior studies have established roles for a number of conserved residues that hydrogen bond to ligands of the [2fe-2s] cluster. we have constructed site-specific variants at two of these residues, measured their thermodynamic and functional properties, and determined atomic resolution x-ray crystal structures for the native protein at 1.2 a re ...	2007	17223530
complete kinetic mechanism of homoisocitrate dehydrogenase from saccharomyces cerevisiae.	the kinetic mechanism of homoisocitrate dehydrogenase from saccharomyces cerevisiae was determined using initial velocity studies in the absence and presence of product and dead end inhibitors in both reaction directions. data suggest a steady state random kinetic mechanism. the dissociation constant of the mg-homoisocitrate complex (mghic) was estimated to be 11 +/- 2 mm as measured using mg2+ as a shift reagent. initial velocity data indicate the mghic complex is the reactant in the direction ...	2007	17223711
intermediates: ubiquitous species on folding energy landscapes?	although intermediates have long been recognised as fascinating species that form during the folding of large proteins, the role that intermediates play in the folding of small, single-domain proteins has been widely debated. recent discoveries using new, sensitive methods of detection and studies combining simulation and experiment have now converged on a common vision for folding, involving intermediates as ubiquitous stepping stones en route to the native state. the results suggest that the f ...	2007	17239580
visualizing the atpase cycle in a protein disaggregating machine: structural basis for substrate binding by clpb.	clpb is a ring-shaped molecular chaperone that has the remarkable ability to disaggregate stress-damaged proteins. here we present the electron cryomicroscopy reconstruction of an atp-activated clpb trap mutant, along with reconstructions of clpb in the amppnp, adp, and in the nucleotide-free state. we show that motif 2 of the clpb m domain is positioned between the d1-large domains of neighboring subunits and could facilitate a concerted, atp-driven conformational change in the aaa-1 ring. we f ...	2007	17244533
a novel superfamily containing the beta-grasp fold involved in binding diverse soluble ligands.	domains containing the beta-grasp fold are utilized in a great diversity of physiological functions but their role, if any, in soluble or small molecule ligand recognition is poorly studied.	2007	17250770
post-transcriptional modifications in the small subunit ribosomal rna from thermotoga maritima, including presence of a novel modified cytidine.	post-transcriptional modifications of rna are nearly ubiquitous in the principal rnas involved in translation. however, in the case of rrna the functional roles of modification are far less established than for trna, and are subject to less knowledge in terms of specific nucleoside identities and their sequence locations. post-transcriptional modifications have been studied in the ssu rrna from thermotoga maritima (optimal growth 80 degrees c), one of the most deeply branched organisms in the eu ...	2007	17255199
structural conservation of recf and rad50: implications for dna recognition and recf function.	recf, together with reco and recr, belongs to a ubiquitous group of recombination mediators (rms) that includes eukaryotic proteins such as rad52 and brca2. rms help maintain genome stability in the presence of dna damage by loading reca-like recombinases and displacing single-stranded dna-binding proteins. here, we present the crystal structure of recf from deinococcus radiodurans. recf exhibits a high degree of structural similarity with the head domain of rad50, but lacks its long coiled-coil ...	2007	17255941
asymmetric deceleration of clpb or hsp104 atpase activity unleashes protein-remodeling activity.	two members of the aaa+ superfamily, clpb and hsp104, collaborate with hsp70 and hsp40 to rescue aggregated proteins. however, the mechanisms that elicit and underlie their protein-remodeling activities remain unclear. we report that for both hsp104 and clpb, mixtures of atp and atp-gammas unexpectedly unleash activation, disaggregation and unfolding activities independent of cochaperones. mutations reveal how remodeling activities are elicited by impaired hydrolysis at individual nucleotide-bin ...	2007	17259993
the tail of the parg dna segregation protein remodels parf polymers and enhances atp hydrolysis via an arginine finger-like motif.	the parf protein of plasmid tp228 belongs to the ubiquitous superfamily of para atpases that drive dna segregation in bacteria. atp-bound parf polymerizes into multistranded filaments. the partner protein parg is dimeric, consisting of c-termini that interweave into a ribbon-helix-helix domain contacting the centromeric dna and unstructured n-termini. parg stimulates atp hydrolysis by parf approximately 30-fold. here, we establish that the mobile tails of parg are crucial for this enhancement an ...	2007	17261809
region 1.2 of the rna polymerase sigma subunit controls recognition of the -10 promoter element.	recognition of the -10 promoter consensus element by region 2 of the bacterial rna polymerase sigma subunit is a key step in transcription initiation. sigma also functions as an elongation factor, inducing transcription pausing by interacting with transcribed dna non-template strand sequences that are similar to the -10 element sequence. here, we show that the region 1.2 of escherichia coli sigma70, whose function was heretofore unknown, is strictly required for efficient recognition of the non- ...	2007	17268549
release factors 2 from escherichia coli and thermus thermophilus: structural, spectroscopic and microcalorimetric studies.	prokaryotic class i release factors (rfs) respond to mrna stop codons and terminate protein synthesis. they interact with the ribosomal decoding site and the peptidyl-transferase centre bridging these 75 a distant ribosomal centres. for this an elongated rf conformation, with partially unfolded core domains ii.iii.iv is required, which contrasts the known compact rf crystal structures. the crystal structure of thermus thermophilus rf2 was determined and compared with solution structure of t. the ...	2007	17272297
characterization of a pseudomonad 2-nitrobenzoate nitroreductase and its catabolic pathway-associated 2-hydroxylaminobenzoate mutase and a chemoreceptor involved in 2-nitrobenzoate chemotaxis.	pseudomonas fluorescens strain ku-7 is a prototype microorganism that metabolizes 2-nitrobenzoate (2-nba) via the formation of 3-hydroxyanthranilate (3-haa), a known antioxidant and reductant. the initial two steps leading to the sequential formation of 2-hydroxy/aminobenzoate and 3-haa are catalyzed by a nadph-dependent 2-nba nitroreductase (nbaa) and 2-hydroxylaminobenzoate mutase (nbab), respectively. the 216-amino-acid protein nbaa is 78% identical to a plasmid-encoded hypothetical conserved ...	2007	17277060
purification, crystallization and preliminary x-ray analysis of the regulatory subunit of aspartate kinase from thermus thermophilus.	aspartate kinase (ak) from thermus thermophilus, which catalyzes the first step of threonine and methionine biosynthesis, is regulated via feedback inhibition by the end product threonine. to elucidate the mechanism of regulation of ak, the regulatory subunit (the beta subunit of t. thermophilus ak) was crystallized in the presence of the inhibitor threonine. diffraction data were collected to 2.15 a at a synchrotron source. the crystal belongs to the cubic space group p4(3)32 or p4(1)32, with u ...	2007	17277448
comparison of the xylose reductase-xylitol dehydrogenase and the xylose isomerase pathways for xylose fermentation by recombinant saccharomyces cerevisiae.	two heterologous pathways have been used to construct recombinant xylose-fermenting saccharomyces cerevisiae strains: i) the xylose reductase (xr) and xylitol dehydrogenase (xdh) pathway and ii) the xylose isomerase (xi) pathway. in the present study, the pichia stipitis xr-xdh pathway and the piromyces xi pathway were compared in an isogenic strain background, using a laboratory host strain with genetic modifications known to improve xylose fermentation (overexpressed xylulokinase, overexpresse ...	2007	17280608
g-ribo: a new structural motif in ribosomal rna.	analysis of the available crystal structures of the ribosome and of its subunits has revealed a new rna motif that we call g-ribo. the motif consists of two double helices positioned side-by-side and connected by an unpaired region. the juxtaposition of the two helices is kept by a complex system of tertiary interactions spread over several layers of stacked nucleotides. in the center of this arrangement, the ribose of a nucleotide from one helix is specifically packed with the ribose and the mi ...	2007	17283211
new bioinformatic tools for analysis of nucleotide modifications in eukaryotic rrna.	this report presents a valuable new bioinformatics package for research on rrna nucleotide modifications in the ribosome, especially those created by small nucleolar rna:protein complexes (snornps). the interactive service, which is not available elsewhere, enables a user to visualize the positions of pseudouridines, 2'-o-methylations, and base methylations in three-dimensional space in the ribosome and also in linear and secondary structure formats of ribosomal rna. our tools provide additional ...	2007	17283215
deinococcus glutaminyl-trna synthetase is a chimer between proteins from an ancient and the modern pathways of aminoacyl-trna formation.	glutaminyl-trna synthetase from deinococcus radiodurans possesses a c-terminal extension of 215 residues appending the anticodon-binding domain. this domain constitutes a paralog of the yqey protein present in various organisms and part of it is present in the c-terminal end of the gatb subunit of gatcab, a partner of the indirect pathway of gln-trna(gln) formation. to analyze the peculiarities of the structure-function relationship of this glnrs related to the yqey domain, a structure of the pr ...	2007	17284460
the structure of free l11 and functional dynamics of l11 in free, l11-rrna(58 nt) binary and l11-rrna(58 nt)-thiostrepton ternary complexes.	the l11 binding site is one of the most important functional sites in the ribosome. the n-terminal domain of l11 has been implicated as a "reversible switch" in facilitating the coordinated movements associated with ef-g-driven gtp hydrolysis. the reversible switch mechanism has been hypothesized to require conformational flexibility involving re-orientation and re-positioning of the two l11 domains, and warrants a close examination of the structure and dynamics of l11. here we report the soluti ...	2007	17292917
widespread occurrence and genomic context of unusually small polyketide synthase genes in microbial consortia associated with marine sponges.	numerous marine sponges harbor enormous amounts of as-yet-uncultivated bacteria in their tissues. there is increasing evidence that these symbionts play an important role in the synthesis of protective metabolites, many of which are of great pharmacological interest. in this study, genes for the biosynthesis of polyketides, one of the most important classes of bioactive natural products, were systematically investigated in 20 demosponge species from different oceans. unexpectedly, the sponge met ...	2007	17293531
in vitro trans-translation of thermus thermophilus: ribosomal protein s1 is not required for the early stage of trans-translation.	transfer-messenger rna (tmrna) plays a dual role as a trna and an mrna in trans-translation, during which the ribosome replaces mrna with tmrna encoding the tag-peptide. these processes have been suggested to involve several tmrna-binding proteins, including smpb and ribosomal protein s1. to investigate the molecular mechanism of trans-translation, we developed in vitro systems using purified ribosome, elongation factors, tmrna and smpb from thermus thermophilus. a stalled ribosome in complex wi ...	2007	17299130
bacterial toxicity of potassium tellurite: unveiling an ancient enigma.	biochemical, genetic, enzymatic and molecular approaches were used to demonstrate, for the first time, that tellurite (teo(3) (2-)) toxicity in e. coli involves superoxide formation. this radical is derived, at least in part, from enzymatic teo(3) (2-) reduction. this conclusion is supported by the following observations made in k(2)teo(3)-treated e. coli bw25113: i) induction of the ibpa gene encoding for the small heat shock protein ibpa, which has been associated with resistance to superoxide ...	2007	17299591
toward understanding phosphoseryl-trnacys formation: the crystal structure of methanococcus maripaludis phosphoseryl-trna synthetase.	a number of archaeal organisms generate cys-trna(cys) in a two-step pathway, first charging phosphoserine (sep) onto trna(cys) and subsequently converting it to cys-trna(cys). we have determined, at 3.2-a resolution, the structure of the methanococcus maripaludis phosphoseryl-trna synthetase (seprs), which catalyzes the first step of this pathway. the structure shows that seprs is a class ii, alpha(4) synthetase whose quaternary structure arrangement of subunits closely resembles that of the het ...	2007	17301225
genetic engineering of zymobacter palmae for production of ethanol from xylose.	its metabolic characteristics suggest that zymobacter palmae gen. nov., sp. nov. could serve as a useful new ethanol-fermenting bacterium, but its biotechnological exploitation will require certain genetic modifications. we therefore engineered z. palmae so as to broaden the range of its fermentable sugar substrates to include the pentose sugar xylose. the escherichia coli genes encoding the xylose catabolic enzymes xylose isomerase, xylulokinase, transaldolase, and transketolase were introduced ...	2007	17308178
kinetic discrimination of trna identity by the conserved motif 2 loop of a class ii aminoacyl-trna synthetase.	the selection of trnas by their cognate aminoacyl-trna synthetases is critical for ensuring the fidelity of protein synthesis. while nucleotides that comprise trna identity sets have been readily identified, their specific role in the elementary steps of aminoacylation is poorly understood. by use of a rapid kinetics analysis employing mutants in trna(his) and its cognate aminoacyl-trna synthetase, the role of trna identity in aminoacylation was investigated. while mutations in the trna anticodo ...	2007	17317626
the structures of antibiotics bound to the e site region of the 50 s ribosomal subunit of haloarcula marismortui: 13-deoxytedanolide and girodazole.	crystal structures of the 50 s ribosomal subunit from haloarcula marismortui complexed with two antibiotics have identified new sites at which antibiotics interact with the ribosome and inhibit protein synthesis. 13-deoxytedanolide binds to the e site of the 50 s subunit at the same location as the cca of trna, and thus appears to inhibit protein synthesis by competing with deacylated trnas for e site binding. girodazole binds near the e site region, but is somewhat buried and may inhibit trna b ...	2007	17321546
structure of the type iii pantothenate kinase from bacillus anthracis at 2.0 a resolution: implications for coenzyme a-dependent redox biology.	coenzyme a (coash) is the major low-molecular weight thiol in staphylococcus aureus and a number of other bacteria; the crystal structure of the s. aureus coenzyme a-disulfide reductase (coadr), which maintains the reduced intracellular state of coash, has recently been reported [mallett, t.c., wallen, j.r., karplus, p.a., sakai, h., tsukihara, t., and claiborne, a. (2006) biochemistry 45, 11278-89]. in this report we demonstrate that coash is the major thiol in bacillus anthracis; a bioinformat ...	2007	17323930
a retro-evolution study of cdp-6-deoxy-d-glycero-l-threo-4-hexulose-3-dehydrase (e1) from yersinia pseudotuberculosis: implications for c-3 deoxygenation in the biosynthesis of 3,6-dideoxyhexoses.	cdp-6-deoxy-l-threo-d-glycero-4-hexulose-3-dehydrase (e1), which catalyzes c-3 deoxygenation of cdp-4-keto-6-deoxyglucose in the biosynthesis of 3,6-dideoxyhexoses, shares a modest sequence identity with other b6-dependent enzymes, albeit with two important distinctions. it is a rare example of a b6-dependent enzyme that harbors a [2fe-2s] cluster, and a highly conserved lysine that serves as an anchor for plp in most b6-dependent enzymes is replaced by histidine at position 220 in e1. since alt ...	2007	17323931
efficient optimization of crystallization conditions by manipulation of drop volume ratio and temperature.	an efficient optimization method for the crystallization of biological macromolecules has been developed and tested. this builds on a successful high-throughput technique for the determination of initial crystallization conditions. the optimization method takes an initial condition identified through screening and then varies the concentration of the macromolecule, precipitant, and the growth temperature in a systematic manner. the amount of sample and number of steps is minimized and no biochem ...	2007	17327388
x-ray crystallographic analysis of the sulfur carrier protein soxy from chlorobium limicola f. thiosulfatophilum reveals a tetrameric structure.	dissimilatory oxidation of thiosulfate in the green sulfur bacterium chlorobium limicola f. thiosulfatophilum is carried out by the ubiquitous sulfur-oxidizing (sox) multi-enzyme system. in this system, soxy plays a key role, functioning as the sulfur substrate-binding protein that offers its sulfur substrate, which is covalently bound to a conserved c-terminal cysteine, to another oxidizing sox enzyme. here, we report the crystal structures of a stand-alone soxy protein of c. limicola f. thiosu ...	2007	17327392
directed mutagenesis identifies amino acid residues involved in elongation factor tu binding to yeast phe-trnaphe.	the co-crystal structure of thermus aquaticus elongation factor tu.guanosine 5'- [beta,gamma-imido]triphosphate (ef-tu.gdpnp) bound to yeast phe-trna(phe) reveals that ef-tu interacts with the trna body primarily through contacts with the phosphodiester backbone. twenty amino acids in the trna binding cleft of thermus thermophilus ef-tu were each mutated to structurally conservative alternatives and the affinities of the mutant proteins to yeast phe-trna(phe) determined. eleven of the 20 mutatio ...	2007	17328911
structure of a upf0150-family protein from thermus thermophilus hb8.	ttha0281 is a hypothetical protein from thermus thermophilus hb8 that belongs to an uncharacterized protein family, upf0150, in the pfam database and to cog1598 in the national center for biotechnology information database of clusters of orthologous groups. the x-ray crystal structure of the protein was determined by a multiple-wavelength anomalous dispersion technique and was refined at 1.9 a resolution to a final r factor of 18.5%. the ttha0281 monomer adopts an alpha-beta-beta-beta-alpha fold ...	2007	17329807
cloning, expression, purification, crystallization and preliminary x-ray crystallographic analysis of initiation factor 1 from mycobacterium tuberculosis.	initiation factor 1 (if-1; rv3462c) from mycobacterium tuberculosis, a component of the 30s initiation complex, was cloned and heterologously expressed in escherichia coli. the protein was purified by affinity and size-exclusion chromatography and crystallized. a complete data set has been collected to high resolution. the crystals belonged to space group p2(1)2(1)2, with two molecules per asymmetric unit which are related by translational symmetry.	2007	17329809
an improved definition of the rna-binding specificity of secis-binding protein 2, an essential component of the selenocysteine incorporation machinery.	by binding to secis elements located in the 3'-utr of selenoprotein mrnas, the protein sbp2 plays a key role in the assembly of the selenocysteine incorporation machinery. sbp2 contains an l7ae/l30 rna-binding domain similar to that of protein 15.5k/snu13p, which binds k-turn motifs with a 3-nt bulge loop closed by a tandem of g.a and a.g pairs. here, by selex experiments, we demonstrate the capacity of sbp2 to bind such k-turn motifs with a protruding u residue. however, we show that conversion ...	2007	17332014
a sigma-core interaction of the rna polymerase holoenzyme that enhances promoter escape.	the sigma subunit of bacterial rna polymerase (rnap) is required for promoter-specific transcription initiation and can also participate in downstream events. several functionally important intersubunit interactions between escherichia coli sigma(70) and the core enzyme (alpha(2)betabeta'omega) have been defined. these include an interaction between conserved region 2 of sigma(70) (sigma(2)) and the coiled-coil domain of beta' (beta' coiled-coil) that is required for sequence-specific interactio ...	2007	17332752
elongation factor tu3 (ef-tu3) from the kirromycin producer streptomyces ramocissimus is resistant to three classes of ef-tu-specific inhibitors.	the antibiotic kirromycin inhibits prokaryotic protein synthesis by immobilizing elongation factor tu (ef-tu) on the elongating ribosome. streptomyces ramocissimus, the producer of kirromycin, contains three tuf genes. while tuf1 and tuf2 encode kirromycin-sensitive ef-tu species, the function of tuf3 is unknown. here we demonstrate that ef-tu3, in contrast to ef-tu1 and ef-tu2, is resistant to three classes of ef-tu-targeted antibiotics: kirromycin, pulvomycin, and ge2270a. a mixture of ef-tu1 ...	2007	17337575
in vivo modulation of a dnaj homolog, cbpa, by cbpm.	cbpa, an escherichia coli dnaj homolog, can function as a cochaperone for the dnak/hsp70 chaperone system, and its in vitro activity can be modulated by cbpm. we discovered that cbpm specifically inhibits the in vivo activity of cbpa, preventing it from functioning in cell growth and division. furthermore, we have shown that cbpm interacts with cbpa in vivo during stationary phase, suggesting that the inhibition of activity is a result of the interaction. these results reveal that the activity o ...	2007	17337578
structural and evolutionary bioinformatics of the spout superfamily of methyltransferases.	spout methyltransferases (mtases) are a large class of s-adenosyl-l-methionine-dependent enzymes that exhibit an unusual alpha/beta fold with a very deep topological knot. in 2001, when no crystal structures were available for any of these proteins, anantharaman, koonin, and aravind identified homology between spou and trmd mtases and defined the spout superfamily. since then, multiple crystal structures of knotted mtases have been solved and numerous new homologous sequences appeared in the dat ...	2007	17338813
structure and kinetics of monofunctional proline dehydrogenase from thermus thermophilus.	proline dehydrogenase (prodh) and delta(1)-pyrroline-5-carboxylate dehydrogenase (p5cdh) catalyze the two-step oxidation of proline to glutamate. they are distinct monofunctional enzymes in all eukaryotes and some bacteria but are fused into bifunctional enzymes known as proline utilization a (puta) in other bacteria. here we report the first structure and biochemical data for a monofunctional prodh. the 2.0-a resolution structure of thermus thermophilus prodh reveals a distorted (betaalpha)(8) ...	2007	17344208
surprising arginine biosynthesis: a reappraisal of the enzymology and evolution of the pathway in microorganisms.	major aspects of the pathway of de novo arginine biosynthesis via acetylated intermediates in microorganisms must be revised in light of recent enzymatic and genomic investigations. the enzyme n-acetylglutamate synthase (nags), which used to be considered responsible for the first committed step of the pathway, is present in a limited number of bacterial phyla only and is absent from archaea. in many bacteria, shorter proteins related to the gcn5-related n-acetyltransferase family appear to acet ...	2007	17347518
insertion sequence diversity in archaea.	insertion sequences (iss) can constitute an important component of prokaryotic (bacterial and archaeal) genomes. over 1,500 individual iss are included at present in the isfinder database (www-is.biotoul.fr), and these represent only a small portion of those in the available prokaryotic genome sequences and those that are being discovered in ongoing sequencing projects. in spite of this diversity, the transposition mechanisms of only a few of these ubiquitous mobile genetic elements are known, a ...	2007	17347521
widespread distribution of archaeal reverse gyrase in thermophilic bacteria suggests a complex history of vertical inheritance and lateral gene transfers.	reverse gyrase, an enzyme of uncertain funtion, is present in all hyperthermophilic archaea and bacteria. previous phylogenetic studies have suggested that the gene for reverse gyrase has an archaeal origin and was transferred laterally (lgt) to the ancestors of the two bacterial hyperthermophilic phyla, thermotogales and aquificales. here, we performed an in-depth analysis of the evolutionary history of reverse gyrase in light of genomic progress. we found genes coding for reverse gyrase in the ...	2007	17350929
degradation of alkyl methyl ketones by pseudomonas veronii mek700.	pseudomonas veronii mek700 was isolated from a biotrickling filter cleaning 2-butanone-loaded waste air. the strain is able to grow on 2-butanone and 2-hexanol. the genes for degradation of short chain alkyl methyl ketones were identified by transposon mutagenesis using a newly designed transposon, mini-tn5495, and cloned in escherichia coli. dna sequence analysis of a 15-kb fragment revealed three genes involved in methyl ketone degradation. the deduced amino acid sequence of the first gene, me ...	2007	17351032
in vivo and in vitro investigation of bacterial type b rnase p interaction with trna 3'-cca.	for catalysis by bacterial type b rnase p, the importance of a specific interaction with p(recursor)trna 3'-cca termini is yet unclear. we show that mutation of one of the two g residues assumed to interact with 3'-cca in type b rnase p rnas inhibits cell growth, but cell viability is at least partially restored at increased rnase p levels due to rnase p protein overexpression. the in vivo defects of the mutant enzymes correlated with an enzyme defect at low mg(2+) in vitro. for bacillus subtili ...	2007	17355991
potential and utilization of thermophiles and thermostable enzymes in biorefining.	in today's world, there is an increasing trend towards the use of renewable, cheap and readily available biomass in the production of a wide variety of fine and bulk chemicals in different biorefineries. biorefineries utilize the activities of microbial cells and their enzymes to convert biomass into target products. many of these processes require enzymes which are operationally stable at high temperature thus allowing e.g. easy mixing, better substrate solubility, high mass transfer rate, and ...	2007	17359551
genomic identification and in vitro reconstitution of a complete biosynthetic pathway for the osmolyte di-myo-inositol-phosphate.	di-myo-inositol 1,1'-phosphate (dip) is a major osmoprotecting metabolite in a number of hyperthermophilic species of archaea and bacteria. although the dip biosynthesis pathway was previously proposed, genes encoding only two of the four required enzymes, inositol-1-phosphate synthase and inositol monophosphatase, were identified. in this study we used a comparative genomic analysis to predict two additional genes of this pathway (termed dipa and dipb) that remained missing. in thermotoga marit ...	2007	17360515
regulation of the stringent response is the essential function of the conserved bacterial g protein cgta in vibrio cholerae.	the gene encoding the conserved bacterial g protein cgta (obg) is essential for viability in every organism in which it has been studied. cgta has been reported to be involved in several diverse bacterial functions, including ribosome assembly, dna repair, sporulation, and morphological development. however, none of these functions have been identified as essential. here we show that depletion of cgta in vibrio cholerae causes global changes in gene expression that are consistent with induction ...	2007	17360576
transcription activation mediated by a cyclic amp receptor protein from thermus thermophilus hb8.	the extremely thermophilic bacterium thermus thermophilus hb8, which belongs to the phylum deinococcus-thermus, has an open reading frame encoding a protein belonging to the cyclic amp (camp) receptor protein (crp) family present in many bacteria. the protein named t. thermophilus crp is highly homologous to the crp family proteins from the phyla firmicutes, actinobacteria, and cyanobacteria, and it forms a homodimer and interacts with camp. crp mrna and intracellular camp were detected in this ...	2007	17369302
temperature-dependent rnp conformational rearrangements: analysis of binary complexes of primary binding proteins with 16 s rrna.	ribonucleoprotein particles (rnps) are important components of all living systems, and the assembly of these particles is an intricate, often multistep, process. the 30 s ribosomal subunit is composed of one large rna (16 s rrna) and 21 ribosomal proteins (r-proteins). in vitro studies have revealed that assembly of the 30 s subunit is a temperature-dependent process involving sequential binding of r-proteins and conformational changes of 16 s rrna. additionally, a temperature-dependent conforma ...	2007	17376481
blub cannibalizes flavin to form the lower ligand of vitamin b12.	vitamin b12 (cobalamin) is among the largest known non-polymeric natural products, and the only vitamin synthesized exclusively by microorganisms. the biosynthesis of the lower ligand of vitamin b(12), 5,6-dimethylbenzimidazole (dmb), is poorly understood. recently, we discovered that a sinorhizobium meliloti gene, blub, is necessary for dmb biosynthesis. here we show that blub triggers the unprecedented fragmentation and contraction of the bound flavin mononucleotide cofactor and cleavage of th ...	2007	17377583
a single residue in leucyl-trna synthetase affecting amino acid specificity and trna aminoacylation.	human mitochondrial leucyl-trna synthetase (hs mt leurs) achieves high aminoacylation fidelity without a functional editing active site, representing a rare example of a class i aminoacyl-trna synthetase (aars) that does not proofread its products. previous studies demonstrated that the enzyme achieves high selectivity by using a more specific synthetic active site that is not prone to errors under physiological conditions. interestingly, the synthetic active site of hs mt leurs displays a high ...	2007	17378584
new photoreactive trna derivatives for probing the peptidyl transferase center of the ribosome.	three new photoreactive trna derivatives have been synthesized for use as probes of the peptidyl transferase center of the ribosome. in two of these derivatives, the 3' adenosine of yeast trna(phe) has been replaced by either 2-azidodeoxyadenosine or 2-azido-2'-o-methyl adenosine, while in a third the 3'-terminal 2-azidodeoxyadenosine of the trna is joined to puromycin via a phosphoramidate linkage to generate a photoreactive transition-state analog. all three derivatives bind to the p site of 7 ...	2007	17379815
anticodon-dependent conservation of bacterial trna gene sequences.	the residues in trna that account for its tertiary fold and for its specific aminoacylation are well understood. in contrast, relatively little is known about the residues in trna that dictate its ability to transit the different sites of the ribosome. yet protein synthesis cannot occur unless trna properly engages with the ribosome. this study analyzes trna gene sequences from 145 fully sequenced bacterial genomes. grouping the sequences according to the anticodon triplet reveals that many resi ...	2007	17379816
structural biology of rna silencing and its functional implications.	we outline structure-function contributions from our laboratories on protein-rna recognition events that monitor sirna length, 5 -phosphate and 2-nucleotide 3 overhangs, as well as the architecture of argonaute, its externally bound sirna complex, and argonaute-based models involving guide-strand-mediated mrna binding, cleavage, and release.	2006	17381284
ribosomal rna guanine-(n2)-methyltransferases and their targets.	five nearly universal methylated guanine-(n2) residues are present in bacterial rrna in the ribosome. to date four out of five ribosomal rna guanine-(n2)-methyltransferases are described. rsmc(yjjt) methylates g1207 of the 16s rrna. rlmg(ygjo) and rlml(ycby) are responsible for the 23s rrna m(2)g1835 and m(2)g2445 formation, correspondingly. rsmd(yhhf) is necessary for methylation of g966 residue of 16s rrna. structure of escherichia coli rsmd(yhhf) methyltransferase and the structure of the met ...	2007	17389639
functional anthology of intrinsic disorder. 3. ligands, post-translational modifications, and diseases associated with intrinsically disordered proteins.	currently, the understanding of the relationships between function, amino acid sequence, and protein structure continues to represent one of the major challenges of the modern protein science. as many as 50% of eukaryotic proteins are likely to contain functionally important long disordered regions. many proteins are wholly disordered but still possess numerous biologically important functions. however, the number of experimentally confirmed disordered proteins with known biological functions is ...	2007	17391016
extrachromosomal element capture and the evolution of multiple replication origins in archaeal chromosomes.	in all three domains of life, dna replication begins at specialized loci termed replication origins. in bacteria, replication initiates from a single, clearly defined site. in contrast, eukaryotic organisms exploit a multitude of replication origins, dividing their genomes into an array of short contiguous units. recently, the multiple replication origin paradigm has also been demonstrated within the archaeal domain of life, with the discovery that the hyperthermophilic archaeon sulfolobus has t ...	2007	17392430
mechanisms for stabilisation and the maintenance of solubility in proteins from thermophiles.	the database of protein structures contains representatives from organisms with a range of growth temperatures. various properties have been studied in a search for the molecular basis of protein adaptation to higher growth temperature. charged groups have emerged as key distinguishing factors for proteins from thermophiles and mesophiles.	2007	17394655
discovery of a thermophilic protein complex stabilized by topologically interlinked chains.	a growing number of organisms have been discovered inhabiting extreme environments, including temperatures in excess of 100 degrees c. how cellular proteins from such organisms retain their native folds under extreme conditions is still not fully understood. recent computational and structural studies have identified disulfide bonding as an important mechanism for stabilizing intracellular proteins in certain thermophilic microbes. here, we present the first proteomic analysis of intracellular d ...	2007	17395198
nanodiscs unravel the interaction between the secyeg channel and its cytosolic partner seca.	the translocon is a membrane-embedded protein assembly that catalyzes protein movement across membranes. the core translocon, the secyeg complex, forms oligomers, but the protein-conducting channel is at the center of the monomer. defining the properties of the secyeg protomer is thus crucial to understand the underlying function of oligomerization. we report here the reconstitution of a single secyeg complex into nano-scale lipid bilayers, termed nanodiscs. these water-soluble particles allow o ...	2007	17396152
transcriptional regulatory network discovery via multiple method integration: application to e. coli k12.	transcriptional regulatory network (trn) discovery from one method (e.g. microarray analysis, gene ontology, phylogenic similarity) does not seem feasible due to lack of sufficient information, resulting in the construction of spurious or incomplete trns. we develop a methodology, trnd, that integrates a preliminary trn, microarray data, gene ontology and phylogenic similarity to accurately discover trns and apply the method to e. coli k12. the approach can easily be extended to include other me ...	2007	17397539
diversity and abundance of nitrate reductase genes (narg and napa), nitrite reductase genes (nirs and nrfa), and their transcripts in estuarine sediments.	estuarine systems are the major conduits for the transfer of nitrate from agricultural and other terrestrial-anthropogenic sources into marine ecosystems. within estuarine sediments some microbially driven processes (denitrification and anammox) result in the net removal of nitrogen from the environment, while others (dissimilatory nitrate reduction to ammonium) do not. in this study, molecular approaches have been used to investigate the diversity, abundance, and activity of the nitrate-reducin ...	2007	17400770
structure probing of tmrna in distinct stages of trans-translation.	ribosomes stalled on problematic mrnas in bacterial cells can be rescued by transfer-messenger rna (tmrna), its helper protein (small protein b, smpb), and elongation factor tu (ef-tu) through a mechanism called trans-translation. in this work we used lead(ii) footprinting to probe the interactions of tmrna with smpb and other components of the translation machinery at different steps of the trans-translation cycle. ribosomes with a short nascent peptide stalled on a truncated mrna were reacted ...	2007	17400816
crystal structure of the map kinase binding domain and the catalytic domain of human mkp5.	map kinase phosphatases (mkps) have crucial roles in regulating the signaling activity of map kinases and are potential targets for drug discovery against human diseases. these enzymes contain a catalytic domain (cd) as well as a binding domain (bd) that help recognize the target map kinase. we report here the crystal structures at up to 2.2 a resolution of the bd and cd of human mkp5 and compare them to the known structures from other mkps. dramatic structural differences are observed between t ...	2007	17400920
purification, crystallization and preliminary x-ray diffraction study on pyrimidine nucleoside phosphorylase ttha1771 from thermus thermophilus hb8.	pyrimidine nucleoside phosphorylase (pynp) catalyzes the reversible phosphorolysis of pyrimidines in the nucleotide-synthesis salvage pathway. in order to study the structure-thermostability relationship of this enzyme, pynp from the extreme thermophile thermus thermophilus hb8 (ttha1771) has been cloned, overexpressed and purified. the ttha1771 protein was crystallized at 291 k using the oil-microbatch method with peg 4000 as a precipitant. a native data set was collected to 1.8 a resolution us ...	2007	17401202
cloning, expression, purification, crystallization and preliminary x-ray crystallographic study of molybdopterin synthase from thermus thermophilus hb8.	thermus thermophilus is a gram-negative aerobic thermophilic eubacterium which can grow at temperatures ranging from 323 to 355 k. in addition to their importance in thermostability or adaptation strategies for survival at high temperatures, the thermostable enzymes in thermophilic organisms contribute to a wide range of biotechnological applications. the molybdenum cofactor in all three kingdoms consists of a tricyclic pyranopterin termed molybdopterin that bears the cis-dithiolene group respon ...	2007	17401207
a unique insert of leucyl-trna synthetase is required for aminoacylation and not amino acid editing.	leucyl-trna synthetase (leurs) is a class i enzyme, which houses its aminoacylation active site in a canonical core that is defined by a rossmann nucleotide binding fold. in addition, many leurss bear a unique polypeptide insert comprised of about 50 amino acids located just upstream of the conserved kmsks sequence. the role of this leucine-specific domain (ls-domain) remains undefined. we hypothesized that this domain may be important for substrate recognition in aminoacylation and/or amino aci ...	2007	17407263
structures of trnas with an expanded anticodon loop in the decoding center of the 30s ribosomal subunit.	during translation, some +1 frameshift mrna sites are decoded by frameshift suppressor trnas that contain an extra base in their anticodon loops. similarly engineered trnas have been used to insert nonnatural amino acids into proteins. here, we report crystal structures of two anticodon stem-loops (asls) from trnas known to facilitate +1 frameshifting bound to the 30s ribosomal subunit with their cognate mrnas. asl(cccg) and asl(accc) (5'-3' nomenclature) form unpredicted anticodon-codon interac ...	2007	17416634
the active ring-like structure of seca revealed by electron crystallography: conformational change upon interaction with secb.	seca is a multifunctional protein involved in protein translocation in bacteria. the structure of seca on membrane is dramatically altered compared with that in solution, accompanying with functional changes. we previously reported the formation of a novel ring-like structure of seca on lipid layers, which may constitute part of the preprotein translocation channel. in the present work, two-dimensional crystallization of escherichia coli seca on lipid monolayers was performed to reveal the struc ...	2007	17419072
branchclust: a phylogenetic algorithm for selecting gene families.	automated methods for assembling families of orthologous genes include those based on sequence similarity scores and those based on phylogenetic approaches. the first are easy to automate but usually they do not distinguish between paralogs and orthologs or have restriction on the number of taxa. phylogenetic methods often are based on reconciliation of a gene tree with a known rooted species tree; a limitation of this approach, especially in case of prokaryotes, is that the species tree is ofte ...	2007	17425803
kinetic and spectroscopic characterization of type ii isopentenyl diphosphate isomerase from thermus thermophilus: evidence for formation of substrate-induced flavin species.	type ii isopentenyl diphosphate (ipp) isomerase catalyzes the interconversion of ipp and dimethylallyl diphosphate (dmapp). although the reactions catalyzed by the type ii enzyme and the well-studied type i ipp isomerase are identical, the type ii protein requires reduced flavin for activity. the chemical mechanism, including the role of flavin, has not been established for type ii ipp isomerase. recombinant type ii ipp isomerase from thermus thermophilus hb27 was purified by ni2+ affinity chrom ...	2007	17428035