Publications

ribosomes containing mutants of l4 ribosomal protein from thermus thermophilus display multiple defects in ribosomal functions and sensitivity against erythromycin.	protein l4 from thermus thermophilus (tthl4) was heterologously overproduced in escherichia coli cells. to study the implication of the extended loop of tthl4 in the exit-tunnel and peptidyltransferase functions, the highly conserved e56 was replaced by d or q, while the semiconserved g55 was changed to e or s. moreover, the sequence -g55e56- was inverted to -e55g56-. when we incorporated these mutants into e. coli ribosomes and investigated their impact on poly(phe) synthesis, high variations i ...	2005	16244130
solution probing of metal ion binding by helix 27 from escherichia coli 16s rrna.	helix (h)27 from escherichia coli 16s ribosomal (r)rna is centrally located within the small (30s) ribosomal subunit, immediately adjacent to the decoding center. bacterial 30s subunit crystal structures depicting mg(2+) binding sites resolve two magnesium ions within the vicinity of h27: one in the major groove of the g886-u911 wobble pair, and one within the gcaa tetraloop. binding of such metal cations is generally thought to be crucial for rna folding and function. to ask how metal ion-rna i ...	2005	16244134
a mutation in the anticodon of a single trnaala is sufficient to confer auxin resistance in arabidopsis.	auxin-resistant mutants have been useful for dissecting the mechanisms that underlie auxin-mediated biological processes. here we report the isolation and molecular characterization of a novel auxin-resistant mutant in arabidopsis (arabidopsis thaliana). like known mutated aux/iaa transcription factors, the mutant described here displayed dominant resistance to exogenously supplied auxins (sirtinol, 2,4-dichlorophenoxyacetic acid, indole-3-acetic acid) and a host of pleiotropic phenotypes, inclu ...	2005	16244142
a colorimetric method for point mutation detection using high-fidelity dna ligase.	the present study reported proof-of-principle for a genotyping assay approach that can detect single nucleotide polymorphisms (snps) through the gold nanoparticle assembly and the ligase reaction. by incorporating the high-fidelity dna ligase (tth dna ligase) into the allele-specific ligation-based gold nanoparticle assembly, this assay provided a convenient yet powerful colorimetric detection that enabled a straightforward single-base discrimination without the need of precise temperature contr ...	2005	16257979
kinetic analysis of the metal binding mechanism of escherichia coli manganese superoxide dismutase.	the acquisition of a catalytic metal cofactor is an essential step in the maturation of every metalloenzyme, including manganese superoxide dismutase (mnsod). in this study, we have taken advantage of the quenching of intrinsic protein fluorescence by bound metal ions to continuously monitor the metallation reaction of escherichia coli mnsod in vitro, permitting a detailed kinetic characterization of the uptake mechanism. apo-mnsod metallation kinetics are "gated", zero order in metal ion for bo ...	2006	16258041
kinetic analysis of the metal binding mechanism of escherichia coli manganese superoxide dismutase.	the acquisition of a catalytic metal cofactor is an essential step in the maturation of every metalloenzyme, including manganese superoxide dismutase (mnsod). in this study, we have taken advantage of the quenching of intrinsic protein fluorescence by bound metal ions to continuously monitor the metallation reaction of escherichia coli mnsod in vitro, permitting a detailed kinetic characterization of the uptake mechanism. apo-mnsod metallation kinetics are "gated", zero order in metal ion for bo ...	2006	16258041
domain ii plays a crucial role in the function of ribosome recycling factor.	rrf (ribosome recycling factor) consists of two domains, and in concert with ef-g (elongation factor-g), triggers dissociation of the post-termination ribosomal complex. however, the function of the individual domains of rrf remains unclear. to clarify this, two rrf chimaeras, ecodi/ttedii and ttedi/ecodii, were created by domain swaps between the proteins from escherichia coli and thermoanaerobacter tengcongensis. the ribosome recycling activity of the rrf chimaeras was compared with their wild ...	2006	16262604
enzymatic and genetic characterization of carbon and energy metabolisms by deep-sea hydrothermal chemolithoautotrophic isolates of epsilonproteobacteria.	the carbon and energy metabolisms of a variety of cultured chemolithoautotrophic epsilonproteobacteria from deep-sea hydrothermal environments were characterized by both enzymatic and genetic analyses. all the epsilonproteobacteria tested had all three key reductive tricarboxylic acid (rtca) cycle enzymatic activities--atp-dependent citrate lyase, pyruvate:ferredoxin oxidoreductase, and 2-oxoglutarate:ferredoxin oxidoreductase--while they had no ribulose 1,5-bisphosphate carboxylase (rubisco) ac ...	2005	16269773
identification of pilus-like structures and genes in microcystis aeruginosa pcc7806.	four putative type iv pilus genes from the toxic, naturally transformable microcystis aeruginosa pcc7806 were identified. three of these genes were clustered in an arrangement which is identical to that from other cyanobacterial genomes. type iv pilus-like appendages were also observed by electron microscopy.	2005	16269818
homology-model-guided site-specific mutagenesis reveals the mechanisms of substrate binding and product-regulation of adenosine kinase from leishmania donovani.	despite designating catalytic roles of asp299 and arg131 during the transfer of gamma-phosphate from atp to ado (adenosine) [r. datta, das, sen, chakraborty, adak, mandal and a. k. datta (2005) biochem. j. 387, 591-600], the mechanisms that determine binding of substrate and cause product inhibition of adenosine kinase from leishmania donovani remained unclear. in the present study, employing homology-model-guided site-specific protein mutagenesis, we show that asp16 is indispensable, since its ...	2006	16271040
structural basis for transcription inhibition by tagetitoxin.	tagetitoxin (tgt) inhibits transcription by an unknown mechanism. a structure at a resolution of 2.4 a of the thermus thermophilus rna polymerase (rnap)-tgt complex revealed that the tgt-binding site within the rnap secondary channel overlaps that of the stringent control effector ppgpp, which partially protects rnap from tgt inhibition. tgt binding is mediated exclusively through polar interactions with the beta and beta' residues whose substitutions confer resistance to tgt in vitro. important ...	2005	16273103
crystal structures of the editing domain of escherichia coli leucyl-trna synthetase and its complexes with met and ile reveal a lock-and-key mechanism for amino acid discrimination.	aarss (aminoacyl-trna synthetases) are responsible for the covalent linking of amino acids to their cognate trnas via the aminoacylation reaction and play a vital role in maintaining the fidelity of protein synthesis. leurs (leucyl-trna synthetase) can link not only the cognate leucine but also the nearly cognate residues ile and met to trna(leu). the editing domain of leurs deacylates the mischarged ile-trna(leu) and met-trna(leu). we report here the crystal structures of ecleurs-ed (the editin ...	2006	16277600
structure of a central stalk subunit f of prokaryotic v-type atpase/synthase from thermus thermophilus.	the crystal structure of subunit f of vacuole-type atpase/synthase (prokaryotic v-atpase) was determined to of 2.2 a resolution. the subunit reveals unexpected structural similarity to the response regulator proteins that include the escherichia coli chemotaxis response regulator chey. the structure was successfully placed into the low-resolution em structure of the prokaryotic holo-v-atpase at a location indicated by the results of crosslinking experiments. the crystal structure, together with ...	2005	16281059
crystal structure and rna binding of the rpb4/rpb7 subunits of human rna polymerase ii.	the rpb4 and rpb7 subunits of eukaryotic rna polymerase ii (rnap(ii)) form a heterodimer that protrudes from the 10-subunit core of the enzyme. we have obtained crystals of the human rpb4/rpb7 heterodimer and determined the structure to 2.7 a resolution. the presence of putative rna-binding domains on the rpb7 subunit and the position of the heterodimer close to the rna exit groove in the 12 subunit yeast polymerase complex strongly suggests a role for the heterodimer in binding and stabilizing ...	2005	16282592
conserved quantitative stability/flexibility relationships (qsfr) in an orthologous rnase h pair.	many reports qualitatively describe conserved stability and flexibility profiles across protein families, but biophysical modeling schemes have not been available to robustly quantify both. here we investigate an orthologous rnase h pair by using a minimal distance constraint model (dcm). the dcm is an all atom microscopic model [jacobs and dallakyan, biophys j 2005;88(2):903-915] that accurately reproduces heat capacity measurements [livesay et al., febs lett 2004;576(3):468-476], and is unique ...	2006	16287093
extending ribosomal protein identifications to unsequenced bacterial strains using matrix-assisted laser desorption/ionization mass spectrometry.	a protocol has been developed that allows protein identifications using available dna-based or protein sequences from a reference strain of a bacterial species to be extended to bacterial strains for which no prior dna-based or protein sequence information exists. the protocol is predicated on careful isolation of a specific sub-cellular group of proteins. in this study, ribosomal proteins were chosen due to their high relative abundance and similarity in copy number per cell. after isolation of ...	2005	16287167
control of phosphate release from elongation factor g by ribosomal protein l7/12.	ribosomal protein l7/12 is crucial for the function of elongation factor g (ef-g) on the ribosome. here, we report the localization of a site in the c-terminal domain (ctd) of l7/12 that is critical for the interaction with ef-g. single conserved surface amino acids were replaced in the ctd of l7/12. whereas mutations in helices 5 and 6 had no effect, replacements of v66, i69, k70, and r73 in helix 4 increased the michaelis constant (km) of ef-g.gtp for the ribosome, suggesting an involvement of ...	2005	16292341
a guild of 45 crispr-associated (cas) protein families and multiple crispr/cas subtypes exist in prokaryotic genomes.	clustered regularly interspaced short palindromic repeats (crisprs) are a family of dna direct repeats found in many prokaryotic genomes. repeats of 21-37 bp typically show weak dyad symmetry and are separated by regularly sized, nonrepetitive spacer sequences. four crispr-associated (cas) protein families, designated cas1 to cas4, are strictly associated with crispr elements and always occur near a repeat cluster. some spacers originate from mobile genetic elements and are thought to confer "im ...	2005	16292354
miniseed3 (mini3), a wrky family gene, and haiku2 (iku2), a leucine-rich repeat (lrr) kinase gene, are regulators of seed size in arabidopsis.	we have identified mutant alleles of two sporophytically acting genes, haiku2 (iku2) and miniseed3 (mini3). homozygotes of these alleles produce a small seed phenotype associated with reduced growth and early cellularization of the endosperm. this phenotype is similar to that described for another seed size gene, iku1. mini3 encodes wrky10, a wrky class transcription factor. mini3 promoter::gus fusions show the gene is expressed in pollen and in the developing endosperm from the two nuclei stage ...	2005	16293693
regulation through the rna polymerase secondary channel. structural and functional variability of the coiled-coil transcription factors.	gre factors enhance the intrinsic endonucleolytic activity of rna polymerase to rescue arrested transcription complexes and are thought to confer the high fidelity and processivity of rna synthesis. the gre factors insert the extended alpha-helical coiled-coil domains into the rna polymerase secondary channel to position two invariant acidic residues at the coiled-coil tip near the active site to stabilize the catalytic metal ion. gfh1, a grea homolog from thermus thermophilus, inhibits rather t ...	2006	16298991
multiplexed tandem pcr: gene profiling from small amounts of rna using sybr green detection.	multiplexed tandem pcr (mt-pcr) is a process for highly multiplexed gene expression profiling. in the first step, multiple primer pairs are added to the rna to be analysed together with reverse transcriptase and taq dna polymerase. following reverse transcription, the multiplexed amplicons are simultaneously amplified for a small number of cycles so as to avoid competition between amplicons. the reaction product is then diluted and analysed in multiple individual pcrs using primers nested inside ...	2005	16314310
accessibility of 18s rrna in human 40s subunits and 80s ribosomes at physiological magnesium ion concentrations--implications for the study of ribosome dynamics.	protein biosynthesis requires numerous conformational rearrangements within the ribosome. the structural core of the ribosome is composed of rna and is therefore dependent on counterions such as magnesium ions for function. many steps of translation can be compromised or inhibited if the concentration of mg(2+) is too low or too high. conditions previously used to probe the conformation of the mammalian ribosome in vitro used high mg(2+) concentrations that we find completely inhibit translation ...	2005	16314459
the membrane protein data bank.	the membrane protein data bank (mpdb) is an online, searchable, relational database of structural and functional information on integral, anchored and peripheral membrane proteins and peptides. data originates from the protein data bank and other databases, and from the literature. structures are based on x-ray and electron diffraction, nuclear magnetic resonance and cryoelectron microscopy. the mpdb is searchable online by protein characteristic, structure determination method, crystallization ...	2005	16314922
the membrane protein data bank.	the membrane protein data bank (mpdb) is an online, searchable, relational database of structural and functional information on integral, anchored and peripheral membrane proteins and peptides. data originates from the protein data bank and other databases, and from the literature. structures are based on x-ray and electron diffraction, nuclear magnetic resonance and cryoelectron microscopy. the mpdb is searchable online by protein characteristic, structure determination method, crystallization ...	2005	16314922
an assembly landscape for the 30s ribosomal subunit.	self-assembling macromolecular machines drive fundamental cellular processes, including transcription, messenger rna processing, translation, dna replication and cellular transport. the ribosome, which carries out protein synthesis, is one such machine, and the 30s subunit of the bacterial ribosome is the preeminent model system for biophysical analysis of large rna-protein complexes. our understanding of 30s assembly is incomplete, owing to the challenges of monitoring the association of many c ...	2005	16319883
compatible solutes of the hyperthermophile palaeococcus ferrophilus: osmoadaptation and thermoadaptation in the order thermococcales.	the effect of salinity and growth temperature on the accumulation of intracellular organic solutes was examined in the hyperthermophilic archaeon palaeococcus ferrophilus. the genus palaeococcus represents a deep-branching lineage of the order thermococcales, which diverged before thermococcus and pyrococcus. palaeococcus ferrophilus accumulated mannosylglycerate, glutamate, and aspartate as major compatible solutes. unlike members of the genera pyrococcus and thermococcus, palaeococcus ferrophi ...	2005	16332790
comparative genomic analyses of the bacterial phosphotransferase system.	we report analyses of 202 fully sequenced genomes for homologues of known protein constituents of the bacterial phosphoenolpyruvate-dependent phosphotransferase system (pts). these included 174 bacterial, 19 archaeal, and 9 eukaryotic genomes. homologues of pts proteins were not identified in archaea or eukaryotes, showing that the horizontal transfer of genes encoding pts proteins has not occurred between the three domains of life. of the 174 bacterial genomes (136 bacterial species) analyzed, ...	2005	16339738
the proficiency of a thermophilic chorismate mutase enzyme is solely through an entropic advantage in the enzyme reaction.	a study of the thermus thermophilus chorismate mutase (ttcm) is described by using quantum mechanics (self-consistent-charge density-functional tight binding)/molecular mechanics, umbrella sampling, and the weighted histogram analysis method. the computed free energies of activation for the reactions in water and ttcm are comparable to the experimental values. the free energies for formation of near attack conformer have been determined to be 8.06 and 0.05 kcal/mol in water and ttcm, respectivel ...	2005	16344484
resistance of thermus spp. to potassium tellurite.	two members of the genus thermus were examined for their resistance to toxic inorganic compounds. they both proved to be fairly resistant to tellurite and selenite and to many other heavy metal salts. cell extracts of thermus thermophilus hb8 and of t. flavus at-62 catalyze the reduction of k(2)teo(3) in a reaction which is dependent on nadh oxidation.	1988	16347571
production and extracellular secretion of aqualysin i (a thermophilic subtilisin-type protease) in a host-vector system for thermus thermophilus.	aqualysin i is synthesized as a large precursor, processed, and secreted into the culture medium by thermus aquaticus yt-1. an expression plasmid for the aqualysin i gene in t. thermophilus hb27 was constructed. t. thermophilus cells harboring the recombinant plasmid produced correctly processed aqualysin i, and the mature enzyme was secreted into the culture medium.	1991	16348594
recombination-deficient mutants of an extreme thermophile, thermus thermophilus.	recombination-deficient strains of the extreme thermophile thermus thermophilus have been prepared from a leucine-isoleucine mutant strain (nm6). the availability of such recombination-deficient thermophilic bacterial strains may provide especially good hosts for work with plasmid vectors.	1993	16349029
a low-cost open-source snp genotyping platform for association mapping applications.	association mapping aimed at identifying dna polymorphisms that contribute to variation in complex traits entails genotyping a large number of single-nucleotide polymorphisms (snps) in a very large panel of individuals. few technologies, however, provide inexpensive high-throughput genotyping. here, we present an efficient approach developed specifically for genotyping large fixed panels of diploid individuals. the cost-effective, open-source nature of our methodology may make it particularly at ...	2005	16356268
protein-protein interactions of the hyperthermophilic archaeon pyrococcus horikoshii ot3.	although 2,061 proteins of pyrococcus horikoshii ot3, a hyperthermophilic archaeon, have been predicted from the recently completed genome sequence, the majority of proteins show no similarity to those from other organisms and are thus hypothetical proteins of unknown function. because most proteins operate as parts of complexes to regulate biological processes, we systematically analyzed protein-protein interactions in pyrococcus using the mammalian two-hybrid system to determine the function o ...	2005	16356270
the fidelity of translation initiation: reciprocal activities of eif1, if3 and ycih.	eukaryotic initiation factor eif1 and the functional c-terminal domain of prokaryotic initiation factor if3 maintain the fidelity of initiation codon selection in eukaryotes and prokaryotes, respectively, and bind to the same regions of small ribosomal subunits, between the platform and initiator trna. here we report that these nonhomologous factors can bind to the same regions of heterologous subunits and perform their functions in heterologous systems in a reciprocal manner, discriminating aga ...	2005	16362046
the fidelity of translation initiation: reciprocal activities of eif1, if3 and ycih.	eukaryotic initiation factor eif1 and the functional c-terminal domain of prokaryotic initiation factor if3 maintain the fidelity of initiation codon selection in eukaryotes and prokaryotes, respectively, and bind to the same regions of small ribosomal subunits, between the platform and initiator trna. here we report that these nonhomologous factors can bind to the same regions of heterologous subunits and perform their functions in heterologous systems in a reciprocal manner, discriminating aga ...	2005	16362046
the structural biology center 19id undulator beamline: facility specifications and protein crystallographic results.	the 19id undulator beamline of the structure biology center has been designed and built to take full advantage of the high flux, brilliance and quality of x-ray beams delivered by the advanced photon source. the beamline optics are capable of delivering monochromatic x-rays with photon energies from 3.5 to 20 kev (3.5-0.6 a wavelength) with fluxes up to 8-18 x 10(12) photons s(-1) (depending on photon energy) onto cryogenically cooled crystal samples. the size of the beam (full width at half-max ...	2005	16371706
the structural biology center 19id undulator beamline: facility specifications and protein crystallographic results.	the 19id undulator beamline of the structure biology center has been designed and built to take full advantage of the high flux, brilliance and quality of x-ray beams delivered by the advanced photon source. the beamline optics are capable of delivering monochromatic x-rays with photon energies from 3.5 to 20 kev (3.5-0.6 a wavelength) with fluxes up to 8-18 x 10(12) photons s(-1) (depending on photon energy) onto cryogenically cooled crystal samples. the size of the beam (full width at half-max ...	2005	16371706
asnb is involved in natural resistance of mycobacterium smegmatis to multiple drugs.	mycobacteria are naturally resistant to most common antibiotics and chemotherapeutic agents. the underlying molecular mechanisms are not fully understood. in this paper, we describe a hypersensitive mutant of mycobacterium smegmatis, ms 2-39, which was isolated by screening for transposon insertion mutants of m. smegmatis mc2155 that exhibit increased sensitivity to rifampin, erythromycin, or novobiocin. the mutant ms 2-39 exhibited increased sensitivity to all three of the above mentioned antib ...	2006	16377694
the tmrdb and srpdb resources.	maintained at the university of texas health science center at tyler, texas, the tmrna database (tmrdb) is accessible at the url http://psyche.uthct.edu/dbs/tmrdb/tmrdb.html with mirror sites located at auburn university, auburn, alabama (http://www.ag.auburn.edu/mirror/tmrdb/) and the royal veterinary and agricultural university, denmark (http://tmrdb.kvl.dk/). the signal recognition particle database (srpdb) at http://psyche.uthct.edu/dbs/srpdb/srpdb.html is mirrored at http://srpdb.kvl.dk/ an ...	2006	16381838
the tmrdb and srpdb resources.	maintained at the university of texas health science center at tyler, texas, the tmrna database (tmrdb) is accessible at the url http://psyche.uthct.edu/dbs/tmrdb/tmrdb.html with mirror sites located at auburn university, auburn, alabama (http://www.ag.auburn.edu/mirror/tmrdb/) and the royal veterinary and agricultural university, denmark (http://tmrdb.kvl.dk/). the signal recognition particle database (srpdb) at http://psyche.uthct.edu/dbs/srpdb/srpdb.html is mirrored at http://srpdb.kvl.dk/ an ...	2006	16381838
the allosteric transition in dnak probed by infrared difference spectroscopy. concerted atp-induced rearrangement of the substrate binding domain.	the biological activity of dnak, the bacterial representative of the hsp70 protein family, is regulated by the allosteric interaction between its nucleotide and peptide substrate binding domains. despite the importance of the nucleotide-induced cycling of dnak between substrate-accepting and releasing states, the heterotropic allosteric mechanism remains as yet undefined. to further characterize this mechanism, the nucleotide-induced absorbance changes in the vibrational spectrum of wild-type dn ...	2006	16384998
production of recombinant and tagged proteins in the hyperthermophilic archaeon sulfolobus solfataricus.	many systems are available for the production of recombinant proteins in bacterial and eukaryotic model organisms, which allow us to study proteins in their native hosts and to identify protein-protein interaction partners. in contrast, only a few transformation systems have been developed for archaea, and no system for high-level gene expression existed for hyperthermophilic organisms. recently, a virus-based shuttle vector with a reporter gene was developed for the crenarchaeote sulfolobus sol ...	2006	16391031
involvement of nark1 and nark2 proteins in transport of nitrate and nitrite in the denitrifying bacterium pseudomonas aeruginosa pao1.	two transmembrane proteins were tentatively classified as nark1 and nark2 in the pseudomonas genome project and hypothesized to play an important physiological role in nitrate/nitrite transport in pseudomonas aeruginosa. the nark1 and nark2 genes are located in a cluster along with the structural genes for the nitrate reductase complex. our studies indicate that the transcription of all these genes is initiated from a single promoter and that the gene complex nark1k2ghji constitutes an operon. u ...	2006	16391109
bioinformatic analysis of an unusual gene-enzyme relationship in the arginine biosynthetic pathway among marine gamma proteobacteria: implications concerning the formation of n-acetylated intermediates in prokaryotes.	the n-acetylation of l-glutamate is regarded as a universal metabolic strategy to commit glutamate towards arginine biosynthesis. until recently, this reaction was thought to be catalyzed by either of two enzymes: (i) the classical n-acetylglutamate synthase (nags, gene arga) first characterized in escherichia coli and pseudomonas aeruginosa several decades ago and also present in vertebrates, or (ii) the bifunctional version of ornithine acetyltransferase (oat, gene argj) present in bacteria, a ...	2006	16409639
comparative genomics of multidrug resistance in acinetobacter baumannii.	acinetobacter baumannii is a species of nonfermentative gram-negative bacteria commonly found in water and soil. this organism was susceptible to most antibiotics in the 1970s. it has now become a major cause of hospital-acquired infections worldwide due to its remarkable propensity to rapidly acquire resistance determinants to a wide range of antibacterial agents. here we use a comparative genomic approach to identify the complete repertoire of resistance genes exhibited by the multidrug-resist ...	2006	16415984
size matters: a view of selenocysteine incorporation from the ribosome.	this review focuses on the known factors required for selenocysteine (sec) incorporation in eukaryotes and highlights recent findings that have compelled us to propose a new model for the mechanism of sec incorporation. in light of this data we also review the controversial aspects of the previous model specifically regarding the proposed interaction between sbp2 and eefsec. in addition, the relevance of two recently discovered factors in the recoding of sec are reviewed. the role of the ribosom ...	2005	16416259
size matters: a view of selenocysteine incorporation from the ribosome.	this review focuses on the known factors required for selenocysteine (sec) incorporation in eukaryotes and highlights recent findings that have compelled us to propose a new model for the mechanism of sec incorporation. in light of this data we also review the controversial aspects of the previous model specifically regarding the proposed interaction between sbp2 and eefsec. in addition, the relevance of two recently discovered factors in the recoding of sec are reviewed. the role of the ribosom ...	2005	16416259
structure-function analysis of the kinase-cpd domain of yeast trna ligase (trl1) and requirements for complementation of trna splicing by a plant trl1 homolog.	trl1 is an essential 827 amino acid enzyme that executes the end-healing and end-sealing steps of trna splicing in saccharomyces cerevisiae. trl1 consists of two domains--an n-terminal ligase component and a c-terminal 5'-kinase/2',3'-cyclic phosphodiesterase (cpd) component--that can function in trna splicing in vivo when expressed as separate polypeptides. to understand the structural requirements for the kinase-cpd domain, we performed an alanine scan of 30 amino acids that are conserved in t ...	2006	16428247
function and evolution of plasmid-borne genes for pyrimidine biosynthesis in borrelia spp.	the thyx gene for thymidylate synthase of the lyme borreliosis (lb) agent borrelia burgdorferi is located in a 54-kb linear plasmid. in the present study, we identified an orthologous thymidylate synthase gene in the relapsing fever (rf) agent borrelia hermsii, located it in a 180-kb linear plasmid, and demonstrated its expression. the functions of the b. hermsii and b. burgdorferi thyx gene products were evaluated both in vivo, by complementation of a thymidylate synthase-deficient escherichia ...	2006	16428394
characterization of the biosynthetic pathway of glucosylglycerate in the archaeon methanococcoides burtonii.	the pathway for the synthesis of the organic solute glucosylglycerate (gg) is proposed based on the activities of the recombinant glucosyl-3-phosphoglycerate synthase (gpgs) and glucosyl-3-phosphoglycerate phosphatase (gpgp) from methanococcoides burtonii. a mannosyl-3-phosphoglycerate phosphatase gene homologue (mpgp) was found in the genome of m. burtonii (http://www.jgi.doe.gov), but an mpgs gene coding for mannosyl-3-phosphoglycerate synthase (mpgs) was absent. the gene upstream of the mpgp ...	2006	16428406
crystal structures of nitroalkane oxidase: insights into the reaction mechanism from a covalent complex of the flavoenzyme trapped during turnover.	nitroalkane oxidase (nao) from fusarium oxysporum catalyzes the oxidation of neutral nitroalkanes to the corresponding aldehydes or ketones with the production of h(2)o(2) and nitrite. the flavoenzyme is a new member of the acyl-coa dehydrogenase (acad) family, but it does not react with acyl-coa substrates. we present the 2.2 a resolution crystal structure of nao trapped during the turnover of nitroethane as a covalent n5-fad adduct (es). the homotetrameric structure of es was solved by mad p ...	2006	16430210
identification and characterization of rsme, the founding member of a new rna base methyltransferase family.	a variety of rna methyltransferases act during ribosomal rna maturation to modify nucleotides in a site-specific manner. however, of the 10 base-methylated nucleotides present in the small ribosomal subunit of escherichia coli, only three enzymes responsible for modification of four bases are known. here, we show that the protein encoded by yggj, a member of the uncharacterized duf558 protein family of predicted alpha/beta (trefoil) knot methyltransferases is responsible for methylation at u1498 ...	2006	16431987
mutations conferring aminoglycoside and spectinomycin resistance in borrelia burgdorferi.	we have isolated and characterized in vitro mutants of the lyme disease agent borrelia burgdorferi that are resistant to spectinomycin, kanamycin, gentamicin, or streptomycin, antibiotics that target the small subunit of the ribosome. 16s rrna mutations a1185g and c1186u, homologous to escherichia coli nucleotides a1191 and c1192, conferred >2,200-fold and 1,300-fold resistance to spectinomycin, respectively. a 16s rrna a1402g mutation, homologous to e. coli a1408, conferred >90-fold resistance ...	2006	16436695
two conformational states in the crystal structure of the homo sapiens cytoplasmic ribosomal decoding a site.	the decoding a site of the small ribosomal subunit is an rna molecular switch, which monitors codon-anticodon interactions to guarantee translation fidelity. we have solved the crystal structure of an rna fragment containing two homo sapiens cytoplasmic a sites. each of the two a sites presents a different conformational state. in one state, adenines a1492 and a1493 are fully bulged-out with c1409 forming a wobble-like pair to a1491. in the second state, adenines a1492 and a1493 form non-watson- ...	2006	16452297
structure of the tetrahymena thermophila telomerase rna helix ii template boundary element.	telomere addition by telomerase requires an internal templating sequence located in the rna subunit of telomerase. the correct boundary definition of this template sequence is essential for the proper addition of the nucleotide repeats. incorporation of incorrect telomeric repeats onto the ends of chromosomes has been shown to induce chromosomal instability in ciliate, yeast and human cells. a 5' template boundary defining element (tbe) has been identified in human, yeast and ciliate telomerase ...	2006	16452301
the post-translational synthesis of a polyamine-derived amino acid, hypusine, in the eukaryotic translation initiation factor 5a (eif5a).	the eukaryotic translation initiation factor 5a (eif5a) is the only cellular protein that contains the unique polyamine-derived amino acid, hypusine [nepsilon-(4-amino-2-hydroxybutyl)lysine]. hypusine is formed in eif5a by a novel post-translational modification reaction that involves two enzymatic steps. in the first step, deoxyhypusine synthase catalyzes the cleavage of the polyamine spermidine and transfer of its 4-aminobutyl moiety to the epsilon-amino group of one specific lysine residue of ...	2006	16452303
methionine oxidation of monomeric lambda repressor: the denatured state ensemble under nondenaturing conditions.	although poorly understood, the properties of the denatured state ensemble are critical to the thermodynamics and the kinetics of protein folding. the most relevant conformations to cellular protein folding are the ones populated under physiological conditions. to avoid the problem of low expression that is seen with unstable variants, we used methionine oxidation to destabilize monomeric lambda repressor and predominantly populate the denatured state under nondenaturing buffer conditions. the d ...	2006	16452618
molecular dynamics simulations of sarcin-ricin rrna motif.	explicit solvent molecular dynamics (md) simulations were carried out for sarcin-ricin domain (srd) motifs from 23s (escherichia coli) and 28s (rat) rrnas. the srd motif consists of gaga tetraloop, g-bulged cross-strand a-stack, flexible region and duplex part. detailed analysis of the overall dynamics, base pairing, hydration, cation binding and other srd features is presented. the srd is surprisingly static in multiple 25 ns long simulations and lacks any non-local motions, with root mean squa ...	2006	16456030
type a and b rnase p rnas are interchangeable in vivo despite substantial biophysical differences.	we show that structural type a and b bacterial ribonuclease p (rnase p) rnas can fully replace each other in vivo despite the many reported differences in their biogenesis, biochemical/biophysical properties and enzyme function in vitro. our findings suggest that many of the reported idiosyncrasies of type a and b enzymes either do not reflect the in vivo situation or are not crucial for rnase p function in vivo, at least under standard growth conditions. the discrimination of mature trna by rna ...	2006	16470227
isolation of a site-specifically modified rna from an unmodified transcript.	natural rnas contain many base modifications that have specific biological functions. the ability to functionally dissect individual modifications is facilitated by the identification and cloning of enzymes responsible for these modifications, but is hindered by the difficulty of isolating site-specifically modified rnas away from unmodified transcripts. using the m1g37 and m1a58 methyl modifications of trna as two examples, we demonstrate that non-pairing base modifications protect rnas against ...	2006	16473844
trna properties help shape codon pair preferences in open reading frames.	translation elongation is an accurate and rapid process, dependent upon efficient juxtaposition of trnas in the ribosomal a- and p-sites. here, we sought evidence of a- and p-site trna interaction by examining bias in codon pair choice within open reading frames from a range of genomes. three distinct and marked effects were revealed once codon and dipeptide biases had been subtracted. first, in the majority of genomes, codon pair preference is primarily determined by a tetranucleotide combinati ...	2006	16473853
crystal structures of two putative phosphoheptose isomerases.		2006	16477602
nucleic acid visualization with ucsf chimera.	with the increase in the number of large, 3d, high-resolution nucleic acid structures, particularly of the 30s and 50s ribosomal subunits and the intact bacterial ribosome, advancements in the visualization of nucleic acid structural features are essential. large molecular structures are complicated and detailed, and one goal of visualization software is to allow the user to simplify the display of some features and accent others. we describe an extension to the ucsf chimera molecular visualizat ...	2006	16478715
compositional discordance between prokaryotic plasmids and host chromosomes.	most plasmids depend on the host replication machinery and possess partitioning genes. these properties confine plasmids to a limited range of hosts, yielding a close and presumably stable relationship between plasmid and host. hence, it is anticipated that due to amelioration the dinucleotide composition of plasmids is similar to that of the genome of their hosts. however, plasmids are also thought to play a major role in horizontal gene transfer and thus are frequently exchanged between hosts, ...	2006	16480495
effects of streptomycin resistance mutations on posttranslational modification of ribosomal protein s12.	ribosomal protein s12 contains a highly conserved aspartic acid residue that is posttranslationally beta-methylthiolated. using mass spectrometry, we have determined the modification states of several s12 mutants of thermus thermophilus and conclude that beta-methylthiolation is not a determinant of the streptomycin phenotype.	2006	16484214
the molecular architecture of the metalloprotease ftsh.	the atp-dependent integral membrane protease ftsh is universally conserved in bacteria. orthologs exist in chloroplasts and mitochondria, where in humans the loss of a close ftsh-homolog causes a form of spastic paraplegia. ftsh plays a crucial role in quality control by degrading unneeded or damaged membrane proteins, but it also targets soluble signaling factors like sigma(32) and lambda-cii. we report here the crystal structure of a soluble ftsh construct that is functional in caseinolytic an ...	2006	16484367
dependency map of proteins in the small ribosomal subunit.	the assembly of the ribosome has recently become an interesting target for antibiotics in several bacteria. in this work, we extended an analytical procedure to determine native state fluctuations and contact breaking to investigate the protein stability dependence in the 30s small ribosomal subunit of thermus thermophilus. we determined the causal influence of the presence and absence of proteins in the 30s complex on the binding free energies of other proteins. the predicted dependencies are i ...	2006	16485038
recj exonuclease: substrates, products and interaction with ssb.	the recj exonuclease from escherichia coli degrades single-stranded dna (ssdna) in the 5'-3' direction and participates in homologous recombination and mismatch repair. the experiments described here address recj's substrate requirements and reaction products. recj complexes on a variety of 5' single-strand tailed substrates were analyzed by electrophoretic mobility shift in the absence of mg2+ ion required for substrate degradation. recj required single-stranded tails of 7 nt or greater for rob ...	2006	16488881
ribose 2'-hydroxyl groups in the 5' strand of the acceptor arm of p-site trna are not essential for ef-g catalyzed translocation.	the coupled movement of trna-mrna complex through the ribosome is a fundamental step during the protein elongation process. we demonstrate that the ribosome will translocate a p-site-bound trna(met) with a break in the phosphodiester backbone between positions 17 and 18 in the d-loop. crystallographic data showed that the acceptor arms of p- and e-site trna interact extensively with the ribosomal large subunit. therefore, we used this fragmented p-site-bound trna(met) to investigate the contribu ...	2006	16489185
defining the primary route for lutein synthesis in plants: the role of arabidopsis carotenoid beta-ring hydroxylase cyp97a3.	lutein, a dihydroxy derivative of alpha-carotene (beta,epsilon-carotene), is the most abundant carotenoid in photosynthetic plant tissues where it plays important roles in light-harvesting complex-ii structure and function. the synthesis of lutein from lycopene requires at least four distinct enzymatic reactions: beta- and epsilon-ring cyclizations and hydroxylation of each ring at the c-3 position. three carotenoid hydroxylases have already been identified in arabidopsis, two nonheme diiron bet ...	2006	16492736
molecular localization of a ribosome-dependent atpase on escherichia coli ribosomes.	we have previously isolated and described an escherichia coli ribosome-bound atpase, rbba, that is required for protein synthesis in the presence of atp, gtp and the elongation factors, ef-tu and ef-g. the gene encoding rbba, yhih, has been cloned and the deduced protein sequence harbors two atp-motifs and one rna-binding motif and is homologous to the fungal ef-3. here, we describe the isolation and assay of a truncated form of the rbba protein that is stable to overproduction and purification. ...	2006	16495476
identification of hepta- and octo-uridine stretches as sole signals for programmed +1 and -1 ribosomal frameshifting during translation of sars-cov orf 3a variants.	programmed frameshifting is one of the translational recoding mechanisms that read the genetic code in alternative ways. this process is generally programmed by signals at defined locations in a specific mrna. in this study, we report the identification of hepta- and octo-uridine stretches as sole signals for programmed +1 and -1 ribosomal frameshifting during translation of severe acute respiratory syndrome coronavirus (sars-cov) orf 3a variants. sars-cov orf 3a encodes a minor structural prote ...	2006	16500894
crystallization of leucyl-trna synthetase complexed with trnaleu from the archaeon pyrococcus horikoshii.	all five trnaleu isoacceptors from the archaeon pyrococcus horikoshii have been transcribed in vitro and purified. the leucyl-trna synthetase (leurs) from p. horikoshii was overexpressed in escherichia coli and purified, and cocrystallizations with each of the trnaleu isoacceptors were attempted. cocrystals were obtained by the hanging-drop vapour-diffusion method, but only when the trnaleu isoacceptor with the anticodon caa was used. electrophoretic analyses revealed that the crystals contain b ...	2005	16508082
crystallization of leucyl-trna synthetase complexed with trnaleu from the archaeon pyrococcus horikoshii.	all five trnaleu isoacceptors from the archaeon pyrococcus horikoshii have been transcribed in vitro and purified. the leucyl-trna synthetase (leurs) from p. horikoshii was overexpressed in escherichia coli and purified, and cocrystallizations with each of the trnaleu isoacceptors were attempted. cocrystals were obtained by the hanging-drop vapour-diffusion method, but only when the trnaleu isoacceptor with the anticodon caa was used. electrophoretic analyses revealed that the crystals contain b ...	2005	16508082
purification, crystallization and preliminary crystallographic analysis of the vacuole-type atpase subunit e from pyrococcus horikoshii ot3.	the vacuole-type atpases in eukaryotic cells translocate protons across various biological membranes including the vacuolar membrane by consuming atp molecules. the e subunit of the multisubunit complex v-atpase from pyrococcus horikoshii ot3, which has a molecular weight of 22.88 kda, has been cloned, overexpressed in escherichia coli, purified and crystallized by the microbatch method using peg 4000 as a precipitant at 296 k. a data set to 1.85 a resolution with 98.8% completeness and an rmerg ...	2005	16508090
purification, crystallization and preliminary crystallographic analysis of the vacuole-type atpase subunit e from pyrococcus horikoshii ot3.	the vacuole-type atpases in eukaryotic cells translocate protons across various biological membranes including the vacuolar membrane by consuming atp molecules. the e subunit of the multisubunit complex v-atpase from pyrococcus horikoshii ot3, which has a molecular weight of 22.88 kda, has been cloned, overexpressed in escherichia coli, purified and crystallized by the microbatch method using peg 4000 as a precipitant at 296 k. a data set to 1.85 a resolution with 98.8% completeness and an rmerg ...	2005	16508090
a structural model for the large subunit of the mammalian mitochondrial ribosome.	protein translation is essential for all forms of life and is conducted by a macromolecular complex, the ribosome. evolutionary changes in protein and rna sequences can affect the 3d organization of structural features in ribosomes in different species. the most dramatic changes occur in animal mitochondria, whose genomes have been reduced and altered significantly. the rna component of the mitochondrial ribosome (mitoribosome) is reduced in size, with a compensatory increase in protein content. ...	2006	16510155
specific functional interactions of nucleotides at key -3 and +4 positions flanking the initiation codon with components of the mammalian 48s translation initiation complex.	eukaryotic initiation factor (eif) 1 maintains the fidelity of initiation codon selection and enables mammalian 43s preinitiation complexes to discriminate against aug codons with a context that deviates from the optimum sequence gcc(a/g)ccaugg, in which the purines at (-)3 and (+)4 positions are most important. we hypothesize that eif1 acts by antagonizing conformational changes that occur in ribosomal complexes upon codon-anticodon base-pairing during 48s initiation complex formation, and that ...	2006	16510876
overproduction and preliminary crystallographic study of a human kynurenine aminotransferase ii homologue from pyrococcus horikoshii ot3.	the pyrococcus horikoshii ot3 genome contains a gene encoding a human kynurenine aminotransferase ii (kat ii) homologue, which consists of 428 amino-acid residues and shows an amino-acid sequence identity of 30% to human kat ii. this gene was overexpressed in escherichia coli and the recombinant protein (ph-kat ii) was purified. gel-filtration chromatography showed that ph-kat ii exists as a homodimer. ph-kat ii exhibited enzymatic activity that catalyzes the transamination of l-kynurenine to pr ...	2005	16511030
structure of the pseudouridine synthase rsua from haemophilus influenzae.	the structure of the pseudouridine synthase rsua from haemophilus influenza, which catalyzes the conversion of uridine to pseudouridine at a single position within 16s ribosomal rna, has been determined at 1.59 a resolution and compared with that of escherichia coli rsua. the h. influenza enzyme contains an n-terminal s4-like alpha3beta4 domain followed by a catalytic domain, as observed in the structure of e. coli rsua. whereas the individual domains of e. coli and h. influenza rsua are structu ...	2005	16511038
crystallization and preliminary x-ray crystallographic analysis of a conserved domain in plants and prokaryotes from pyrococcus horikoshii ot3.	a plant- and prokaryote-conserved domain (ppc) has previously been found in at-hook motif nuclear localized protein 1 (ahl1) localized in the nuclear matrix of arabidopsis thaliana (atahl1). atahl1 has a dna-binding function. mutation analyses of atahl1 has previously revealed that the hydrophobic region of the ppc domain is essential for its nuclear localization. in this study, the ppc of the hyperthermophilic archaebacterium pyrococcus horikoshii (phppc) was crystallized using the hanging-drop ...	2005	16511056
structure of purine nucleoside phosphorylase (deod) from bacillus anthracis.	protein structures from the causative agent of anthrax (bacillus anthracis) are being determined as part of a structural genomics programme. amongst initial candidates for crystallographic analysis are enzymes involved in nucleotide biosynthesis, since these are recognized as potential targets in antibacterial therapy. purine nucleoside phosphorylase is a key enzyme in the purine-salvage pathway. the crystal structure of purine nucleoside phosphorylase (deod) from b. anthracis has been solved by ...	2005	16511068
crystallization and preliminary x-ray crystallographic analysis of yeast nad+-specific isocitrate dehydrogenase.	nad+-specific isocitrate dehydrogenase (idh; ec 1.1.1.41) is a complex allosterically regulated enzyme in the tricarboxylic acid cycle. yeast idh is believed to be an octamer containing four catalytic idh2 and four regulatory idh1 subunits. crystals of yeast idh have been obtained and optimized using sodium citrate, a competitive inhibitor of the enzyme, as the precipitating agent. the crystals belong to space group r3, with unit-cell parameters a = 302.0, c = 112.1 a. diffraction data were coll ...	2005	16511075
preparation, crystallization and preliminary x-ray analysis of yjcg protein from bacillus subtilis.	bacillus subtilis yjcg is a functionally uncharacterized protein with 171 residues that has no structural homologue in the protein data bank. however, it shows sequence homology to bacterial and archaeal 2'-5' rna ligases. in order to identify its exact function via structural studies, the yjcg gene was amplified from b. subtilis genomic dna and cloned into the expression vector pet21-dest. the protein was expressed in a soluble form in escherichia coli and was purified to homogeneity. crystals ...	2005	16511078
crystallization and preliminary crystallographic analysis of a flavoprotein nadh oxidase from lactobacillus brevis.	nadh oxidase (nox) from lactobacillus brevis is a homotetrameric flavoenzyme composed of 450 amino acids per subunit. the molecular weight of each monomer is 48.8 kda. the enzyme catalyzes the oxidation of two equivalents of nadh and reduces one equivalent of oxygen to yield two equivalents of water, without releasing hydrogen peroxide after the reduction of the first equivalent of nadh. crystals of this protein were grown in the presence of 34% polyethylene glycol monomethyl ether 2000, 0.1 m s ...	2005	16511087
overexpression, purification and crystallographic analysis of a unique adenosine kinase from mycobacterium tuberculosis.	adenosine kinase from mycobacterium tuberculosis is the only prokaryotic adenosine kinase that has been isolated and characterized. the enzyme catalyzes the phosphorylation of adenosine to adenosine monophosphate and is involved in the activation of 2-methyladenosine, a compound that has demonstrated selective activity against m. tuberculosis. the mechanism of action of 2-methyladenosine is likely to be different from those of current tuberculosis treatments and this compound (or other adenosine ...	2005	16511094
expression, purification, crystallization and preliminary x-ray analysis of a nucleoside kinase from the hyperthermophile methanocaldococcus jannaschii.	methanocaldococcus jannaschii nucleoside kinase (mjnk) is an atp-dependent non-allosteric phosphotransferase that shows high catalytic activity for guanosine, inosine and cytidine. mjnk is a member of the phosphofructokinase b family, but participates in the biosynthesis of nucleoside monophosphates rather than in glycolysis. mjnk was crystallized as the apoenzyme as well as in complex with an atp analogue and mg2+. the latter crystal form was also soaked with fructose-6-phosphate. synchrotron-r ...	2005	16511104
crystallization and avoiding the problem of hemihedral twinning in crystals of delta1-pyrroline-5-carboxylate dehydrogenase from thermus thermophilus.	delta1-pyrroline-5-carboxylate dehydrogenase from thermus thermophilus (ttp5cdh) has been crystallized in a citrate-bound form (ttp5cdh-cit). the crystals diffracted to well beyond 2 a resolution, but exhibited perfect or near-perfect hemihedral twinning. variation of crystallization conditions resulted in the growth of larger untwinned crystals or crystals with significantly reduced twin content, all with similar unit-cell parameters. the soaking of ttp5cdh-cit crystals in citrate-free solution ...	2005	16511109
a double mutation of escherichia coli2c-methyl-d-erythritol-2,4-cyclodiphosphate synthase disrupts six hydrogen bonds with, yet fails to prevent binding of, an isoprenoid diphosphate.	the essential enzyme 2c-methyl-d-erythritol-2,4-cyclodiphosphate (mecp) synthase, found in most eubacteria and the apicomplexan parasites, participates in isoprenoid-precursor biosynthesis and is a validated target for the development of broad-spectrum antimicrobial drugs. the structure and mechanism of the enzyme have been elucidated and the recent exciting finding that the enzyme actually binds diphosphate-containing isoprenoids at the interface formed by the three subunits that constitute the ...	2005	16511114
structure of a class ii trmh trna-modifying enzyme from aquifex aeolicus.	biological rnas contain a variety of post-transcriptional modifications that facilitate their efficient function in the cellular environment. one of the two most common forms of modification is methylation of the 2'-hydroxyl group of the ribose sugar, which is performed by a number of s-adenosylmethionine (sam) dependent methyltransferases. in bacteria, many of these modifications in trna and rrna are carried out by the alpha/beta-knot superfamily of enzymes, whose sam-binding pocket is created ...	2005	16511140
cloning, purification and crystallization of thermus thermophilus proline dehydrogenase.	nature recycles l-proline by converting it to l-glutamate. this four-electron oxidation process is catalyzed by the two enzymes: proline dehydrogenase (prodh) and delta1-pyrroline-5-carboxylate dehydrogenase. this note reports the cloning, purification and crystallization of thermus thermophilus prodh, which is the prototype of a newly discovered superfamily of bacterial monofunctional prodhs. the results presented here include production of a monodisperse protein solution through use of the det ...	2005	16511143
structures of a putative rna 5-methyluridine methyltransferase, thermus thermophilus ttha1280, and its complex with s-adenosyl-l-homocysteine.	the thermus thermophilus hypothetical protein ttha1280 belongs to a family of predicted s-adenosyl-l-methionine (adomet) dependent rna methyltransferases (mtases) present in many bacterial and archaeal species. inspection of amino-acid sequence motifs common to class i rossmann-fold-like mtases suggested a specific role as an rna 5-methyluridine mtase. selenomethionine (semet) labelled and native versions of the protein were expressed, purified and crystallized. two crystal forms of the semet-la ...	2005	16511182
crystallization and preliminary x-ray crystallographic study of the wild type and two mutants of the cp1 hydrolytic domain from aquifex aeolicus leucyl-trna synthetase.	the editing or hydrolytic cp1 domain of leucyl-trna synthetase (leurs) hydrolyses several misactivated amino acids. the cp1 domain of aquifex aeolicus leurs was expressed, purified and crystallized by the hanging-drop vapour-diffusion method using ammonium sulfate as precipitant. crystals belong to space group p2(1)2(1)2(1), with unit-cell parameters a = 38.8, b = 98.4, c = 116.7 a. crystals diffract to beyond 1.8 a resolution and contain two monomers in the asymmetric unit. two cp1 mutants in w ...	2005	16511190
crystallization and preliminary x-ray analysis of cryptochrome 3 from arabidopsis thaliana.	cryptochromes are flavoproteins which serve as blue-light receptors in plants, animals, fungi and prokaryotes and belong to the same protein family as the catalytically active dna photolyases. cryptochrome 3 from the plant arabidopsis thaliana (cry3; 525 amino acids, 60.7 kda) is a representative of the novel crydash subfamily of uv-a/blue-light receptors and has been expressed as a mature fad-containing protein in escherichia coli without the signal sequence that directs the protein into plant ...	2005	16511200
structure of a conserved hypothetical protein, ttha0849 from thermus thermophilus hb8, at 2.4 a resolution: a putative member of the star-related lipid-transfer (start) domain superfamily.	the crystal structure of a conserved hypothetical protein, ttha0849 from thermus thermophilus hb8, has been determined at 2.4 a resolution as a part of a structural and functional genomics project on t. thermophilus hb8. the main-chain folding shows a compact alpha+beta motif, forming a hydrophobic cavity in the molecule. a structural similarity search reveals that it resembles those steroidogenic acute regulatory proteins that contain the lipid-transfer (start) domain, even though ttha0849 show ...	2005	16511226
purification, crystallization and preliminary x-ray crystallographic study of the l-fuculose-1-phosphate aldolase (fuca) from thermus thermophilus hb8.	fuculose phosphate aldolase catalyzes the reversible cleavage of l-fuculose-1-phosphate to dihydroxyacetone phosphate and l-lactaldehyde. the protein from thermus thermophilus hb8 is a biological tetramer with a subunit molecular weight of 21 591 da. purified fuca has been crystallized using sitting-drop vapour-diffusion and microbatch techniques at 293 k. the crystals belong to space group p4, with unit-cell parameters a = b = 100.94, c = 45.87 a. the presence of a dimer of the enzyme in the as ...	2005	16511238
cloning, expression, purification, crystallization and initial crystallographic analysis of transcription elongation factors greb from escherichia coli and gfh1 from thermus thermophilus.	the escherichia coli gene encoding the transcription cleavage factor greb and the thermus thermophilus gene encoding the anti-grea transcription factor gfh1 were cloned and expressed and the purified proteins were crystallized by the sitting-drop vapor-diffusion technique. the greb and gfh1 crystals, which were improved by macroseeding, belong to space group p4(1)2(1)2 (or p4(3)2(1)2), with unit-cell parameters a = b = 148, c = 115.2 a and a = b = 59.3, c = 218.9 a, respectively. complete diffra ...	2006	16511259
expression, purification, crystallization and preliminary x-ray analysis of the human ruvb-like protein ruvbl1.	ruvbl1, an evolutionary highly conserved protein related to the aaa+ family of atpases, has been crystallized using the hanging-drop vapour-diffusion method at 293 k. the crystals are hexagonal and belong to space group p6, with unit-cell parameters a = b = 207.1, c = 60.7 a and three molecules in the asymmetric unit.	2006	16511264
expression, purification, crystallization and preliminary x-ray analysis of the human ruvb-like protein ruvbl1.	ruvbl1, an evolutionary highly conserved protein related to the aaa+ family of atpases, has been crystallized using the hanging-drop vapour-diffusion method at 293 k. the crystals are hexagonal and belong to space group p6, with unit-cell parameters a = b = 207.1, c = 60.7 a and three molecules in the asymmetric unit.	2006	16511264
purification, crystallization and preliminary characterization of a putative lmbe-like deacetylase from bacillus cereus.	the bacillus cereus bc1534 protein, a putative deacetylase from the lmbe family, has been purified to homogeneity and crystallized using the hanging-drop vapour-diffusion method. crystals of the 26 kda protein grown from mpd and acetate buffer belong to space group r32, with unit-cell parameters a = b = 76.7, c = 410.5 a (in the hexagonal setting). a complete native data set was collected to a resolution of 2.5 a from a single cryoprotected crystal using synchrotron radiation. as bc1534 shows si ...	2006	16511317