Publications

purification, crystallization and preliminary x-ray characterization of a human mitochondrial phenylalanyl-trna synthetase.	human monomeric mitochondrial phenylalanyl-trna synthetase (mitphers) is an enzyme that catalyzes the charging of trna with the cognate amino acid phenylalanine. human mitphers is a chimera of the bacterial alpha-subunit of phers and the b8 domain of its beta-subunit. together, the alpha-subunit and the 'rnp-domain' (b8 domain) at the c-terminus form the minimal structural set to construct an enzyme with phenylalanylation activity. the recombinant human mitphers was purified to homogeneity and c ...	2007	17768348
crystallization and preliminary x-ray crystallographic analysis of a 40 kda n-terminal fragment of the yeast prion-remodeling factor hsp104.	a 40 kda n-terminal fragment of saccharomyces cerevisiae hsp104 was crystallized in two different crystal forms. native 1 diffracted to 2.6 a resolution and belonged to space group p2(1)2(1)2(1), with unit-cell parameters a = 66.6, b = 75.8, c = 235.7 a. native 2 diffracted to 2.9 a resolution and belonged to space group p6(1)22 or p6(5)22, with unit-cell parameters a = 179.1, b = 179.1, c = 69.7 a. this is the first report of the crystallization of a eukaryotic member of the hsp100 family of mo ...	2007	17768355
purification, crystallization and preliminary x-ray analysis of the fumarylacetoacetase family member ttha0809 from thermus thermophilus hb8.	fumarylacetoacetase catalyzes the final step of tyrosine and phenylalanine catabolism. a recombinant form of the fumarylacetoacetase family member ttha0809 from thermus thermophilus hb8 has been crystallized by the oil-microbatch method using sodium chloride as a precipitating agent. the crystals belong to the monoclinic space group p2(1), with unit-cell parameters a = 93.3, b = 73.4, c = 122.6 a, beta = 111.8 degrees. the crystals are most likely to contain two dimers in the asymmetric unit, wi ...	2007	17768357
ribosome biogenesis and the translation process in escherichia coli.	translation, the decoding of mrna into protein, is the third and final element of the central dogma. the ribosome, a nucleoprotein particle, is responsible and essential for this process. the bacterial ribosome consists of three rrna molecules and approximately 55 proteins, components that are put together in an intricate and tightly regulated way. when finally matured, the quality of the particle, as well as the amount of active ribosomes, must be checked. the focus of this review is ribosome b ...	2007	17804668
nmr analysis of [methyl-13c]methionine uvrb from bacillus caldotenax reveals uvrb-domain 4 heterodimer formation in solution.	uvrb is a central dna damage recognition protein involved in bacterial nucleotide excision repair. structural information has been limited by the apparent disorder of the c-terminal domain 4 in crystal structures of intact uvrb; in solution, the isolated domain 4 is found to form a helix-loop-helix dimer. in order to gain insight into the behavior of uvrb in solution, we have performed nmr studies on [methyl-13c]methionine-labeled uvrb from bacillus caldotenax (molecular mass=75 kda). the 13 met ...	2007	17822711
elongation factor 1a mediates the specificity of mitochondrial trna import in t. brucei.	mitochondrial trna import is widespread in eukaryotes. yet, the mechanism that determines its specificity is unknown. previous in vivo experiments using the trnas(met), trna(ile) and trna(lys) have suggested that the t-stem nucleotide pair 51:63 is the main localization determinant of trnas in trypanosoma brucei. in the cytosol-specific initiator trna(met), this nucleotide pair is identical to the main antideterminant that prevents interaction with cytosolic elongation factor (eef1a). here we sh ...	2007	17853889
structural and kinetic characterization of quinolinate phosphoribosyltransferase (hqprtase) from homo sapiens.	human quinolinate phosphoribosyltransferase (ec 2.4.2.19) (hqprtase) is a member of the type ii phosphoribosyltransferase family involved in the catabolism of quinolinic acid (qa). it catalyses the formation of nicotinic acid mononucleotide from quinolinic acid, which involves a phosphoribosyl transfer reaction followed by decarboxylation. hqprtase has been implicated in a number of neurological conditions and in order to study it further, we have carried out structural and kinetic studies on re ...	2007	17868694
substrate specificity and properties of the escherichia coli 16s rrna methyltransferase, rsme.	the small ribosome subunit of escherichia coli contains 10 base-methylated sites distributed in important functional regions. at present, seven enzymes responsible for methylation of eight bases are known, but most of them have not been well characterized. one of these enzymes, rsme, was recently identified and shown to specifically methylate u1498. here we describe the enzymatic properties and substrate specificity of rsme. the enzyme forms dimers in solution and is most active in the presence ...	2007	17872509
conformational energy and structure in canonical and noncanonical forms of trna determined by temperature analysis of the rate of s(4)u8-c13 photocrosslinking.	bacterial trnas frequently have 4-thiouridine (s(4)u) modification at position 8, which is adjacent to the c13-g22-m(7)g46 base triple in the elbow region of the trna tertiary structure. irradiation with light in the uva range induces an efficient photocrosslink between s(4)u8 and c13. the temperature dependence of the rate constants for photocrosslinking between the s(4)u8 and c13 has been used to investigate the trna conformational energy and structure in escherichia coli trna(val), trna(phe), ...	2007	17872510
phosphopantetheine adenylyltransferase from escherichia coli: investigation of the kinetic mechanism and role in regulation of coenzyme a biosynthesis.	phosphopantetheine adenylyltransferase (ppat) from escherichia coli is an essential hexameric enzyme that catalyzes the penultimate step in coenzyme a (coa) biosynthesis and is a target for antibacterial drug discovery. the enzyme utilizes mg-atp and phosphopantetheine (php) to generate dephospho-coa (dpcoa) and pyrophosphate. when overexpressed in e. coli, ppat copurifies with tightly bound coa, suggesting a feedback inhibitory role for this cofactor. using an enzyme-coupled assay for the forwa ...	2007	17873050
pathogenic mechanism of a human mitochondrial trnaphe mutation associated with myoclonic epilepsy with ragged red fibers syndrome.	human mitochondrial trna (hmt-trna) mutations are associated with a variety of diseases including mitochondrial myopathies, diabetes, encephalopathies, and deafness. because the current understanding of the precise molecular mechanisms of these mutations is limited, there is no efficient method to treat their associated mitochondrial diseases. here, we use a variety of known mutations in hmt-trna(phe) to investigate the mechanisms that lead to malfunctions. we tested the impact of hmt-trna(phe) ...	2007	17878308
human ribosomal protein s13 regulates expression of its own gene at the splicing step by a feedback mechanism.	the expression of ribosomal protein (rp) genes is regulated at multiple levels. in yeast, two genes are autoregulated by feedback effects of the protein on pre-mrna splicing. here, we have investigated whether similar mechanisms occur in eukaryotes with more complicated and highly regulated splicing patterns. comparisons of the sequences of ribosomal protein s13 gene (rps13) among mammals and birds revealed that intron 1 is more conserved than the other introns. transfection of hek 293 cells wit ...	2007	17881366
role of hsp104 in the propagation and inheritance of the [het-s] prion.	the chaperones of the clpb/hsp100 family play a central role in thermotolerance in bacteria, plants, and fungi by ensuring solubilization of heat-induced protein aggregates. in addition in yeast, hsp104 was found to be required for prion propagation. herein, we analyze the role of podospora anserina hsp104 (pahsp104) in the formation and propagation of the [het-s] prion. we show that deltapahsp104 strains propagate [het-s], making [het-s] the first native fungal prion to be propagated in the abs ...	2007	17881723
saturation mutagenesis of a +1 programmed frameshift-inducing mrna sequence derived from a yeast retrotransposon.	errors during the process of translating mrna information into protein products occur infrequently. frameshift errors occur less frequently than other types of errors, suggesting that the translational machinery has more robust mechanisms for precluding that kind of error. despite these mechanisms, mrna sequences have evolved that increase the frequency up to 10,000-fold. these sequences, termed programmed frameshift sites, usually consist of a heptameric nucleotide sequence, at which the change ...	2007	17881742
dissection of 16s rrna methyltransferase (ksga) function in escherichia coli.	a 16s rrna methyltransferase, ksga, identified originally in escherichia coli is highly conserved in all living cells, from bacteria to humans. ksga orthologs in eukaryotes possess functions in addition to their rrna methyltransferase activity. e. coli era is an essential gtp-binding protein. we recently observed that ksga functions as a multicopy suppressor for the cold-sensitive cell growth of an era mutant [era(e200k)] strain (q. lu and m. inouye, j. bacteriol. 180:5243-5246, 1998). here we o ...	2007	17890303
flavin-dependent thymidylate synthase thyx activity: implications for the folate cycle in bacteria.	although flavin-dependent thyx proteins show thymidylate synthase activity in vitro and functionally complement thya defects in heterologous systems, direct proof of their cellular functions is missing. using insertional mutagenesis of rhodobacter capsulatus thyx, we constructed the first defined thyx inactivation mutant. phenotypic analyses of the obtained mutant strain confirmed that r. capsulatus thyx is required for de novo thymidylate synthesis. full complementation of the r. capsulatus thy ...	2007	17890305
deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks.	bacteria of the genus deinococcus are extremely resistant to ionizing radiation (ir), ultraviolet light (uv) and desiccation. the mesophile deinococcus radiodurans was the first member of this group whose genome was completely sequenced. analysis of the genome sequence of d. radiodurans, however, failed to identify unique dna repair systems. to further delineate the genes underlying the resistance phenotypes, we report the whole-genome sequence of a second deinococcus species, the thermophile de ...	2007	17895995
functional analysis of the gtpases enga and yhbz encoded by salmonella typhimurium.	the s. typhimurium genome encodes proteins, designated enga and yhbz, which have a high sequence identity with the gtpases enga/der and obge/cgtae of escherichia coli. the wild-type activity of the e. coli proteins is essential for normal ribosome maturation and cell viability. in order to characterize the potential involvement of the salmonella typhimurium enga and yhbz proteins in ribosome biology, we used high stringency affinity chromatography experiments to identify strongly binding ribosom ...	2007	17905831
evaluation of the staphylococcus aureus class c nonspecific acid phosphatase (saps) as a reporter for gene expression and protein secretion in gram-negative and gram-positive bacteria.	a phosphatase secreted by staphylococcus aureus strain 154 has previously been characterized and classified as a new member of the bacterial class c family of nonspecific acid phosphatases. as the acid phosphatase activity can be easily detected with a cost-effective plate screen assay, quantitatively measured by a simple enzyme assay, and detected by zymography, its potential use as a reporter system was investigated. the s. aureus acid phosphatase (saps) gene has been cloned and expressed from ...	2007	17905879
identification of promoters recognized by rna polymerase-sigmae holoenzyme from thermus thermophilus hb8.	thermus thermophilus sigma(e), an extracytoplasmic function sigma factor from the extremely thermophilic bacterium thermus thermophilus hb8, bound to the rna polymerase core enzyme and showed transcriptional activity. with the combination of in vitro transcription assay and genechip technology, we identified three promoters recognized by sigma(e). the predicted consensus promoter sequence for sigma(e) is 5'-ca(a/t)(a/c)c(a/c)-n(15)-ccgta-3'.	2007	17905996
electron transport chain of saccharomyces cerevisiae mitochondria is inhibited by h2o2 at succinate-cytochrome c oxidoreductase level without lipid peroxidation involvement.	the deleterious effects of h202 on the electron transport chain of yeast mitochondria and on mitochondrial lipid peroxidation were evaluated. exposure to h2o2 resulted in inhibition of the oxygen consumption in the uncoupled and phosphorylating states to 69% and 65%, respectively. the effect of h2o2 on the respiratory rate was associated with an inhibition of succinate-ubiquinone and succinate-dcip oxidoreductase activities. inhibitory effect of h2o2 on respiratory complexes was almost completel ...	2007	17907001
x-ray structures of two proteins belonging to pfam duf178 revealed unexpected structural similarity to the duf191 pfam family.	pfam is a comprehensive collection of protein domains and families, with a range of well-established information including genome annotation. pfam has two large series of functionally uncharacterized families, known as domains of unknown function (dufs) and uncharacterized protein families (upfs).	2007	17908300
cocrystallizing natural rna with its unnatural mirror image: biochemical and preliminary x-ray diffraction analysis of a 5s rrna a-helix racemate.	chemically synthesized rnas with the unnatural l-configuration possess enhanced in vivo stability and nuclease resistance, which is a highly desirable property for pharmacological applications. for a structural comparison, both l- and d-rna oligonucleotides of a shortened thermus flavus 5s rrna a-helix were chemically synthesized. the enantiomeric rna duplexes were stochiometrically cocrystallized as a racemate, which enabled analysis of the d- and l-rna enantiomers in the same crystals. in addi ...	2007	17909284
human trna(gly) acceptor-stem microhelix: crystallization and preliminary x-ray diffraction analysis at 1.2 a resolution.	the major dissimilarities between the eukaryotic/archaebacterial-type and eubacterial-type glycyl-trna synthetase systems (glyrs; class ii aminoacyl-trna synthetases) represent an intriguing example of evolutionarily divergent solutions to similar biological functions. the differences in the identity elements of the respective trna(gly) systems are located within the acceptor stem and include the discriminator base u73. in the present work, the human trna(gly) acceptor-stem microhelix was crysta ...	2007	17909289
functional smpb-ribosome interactions require tmrna.	small protein b (smpb) is a requisite component of the transfer messenger rna (tmrna)-mediated bacterial translational quality control system known as trans-translation. the initial binding of tmrna and its subsequent accommodation into the ribosomal a-site are activities intimately linked to smpb protein function. from a mechanistic perspective, two key unanswered questions that require further investigation are: 1) what constitutes a stalled ribosome recognition complex and 2) does smpb pre-bi ...	2007	17911096
analysis of gene order data supports vertical inheritance of the leukotoxin operon and genome rearrangements in the 5' flanking region in genus mannheimia.	the mannheimia subclades belong to the same bacterial genus, but have taken divergent paths toward their distinct lifestyles. for example, m. haemolytica + m. glucosida are potential pathogens of the respiratory tract in the mammalian suborder ruminantia, whereas m. ruminalis, the supposed sister group, lives as a commensal in the ovine rumen. we have tested the hypothesis that vertical inheritance of the leukotoxin (lktcabd) operon has occurred from the last common ancestor of genus mannheimia ...	2007	17915007
the carboxy-terminal coiled-coil of the rna polymerase beta'-subunit is the main binding site for gre factors.	bacterial gre transcript cleavage factors stimulate the intrinsic endonucleolytic activity of rna polymerase (rnap) to rescue stalled transcription complexes. they bind to rnap and extend their coiled-coil (cc) domains to the catalytic centre through the secondary channel. three existing models for the gre-rnap complex postulate congruent mechanisms of gre-assisted catalysis, while offering conflicting views of the gre-rnap interactions. here, we report the greb structure of escherichia coli. th ...	2007	17917675
evolution and functional characterization of the rh50 gene from the ammonia-oxidizing bacterium nitrosomonas europaea.	the family of ammonia and ammonium channel proteins comprises the amt proteins, which are present in all three domains of life with the notable exception of vertebrates, and the homologous rh proteins (rh50 and rh30) that have been described thus far only in eukaryotes. the existence of an rh50 gene in bacteria was first revealed by the genome sequencing of the ammonia-oxidizing bacterium nitrosomonas europaea. here we have used a phylogenetic approach to study the evolution of the n. europaea r ...	2007	17921289
orotate phosphoribosyltransferase from corynebacterium ammoniagenes lacking a conserved lysine.	the pyre gene, encoding orotate phosphoribosyltransferase (oprtase), was cloned by nested pcr and colony blotting from corynebacterium ammoniagenes atcc 6872, which is widely used in nucleotide production. sequence analysis shows that there is a lack of an important conserved lysine (lys 73 in salmonella enterica serovar typhimurium oprtase) in the c. ammoniagenes oprtase. this lysine has been considered to contribute to the initiation of catalysis. the enzyme was overexpressed and purified from ...	2007	17921291
insights into hsp70 chaperone activity from a crystal structure of the yeast hsp110 sse1.	classic hsp70 chaperones assist in diverse processes of protein folding and translocation, and hsp110s had seemed by sequence to be distant relatives within an hsp70 superfamily. the 2.4 a resolution structure of sse1 with atp shows that hsp110s are indeed hsp70 relatives, and it provides insight into allosteric coupling between sites for atp and polypeptide-substrate binding in hsp70s. subdomain structures are similar in intact sse1(atp) and in the separate hsp70 domains, but conformational dis ...	2007	17923091
genetic and phenotypic identification of fusidic acid-resistant mutants with the small-colony-variant phenotype in staphylococcus aureus.	small-colony variants (scvs) of staphylococcus aureus are a slow-growing subpopulation whose phenotypes can include resistance to aminoglycosides, defects in electron transport, and enhanced persistence in mammalian cells. here we show that a subset of mutants selected as scvs by reduced susceptibility to aminoglycosides are resistant to the antibiotic fusidic acid (fa) and conversely that a subset of mutants selected for resistance to fa are scvs. mutation analysis reveals different genetic cla ...	2007	17923494
a cysteine-rich ccg domain contains a novel [4fe-4s] cluster binding motif as deduced from studies with subunit b of heterodisulfide reductase from methanothermobacter marburgensis.	heterodisulfide reductase (hdr) of methanogenic archaea with its active-site [4fe-4s] cluster catalyzes the reversible reduction of the heterodisulfide (com-s-s-cob) of the methanogenic coenzyme m (com-sh) and coenzyme b (cob-sh). com-hdr, a mechanistic-based paramagnetic intermediate generated upon half-reaction of the oxidized enzyme with com-sh, is a novel type of [4fe-4s]3+ cluster with com-sh as a ligand. subunit hdrb of the methanothermobacter marburgensis hdrabc holoenzyme contains two cy ...	2007	17929940
interactions and dynamics of the shine dalgarno helix in the 70s ribosome.	the crystal structure of an initiation-like 70s ribosome complex containing an 8-bp shine-dalgarno (sd) helix was determined at 3.8-a resolution. translation-libration-screw analysis showed that the inherent anisotropic motions of the sd helix were biased along its helical axis, suggesting that during the first step of translocation, the sd helix moves along its helical screw axis. contacts between the sd helix and the ribosome were primarily through interactions with helices 23a, 26, and 28 of ...	2007	17940016
the wobble hypothesis revisited: uridine-5-oxyacetic acid is critical for reading of g-ending codons.	according to crick's wobble hypothesis, trnas with uridine at the wobble position (position 34) recognize a- and g-, but not u- or c-ending codons. however, u in the wobble position is almost always modified, and salmonella enterica trnas containing the modified nucleoside uridine-5-oxyacetic acid (cmo(5)u34) at this position are predicted to recognize u- (but not c-) ending codons, in addition to a- and g-ending codons. we have constructed a set of s. enterica mutants with only the cmo(5)u-cont ...	2007	17942742
a systematic evaluation of the function of the protein-remodeling factor hsp104 in [psi+] prion propagation in s. cerevisiae by comprehensive chromosomal mutations.	the yeast prion [psi(+)] represents an aggregated state of the translational release factor sup35 (erf3) and deprives termination complexes of functional sup35, resulting in nonsense codon suppression. protein-remodeling factor hsp104 is involved in thermotolerance and [psi(+)] propagation, however the structure-and-function relationship of hsp104 for [psi(+)] remains unclear. in this study, we engineered 58 chromosomal hsp104 mutants that affect residues considered structurally or functionally ...	2007	19164920
reversible dissociation of flavin mononucleotide from the mammalian membrane-bound nadh: ubiquinone oxidoreductase (complex i).	conditions for the reversible dissociation of flavin mononucleotide (fmn) from the membrane-bound mitochondrial nadh:ubiquinone oxidoreductase (complex i) are described. the catalytic activities of the enzyme, i.e. rotenone-insensitive nadh:hexaammineruthenium iii reductase and rotenone-sensitive nadh:quinone reductase decline when bovine heart submitochondrial particles are incubated with nadh in the presence of rotenone or cyanide at alkaline ph. fmn protects and fully restores the nadh-induce ...	2007	18037377
the hsp70 chaperone system maintains high concentrations of active proteins and suppresses atp consumption during heat shock.	hsp70 chaperones assist protein folding by cycling between the atp-bound t state with low affinity for substrates and the adp-bound r state with high affinity for substrates. the transition from the t to r state is catalyzed by the synergistic action of the substrate and dnaj cochaperones. the reverse transition from the r state to the t state is accelerated by the nucleotide exchange factor grpe. these two processes, t-to-r and r-to-t conversion, are affected differently by temperature change. ...	2007	19003436
the structure of mycobacteria 2c-methyl-d-erythritol-2,4-cyclodiphosphate synthase, an essential enzyme, provides a platform for drug discovery.	the prevalence of tuberculosis, the prolonged and expensive treatment that this disease requires and an increase in drug resistance indicate an urgent need for new treatments. the 1-deoxy-d-xylulose 5-phosphate pathway of isoprenoid precursor biosynthesis is an attractive chemotherapeutic target because it occurs in many pathogens, including mycobacterium tuberculosis, and is absent from humans. to underpin future drug development it is important to assess which enzymes in this biosynthetic path ...	2007	17956607
interaction of smpb with ribosome from directed hydroxyl radical probing.	to add a tag-peptide for degradation to the nascent polypeptide in a stalled ribosome, an unusual translation called trans-translation is facilitated by transfer-messenger rna (tmrna) having an upper half of the trna structure and the sequence encoding the tag-peptide except the first alanine. during this event, tmrna enters the vacant a-site of the stalled ribosome without a codon-anticodon interaction, but with a protein factor smpb. here, we studied the sites and modes of binding of smpb to t ...	2007	17959652
domain i of ribosomal protein l1 is sufficient for specific rna binding.	ribosomal protein l1 has a dual function as a ribosomal protein binding 23s rrna and as a translational repressor binding its mrna. l1 is a two-domain protein with n- and c-termini located in domain i. earlier it was shown that l1 interacts with the same targets on both rrna and mrna mainly through domain i. we have suggested that domain i is necessary and sufficient for specific rna-binding by l1. to test this hypothesis, a truncation mutant of l1 from thermus thermophilus, representing domain ...	2007	17962298
mutational analysis of s12 protein and implications for the accuracy of decoding by the ribosome.	the fidelity of aminoacyl-trna selection by the ribosome depends on a conformational switch in the decoding center of the small ribosomal subunit induced by cognate but not by near-cognate aminoacyl-trna. the aminoglycosides paromomycin and streptomycin bind to the decoding center and induce related structural rearrangements that explain their observed effects on miscoding. structural and biochemical studies have identified ribosomal protein s12 (as well as specific nucleotides in 16s ribosomal ...	2007	17967466
novel hexamerization motif is discovered in a conserved cytoplasmic protein from salmonella typhimurium.	the cytoplasmic protein stm3548 of unknown function obtained from a strain of salmonella typhimurium was determined by x-ray crystallography at a resolution of 2.25 a. the asymmetric unit contains a hexamer of structurally identical monomers. the monomer is a globular domain with a long beta-hairpin protrusion that distinguishes this structure. this beta-hairpin occupies a central position in the hexamer, and its residues participate in the majority of interactions between subunits of the hexame ...	2007	17968677
translation initiation region sequence preferences in escherichia coli.	the mrna translation initiation region (tir) comprises the initiator codon, shine-dalgarno (sd) sequence and translational enhancers. probably the most abundant class of enhancers contains a/u-rich sequences. we have tested the influence of sd sequence length and the presence of enhancers on the efficiency of translation initiation.	2007	17973990
zinc is the metal cofactor of borrelia burgdorferi peptide deformylase.	peptide deformylase (pdf, e.c. 3.5.1.88) catalyzes the removal of n-terminal formyl groups from nascent ribosome-synthesized polypeptides. pdf contains a catalytically essential divalent metal ion, which is tetrahedrally coordinated by three protein ligands (his, his, and cys) and a water molecule. previous studies revealed that the metal cofactor is a fe2+ ion in escherichia coli and many other bacterial pdfs. in this work, we found that pdfs from two iron-deficient bacteria, borrelia burgdorfe ...	2007	17977509
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
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
a thin-layer electrophoretic assay for asp-trnaasn/glu-trnagln amidotransferase.		2007	17113030
a thin-layer electrophoretic assay for asp-trnaasn/glu-trnagln amidotransferase.		2007	17113030
interpretation of electron density with stereographic roadmap projections.	the program rivem (radial interpretation of viral electron density maps) was developed to project density radially onto a sphere that is then presented as a stereographic diagram. this permits features resulting from an asymmetric reconstruction to be projected and positioned onto an icosahedral virus surface. the features that constitute the viral surface can also be simultaneously represented in terms of atoms, amino acid residues, potential charge distribution, and surface topology. the proce ...	2007	17116403
interpretation of electron density with stereographic roadmap projections.	the program rivem (radial interpretation of viral electron density maps) was developed to project density radially onto a sphere that is then presented as a stereographic diagram. this permits features resulting from an asymmetric reconstruction to be projected and positioned onto an icosahedral virus surface. the features that constitute the viral surface can also be simultaneously represented in terms of atoms, amino acid residues, potential charge distribution, and surface topology. the proce ...	2007	17116403
mechanism of template-independent nucleotide incorporation catalyzed by a template-dependent dna polymerase.	numerous template-dependent dna polymerases are capable of catalyzing template-independent nucleotide additions onto blunt-end dna. such non-canonical activity has been hypothesized to increase the genomic hypermutability of retroviruses including human immunodeficiency viruses. here, we employed pre-steady state kinetics and x-ray crystallography to establish a mechanism for blunt-end additions catalyzed by sulfolobus solfataricus dpo4. our kinetic studies indicated that the first blunt-end dat ...	2007	17095011
mechanism of template-independent nucleotide incorporation catalyzed by a template-dependent dna polymerase.	numerous template-dependent dna polymerases are capable of catalyzing template-independent nucleotide additions onto blunt-end dna. such non-canonical activity has been hypothesized to increase the genomic hypermutability of retroviruses including human immunodeficiency viruses. here, we employed pre-steady state kinetics and x-ray crystallography to establish a mechanism for blunt-end additions catalyzed by sulfolobus solfataricus dpo4. our kinetic studies indicated that the first blunt-end dat ...	2007	17095011
mutagenesis of rat acyl-coa synthetase 4 indicates amino acids that contribute to fatty acid binding.	although each of the five mammalian long-chain acyl-coa synthetases (acsl) can bind saturated and unsaturated fatty acids ranging from 12 to 22 carbons, acsl4 prefers longer chain polyunsaturated fatty acids. in order to gain a better understanding of acsl4 fatty acid binding, we based a mutagenesis approach on sequence alignments related to ttlc-facs crystallized from thermus thermophilus hb8. four residues selected for mutagenesis corresponded to residues in ttlc-facs that comprise the fatty a ...	2007	17110164
the role of specific 2'-hydroxyl groups in the stabilization of the folded conformation of kink-turn rna.	the role of 2'-hydroxyl groups in stabilizing the tightly kinked geometry of the kink-turn (k-turn) has been investigated. individual 2'-oh groups have been removed by chemical synthesis, and the kinking of the rna has been studied by gel electrophoresis and fluorescence resonance energy transfer. the results have been analyzed by reference to a database of 11 different crystallographic structures of k-turns. the potential hydrogen bonds fall into several classes. the most important are those in ...	2007	17158708
infantile encephalopathy and defective mitochondrial dna translation in patients with mutations of mitochondrial elongation factors efg1 and eftu.	mitochondrial protein translation is a complex process performed within mitochondria by an apparatus composed of mitochondrial dna (mtdna)-encoded rnas and nuclear dna-encoded proteins. although the latter by far outnumber the former, the vast majority of mitochondrial translation defects in humans have been associated with mutations in rna-encoding mtdna genes, whereas mutations in protein-encoding nuclear genes have been identified in a handful of cases. genetic investigation involving patient ...	2007	17160893
infantile encephalopathy and defective mitochondrial dna translation in patients with mutations of mitochondrial elongation factors efg1 and eftu.	mitochondrial protein translation is a complex process performed within mitochondria by an apparatus composed of mitochondrial dna (mtdna)-encoded rnas and nuclear dna-encoded proteins. although the latter by far outnumber the former, the vast majority of mitochondrial translation defects in humans have been associated with mutations in rna-encoding mtdna genes, whereas mutations in protein-encoding nuclear genes have been identified in a handful of cases. genetic investigation involving patient ...	2007	17160893
oligomeric states of the seca and secyeg core components of the bacterial sec translocon.	many proteins synthesized in the cytoplasm ultimately function in non-cytoplasmic locations. in escherichia coli, the general secretory (sec) pathway transports the vast majority of these proteins. two fundamental components of the sec transport pathway are the secyeg heterotrimeric complex that forms the channel through the cytoplasmic membrane, and seca, the atpase that drives the preprotein to and across the membrane. this review focuses on what is known about the oligomeric states of these c ...	2007	17011510
oligomeric states of the seca and secyeg core components of the bacterial sec translocon.	many proteins synthesized in the cytoplasm ultimately function in non-cytoplasmic locations. in escherichia coli, the general secretory (sec) pathway transports the vast majority of these proteins. two fundamental components of the sec transport pathway are the secyeg heterotrimeric complex that forms the channel through the cytoplasmic membrane, and seca, the atpase that drives the preprotein to and across the membrane. this review focuses on what is known about the oligomeric states of these c ...	2007	17011510
coordinate expression of the acetyl coenzyme a carboxylase genes, accb and accc, is necessary for normal regulation of biotin synthesis in escherichia coli.	transcription of the biotin (bio) biosynthetic operon of escherichia coli is negatively regulated by the bira protein, an atypical repressor protein in that it is also an enzyme. the bira-catalyzed reaction involves the covalent attachment of biotin to accb, a subunit of acetyl coenzyme (acetyl-coa) carboxylase. the two functions of bira allow regulation of the bio operon to respond to the intracellular concentrations of both biotin and unbiotinylated accb. we report here that bio operon express ...	2007	17056747
coordinate expression of the acetyl coenzyme a carboxylase genes, accb and accc, is necessary for normal regulation of biotin synthesis in escherichia coli.	transcription of the biotin (bio) biosynthetic operon of escherichia coli is negatively regulated by the bira protein, an atypical repressor protein in that it is also an enzyme. the bira-catalyzed reaction involves the covalent attachment of biotin to accb, a subunit of acetyl coenzyme (acetyl-coa) carboxylase. the two functions of bira allow regulation of the bio operon to respond to the intracellular concentrations of both biotin and unbiotinylated accb. we report here that bio operon express ...	2007	17056747
structural and biochemical characterization of human orphan dhrs10 reveals a novel cytosolic enzyme with steroid dehydrogenase activity.	to this day, a significant proportion of the human genome remains devoid of functional characterization. in this study, we present evidence that the previously functionally uncharacterized product of the human dhrs10 gene is endowed with 17beta-hsd (17beta-hydroxysteroid dehydrogenase) activity. 17beta-hsd enzymes are primarily involved in the metabolism of steroids at the c-17 position and also of other substrates such as fatty acids, prostaglandins and xenobiotics. in vitro, dhrs10 converts na ...	2007	17067289
biosynthesis of phosphoserine in the methanococcales.	methanococcus maripaludis and methanocaldococcus jannaschii produce cysteine for protein synthesis using a trna-dependent pathway. these methanogens charge trna(cys) with l-phosphoserine, which is also an intermediate in the predicted pathways for serine and cystathionine biosynthesis. to establish the mode of phosphoserine production in methanococcales, cell extracts of m. maripaludis were shown to have phosphoglycerate dehydrogenase and phosphoserine aminotransferase activities. the heterologo ...	2007	17071763
biosynthesis of phosphoserine in the methanococcales.	methanococcus maripaludis and methanocaldococcus jannaschii produce cysteine for protein synthesis using a trna-dependent pathway. these methanogens charge trna(cys) with l-phosphoserine, which is also an intermediate in the predicted pathways for serine and cystathionine biosynthesis. to establish the mode of phosphoserine production in methanococcales, cell extracts of m. maripaludis were shown to have phosphoglycerate dehydrogenase and phosphoserine aminotransferase activities. the heterologo ...	2007	17071763
genome evolution and the emergence of fruiting body development in myxococcus xanthus.	lateral gene transfer (lgt) is thought to promote speciation in bacteria, though well-defined examples have not been put forward.	2007	18159227
structure of the minimized alpha/beta-hydrolase fold protein from thermus thermophilus hb8.	the gene encoding ttha1544 is a singleton found in the thermus thermophilus hb8 genome and encodes a 131-amino-acid protein. the crystal structure of ttha1544 has been determined at 2.0 a resolution by the single-wavelength anomalous dispersion method in order to elucidate its function. there are two molecules in the asymmetric unit. each molecule consists of four alpha-helices and six beta-strands, with the beta-strands composing a central beta-sheet. a structural homology search revealed that ...	2007	18084077
structure of bacillus subtilis superoxide dismutase.	the soda gene of bacillus subtilis was expressed in escherichia coli, purified and crystallized. the crystal structure of mnsod was solved by molecular replacement with four dimers per asymmetric unit and refined to an r factor of 21.1% at 1.8 a resolution. the dimer structure is very similar to that of the related enzyme from b. anthracis. larger structural differences were observed with the human mnsod, which has one less helix in the helical domain and a longer loop between two beta-strands a ...	2007	18084079
an unexpected outcome of surface engineering an integral membrane protein: improved crystallization of cytochrome ba(3) from thermus thermophilus.	past work has shown that it is feasible to mutate surface residues of soluble proteins and to a lesser extent membrane proteins in order to improve their crystallization behavior. described here is a successful application of this approach to the integral membrane protein thermus thermophilus cytochrome ba(3) oxidase. two mutant forms of this enzyme (i-k258r and i-k258r/ii-e4q) were created in which symmetrical crystal contacts within crystals of wild-type enzyme were modified. these mutant prot ...	2007	18084085
dodecamer rotor ring defines h+/atp ratio for atp synthesis of prokaryotic v-atpase from thermus thermophilus.	atp synthesis by v-atpase from the thermophilic bacterium thermus thermophilus driven by the acid-base transition was investigated. the rate of atp synthesis increased in parallel with the increase in proton motive force (pmf) >110 mv, which is composed of a difference in proton concentration (deltaph) and the electrical potential differences (deltapsi) across membranes. the optimum rate of synthesis reached 85 s(-1), and the h(+)/atp ratio of 4.0 +/- 0.1 was obtained. atp was synthesized at a c ...	2007	18077374
soj (para) dna binding is mediated by conserved arginines and is essential for plasmid segregation.	soj is a member of the para family of atpases involved in plasmid and chromosomal segregation. it binds nonspecifically and cooperatively to dna although the function of this binding is unknown. here, we show that mutation of conserved arginine residues that map to the surface of bacillus subtilis soj caused only minimal effects on nucleotide-dependent dimerization but had dramatic effects on dna binding. using a model plasmid partitioning system in escherichia coli, we find that soj dna-binding ...	2007	18077387
pseudouridylation of helix 69 of 23s rrna is necessary for an effective translation termination.	escherichia coli strains with inactivated rlud genes were previously found to lack the conserved pseudouridines in helix 69 of 23s ribosomal rna and to grow slowly. a suppressor mutant was isolated with a near normal growth rate that had changed the conserved glu-172 codon to a lys codon in prfb, encoding translation termination factor rf2. when nonsense suppression in strains with all combinations of prfb(+)/prfb(e172k) and rlud(+)/rlud::cat was analyzed, misreading of all three stop codons as ...	2007	18032607
carotenoid biosynthesis in the primitive red alga cyanidioschyzon merolae.	cyanidioschyzon merolae is considered to be one of the most primitive of eukaryotic photosynthetic organisms. to obtain insights into the origin and evolution of the pathway of carotenoid biosynthesis in eukaryotic plants, the carotenoid content of c. merolae was ascertained, genes encoding enzymes of carotenoid biosynthesis in this unicellular red alga were identified, and the activities of two candidate pathway enzymes of particular interest, lycopene cyclase and beta-carotene hydroxylase, wer ...	2007	17085635
carotenoid biosynthesis in the primitive red alga cyanidioschyzon merolae.	cyanidioschyzon merolae is considered to be one of the most primitive of eukaryotic photosynthetic organisms. to obtain insights into the origin and evolution of the pathway of carotenoid biosynthesis in eukaryotic plants, the carotenoid content of c. merolae was ascertained, genes encoding enzymes of carotenoid biosynthesis in this unicellular red alga were identified, and the activities of two candidate pathway enzymes of particular interest, lycopene cyclase and beta-carotene hydroxylase, wer ...	2007	17085635
cloning, expression, purification, crystallization and preliminary x-ray diffraction analysis of universal stress protein f (ynaf) from salmonella typhimurium.	the universal stress protein uspf (ynaf) is a small cytoplasmic bacterial protein. the expression of stress proteins is enhanced when cells are exposed to heat shock, nutrition starvation and certain other stress-inducing agents. ynaf promotes cell survival during prolonged exposure to stress and may activate a general mechanism for stress endurance. this manuscript reports preliminary crystallographic studies on ynaf from salmonella typhimurium. the gene coding for ynaf was cloned and overexpre ...	2007	18007050
crystallization and preliminary x-ray diffraction studies of tetrameric malate dehydrogenase from the novel antarctic psychrophile flavobacterium frigidimaris kuc-1.	flavobacterium frigidimaris kuc-1 is a novel psychrotolerant bacterium isolated from antarctic seawater. malate dehydrogenase (mdh) is an essential metabolic enzyme in the citric acid cycle and has been cloned, overexpressed and purified from f. frigidimaris kuc-1. in contrast to the already known dimeric form of mdh from the psychrophile aquaspirillium arcticum, f. frigidimaris mdh exists as a tetramer. it was crystallized at 288 k by the hanging-drop vapour-diffusion method using ammonium sulf ...	2007	18007057
structural basis of j cochaperone binding and regulation of hsp70.	the many protein processing reactions of the atp-hydrolyzing hsp70s are regulated by j cochaperones, which contain j domains that stimulate hsp70 atpase activity and accessory domains that present protein substrates to hsp70s. we report the structure of a j domain complexed with a j responsive portion of a mammalian hsp70. the j domain activates atpase activity by directing the linker that connects the hsp70 nucleotide binding domain (nbd) and substrate binding domain (sbd) toward a hydrophobic ...	2007	17996706
structural aspects of rbfa action during small ribosomal subunit assembly.	ribosome binding factor a (rbfa) is a bacterial cold shock response protein, required for an efficient processing of the 5' end of the 16s ribosomal rna (rrna) during assembly of the small (30s) ribosomal subunit. here we present a crystal structure of thermus thermophilus (tth) rbfa and a three-dimensional cryo-electron microscopic (em) map of the tth 30s*rbfa complex. rbfa binds to the 30s subunit in a position overlapping the binding sites of the a and p site trnas, and rbfa's functionally im ...	2007	17996707
two distinct components of release factor function uncovered by nucleophile partitioning analysis.	during translation termination, release factor (rf) protein catalyzes a hydrolytic reaction in the large subunit peptidyl transferase center to release the finished polypeptide chain. while the mechanism of catalysis of peptide release remains obscure, important contributing factors have been identified, including conserved active-site nucleotides and a ggq tripeptide motif in the rf. here we describe pre-steady-state kinetic and nucleophile competition experiments to examine rf contributions to ...	2007	17996709
fourier transform infrared characterization of a cub-nitrosyl complex in cytochrome ba3 from thermus thermophilus: relevance to no reductase activity in heme-copper terminal oxidases.	the two heme-copper terminal oxidases of thermus thermophilus have been shown to catalyze the two-electron reduction of nitric oxide (no) to nitrous oxide (n2o) [giuffre, a.; stubauer, g.; sarti, p.; brunori, m.; zumft, w. g.; buse, g.; soulimane, t. proc. natl. acad. sci. u.s.a. 1999, 96, 14718-14723]. while it is well-established that no binds to the reduced heme a3 to form a low-spin heme {feno}7 species, the role cub plays in the binding of the second no remains unclear. here we present low- ...	2007	17997553
loss of a universal trna feature.	trna(his) has thus far always been found with one of the most distinctive of trna features, an extra 5' nucleotide that is usually a guanylate. trna(his) genes in a disjoint alphaproteobacterial group comprising the rhizobiales, rhodobacterales, caulobacterales, parvularculales, and pelagibacter generally fail to encode this extra guanylate, unlike those of other alphaproteobacteria and bacteria in general. rather than adding an extra 5' guanylate posttranscriptionally as eukaryotes do, evidence ...	2007	17172343
loss of a universal trna feature.	trna(his) has thus far always been found with one of the most distinctive of trna features, an extra 5' nucleotide that is usually a guanylate. trna(his) genes in a disjoint alphaproteobacterial group comprising the rhizobiales, rhodobacterales, caulobacterales, parvularculales, and pelagibacter generally fail to encode this extra guanylate, unlike those of other alphaproteobacteria and bacteria in general. rather than adding an extra 5' guanylate posttranscriptionally as eukaryotes do, evidence ...	2007	17172343
x-ray crystal structure of mycobacterium tuberculosis beta-ketoacyl acyl carrier protein synthase ii (mtkasb).	mycolic acids are long chain alpha-alkyl branched, beta-hydroxy fatty acids that represent a characteristic component of the mycobacterium tuberculosis cell wall. through their covalent attachment to peptidoglycan via an arabinogalactan polysaccharide, they provide the basis for an essential outer envelope membrane. mycobacteria possess two fatty acid synthases (fas); fas-i carries out de novo synthesis of fatty acids while fas-ii is considered to elongate medium chain length fatty acyl primers ...	2007	17174327
x-ray crystal structure of mycobacterium tuberculosis beta-ketoacyl acyl carrier protein synthase ii (mtkasb).	mycolic acids are long chain alpha-alkyl branched, beta-hydroxy fatty acids that represent a characteristic component of the mycobacterium tuberculosis cell wall. through their covalent attachment to peptidoglycan via an arabinogalactan polysaccharide, they provide the basis for an essential outer envelope membrane. mycobacteria possess two fatty acid synthases (fas); fas-i carries out de novo synthesis of fatty acids while fas-ii is considered to elongate medium chain length fatty acyl primers ...	2007	17174327
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
small but versatile: the extraordinary functional and structural diversity of the beta-grasp fold.	the beta-grasp fold (beta-gf), prototyped by ubiquitin (ub), has been recruited for a strikingly diverse range of biochemical functions. these functions include providing a scaffold for different enzymatic active sites (e.g. nudix phosphohydrolases) and iron-sulfur clusters, rna-soluble-ligand and co-factor-binding, sulfur transfer, adaptor functions in signaling, assembly of macromolecular complexes and post-translational protein modification. to understand the basis for the functional versatil ...	2007	17605815
assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data.	comparison of completely sequenced microbial genomes has revealed how fluid these genomes are. detecting synteny blocks requires reliable methods to determining the orthologs among the whole set of homologs detected by exhaustive comparisons between each pair of completely sequenced genomes. this is a complex and difficult problem in the field of comparative genomics but will help to better understand the way prokaryotic genomes are evolving.	2007	18047665
separating the effects of mutation and selection in producing dna skew in bacterial chromosomes.	many bacterial chromosomes display nucleotide asymmetry, or skew, between the leading and lagging strands of replication. mutational differences between these strands result in an overall pattern of skew that is centered about the origin of replication. such a pattern could also arise from selection coupled with a bias for genes coded on the leading strand. the relative contributions of selection and mutation in producing compositional skew are largely unknown.	2007	17935620
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
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
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
conserved lipid-binding sites in membrane proteins: a focus on cytochrome c oxidase.	specific interactions between lipids and membrane proteins have been observed in recent high-resolution crystal structures of membrane proteins. a number of cytochrome oxidase structures were analyzed, along with many amino acid sequences of membrane-spanning regions aligned according to their location in the membrane. the results reveal conservation of lipid-binding sites and of the residues that form them. these studies imply that bound lipids have important roles that are crucial to the assem ...	2007	17719219
spectroscopic characterization of heme iron-nitrosyl species and their role in no reductase mechanisms in diiron proteins.		2007	17534533
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
identification of genes encoding trna modification enzymes by comparative genomics.	as the molecular adapters between codons and amino acids, transfer-rnas are pivotal molecules of the genetic code. the coding properties of a trna molecule do not reside only in its primary sequence. posttranscriptional nucleoside modifications, particularly in the anticodon loop, can modify cognate codon recognition, affect aminoacylation properties, or stabilize the codon-anticodon wobble base pairing to prevent ribosomal frameshifting. despite a wealth of biophysical and structural knowledge ...	2007	17673083
the [fefe] hydrogenase of nyctotherus ovalis has a chimeric origin.	the hydrogenosomes of the anaerobic ciliate nyctotherus ovalis show how mitochondria can evolve into hydrogenosomes because they possess a mitochondrial genome and parts of an electron-transport chain on the one hand, and a hydrogenase on the other hand. the hydrogenase permits direct reoxidation of nadh because it consists of a [fefe] hydrogenase module that is fused to two modules, which are homologous to the 24 kda and the 51 kda subunits of a mitochondrial complex i.	2007	18021395
similarity search for local protein structures at atomic resolution by exploiting a database management system.	a method to search for local structural similarities in proteins at atomic resolution is presented. it is demonstrated that a huge amount of structural data can be handled within a reasonable cpu time by using a conventional relational database management system with appropriate indexing of geometric data. this method, which we call geometric indexing, can enumerate ligand binding sites that are structurally similar to sub-structures of a query protein among more than 160,000 possible candidates ...	2007	27857569