Publications

multiple defects in translation associated with altered ribosomal protein l4.	the ribosomal proteins l4 and l22 form part of the peptide exit tunnel in the large ribosomal subunit. in escherichia coli, alterations in either of these proteins can confer resistance to the macrolide antibiotic, erythromycin. the structures of the 30s as well as the 50s subunits from each antibiotic resistant mutant differ from wild type in distinct ways and l4 mutant ribosomes have decreased peptide bond-forming activity. our analyses of the decoding properties of both mutants show that ribo ...	2004	15509870
a novel archaeal alanine dehydrogenase homologous to ornithine cyclodeaminase and mu-crystallin.	a novel alanine dehydrogenase (aladh) showing no significant amino acid sequence homology with previously known bacterial aladhs was purified to homogeneity from the soluble fraction of the hyperthermophilic archaeon archaeoglobus fulgidus. aladh catalyzed the reversible, nad+-dependent deamination of l-alanine to pyruvate and nh4+. nadp(h) did not serve as a coenzyme. the enzyme is a homodimer of 35 kda per subunit. the km values for l-alanine, nad+, pyruvate, nadh, and nh4+ were estimated at 0 ...	2004	15516582
identification and functional verification of archaeal-type phosphoenolpyruvate carboxylase, a missing link in archaeal central carbohydrate metabolism.	despite the fact that phosphoenolpyruvate carboxylase (pepc) activity has been measured and in some cases even purified from some archaea, the gene responsible for this activity has not been elucidated. using sensitive sequence comparison methods, we detected a highly conserved, uncharacterized archaeal gene family that is distantly related to the catalytic core of the canonical pepc. to verify the predicted function of this archaeal gene family, we cloned a representative from the hyperthermoph ...	2004	15516590
use of an antisense rna strategy to investigate the functional significance of mn-catalase in the extreme thermophile thermus thermophilus.	the expression of an antisense rna revealed that an mn-catalase was required in thermus thermophilus for aerobic but not for anaerobic growth. the antisense system is based on the constitutive expression of a "bicistronic" transcript consisting of the kanamycin resistance gene mrna followed by the antisense rna against the selected target.	2004	15516595
cold sensitivity of thermophilic and mesophilic rna polymerases.	rna polymerase from mesophilic deinococcus radiodurans displays the same cold sensitivity of promoter opening as rna polymerase from the closely related thermophilic thermus aquaticus. this suggests that, contrary to the accepted view, cold sensitivity of promoter opening by thermophilic rna polymerases may not be a consequence of their thermostability.	2004	15516599
staphylococcus aureus isdg and isdi, heme-degrading enzymes with structural similarity to monooxygenases.	heme-degrading enzymes are involved in human diseases ranging from stroke, cancer, and multiple sclerosis to infectious diseases such as malaria, diphtheria, and meningitis. all mammalian and microbial enzymes identified to date are members of the heme oxygenase superfamily and assume similar monomeric structures with an all alpha-helical fold. here we describe the crystal structures of isdg and isdi, two heme-degrading enzymes from staphylococcus aureus. the structures of both enzymes resemble ...	2005	15520015
staphylococcus aureus isdg and isdi, heme-degrading enzymes with structural similarity to monooxygenases.	heme-degrading enzymes are involved in human diseases ranging from stroke, cancer, and multiple sclerosis to infectious diseases such as malaria, diphtheria, and meningitis. all mammalian and microbial enzymes identified to date are members of the heme oxygenase superfamily and assume similar monomeric structures with an all alpha-helical fold. here we describe the crystal structures of isdg and isdi, two heme-degrading enzymes from staphylococcus aureus. the structures of both enzymes resemble ...	2005	15520015
cleavage of double-stranded rna by rnase hi from a thermoacidophilic archaeon, sulfolobus tokodaii 7.	st0753, the orthologous gene of type 1 rnase h found in a thermoacidophilic archaeon, sulfolobus tokodaii, was analyzed. the recombinant st0753 protein exhibited rnase h activity in both in vivo and in vitro assays. the protein expressed in an rnase h-deficient mutant escherichia coli strain functioned to suppress the temperature-sensitive phenotype associated with the lack of rnase h. the in vitro characteristics of the gene's rnase h activity were similar to those of halobacterium rnase hi, th ...	2004	15520465
assembly of the 30s ribosomal subunit: positioning ribosomal protein s13 in the s7 assembly branch.	studies of escherichia coli 30s ribosomal subunit assembly have revealed a hierarchical and cooperative association of ribosomal proteins with 16s ribosomal rna; these results have been used to compile an in vitro 30s subunit assembly map. in single protein addition and omission studies, ribosomal protein s13 was shown to be dependent on the prior association of ribosomal protein s20 for binding to the ribonucleoprotein particle. while the overwhelming majority of interactions revealed in the as ...	2004	15525707
post-transfer editing in vitro and in vivo by the beta subunit of phenylalanyl-trna synthetase.	translation of the genetic code requires attachment of trnas to their cognate amino acids. errors during amino-acid activation and trna esterification are corrected by aminoacyl-trna synthetase-catalyzed editing reactions, as extensively described for aliphatic amino acids. the contribution of editing to aromatic amino-acid discrimination is less well understood. we show that phenylalanyl-trna synthetase misactivates tyrosine and that it subsequently corrects such errors through hydrolysis of ty ...	2004	15526031
testing the conservation of the translational machinery over evolution in diverse environments: assaying thermus thermophilus ribosomes and initiation factors in a coupled transcription-translation system from escherichia coli.	ribosomes from the extreme thermophile thermus thermophilus are capable of translation in a coupled transcription-translation system derived from escherichia coli. at 45 degrees c, t.thermophilus ribosomes translate at approximately 25-30% of the maximal rate of e.coli ribosomes, and synthesize full-length protein. t.thermophilus and e.coli subunits can be combined to effect translation, with the spectrum of proteins produced depending upon the source of the 30s subunit. in this system, t.thermo ...	2004	15534366
the bag or the spindle: the cell factory at the time of systems' biology.	genome programs changed our view of bacteria as cell factories, by making them amenable to systematic rational improvement. as a first step, isolated genes (including those of the metagenome), or small gene clusters are improved and expressed in a variety of hosts. new techniques derived from functional genomics (transcriptome, proteome and metabolome studies) now allow users to shift from this single-gene approach to a more integrated view of the cell, where it is more and more considered as a ...	2004	15537427
interaction of the n-terminal domain of escherichia coli heat-shock protein clpb and protein aggregates during chaperone activity.	the escherichia coli heat-shock protein clpb reactivates protein aggregates in cooperation with the dnak chaperone system. the clpb n-terminal domain plays an important role in the chaperone activity, but its mechanism remains unknown. in this study, we investigated the effect of the clpb n-terminal domain on malate dehydrogenase (mdh) refolding. clpb reduced the yield of mdh refolding by a strong interaction with the intermediate. however, the refolding kinetics was not affected by deletion of ...	2004	15537752
crystal structure of yeast v-atpase subunit c reveals its stator function.	vacuolar h(+)-atpase (v-atpase) has a crucial role in the vacuolar system of eukaryotic cells. it provides most of the energy required for transport systems that utilize the proton-motive force that is generated by atp hydrolysis. some, but not all, of the v-atpase subunits are homologous to those of f-atpase and the nonhomologous subunits determine the unique features of v-atpase. we determined the crystal structure of v-atpase subunit c (vma5p), which does not show any homology with f-atpase s ...	2004	15540116
the driving force for molecular evolution of translation.	it is widely argued that protein synthesis evolved out of an rna world, in which catalytic and other biological functions now carried out by proteins were performed by rnas. however, it is not clear what selective advantage would have provided the driving force for evolution of a primitive translation apparatus, because of the unlikelihood that rudimentary polypeptides would have contributed sufficiently useful biological functions. here, i suggest that the availability of even simple peptides c ...	2004	15547132
artificial tertiary motifs stabilize trans-cleaving hammerhead ribozymes under conditions of submillimolar divalent ions and high temperatures.	tertiary stabilizing motifs (tsms) between terminal loops or internal bulges facilitate folding of natural hammerhead ribozymes (hrz) under physiological conditions. however, both substrate and enzyme strands contribute nucleotides to the tsms of trans-cleaving hrz, complicating the design of hrz that exploit tsms to target specific mrna. to overcome this limitation, we used selex to identify new, artificial tsms that are less sensitive to sequence context. nucleotides in loop ii or in a bulge w ...	2004	15547137
two outer membrane proteins are required for maximal type i secretion of the caulobacter crescentus s-layer protein.	transport of rsaa, the crystalline s-layer subunit protein of caulobacter crescentus, is mediated by a type i secretion mechanism. two proteins have been identified that play the role of the outer membrane protein (omp) component in the rsaa secretion machinery. the genes rsaf(a) and rsaf(b) were identified by similarity to the escherichia coli hemolysin secretion omp tolc by using the c. crescentus genome sequence. the rsaf(a) gene is located several kilobases downstream of the other transporte ...	2004	15547272
chloroplast elongation factor ts pro-protein is an evolutionarily conserved fusion with the s1 domain-containing plastid-specific ribosomal protein-7.	the components of chloroplast translation are similar to those of prokaryotic translation but contain some additional unique features. proteomic analysis of the chlamydomonas reinhardtii chloroplast ribosome identified an s1-like protein, plastid-specific ribosomal protein-7 (psrp-7), as a stoichiometric component of the 30s subunit. here, we report that psrp-7 is part of a polyprotein that contains psrp-7 on its amino end and two translation elongation factor ts (ef-ts) domains at the carboxy e ...	2004	15548736
correspondence between anomalous m- and deltacp-values in protein folding.	proteins folding according to a classical two-state system characteristically show v-shaped chevron plots. we have previously interpreted the symmetrically curved chevron plot of the protein u1a as denaturant-dependent movements in the position of the transition state ensemble (tse). s6, a structural analog of u1a, shows a classical v-shaped chevron plot indicative of straightforward two-state kinetics, but the mutant la30 has a curved unfolding limb, which is most consistent with tse mobility. ...	2004	15557266
divergent anticodon recognition in contrasting glutamyl-trna synthetases.	the pathogenic bacterium helicobacter pylori utilizes two essential glutamyl-trna synthetases (glurs1 and glurs2). these two enzymes are closely related in evolution and yet they aminoacylate contrasting trnas. glurs1 is a canonical discriminating glurs (d-glurs) that biosynthesizes glu-trna(glu) and cannot make glu-trna(gln). in contrast, glurs2 is non-canonical as it is only essential for the production of misacylated glu-trna(gln). the co-existence and evident divergence of these two enzymes ...	2004	15561136
cloning of cvipii nicking and modification system from chlorella virus nys-1 and application of nt.cvipii in random dna amplification.	the cloning and expression of the cvipii dna nicking and modification system encoded by chlorella virus nys-1 is described. the system consists of a co-linear mtase encoding gene (cvipiim) and a nicking endonuclease encoding gene (cvipiint) separated by 12 nt. m.cvipii possesses eight conserved amino acid motifs (i to viii) typical of c5 mtases, but, like another chlorella virus mtase m.cviji, lacks conserved motifs ix and x. in addition to modification of the first cytosine in ccd (d = a, g or ...	2004	15570069
mechanistic approach to the problem of hybridization efficiency in fluorescent in situ hybridization.	in fluorescent in situ hybridization (fish), the efficiency of hybridization between the dna probe and the rrna has been related to the accessibility of the rrna when ribosome content and cell permeability are not limiting. published rrna accessibility maps show that probe brightness is sensitive to the organism being hybridized and the exact location of the target site and, hence, it is highly unpredictable based on accessibility only. in this study, a model of fish based on the thermodynamics ...	2004	15574909
characterization of a novel amylolytic enzyme encoded by a gene from a soil-derived metagenomic library.	it has been estimated that less than 1% of the microorganisms in nature can be cultivated by conventional techniques. thus, the classical approach of isolating enzymes from pure cultures allows the analysis of only a subset of the total naturally occurring microbiota in environmental samples enriched in microorganisms. to isolate useful microbial enzymes from uncultured soil microorganisms, a metagenome was isolated from soil samples, and a metagenomic library was constructed by using the puc19 ...	2004	15574921
in vivo 31p nuclear magnetic resonance investigation of tellurite toxicity in escherichia coli.	here we compare the physiological state of escherichia coli exposed to tellurite or selenite by using the noninvasive technique of phosphorus-31 nuclear magnetic resonance (nmr) spectroscopy. we studied glucose-fed escherichia coli hb101 cells containing either a normal puc8 plasmid with no tellurite resistance determinants present or the ptwt100 plasmid which contains the resistance determinants tehab. no differences could be observed in intracellular atp levels, the presence or absence of a tr ...	2004	15574934
shear rate moderates community diversity in freshwater biofilms.	the development of freshwater multispecies biofilms at solid-liquid interfaces occurs both in quiescent waters and under conditions of high shear rates. however, the influence of hydrodynamic shear rates on bacterial biofilm diversity is poorly understood. we hypothesized that different shear rates would significantly influence biofilm diversity and alter the relative proportions of coaggregating and autoaggregating community isolates. in order to study this hypothesis, freshwater biofilms were ...	2004	15574945
thermoadaptation trait revealed by the genome sequence of thermophilic geobacillus kaustophilus.	we present herein the first complete genome sequence of a thermophilic bacillus-related species, geobacillus kaustophilus hta426, which is composed of a 3.54 mb chromosome and a 47.9 kb plasmid, along with a comparative analysis with five other mesophilic bacillar genomes. upon orthologous grouping of the six bacillar sequenced genomes, it was found that 1257 common orthologous groups composed of 1308 genes (37%) are shared by all the bacilli, whereas 839 genes (24%) in the g.kaustophilus genome ...	2004	15576355
paradoxical homozygous expression from heterozygotes and heterozygous expression from homozygotes as a consequence of transcriptional infidelity through a polyadenine tract in the ap3b1 gene responsible for canine cyclic neutropenia.	canine cyclic neutropenia is an autosomal recessive disease in which the number of neutrophils, the primary blood phagocyte, oscillates between almost zero and normal values with two week frequency. we previously found that the causative mutation is an insertion of an extra adenine residue within a tract of nine a's in exon 21 of the 27 exon canine ap3b1 gene. in the course of identifying the mutation, however, we observed an unusual phenomenon: heterozygous carrier dogs, who have one normal all ...	2004	15576359
nadp-malate dehydrogenase from unicellular green alga chlamydomonas reinhardtii. a first step toward redox regulation?	the determinants of the thioredoxin (trx)-dependent redox regulation of the chloroplastic nadp-malate dehydrogenase (nadp-mdh) from the eukaryotic green alga chlamydomonas reinhardtii have been investigated using site-directed mutagenesis. the results indicate that a single c-terminal disulfide is responsible for this regulation. the redox midpoint potential of this disulfide is less negative than that of the higher plant enzyme. the regulation is of an all-or-nothing type, lacking the fine-tuni ...	2005	15579663
control of rrna synthesis in escherichia coli: a systems biology approach.	the first part of this review contains an overview of the various contributions and models relating to the control of rrna synthesis reported over the last 45 years. the second part describes a systems biology approach to identify the factors and effectors that control the interactions between rna polymerase and rrna (rrn) promoters of escherichia coli bacteria during exponential growth in different media. this analysis is based on measurements of absolute rrn promoter activities as transcripts ...	2004	15590778
4scopmap: automated assignment of protein structures to evolutionary superfamilies.	inference of remote homology between proteins is very challenging and remains a prerogative of an expert. thus a significant drawback to the use of evolutionary-based protein structure classifications is the difficulty in assigning new proteins to unique positions in the classification scheme with automatic methods. to address this issue, we have developed an algorithm to map protein domains to an existing structural classification scheme and have applied it to the scop database.	2004	15598351
pa-agog, the founding member of a new family of archaeal 8-oxoguanine dna-glycosylases.	oxidative damage represents a major threat to genomic stability, as the major product of dna oxidation, 8-oxoguanine (go), frequently mispairs with adenine during replication. in order to prevent these mutagenic events, organisms have evolved go-dna glycosylases that remove this oxidized base from dna. we were interested to find out how go is processed in the hyperthermophilic archaeon pyrobaculum aerophilum, which lives at temperatures around 100 degrees c. to this end, we searched its genome f ...	2004	15604455
enzyme adaptation to alkaline ph: atomic resolution (1.08 a) structure of phosphoserine aminotransferase from bacillus alcalophilus.	the crystal structure of the vitamin b(6)-dependent enzyme phosphoserine aminotransferase from the obligatory alkaliphile bacillus alcalophilus has been determined at 1.08 a resolution. the model was refined to an r-factor of 11.7% (r(free) = 13.9%). the enzyme displays a narrow ph optimum of enzymatic activity at ph 9.0. the final structure was compared to the previously reported structure of the mesophilic phosphoserine aminotransferase from escherichia coli and to that of phosphoserine aminot ...	2005	15608117
the identification of novel rna structural motifs using compadres: an automated approach to structural discovery.	recurring rna structural motifs are important sites of tertiary interaction and as such, are integral to rna macromolecular structure. although numerous rna motifs have been classified and characterized, the identification of new motifs is of great interest. in this study, we discovered four new conformationally recurring motifs: the pi-turn, the omega-turn, the alpha-loop and the c2'-endo mediated flipped adenosine motif. not only do they have complex and interesting structures, but they partic ...	2004	15608296
genetic determinant of intrinsic quinolone resistance in fusobacterium canifelinum.	fourteen fluoroquinolone-resistant fusobacterial strains, originating from cats or dogs, were characterized by sequencing of the 16s-23s and 16s rrna genes and dna-dna hybridization and were described as a new species, fusobacterium canifelinum. all of the strains are intrinsically resistant (mic, >4 g/ml) to levofloxacin and other fluoroquinolones. compared to the quinolone resistance-determining region (gyra) of the susceptible relative f. nucleatum, we found that ser79 was replaced with leuci ...	2005	15616329
x-ray crystallography study on ribosome recycling: the mechanism of binding and action of rrf on the 50s ribosomal subunit.	this study presents the crystal structure of domain i of the escherichia coli ribosome recycling factor (rrf) bound to the deinococcus radiodurans 50s subunit. the orientation of rrf is consistent with the position determined on a 70s-rrf complex by cryoelectron microscopy (cryo-em). alignment, however, requires a rotation of 7 degrees and a shift of the cryo-em rrf by a complete turn of an alpha-helix, redefining the contacts established with ribosomal components. at 3.3 a resolution, rrf is se ...	2004	15616575
x-ray crystallography study on ribosome recycling: the mechanism of binding and action of rrf on the 50s ribosomal subunit.	this study presents the crystal structure of domain i of the escherichia coli ribosome recycling factor (rrf) bound to the deinococcus radiodurans 50s subunit. the orientation of rrf is consistent with the position determined on a 70s-rrf complex by cryoelectron microscopy (cryo-em). alignment, however, requires a rotation of 7 degrees and a shift of the cryo-em rrf by a complete turn of an alpha-helix, redefining the contacts established with ribosomal components. at 3.3 a resolution, rrf is se ...	2004	15616575
selenocysteine trna-specific elongation factor selb is a structural chimaera of elongation and initiation factors.	in all three kingdoms of life, selb is a specialized translation elongation factor responsible for the cotranslational incorporation of selenocysteine into proteins by recoding of a uga stop codon in the presence of a downstream mrna hairpin loop. here, we present the x-ray structures of selb from the archaeon methanococcus maripaludis in the apo-, gdp- and gppnhp-bound form and use mutational analysis to investigate the role of individual amino acids in its aminoacyl-binding pocket. all three s ...	2004	15616587
selenocysteine trna-specific elongation factor selb is a structural chimaera of elongation and initiation factors.	in all three kingdoms of life, selb is a specialized translation elongation factor responsible for the cotranslational incorporation of selenocysteine into proteins by recoding of a uga stop codon in the presence of a downstream mrna hairpin loop. here, we present the x-ray structures of selb from the archaeon methanococcus maripaludis in the apo-, gdp- and gppnhp-bound form and use mutational analysis to investigate the role of individual amino acids in its aminoacyl-binding pocket. all three s ...	2004	15616587
the structure of a rigorously conserved rna element within the sars virus genome.	we have solved the three-dimensional crystal structure of the stem-loop ii motif (s2m) rna element of the sars virus genome to 2.7-a resolution. sars and related coronaviruses and astroviruses all possess a motif at the 3' end of their rna genomes, called the s2m, whose pathogenic importance is inferred from its rigorous sequence conservation in an otherwise rapidly mutable rna genome. we find that this extreme conservation is clearly explained by the requirement to form a highly structured rna ...	2004	15630477
the structure of a rigorously conserved rna element within the sars virus genome.	we have solved the three-dimensional crystal structure of the stem-loop ii motif (s2m) rna element of the sars virus genome to 2.7-a resolution. sars and related coronaviruses and astroviruses all possess a motif at the 3' end of their rna genomes, called the s2m, whose pathogenic importance is inferred from its rigorous sequence conservation in an otherwise rapidly mutable rna genome. we find that this extreme conservation is clearly explained by the requirement to form a highly structured rna ...	2004	15630477
bacterial chromosome segregation: structure and dna binding of the soj dimer--a conserved biological switch.	soj and spo0j of the gram-negative hyperthermophile thermus thermophilus belong to the conserved parab family of bacterial proteins implicated in plasmid and chromosome partitioning. spo0j binds to dna near the replication origin and localises at the poles following initiation of replication. soj oscillates in the nucleoid region in an atp- and spo0j-dependent fashion. here, we show that soj undergoes atp-dependent dimerisation in solution and forms nucleoprotein filaments with dna. crystal stru ...	2005	15635448
high-level overproduction of his-tagged tth dna polymerase in thermus thermophilus.	a new plasmid for the overexpression of his-tagged thermozymes in thermus thermophilus was developed. with this plasmid, soluble and active histidine-tagged dna polymerase from t. thermophilus was overproduced in larger amounts in the thermophile than in escherichia coli. the protein purified from the thermophile was active in pcr.	2005	15640243
isolation and characterization of a thermostable rna ligase 1 from a thermus scotoductus bacteriophage ts2126 with good single-stranded dna ligation properties.	we have recently sequenced the genome of a novel thermophilic bacteriophage designated as ts2126 that infects the thermophilic eubacterium thermus scotoductus. one of the annotated open reading frames (orfs) shows homology to t4 rna ligase 1, an enzyme of great importance in molecular biology, owing to its ability to ligate single-stranded nucleic acids. the orf was cloned, and recombinant protein was expressed, purified and characterized. the recombinant enzyme ligates single-stranded nucleic a ...	2005	15642699
site-specific labeling of the ribosome for single-molecule spectroscopy.	single-molecule fluorescence spectroscopy can reveal mechanistic and kinetic details that may not be observed in static structural and bulk biochemical studies of protein synthesis. one approach requires site-specific and stable attachment of fluorophores to the components of translation machinery. fluorescent tagging of the ribosome is a prerequisite for the observation of dynamic changes in ribosomal conformation during translation using fluorescence methods. modifications of the ribosomal par ...	2005	15647501
membrane protein crystallization in amphiphile phases: practical and theoretical considerations.	integral membrane proteins are amphiphilic molecules. in order to enable chromatographic purification and crystallization, a complementary amphiphilic microenvironment must be created and maintained. various types of amphiphilic phases have been employed in crystallizations and intricate amphiphilic microenvironmental structures have resulted from these and are found inside membrane protein crystals. in this review the process of crystallization is put into the context of amphiphile phase transi ...	2004	15652249
membrane protein crystallization in amphiphile phases: practical and theoretical considerations.	integral membrane proteins are amphiphilic molecules. in order to enable chromatographic purification and crystallization, a complementary amphiphilic microenvironment must be created and maintained. various types of amphiphilic phases have been employed in crystallizations and intricate amphiphilic microenvironmental structures have resulted from these and are found inside membrane protein crystals. in this review the process of crystallization is put into the context of amphiphile phase transi ...	2004	15652249
a vibrational spectral maker for probing the hydrogen-bonding status of protonated asp and glu residues.	hydrogen bonding is a fundamental element in protein structure and function. breaking a single hydrogen bond may impair the stability of a protein. we report an infrared vibrational spectral marker for probing the hydrogen-bond number for buried, protonated asp or glu residues in proteins. ab initio computational studies were performed on hydrogen-bonding interactions of a cooh group with a variety of side-chain model compounds of polar and charged amino acids in vacuum using density function th ...	2005	15653739
crystal structure of mil (mth680): internal duplication and similarity between the imp4/brix domain and the anticodon-binding domain of class iia aminoacyl-trna synthetases.	proteins of the imp4/brix superfamily are involved in ribosomal rna processing, an essential function in all cells. we report the first structure of an imp4/brix superfamily protein, the mil (for methanothermobacter thermautotrophicus imp4-like) protein (gene product mth680), from the archaeon m. thermautotrophicus. the amino- and carboxy-terminal halves of mil show significant structural similarity to one another, suggesting an origin by means of an ancestral duplication. both halves show the s ...	2005	15654320
breaking sieve for steric exclusion of a noncognate amino acid from active site of a trna synthetase.	the genetic code is fixed in aminoacylation reactions catalyzed by aminoacyl-trna synthetases. amino acid discrimination occurs at two sites: one for amino acid activation and aminoacylation and one for editing misactivated amino acids. although the active site sieves out bulkier amino acids, misactivation occurs with substrates whose side chains are smaller than the cognate one. paradoxically, although alanyl-trna synthetase activates glycine as well as alanine, the sterically larger (than alan ...	2005	15657145
the snrnp 15.5k protein folds its cognate k-turn rna: a combined theoretical and biochemical study.	the human 15.5k protein binds to the 5' stem-loop of u4 snrna, promotes the assembly of the spliceosomal u4/u6 snrnp, and is required for the recruitment of the 61k protein and the 20/60/90k protein complex to the u4 snrna. in the crystallographic structure of the 15.5k-u4 snrna complex, the conformation of the rna corresponds to the family of kink-turn (k-turn) structural motifs. we simulated the complex and the free rna, showing how the protein binding and the intrinsic flexibility contribute ...	2005	15659359
ribosomal protein l1 recognizes the same specific structural motif in its target sites on the autoregulatory mrna and 23s rrna.	the rna-binding ability of ribosomal protein l1 is of profound interest since the protein has a dual function as a ribosomal protein binding rrna and as a translational repressor binding its mrna. here, we report the crystal structure of ribosomal protein l1 in complex with a specific fragment of its mrna and compare it with the structure of l1 in complex with a specific fragment of 23s rrna determined earlier. in both complexes, a strongly conserved rna structural motif is involved in l1 bindin ...	2005	15659579
genetic analysis reveals domain interactions of arabidopsis hsp100/clpb and cooperation with the small heat shock protein chaperone system.	we have defined amino acids important for function of the arabidopsis thaliana hsp100/clpb chaperone (athsp101) in acquired thermotolerance by isolating recessive, loss-of-function mutations and a novel semidominant, gain-of-function allele [hot1-4 (a499t)]. the hot1-4 allele is unusual in that it not only fails to develop thermotolerance to 45 degrees c after acclimation at 38 degrees c, but also is sensitive to 38 degrees c, which is a permissive temperature for wild-type and loss-of-function ...	2005	15659638
biogenesis of a putative channel protein, comec, required for dna uptake: membrane topology, oligomerization and formation of disulphide bonds.	comec is a putative channel protein for dna uptake in bacillus subtilis and other genetically transformable bacteria. membrane topology studies suggest a model of comec as a multispanning membrane protein with seven transmembrane segments (tmss), and possibly with one laterally inserted amphipathic helix. we show that comec contains an intramolecular disulphide bond in its n-terminal extracellular loop (between the residues c131 and c172), which is required for the stability of the protein, and ...	2005	15661011
interaction of rrf and ef-g from e. coli and t. thermophilus with ribosomes from both origins--insight into the mechanism of the ribosome recycling step.	ribosome recycling factor (rrf), elongation factor-g (ef-g), and ribosomes from thermus thermophilus (tt-) and escherichia coli (ec-) were used to study the disassembly mechanism of post-termination ribosomal complexes by these factors. with tt-rrf, ec-ef-g can release bound-trna from ec-model post-termination complexes. however, tt-rrf is not released by ec-ef-g from ec-ribosomes. this complex with tt-rrf and ec-ribosomes after the trna release by ec-ef-g is regarded as an intermediate of the d ...	2005	15661844
the diversity of dolichol-linked precursors to asn-linked glycans likely results from secondary loss of sets of glycosyltransferases.	the vast majority of eukaryotes (fungi, plants, animals, slime mold, and euglena) synthesize asn-linked glycans (alg) by means of a lipid-linked precursor dolichol-pp-glcnac2man9glc3. knowledge of this pathway is important because defects in the glycosyltransferases (alg1-alg12 and others not yet identified), which make dolichol-pp-glycans, lead to numerous congenital disorders of glycosylation. here we used bioinformatic and experimental methods to characterize alg glycosyltransferases and doli ...	2005	15665075
stabilization of nucleic acids by unusual polyamines produced by an extreme thermophile, thermus thermophilus.	extreme thermophiles produce two types of unusual polyamine: long linear polyamines such as caldopentamine and caldohexamine, and branched polyamines such as quaternary ammonium compounds [e.g. tetrakis(3-aminopropyl)ammonium]. to clarify the physiological roles of long linear and branched polyamines in thermophiles, we synthesized them chemically and tested their effects on the stability of ds (double-stranded) and ss (single-stranded) dnas and trna in response to thermal denaturation, as measu ...	2005	15673283
the high-affinity maltose/trehalose abc transporter in the extremely thermophilic bacterium thermus thermophilus hb27 also recognizes sucrose and palatinose.	we have studied the transport of trehalose and maltose in the thernophilic bacterium thermus thermophilus hb27, which grows optimally in the range of 70 to 75 degrees c. the k(m) values at 70 degrees c were 109 nm for trehalose and 114 nm for maltose; also, a high k(m) (424 nm) was found for the uptake of sucrose. competition studies showed that a single transporter recognizes trehalose, maltose, and sucrose, while d-galactose, d-fucose, l-rhamnose, l-arabinose, and d-mannose were not competitiv ...	2005	15687184
dna binding: a novel function of pseudomonas aeruginosa type iv pili.	the opportunistic pathogen pseudomonas aeruginosa produces multifunctional, polar, filamentous appendages termed type iv pili. type iv pili are involved in colonization during infection, twitching motility, biofilm formation, bacteriophage infection, and natural transformation. electrostatic surface analysis of modeled pilus fibers generated from p. aeruginosa strain pak, k122-4, and kb-7 pilin monomers suggested that a solvent-exposed band of positive charge may be a common feature of all type ...	2005	15687210
contribution of the atp binding site of pare to susceptibility to novobiocin and quinolones in streptococcus pneumoniae.	in streptococcus pneumoniae, an h103y substitution in the atp binding site of the pare subunit of topoisomerase iv was shown to confer quinolone resistance and hypersensitivity to novobiocin when associated with an s84f change in the a subunit of dna gyrase. we reconstituted in vitro the wild-type topoisomerase iv and its pare mutant. the pare mutant enzyme showed a decreased activity for decatenation at subsaturating atp levels and was more sensitive to inhibition by novobiocin but was as sensi ...	2005	15687222
protein folding: defining a "standard" set of experimental conditions and a preliminary kinetic data set of two-state proteins.	recent years have seen the publication of both empirical and theoretical relationships predicting the rates with which proteins fold. our ability to test and refine these relationships has been limited, however, by a variety of difficulties associated with the comparison of folding and unfolding rates, thermodynamics, and structure across diverse sets of proteins. these difficulties include the wide, potentially confounding range of experimental conditions and methods employed to date and the di ...	2005	15689503
crystal structure of a predicted phosphoribosyltransferase (tt1426) from thermus thermophilus hb8 at 2.01 a resolution.	tt1426, from thermus thermophilus hb8, is a conserved hypothetical protein with a predicted phosphoribosyltransferase (prtase) domain, as revealed by a pfam database search. the 2.01 a crystal structure of tt1426 has been determined by the multiwavelength anomalous dispersion (mad) method. tt1426 comprises a core domain consisting of a central five-stranded beta sheet surrounded by four alpha-helices, and a subdomain in the c terminus. the core domain structure resembles those of the type i prta ...	2005	15689504
analysis of subsecond protein dynamics by amide hydrogen exchange and mass spectrometry using a quenched-flow setup.	amide hydrogen exchange (hx) in combination with mass spectrometry (ms) is a powerful tool to analyze the folding and dynamics of proteins. in the traditional methodology the exchange time is controlled by manual pipetting, thereby limiting the time resolution to several seconds. some conformational changes in proteins, however, occur in the subsecond time scale, making it desirable to perform hx at shorter time intervals down to the limit set by the intrinsic chemical exchange rate. we now repo ...	2005	15689511
processivity clamp gp45 and ssdna-binding-protein gp32 modulate the fidelity of bacteriophage rb69 dna polymerase in a sequence-specific manner, sometimes enhancing and sometimes compromising accuracy.	numerous studies of the impact of accessory proteins upon the fidelity of dna synthesis have provided a complex and sometimes discordant picture. we previously described such an analysis conducted in vitro using various bacteriophage rb69 gp43 mutator dna polymerases with or without the accessory proteins gp32 (which binds single-stranded dna) plus gp45/44/62 (processivity clamp and its loaders). mutations were scored at many sites in the laczalpha mutation reporter sequence. unexpectedly, the a ...	2005	15695359
homology-extended sequence alignment.	we present a profile-profile multiple alignment strategy that uses database searching to collect homologues for each sequence in a given set, in order to enrich their available evolutionary information for the alignment. for each of the alignment sequences, the putative homologous sequences that score above a pre-defined threshold are incorporated into a position-specific pre-alignment profile. the enriched position-specific profile is used for standard progressive alignment, thereby more accura ...	2005	15699183
a previously uncharacterized role for small protein b (smpb) in transfer messenger rna-mediated trans-translation.	ssra is a versatile rna molecule found in all bacteria that functions as both a trna and an mrna. ssra rescues ribosomes stalled on damaged mrnas and directs the tagging and degradation of their aberrant protein products. small protein b (smpb) is required for all known activities of ssra. the two known functions of smpb are binding ssra rna and promoting stable association of the smpb.ssra complex with 70s ribosomes. using mutational analysis and biochemical experiments, we have discovered a pr ...	2005	15699355
quantitative pcr-enhanced immunoassay for measurement of enteroviral immunoglobulin m antibody and diagnosis of aseptic meningitis.	a pcr-enhanced immunoassay (pia) to detect enterovirus (ev) immunoglobulin m (igm) for diagnosis of recent ev infection was recently developed. this test was compared with another ev igm capture technique, the solid-phase reverse immunosorbent test (sprist). fourteen of 43 serum samples from aseptic meningitis patients were positive by pia, whereas 10 were positive by sprist. one of 39 control serum samples was weakly positive by pia. a single-serum-dilution real-time pcr-based pia for ev igm (q ...	2005	15699416
clustering the annotation space of proteins.	current protein clustering methods rely on either sequence or functional similarities between proteins, thereby limiting inferences to one of these areas.	2005	15703069
complete genome sequence of the hyperthermophilic archaeon thermococcus kodakaraensis kod1 and comparison with pyrococcus genomes.	the genus thermococcus, comprised of sulfur-reducing hyperthermophilic archaea, belongs to the order thermococcales in euryarchaeota along with the closely related genus pyrococcus. the members of thermococcus are ubiquitously present in natural high-temperature environments, and are therefore considered to play a major role in the ecology and metabolic activity of microbial consortia within hot-water ecosystems. to obtain insight into this important genus, we have determined and annotated the c ...	2005	15710748
increasing stability of water-soluble pqq glucose dehydrogenase by increasing hydrophobic interaction at dimeric interface.	water-soluble quinoprotein glucose dehydrogenase (pqqgdh-b) from acinetobacter calcoaceticus has a great potential for application as a glucose sensor constituent. because this enzyme shows no activity in its monomeric form, correct quaternary structure is essential for the formation of active enzyme. we have previously reported on the increasing of the stability of pqqgdh-b by preventing the subunit dissociation. previous studies were based on decreasing the entropy of quaternary structure diss ...	2005	15715904
genomic analysis of anaerobic respiration in the archaeon halobacterium sp. strain nrc-1: dimethyl sulfoxide and trimethylamine n-oxide as terminal electron acceptors.	we have investigated anaerobic respiration of the archaeal model organism halobacterium sp. strain nrc-1 by using phenotypic and genetic analysis, bioinformatics, and transcriptome analysis. nrc-1 was found to grow on either dimethyl sulfoxide (dmso) or trimethylamine n-oxide (tmao) as the sole terminal electron acceptor, with a doubling time of 1 day. an operon, dmsreabcd, encoding a putative regulatory protein, dmsr, a molybdopterin oxidoreductase of the dmso reductase family (dmseabc), and a ...	2005	15716436
structure of the nucleotide complex of pyrr, the pyr attenuation protein from bacillus caldolyticus, suggests dual regulation by pyrimidine and purine nucleotides.	pyrr is a protein that regulates the expression of genes and operons of pyrimidine nucleotide biosynthesis (pyr genes) in many bacteria. pyrr acts by binding to specific sequences on pyr mrna and causing transcriptional attenuation when intracellular levels of uridine nucleotides are elevated. pyrr from bacillus subtilis has been purified and extensively studied. in this work, we describe the purification to homogeneity and characterization of recombinant pyrr from the thermophile bacillus caldo ...	2005	15716449
characterization of the atpase and unwinding activities of the yeast dead-box protein has1p and the analysis of the roles of the conserved motifs.	the yeast dead-box protein has1p is required for the maturation of 18s rrna, the biogenesis of 40s r-subunits and for the processing of 27s pre-rrnas during 60s r-subunit biogenesis. we purified recombinant has1p and characterized its biochemical activities. we show that has1p is an rna-dependent atpase in vitro and that it is able to unwind rna/dna duplexes in an atp-dependent manner. we also report a mutational analysis of the conserved residues in motif i (86aktgsgkt93), motif iii (228sat230) ...	2005	15718299
crystal structure and dna-binding analysis of reco from deinococcus radiodurans.	the recfor pathway has been shown to be essential for dna repair through the process of homologous recombination in bacteria and, recently, to be important in the recovery of stalled replication forks following uv irradiation. reco, along with recr, recf, recq and recj, is a principal actor in this fundamental dna repair pathway. here we present the three-dimensional structure of a member of the reco family. the crystal structure of deinococcus radiodurans reco (drreco) reveals possible binding ...	2005	15719017
identification of a new family of putative pd-(d/e)xk nucleases with unusual phylogenomic distribution and a new type of the active site.	prediction of structure and function for uncharacterized protein families by identification of evolutionary links to characterized families and known structures is one of the cornerstones of genomics. theoretical assignment of three-dimensional folds and prediction of protein function even at a very general level can facilitate the experimental determination of the molecular mechanism of action and the role that members of a given protein family fulfill in the cell. here, we predict the three-di ...	2005	15720711
hinge-like motions in rna kink-turns: the role of the second a-minor motif and nominally unpaired bases.	kink-turn (k-turn) motifs are asymmetric internal loops found at conserved positions in diverse rnas, with sharp bends in phosphodiester backbones producing v-shaped structures. explicit-solvent molecular dynamics simulations were carried out for three k-turns from 23s rrna, i.e., kt-38 located at the base of the a-site finger, kt-42 located at the base of the l7/l12 stalk, and kt-58 located in domain iii, and for the k-turn of human u4 snrna. the simulations reveal hinge-like k-turn motions on ...	2005	15722438
separation of mutation avoidance and antirecombination functions in an escherichia coli muts mutant.	dna mismatch repair in escherichia coli has been shown to be involved in two distinct processes: mutation avoidance, which removes potential mutations arising as replication errors, and antirecombination which prevents recombination between related, but not identical (homeologous), dna sequences. we show that cells with the mutsdelta800 mutation (which removes the c-terminal 53 amino acids of muts) on a multicopy plasmid are proficient for mutation avoidance. in interspecies genetic crosses, how ...	2005	15731339
tolerance of the rieske-type [2fe-2s] cluster in recombinant ferredoxin bpha3 from pseudomonas sp. kks102 to histidine ligand mutations.	bpha3 from pseudomonas sp. kks102 is a rieske-type [2fe-2s] ferredoxin that transfers electrons from an nadh-dependent oxidoreductase, bpha4, to a biphenyl dioxygenase complex. a high-level expression and purification system for the recombinant bpha3 in escherichia coli was constructed. two histidine ligands of the rieske-type cluster in bpha3, were each replaced with serine, cysteine, asparagine and tyrosine. the single mutants, in which either his44 or his65 was replaced with a cysteine residu ...	2005	15733056
evolutionary profiles from the qr factorization of multiple sequence alignments.	we present an algorithm to generate complete evolutionary profiles that represent the topology of the molecular phylogenetic tree of the homologous group. the method, based on the multidimensional qr factorization of numerically encoded multiple sequence alignments, removes redundancy from the alignments and orders the protein sequences by increasing linear dependence, resulting in the identification of a minimal basis set of sequences that spans the evolutionary space of the homologous group of ...	2005	15741270
crystal structure of a novel polyisoprenoid-binding protein from thermus thermophilus hb8.	the isoprenoid quinones exist widely among prokaryotes and eukaryotes. they play essential roles in respiratory electron transport and in controlling oxidative stress and gene regulation. in the isoprenoid quinone biosynthetic pathway, polyprenyl pyrophosphates are used as isoprenoid side-chain precursors. here we report the crystal structure of a novel polyprenyl pyrophosphate binding protein, tt1927b, from thermus thermophilus hb8, complexed with its ligand. this protein belongs to the ycei-li ...	2005	15741337
a mutation in the decoding center of thermus thermophilus 16s rrna suggests a novel mechanism of streptomycin resistance.	a spontaneous kanamycin resistance and capreomycin resistance mutation, a1408g, in the decoding center of 16s rrna, was identified in the extreme thermophile thermus thermophilus. unexpectedly, this mutation also confers resistance to streptomycin. we propose a novel mechanism of streptomycin resistance by which a1408g influences conformational changes in 16s rrna during trna selection.	2005	15743969
modular rna architecture revealed by computational analysis of existing pseudoknots and ribosomal rnas.	modular architecture is a hallmark of rna structures, implying structural, and possibly functional, similarity among existing rnas. to systematically delineate the existence of smaller topologies within larger structures, we develop and apply an efficient rna secondary structure comparison algorithm using a newly developed two-dimensional rna graphical representation. our survey of similarity among 14 pseudoknots and subtopologies within ribosomal rnas (rrnas) uncovers eight pairs of structurall ...	2005	15745998
the acetate switch.	to succeed, many cells must alternate between life-styles that permit rapid growth in the presence of abundant nutrients and ones that enhance survival in the absence of those nutrients. one such change in life-style, the "acetate switch," occurs as cells deplete their environment of acetate-producing carbon sources and begin to rely on their ability to scavenge for acetate. this review explains why, when, and how cells excrete or dissimilate acetate. the central components of the "switch" (phos ...	2005	15755952
initiation of protein synthesis in bacteria.	valuable information on translation initiation is available from biochemical data and recently solved structures. we present a detailed description of current knowledge about the structure, function, and interactions of the individual components involved in bacterial translation initiation. the first section describes the ribosomal features relevant to the initiation process. subsequent sections describe the structure, function, and interactions of the mrna, the initiator trna, and the initiatio ...	2005	15755955
the interaction between sigma70 and the beta-flap of escherichia coli rna polymerase inhibits extension of nascent rna during early elongation.	the sigma-subunit of bacterial rna polymerase (rnap) is required for promoter-specific transcription initiation. this function depends on specific intersubunit interactions that occur when sigma associates with the rnap core enzyme to form rnap holoenzyme. among these interactions, that between conserved region 4 of sigma and the flap domain of the rnap beta-subunit (beta-flap) is critical for recognition of the major class of bacterial promoters. here, we describe the isolation of amino acid su ...	2005	15761057
chemical engineering of the peptidyl transferase center reveals an important role of the 2'-hydroxyl group of a2451.	the main enzymatic reaction of the large ribosomal subunit is peptide bond formation. ribosome crystallography showed that a2451 of 23s rrna makes the closest approach to the attacking amino group of aminoacyl-trna. mutations of a2451 had relatively small effects on transpeptidation and failed to unequivocally identify the crucial functional group(s). here, we employed an in vitro reconstitution system for chemical engineering the peptidyl transferase center by introducing non-natural nucleoside ...	2005	15767286
the application of cluster analysis in the intercomparison of loop structures in rna.	we have developed a computational approach for the comparison and classification of rna loop structures. hairpin or interior loops identified in atomic resolution rna structures were intercompared by conformational matching. the root-mean-square deviation (rmsd) values between all pairs of rna fragments of interest, even if from different molecules, are calculated. subsequently, cluster analysis is performed on the resulting matrix of rmsd distances using the unweighted pair group method with ar ...	2005	15769871
molecular analysis of a synthetic tetracycline-binding riboswitch.	riboswitches are newly discovered regulatory elements that consist solely of rna, sense their ligand in a preformed binding pocket, and perform a conformational switch in response to ligand binding, resulting in altered gene expression. regulation by a tetracycline (tc)-binding aptamer when inserted into the 5' untranslated region (utr) of a reporter gene exhibits all characteristics of a riboswitch. chemical and enzymatic probing reveals that the aptamer consists of two stems, p1 and p2, which ...	2005	15769877
hsp70 chaperones: cellular functions and molecular mechanism.	hsp70 proteins are central components of the cellular network of molecular chaperones and folding catalysts. they assist a large variety of protein folding processes in the cell by transient association of their substrate binding domain with short hydrophobic peptide segments within their substrate proteins. the substrate binding and release cycle is driven by the switching of hsp70 between the low-affinity atp bound state and the high-affinity adp bound state. thus, atp binding and hydrolysis a ...	2005	15770419
transcriptional slippage in bacteria: distribution in sequenced genomes and utilization in is element gene expression.	transcription slippage occurs on certain patterns of repeat mononucleotides, resulting in synthesis of a heterogeneous population of mrnas. individual mrna molecules within this population differ in the number of nucleotides they contain that are not specified by the template. when transcriptional slippage occurs in a coding sequence, translation of the resulting mrnas yields more than one protein product. except where the products of the resulting mrnas have distinct functions, transcription sl ...	2005	15774026
leucyl-trna synthetase from the ancestral bacterium aquifex aeolicus contains relics of synthetase evolution.	the editing reactions catalyzed by aminoacyl-trna synthetases are critical for the faithful protein synthesis by correcting misactivated amino acids and misaminoacylated trnas. we report that the isolated editing domain of leucyl-trna synthetase from the deep-rooted bacterium aquifex aeolicus (alphabeta-leurs) catalyzes the hydrolytic editing of both mischarged trna(leu) and minihelix(leu). within the domain, we have identified a crucial 20-amino-acid peptide that confers editing capacity when t ...	2005	15775966
ldpa: a component of the circadian clock senses redox state of the cell.	the endogenous 24-h (circadian) rhythms exhibited by the cyanobacterium synechococcus elongatus pcc 7942 and other organisms are entrained by a variety of environmental factors. in cyanobacteria, the mechanism that transduces environmental input signals to the central oscillator of the clock is not known. an earlier study identified ldpa as a gene involved in light-dependent modulation of the circadian period, and a candidate member of a clock-entraining input pathway. here, we report that the l ...	2005	15775978
graphical representation of ribosomal rna probe accessibility data using arb software package.	taxon specific hybridization probes in combination with a variety of commonly used hybridization formats nowadays are standard tools in microbial identification. a frequently applied technology, fluorescence in situ hybridization (fish), besides single cell identification, allows the localization and functional studies of the microbial community composition. careful in silico design and evaluation of potential oligonucleotide probe targets is therefore crucial for performing successful hybridiza ...	2005	15777482
modification at position 9 with 1-methyladenosine is crucial for structure and function of nematode mitochondrial trnas lacking the entire t-arm.	the mitochondria of the nematode ascaris suum have trnas with unusual secondary structures that lack either the t-arm or d-arm found in most other organisms. of the twenty-two trna species present in the mitochondria of a.suum, twenty lack the entire t-arm and two serine trnas lack the d-arm. to understand how such unusual trnas work in the nematode mitochondrial translation system, we analyzed post-transcriptional modifications of 11 mitochondrial trna species purified from a.suum, 10 of which ...	2005	15781491
single-stranded dna-binding protein of deinococcus radiodurans: a biophysical characterization.	the highly conserved bacterial single-stranded dna-binding (ssb) proteins play an important role in dna replication, repair and recombination and are essential for the survival of the cell. they are functional as tetramers, in which four ob(oligonucleotide/oligosaccharide binding)-folds act as dna-binding domains. the protomer of the ssb protein from the extremely radiation-resistant organism deinococcus radiodurans (drassb) has twice the size of the other bacterial ssb proteins and contains two ...	2005	15781492
the thermophilic, homohexameric aminopeptidase of borrelia burgdorferi is a member of the m29 family of metallopeptidases.	proteases are implicated in several aspects of the physiology of microorganisms, as well as in host-pathogen interactions. aminopeptidases are also emerging as novel drug targets in infectious agents. in this study, we have characterized an aminopeptidase from the spirochete borrelia burgdorferi, the causative agent of lyme disease. the aminopeptidolytic activity was identified in cell extracts from b. burgdorferi by using the substrate leucine-7-amido-4-methylcoumarin. a protein displaying this ...	2005	15784569
structure of p-protein of the glycine cleavage system: implications for nonketotic hyperglycinemia.	the crystal structure of the p-protein of the glycine cleavage system from thermus thermophilus hb8 has been determined. this is the first reported crystal structure of a p-protein, and it reveals that p-proteins do not involve the alpha(2)-type active dimer universally observed in the evolutionarily related pyridoxal 5'-phosphate (plp)-dependent enzymes. instead, novel alphabeta-type dimers associate to form an alpha(2)beta(2) tetramer, where the alpha- and beta-subunits are structurally simila ...	2005	15791207
correcting errors in synthetic dna through consensus shuffling.	although efficient methods exist to assemble synthetic oligonucleotides into genes and genomes, these suffer from the presence of 1-3 random errors/kb of dna. here, we introduce a new method termed consensus shuffling and demonstrate its use to significantly reduce random errors in synthetic dna. in this method, errors are revealed as mismatches by re-hybridization of the population. the dna is fragmented, and mismatched fragments are removed upon binding to an immobilized mismatch binding prote ...	2005	15800206
crystal structure of yeast yhr049w/fsh1, a member of the serine hydrolase family.	yhr049w/fsh1 was recently identified in a combined computational and experimental proteomics analysis for the detection of active serine hydrolases in yeast. this analysis suggested that fsh1 might be a serine-type hydrolase belonging to the broad functional alphabeta-hydrolase superfamily. in order to get insight into the molecular function of this gene, it was targeted in our yeast structural genomics project. the crystal structure of the protein confirms that it contains a ser/his/asp catalyt ...	2005	15802654
perspectives on biotechnological applications of archaea.	many archaea colonize extreme environments. they include hyperthermophiles, sulfur-metabolizing thermophiles, extreme halophiles and methanogens. because extremophilic microorganisms have unusual properties, they are a potentially valuable resource in the development of novel biotechnological processes. despite extensive research, however, there are few existing industrial applications of either archaeal biomass or archaeal enzymes. this review summarizes current knowledge about the biotechnolog ...	2002	15803645
molecular analysis of the role of two aromatic aminotransferases and a broad-specificity aspartate aminotransferase in the aromatic amino acid metabolism of pyrococcus furiosus.	the genes encoding aromatic aminotransferase ii (aroat ii) and aspartate aminotransferase (aspat) from pyrococcus furiosus have been identified, expressed in escherichia coli and the recombinant proteins characterized. the aroat ii enzyme was specific for the transamination reaction of the aromatic amino acids, and uses a-ketoglutarate as the amino acceptor. like the previously characterized aroat i, aroat ii has highest efficiency for phenylalanine (k(cat)/km = 923 s(-1) mm(-1)). northern blot ...	2002	15803651