Publications

isolation of a single-stranded dna-binding protein from the methylotrophic yeast, pichia pastoris and its identification as zeta crystallin.	a single-stranded dna (ssdna)-binding protein (ssb) that binds to specific upstream sequences of alcohol oxidase (aox1) promoter of the methylotrophic yeast pichia pastoris has been isolated and identified as zeta crystallin (zta1). the cdna encoding p.pastoris zta1 (ppzta1) was cloned into an escherichia coli expression vector, the recombinant ppzta1 was expressed and purified from e.coli cell lysates. the dna-binding properties of recombinant ppzta1 are identical to those of the ssb present in ...	2006	16914438
elongation complexes of thermus thermophilus rna polymerase that possess distinct translocation conformations.	we have characterized elongation complexes (ecs) of rna polymerase from the extremely thermophilic bacterium, thermus thermophilus. we found that complexes assembled on nucleic acid scaffolds are transcriptionally competent at high temperature (50-80 degrees c) and, depending upon the organization of the scaffold, possess distinct translocation conformations. ecs assembled on scaffolds with a 9 bp rna:dna hybrid are highly stable, resistant to pyrophosphorolysis, and are in the posttranslocated ...	2006	16914440
the "bridging" aspartate 178 in phthalate dioxygenase facilitates interactions between the rieske center and the iron(ii)--mononuclear center.	phthalate dioxygenase (pdo) and its reductase are parts of a two-component rieske dioxygenase system that initiates the aerobic breakdown of phthalate by forming cis-4,5-dihydro-4,5-dihydroxyphthalate (dhd). aspartate d178 in pdo, located near its ferrous mononuclear center, is highly conserved among rieske dioxygenases. the analogous aspartate has been implicated in electron transfer between the mononuclear iron and rieske center in naphthalene dioxygenase [parales et al. (1999) j. bacteriol. 1 ...	2006	16922496
two genes encoding new carotenoid-modifying enzymes in the green sulfur bacterium chlorobium tepidum.	the green sulfur bacterium chlorobium tepidum produces chlorobactene as its primary carotenoid. small amounts of chlorobactene are hydroxylated by the enzyme crtc and then glucosylated and acylated to produce chlorobactene glucoside laurate. the genes encoding the enzymes responsible for these modifications of chlorobactene, ct1987, and ct0967, have been identified by comparative genomics, and these genes were insertionally inactivated in c. tepidum to verify their predicted function. the gene e ...	2006	16923888
antimutator role of the dna glycosylase muty gene in helicobacter pylori.	helicobacter pylori has a highly variable genome with ongoing diversification via inter- and intragenomic recombination and spontaneous mutation. dna repair genes modulating mutation and recombination rates that influence diversification have not been well characterized for h. pylori. to examine the role of putative base excision repair ung and muty glycosylase and xtha apurinic/apyrimidinic endonuclease genes in h. pylori, mutants of each were constructed in strain jp26 by allelic exchange. spo ...	2006	16923889
23s rrna 2058a-->g alteration mediates ketolide resistance in combination with deletion in l22.	resistance to macrolides and ketolides occurs mainly via alterations in rna moieties of the drug-binding site. using an a2058g mutant of mycobacterium smegmatis, additional telithromycin resistance was acquired via deletion of 15 residues from protein l22. molecular modeling, based on the crystal structure of the large ribosomal subunit from deinococcus radiodurans complexed with telithromycin, shows that the telithromycin carbamate group is located in the proximity of the tip of the l22 hairpin ...	2006	16923950
sit down, relax and unwind: structural insights into recq helicase mechanisms.	helicases are specialized molecular motors that separate duplex nucleic acids into single strands. the recq family of helicases functions at the interface of dna replication, recombination and repair in bacterial and eukaryotic cells. they are key, multifunctional enzymes that have been linked to three human diseases: bloom's, werner's and rothmund-thomson's syndromes. this review summarizes recent studies that relate the structures of recq proteins to their biochemical activities.	2006	16935877
role and timing of gtp binding and hydrolysis during ef-g-dependent trna translocation on the ribosome.	the translocation of trna and mrna through the ribosome is promoted by elongation factor g (ef-g), a gtpase that hydrolyzes gtp during the reaction. recently, it was reported that, in contrast to previous observations, the affinity of ef-g was much weaker for gtp than for gdp and that ribosome-catalyzed gdp-gtp exchange would be required for translocation [zavialov av, hauryliuk vv, ehrenberg m (2005) j biol 4:9]. we have reinvestigated gtp/gdp binding and show that ef-g binds gtp and gdp with a ...	2006	16940356
structure of the stand-alone ram-domain protein from thermus thermophilus hb8.	the stand-alone ram (regulation of amino-acid metabolism) domain protein sraa from thermus thermophilus hb8 (ttha0845) was crystallized in the presence of zinc ions. the x-ray crystal structure was determined using a multiple-wavelength anomalous dispersion technique and was refined at 2.4 a resolution to a final r factor of 25.0%. the monomeric structure is a betaalphabetabetaalphabeta fold and it dimerizes mainly through interactions between the antiparallel beta-sheets. furthermore, five sraa ...	2006	16946463
cloning, expression, purification, crystallization and initial crystallographic analysis of the preprotein translocation atpase seca from thermus thermophilus.	the thermus thermophilus gene encoding the preprotein translocation atpase seca was cloned and expressed and the purified protein was crystallized by the hanging-drop vapour-diffusion technique in two different space groups p3(1(2))21 (a = b = 168.6, c = 149.8 a) and p6(1(5))22 (a = b = 130.9, c = 564.6 a). the crystals, improved by macroseeding, diffracted to beyond 2.8 and 3.5 a resolution for the trigonal and hexagonal crystal forms, respectively. structure determination using the multiple is ...	2006	16946477
a counterintuitive mg2+-dependent and modification-assisted functional folding of mitochondrial trnas.	mitochondrial trnas (mtrnas) often lack domains and posttranscriptional modifications that are found in cytoplasmic trnas. these structural and chemical elements normally stabilize the folding of cytoplasmic trnas into canonical structures that are competent for aminoacylation and translation. for example, the dihydrouridine (d) stem and loop domain is involved in the tertiary structure of cytoplasmic trnas through hydrogen bonds and a mg2+ bridge to the ribothymidine (t) stem and loop domain. t ...	2006	16949614
easi--enrichment of alternatively spliced isoforms.	alternative splicing produces more than one protein from the majority of genes and the rarer forms can have dominant functions. instability of alternative transcripts can also hinder the study of regulation of gene expression by alternative splicing. to investigate the true extent of alternative splicing we have developed a simple method of enriching alternatively spliced isoforms (easi) from pcrs using beads charged with thermus aquaticus single-stranded dna-binding protein (t.aq ssb). this dir ...	2006	16951290
tungsten transport protein a (wtpa) in pyrococcus furiosus: the first member of a new class of tungstate and molybdate transporters.	a novel tungstate and molybdate binding protein has been discovered from the hyperthermophilic archaeon pyrococcus furiosus. this tungstate transport protein a (wtpa) is part of a new abc transporter system selective for tungstate and molybdate. wtpa has very low sequence similarity with the earlier-characterized transport proteins moda for molybdate and tupa for tungstate. its structural gene is present in the genome of numerous archaea and some bacteria. the identification of this new tungstat ...	2006	16952940
mlc of thermus thermophilus: a glucose-specific regulator for a glucose/mannose abc transporter in the absence of the phosphotransferase system.	we report the presence of mlc in a thermophilic bacterium. mlc is known as a global regulator of sugar metabolism in gram-negative enteric bacteria that is controlled by sequestration to a glucose-transporting eii(glc) of the phosphotransferase system (pts). since thermophilic bacteria do not possess pts, mlc in thermus thermophilus must be differently controlled. dna sequence alignments between mlc from t. thermophilus (mlc(tth)) and mlc from e. coli (mlc(eco)) revealed that mlc(tth) conserved ...	2006	16952948
molecular characterization of disease-associated streptococci of the mitis group that are optochin susceptible.	eight optochin-susceptible (opt(s)) alpha-hemolytic (viridans) streptococcus isolates were characterized at the molecular level. these isolates showed phenotypic characteristics typical of both viridans streptococci and streptococcus pneumoniae. comparison of the sequence of housekeeping genes from these isolates with those of s. pneumoniae, streptococcus mitis, streptococcus oralis, and streptococcus pseudopneumoniae suggested that the opt(s) isolates corresponded to streptococci of the mitis g ...	2006	16971639
conservation and variation between rhodobacter capsulatus and escherichia coli tat systems.	the tat system allows the translocation of folded and often cofactor-containing proteins across biological membranes. here, we show by an interspecies transfer of a complete tat translocon that tat systems are largely, but not fully, interchangeable even between different classes of proteobacteria. the tat apparatus from the alpha-proteobacterium rhodobacter capsulatus was transferred to a tat-deficient escherichia coli strain, which is a gamma-proteobacterium. similar to that of e. coli, the r. ...	2006	16980457
colocation of genes encoding a trna-mrna hybrid and a putative signaling peptide on complementary strands in the genome of the hyperthermophilic bacterium thermotoga maritima.	in the genome of the hyperthermophilic bacterium thermotoga maritima, tm0504 encodes a putative signaling peptide implicated in population density-dependent exopolysaccharide formation. although not noted in the original genome annotation, tm0504 was found to colocate, on the opposite strand, with the gene encoding ssra, a hybrid of trna and mrna (tmrna), which is involved in a trans-translation process related to ribosome rescue and is ubiquitous in bacteria. specific dna probes were designed a ...	2006	16980482
analysis of rnase p protein (rnpa) expression in bacillus subtilis utilizing strains with suppressible rnpa expression.	bacterial rnase p is composed of an rna subunit and a single protein subunit (encoded by the rnpb and rnpa genes, respectively). we constructed bacillus subtilis mutant strains that conditionally express the rnase p protein under control of the xylose promoter (p(xyl)). in one strain (d7), rnpa expression was efficiently repressed in the absence of the inducer xylose, leading to cell growth arrest. growth could be restored by a second functional rnpa allele. this is the first rnase p protein kno ...	2006	16980484
characterization of adhesion threads of deinococcus geothermalis as type iv pili.	deinococcus geothermalis e50051 forms tenuous biofilms on paper machine surfaces. field emission electron microscopy analysis revealed peritrichous appendages which mediated cell-to-surface and cell-to-cell interactions but were absent in planktonically grown cells. the major protein component of the extracellular extract of d. geothermalis had an n-terminal sequence similar to the fimbrial protein pilin annotated in the d. geothermalis dsm 11300 draft sequence. it also showed similarity to the ...	2006	16980504
effects of protein-ligand associations on the subunit interactions of phosphofructokinase from b. stearothermophilus.	differences between the crystal structures of inhibitor-bound and uninhibited forms of phosphofructokinase (pfk) from b. stearothermophilus have led to a structural model for allosteric inhibition by phosphoenolpyruvate (pep) wherein a dimer-dimer interface within the tetrameric enzyme undergoes a quaternary shift. we have developed a labeling and hybridization technique to generate a tetramer with subunits simultaneously containing two different extrinsic fluorophores in known subunit orientati ...	2006	16981693
structural and functional conversion of molecular chaperone clpb from the gram-positive halophilic lactic acid bacterium tetragenococcus halophilus mediated by atp and stress.	in this study, we report the purification, initial structural characterization, and functional analysis of the molecular chaperone clpb from the gram-positive, halophilic lactic acid bacterium tetragenococcus halophilus. a recombinant t. halophilus clpb (clpb(tha)) was overexpressed in escherichia coli and purified by affinity chromatography, hydroxyapatite chromatography, and gel filtration chromatography. as demonstrated by gel filtration chromatography, chemical cross-linking with glutaraldeh ...	2006	16997952
identification of pyruvate carboxylase genes in pseudomonas aeruginosa pao1 and development of a p. aeruginosa-based overexpression system for alpha4- and alpha4beta4-type pyruvate carboxylases.	pyruvate carboxylase (pyc) is an ecologically, medically, and industrially important enzyme. it is widespread in all three domains of life, the archaea, bacteria, and eukarya. pyc catalyzes atp-dependent carboxylation of pyruvate to oxaloacetate. detailed structure-function studies of this enzyme have been hampered due to the unavailability of a facile recombinant overexpression system. except for the alpha4 enzyme from a thermophilic bacillus species, escherichia coli has been unsuitable for ov ...	2006	16997990
genetic characterization of the phenylacetyl-coenzyme a oxygenase from the aerobic phenylacetic acid degradation pathway of escherichia coli.	we show here that the paaabcde genes of the paa cluster responsible for phenylacetate degradation in escherichia coli w encode a five-component oxygenase that hydroxylates phenylacetyl-coenzyme a (coa), the first intermediate of the pathway. the primary structure of the subunits of bacterial phenylacetyl-coa oxygenases revealed that these enzymes constitute the prototype of a new and distinct group of the large bacterial diiron multicomponent oxygenase family.	2006	16997993
structural analysis of kasugamycin inhibition of translation.	the prokaryotic ribosome is an important target of antibiotic action. we determined the x-ray structure of the aminoglycoside kasugamycin (ksg) in complex with the escherichia coli 70s ribosome at 3.5-a resolution. the structure reveals that the drug binds within the messenger rna channel of the 30s subunit between the universally conserved g926 and a794 nucleotides in 16s ribosomal rna, which are sites of ksg resistance. to our surprise, ksg resistance mutations do not inhibit binding of the dr ...	2006	16998486
characterization of the particulate methane monooxygenase metal centers in multiple redox states by x-ray absorption spectroscopy.	the integral membrane enzyme particulate methane monooxygenase (pmmo) converts methane, the most inert hydrocarbon, to methanol under ambient conditions. the 2.8-a resolution pmmo crystal structure revealed three metal sites: a mononuclear copper center, a dinuclear copper center, and a nonphysiological mononuclear zinc center. although not found in the crystal structure, solution samples of pmmo also contain iron. we have used x-ray absorption spectroscopy to analyze the oxidation states and co ...	2006	16999437
crystal structures of the dna-binding domain of escherichia coli proline utilization a flavoprotein and analysis of the role of lys9 in dna recognition.	puta (proline utilization a) from escherichia coli is a 1320-amino-acid residue protein that is both a bifunctional proline catabolic enzyme and an autogenous transcriptional repressor. here, we report the first crystal structure of a puta dna-binding domain along with functional analysis of a mutant puta defective in dna binding. crystals were grown using a polypeptide corresponding to residues 1-52 of e. coli puta (puta52). the 2.1 angstrom resolution structure of puta52 mutant lys9met was det ...	2006	17001030
the nmr structure of an internal loop from 23s ribosomal rna differs from its structure in crystals of 50s ribosomal subunits.	internal loops play an important role in structure and folding of rna and in recognition of rna by other molecules such as proteins and ligands. an understanding of internal loops with propensities to form a particular structure will help predict rna structure, recognition, and function. the structures of internal loops 5' 1009cuaag1013 3'/3' 1168gaagc1164 5' and 5' 998cuaag1002 3'/3' 1157gaagc1153 5' from helix 40 of the large subunit rrna in deinococcus radiodurans and escherichia coli, respec ...	2006	17002278
evolution of new function in the gtp cyclohydrolase ii proteins of streptomyces coelicolor.	the genome sequence of streptomyces coelicolor contains three open reading frames (sco1441, sco2687, and sco6655) that encode proteins with significant (>40%) amino acid identity to gtp cyclohydrolase ii (gch ii), which catalyzes the committed step in the biosynthesis of riboflavin. the physiological significance of the redundancy of these proteins in s. coelicolor is not known. however, the gene contexts of the three proteins are different, suggesting that they may serve alternate biological ni ...	2006	17002314
structural and mutational studies of the amino acid-editing domain from archaeal/eukaryal phenylalanyl-trna synthetase.	to achieve accurate aminoacylation of trnas with their cognate amino acids, errors in aminoacylation are corrected by the "editing" mechanism in several aminoacyl-trna synthetases. phenylalanyl-trna synthetase (phers) hydrolyzes, or edits, misformed tyrosyl-trna with its editing domain in the beta subunit. we report the crystal structure of an n-terminal fragment of the phers beta subunit (phers-beta(n)) from the archaeon, pyrococcus horikoshii, at 1.94-a resolution. phers-beta(n) includes the e ...	2006	17003130
thermostable rnase p rnas lacking p18 identified in the aquificales.	the rnase p rna (rnpb) and protein (rnpa) genes were identified in the two aquificales sulfurihydrogenibium azorense and persephonella marina. in contrast, neither of the two genes has been found in the sequenced genome of their close relative, aquifex aeolicus. as in most bacteria, the rnpa genes of s. azorense and p. marina are preceded by the rpmh gene coding for ribosomal protein l34. this genetic region, including several genes up- and downstream of rpmh, is uniquely conserved among all thr ...	2006	17005927
heat shock proteins, end effectors of myocardium ischemic preconditioning?	the purpose of this study was to investigate (1) whether ischemia-reperfusion increased the content of heat shock protein 72 (hsp72) transcripts and (2) whether myocardial content of hsp72 is increased by ischemic preconditioning so that they can be considered as end effectors of preconditioning. twelve male minipigs (8 protocol, 4 sham) were used, with the following ischemic preconditioning protocol: 3 ischemia and reperfusion 5-minute alternative cycles and last reperfusion cycle of 3 hours. i ...	2006	17009598
substrate recognition, protein dynamics, and iron-sulfur cluster in pseudomonas aeruginosa adenosine 5'-phosphosulfate reductase.	aps reductase catalyzes the first committed step of reductive sulfate assimilation in pathogenic bacteria, including mycobacterium tuberculosis, and is a promising target for drug development. we report the 2.7 a resolution crystal structure of pseudomonas aeruginosa aps reductase in the thiosulfonate intermediate form of the catalytic cycle and with substrate bound. the structure, high-resolution fourier transform ion cyclotron resonance (ft-icr) mass spectrometry, and quantitative kinetic anal ...	2006	17010373
kinetic analysis of the metal binding mechanism of escherichia coli manganese superoxide dismutase.	the acquisition of a catalytic metal cofactor is an essential step in the maturation of every metalloenzyme, including manganese superoxide dismutase (mnsod). in this study, we have taken advantage of the quenching of intrinsic protein fluorescence by bound metal ions to continuously monitor the metallation reaction of escherichia coli mnsod in vitro, permitting a detailed kinetic characterization of the uptake mechanism. apo-mnsod metallation kinetics are "gated", zero order in metal ion for bo ...	2006	16258041
kinetic analysis of the metal binding mechanism of escherichia coli manganese superoxide dismutase.	the acquisition of a catalytic metal cofactor is an essential step in the maturation of every metalloenzyme, including manganese superoxide dismutase (mnsod). in this study, we have taken advantage of the quenching of intrinsic protein fluorescence by bound metal ions to continuously monitor the metallation reaction of escherichia coli mnsod in vitro, permitting a detailed kinetic characterization of the uptake mechanism. apo-mnsod metallation kinetics are "gated", zero order in metal ion for bo ...	2006	16258041
domain ii plays a crucial role in the function of ribosome recycling factor.	rrf (ribosome recycling factor) consists of two domains, and in concert with ef-g (elongation factor-g), triggers dissociation of the post-termination ribosomal complex. however, the function of the individual domains of rrf remains unclear. to clarify this, two rrf chimaeras, ecodi/ttedii and ttedi/ecodii, were created by domain swaps between the proteins from escherichia coli and thermoanaerobacter tengcongensis. the ribosome recycling activity of the rrf chimaeras was compared with their wild ...	2006	16262604
asnb is involved in natural resistance of mycobacterium smegmatis to multiple drugs.	mycobacteria are naturally resistant to most common antibiotics and chemotherapeutic agents. the underlying molecular mechanisms are not fully understood. in this paper, we describe a hypersensitive mutant of mycobacterium smegmatis, ms 2-39, which was isolated by screening for transposon insertion mutants of m. smegmatis mc2155 that exhibit increased sensitivity to rifampin, erythromycin, or novobiocin. the mutant ms 2-39 exhibited increased sensitivity to all three of the above mentioned antib ...	2006	16377694
the allosteric transition in dnak probed by infrared difference spectroscopy. concerted atp-induced rearrangement of the substrate binding domain.	the biological activity of dnak, the bacterial representative of the hsp70 protein family, is regulated by the allosteric interaction between its nucleotide and peptide substrate binding domains. despite the importance of the nucleotide-induced cycling of dnak between substrate-accepting and releasing states, the heterotropic allosteric mechanism remains as yet undefined. to further characterize this mechanism, the nucleotide-induced absorbance changes in the vibrational spectrum of wild-type dn ...	2006	16384998
production of recombinant and tagged proteins in the hyperthermophilic archaeon sulfolobus solfataricus.	many systems are available for the production of recombinant proteins in bacterial and eukaryotic model organisms, which allow us to study proteins in their native hosts and to identify protein-protein interaction partners. in contrast, only a few transformation systems have been developed for archaea, and no system for high-level gene expression existed for hyperthermophilic organisms. recently, a virus-based shuttle vector with a reporter gene was developed for the crenarchaeote sulfolobus sol ...	2006	16391031
involvement of nark1 and nark2 proteins in transport of nitrate and nitrite in the denitrifying bacterium pseudomonas aeruginosa pao1.	two transmembrane proteins were tentatively classified as nark1 and nark2 in the pseudomonas genome project and hypothesized to play an important physiological role in nitrate/nitrite transport in pseudomonas aeruginosa. the nark1 and nark2 genes are located in a cluster along with the structural genes for the nitrate reductase complex. our studies indicate that the transcription of all these genes is initiated from a single promoter and that the gene complex nark1k2ghji constitutes an operon. u ...	2006	16391109
bioinformatic analysis of an unusual gene-enzyme relationship in the arginine biosynthetic pathway among marine gamma proteobacteria: implications concerning the formation of n-acetylated intermediates in prokaryotes.	the n-acetylation of l-glutamate is regarded as a universal metabolic strategy to commit glutamate towards arginine biosynthesis. until recently, this reaction was thought to be catalyzed by either of two enzymes: (i) the classical n-acetylglutamate synthase (nags, gene arga) first characterized in escherichia coli and pseudomonas aeruginosa several decades ago and also present in vertebrates, or (ii) the bifunctional version of ornithine acetyltransferase (oat, gene argj) present in bacteria, a ...	2006	16409639
comparative genomics of multidrug resistance in acinetobacter baumannii.	acinetobacter baumannii is a species of nonfermentative gram-negative bacteria commonly found in water and soil. this organism was susceptible to most antibiotics in the 1970s. it has now become a major cause of hospital-acquired infections worldwide due to its remarkable propensity to rapidly acquire resistance determinants to a wide range of antibacterial agents. here we use a comparative genomic approach to identify the complete repertoire of resistance genes exhibited by the multidrug-resist ...	2006	16415984
structure-function analysis of the kinase-cpd domain of yeast trna ligase (trl1) and requirements for complementation of trna splicing by a plant trl1 homolog.	trl1 is an essential 827 amino acid enzyme that executes the end-healing and end-sealing steps of trna splicing in saccharomyces cerevisiae. trl1 consists of two domains--an n-terminal ligase component and a c-terminal 5'-kinase/2',3'-cyclic phosphodiesterase (cpd) component--that can function in trna splicing in vivo when expressed as separate polypeptides. to understand the structural requirements for the kinase-cpd domain, we performed an alanine scan of 30 amino acids that are conserved in t ...	2006	16428247
function and evolution of plasmid-borne genes for pyrimidine biosynthesis in borrelia spp.	the thyx gene for thymidylate synthase of the lyme borreliosis (lb) agent borrelia burgdorferi is located in a 54-kb linear plasmid. in the present study, we identified an orthologous thymidylate synthase gene in the relapsing fever (rf) agent borrelia hermsii, located it in a 180-kb linear plasmid, and demonstrated its expression. the functions of the b. hermsii and b. burgdorferi thyx gene products were evaluated both in vivo, by complementation of a thymidylate synthase-deficient escherichia ...	2006	16428394
characterization of the biosynthetic pathway of glucosylglycerate in the archaeon methanococcoides burtonii.	the pathway for the synthesis of the organic solute glucosylglycerate (gg) is proposed based on the activities of the recombinant glucosyl-3-phosphoglycerate synthase (gpgs) and glucosyl-3-phosphoglycerate phosphatase (gpgp) from methanococcoides burtonii. a mannosyl-3-phosphoglycerate phosphatase gene homologue (mpgp) was found in the genome of m. burtonii (http://www.jgi.doe.gov), but an mpgs gene coding for mannosyl-3-phosphoglycerate synthase (mpgs) was absent. the gene upstream of the mpgp ...	2006	16428406
crystal structures of nitroalkane oxidase: insights into the reaction mechanism from a covalent complex of the flavoenzyme trapped during turnover.	nitroalkane oxidase (nao) from fusarium oxysporum catalyzes the oxidation of neutral nitroalkanes to the corresponding aldehydes or ketones with the production of h(2)o(2) and nitrite. the flavoenzyme is a new member of the acyl-coa dehydrogenase (acad) family, but it does not react with acyl-coa substrates. we present the 2.2 a resolution crystal structure of nao trapped during the turnover of nitroethane as a covalent n5-fad adduct (es). the homotetrameric structure of es was solved by mad p ...	2006	16430210
identification and characterization of rsme, the founding member of a new rna base methyltransferase family.	a variety of rna methyltransferases act during ribosomal rna maturation to modify nucleotides in a site-specific manner. however, of the 10 base-methylated nucleotides present in the small ribosomal subunit of escherichia coli, only three enzymes responsible for modification of four bases are known. here, we show that the protein encoded by yggj, a member of the uncharacterized duf558 protein family of predicted alpha/beta (trefoil) knot methyltransferases is responsible for methylation at u1498 ...	2006	16431987
mutations conferring aminoglycoside and spectinomycin resistance in borrelia burgdorferi.	we have isolated and characterized in vitro mutants of the lyme disease agent borrelia burgdorferi that are resistant to spectinomycin, kanamycin, gentamicin, or streptomycin, antibiotics that target the small subunit of the ribosome. 16s rrna mutations a1185g and c1186u, homologous to escherichia coli nucleotides a1191 and c1192, conferred >2,200-fold and 1,300-fold resistance to spectinomycin, respectively. a 16s rrna a1402g mutation, homologous to e. coli a1408, conferred >90-fold resistance ...	2006	16436695
two conformational states in the crystal structure of the homo sapiens cytoplasmic ribosomal decoding a site.	the decoding a site of the small ribosomal subunit is an rna molecular switch, which monitors codon-anticodon interactions to guarantee translation fidelity. we have solved the crystal structure of an rna fragment containing two homo sapiens cytoplasmic a sites. each of the two a sites presents a different conformational state. in one state, adenines a1492 and a1493 are fully bulged-out with c1409 forming a wobble-like pair to a1491. in the second state, adenines a1492 and a1493 form non-watson- ...	2006	16452297
structure of the tetrahymena thermophila telomerase rna helix ii template boundary element.	telomere addition by telomerase requires an internal templating sequence located in the rna subunit of telomerase. the correct boundary definition of this template sequence is essential for the proper addition of the nucleotide repeats. incorporation of incorrect telomeric repeats onto the ends of chromosomes has been shown to induce chromosomal instability in ciliate, yeast and human cells. a 5' template boundary defining element (tbe) has been identified in human, yeast and ciliate telomerase ...	2006	16452301
molecular dynamics simulations of sarcin-ricin rrna motif.	explicit solvent molecular dynamics (md) simulations were carried out for sarcin-ricin domain (srd) motifs from 23s (escherichia coli) and 28s (rat) rrnas. the srd motif consists of gaga tetraloop, g-bulged cross-strand a-stack, flexible region and duplex part. detailed analysis of the overall dynamics, base pairing, hydration, cation binding and other srd features is presented. the srd is surprisingly static in multiple 25 ns long simulations and lacks any non-local motions, with root mean squa ...	2006	16456030
type a and b rnase p rnas are interchangeable in vivo despite substantial biophysical differences.	we show that structural type a and b bacterial ribonuclease p (rnase p) rnas can fully replace each other in vivo despite the many reported differences in their biogenesis, biochemical/biophysical properties and enzyme function in vitro. our findings suggest that many of the reported idiosyncrasies of type a and b enzymes either do not reflect the in vivo situation or are not crucial for rnase p function in vivo, at least under standard growth conditions. the discrimination of mature trna by rna ...	2006	16470227
isolation of a site-specifically modified rna from an unmodified transcript.	natural rnas contain many base modifications that have specific biological functions. the ability to functionally dissect individual modifications is facilitated by the identification and cloning of enzymes responsible for these modifications, but is hindered by the difficulty of isolating site-specifically modified rnas away from unmodified transcripts. using the m1g37 and m1a58 methyl modifications of trna as two examples, we demonstrate that non-pairing base modifications protect rnas against ...	2006	16473844
trna properties help shape codon pair preferences in open reading frames.	translation elongation is an accurate and rapid process, dependent upon efficient juxtaposition of trnas in the ribosomal a- and p-sites. here, we sought evidence of a- and p-site trna interaction by examining bias in codon pair choice within open reading frames from a range of genomes. three distinct and marked effects were revealed once codon and dipeptide biases had been subtracted. first, in the majority of genomes, codon pair preference is primarily determined by a tetranucleotide combinati ...	2006	16473853
crystal structures of two putative phosphoheptose isomerases.		2006	16477602
compositional discordance between prokaryotic plasmids and host chromosomes.	most plasmids depend on the host replication machinery and possess partitioning genes. these properties confine plasmids to a limited range of hosts, yielding a close and presumably stable relationship between plasmid and host. hence, it is anticipated that due to amelioration the dinucleotide composition of plasmids is similar to that of the genome of their hosts. however, plasmids are also thought to play a major role in horizontal gene transfer and thus are frequently exchanged between hosts, ...	2006	16480495
effects of streptomycin resistance mutations on posttranslational modification of ribosomal protein s12.	ribosomal protein s12 contains a highly conserved aspartic acid residue that is posttranslationally beta-methylthiolated. using mass spectrometry, we have determined the modification states of several s12 mutants of thermus thermophilus and conclude that beta-methylthiolation is not a determinant of the streptomycin phenotype.	2006	16484214
the molecular architecture of the metalloprotease ftsh.	the atp-dependent integral membrane protease ftsh is universally conserved in bacteria. orthologs exist in chloroplasts and mitochondria, where in humans the loss of a close ftsh-homolog causes a form of spastic paraplegia. ftsh plays a crucial role in quality control by degrading unneeded or damaged membrane proteins, but it also targets soluble signaling factors like sigma(32) and lambda-cii. we report here the crystal structure of a soluble ftsh construct that is functional in caseinolytic an ...	2006	16484367
dependency map of proteins in the small ribosomal subunit.	the assembly of the ribosome has recently become an interesting target for antibiotics in several bacteria. in this work, we extended an analytical procedure to determine native state fluctuations and contact breaking to investigate the protein stability dependence in the 30s small ribosomal subunit of thermus thermophilus. we determined the causal influence of the presence and absence of proteins in the 30s complex on the binding free energies of other proteins. the predicted dependencies are i ...	2006	16485038
recj exonuclease: substrates, products and interaction with ssb.	the recj exonuclease from escherichia coli degrades single-stranded dna (ssdna) in the 5'-3' direction and participates in homologous recombination and mismatch repair. the experiments described here address recj's substrate requirements and reaction products. recj complexes on a variety of 5' single-strand tailed substrates were analyzed by electrophoretic mobility shift in the absence of mg2+ ion required for substrate degradation. recj required single-stranded tails of 7 nt or greater for rob ...	2006	16488881
molecular localization of a ribosome-dependent atpase on escherichia coli ribosomes.	we have previously isolated and described an escherichia coli ribosome-bound atpase, rbba, that is required for protein synthesis in the presence of atp, gtp and the elongation factors, ef-tu and ef-g. the gene encoding rbba, yhih, has been cloned and the deduced protein sequence harbors two atp-motifs and one rna-binding motif and is homologous to the fungal ef-3. here, we describe the isolation and assay of a truncated form of the rbba protein that is stable to overproduction and purification. ...	2006	16495476
identification of hepta- and octo-uridine stretches as sole signals for programmed +1 and -1 ribosomal frameshifting during translation of sars-cov orf 3a variants.	programmed frameshifting is one of the translational recoding mechanisms that read the genetic code in alternative ways. this process is generally programmed by signals at defined locations in a specific mrna. in this study, we report the identification of hepta- and octo-uridine stretches as sole signals for programmed +1 and -1 ribosomal frameshifting during translation of severe acute respiratory syndrome coronavirus (sars-cov) orf 3a variants. sars-cov orf 3a encodes a minor structural prote ...	2006	16500894
regulation through the rna polymerase secondary channel. structural and functional variability of the coiled-coil transcription factors.	gre factors enhance the intrinsic endonucleolytic activity of rna polymerase to rescue arrested transcription complexes and are thought to confer the high fidelity and processivity of rna synthesis. the gre factors insert the extended alpha-helical coiled-coil domains into the rna polymerase secondary channel to position two invariant acidic residues at the coiled-coil tip near the active site to stabilize the catalytic metal ion. gfh1, a grea homolog from thermus thermophilus, inhibits rather t ...	2006	16298991
homology-model-guided site-specific mutagenesis reveals the mechanisms of substrate binding and product-regulation of adenosine kinase from leishmania donovani.	despite designating catalytic roles of asp299 and arg131 during the transfer of gamma-phosphate from atp to ado (adenosine) [r. datta, das, sen, chakraborty, adak, mandal and a. k. datta (2005) biochem. j. 387, 591-600], the mechanisms that determine binding of substrate and cause product inhibition of adenosine kinase from leishmania donovani remained unclear. in the present study, employing homology-model-guided site-specific protein mutagenesis, we show that asp16 is indispensable, since its ...	2006	16271040
catalases are nad(p)h-dependent tellurite reductases.	reactive oxygen species damage intracellular targets and are implicated in cancer, genetic disease, mutagenesis, and aging. catalases are among the key enzymatic defenses against one of the most physiologically abundant reactive oxygen species, hydrogen peroxide. the well-studied, heme-dependent catalases accelerate the rate of the dismutation of peroxide to molecular oxygen and water with near kinetic perfection. many catalases also bind the cofactors nadph and nadh tenaciously, but, surprising ...	2006	17183702
experimental rugged fitness landscape in protein sequence space.	the fitness landscape in sequence space determines the process of biomolecular evolution. to plot the fitness landscape of protein function, we carried out in vitro molecular evolution beginning with a defective fd phage carrying a random polypeptide of 139 amino acids in place of the g3p minor coat protein d2 domain, which is essential for phage infection. after 20 cycles of random substitution at sites 12-130 of the initial random polypeptide and selection for infectivity, the selected phage s ...	2006	17183728
modeling of phosphomethyl pyrimidine kinase from leptospira interrogans serovar lai strain 56601.	many microorganisms, as well as plants and fungi, synthesize thiamin, but vertebrates do not produce it. phosphomethyl pyrimidine kinase is an enzyme involved in an intermediary step of thiamin biosynthesis from purine molecules. this enzyme is absent in humans. thus, it is a potential chemotherapeutic target for antileptospiral treatment. structure of this enzyme from leptospira interrogans serovar lai strain 56601 has not yet been elucidated. we used the structural template of phosphomethyl py ...	2006	17597880
paradigm development: comparative and predictive 3d modeling of hiv-1 virion infectivity factor (vif).	obtaining structural information about vif is of interest for several reasons that include the study of the interaction of vif with apobec3g, a resistance factor. vif is a potential drug target and its function is essential for the hiv-1 infectivity process. to study vif mechanism of action, we need to decipher its structure. pivotal in this approach is the painstaking prediction of its protein structure. the three-dimensional (3d) crystal structure for vif has not been established. in order to ...	2006	17597910
crystal structures of the editing domain of escherichia coli leucyl-trna synthetase and its complexes with met and ile reveal a lock-and-key mechanism for amino acid discrimination.	aarss (aminoacyl-trna synthetases) are responsible for the covalent linking of amino acids to their cognate trnas via the aminoacylation reaction and play a vital role in maintaining the fidelity of protein synthesis. leurs (leucyl-trna synthetase) can link not only the cognate leucine but also the nearly cognate residues ile and met to trna(leu). the editing domain of leurs deacylates the mischarged ile-trna(leu) and met-trna(leu). we report here the crystal structures of ecleurs-ed (the editin ...	2006	16277600
high precision multi-genome scale reannotation of enzyme function by eficaz.	the functional annotation of most genes in newly sequenced genomes is inferred from similarity to previously characterized sequences, an annotation strategy that often leads to erroneous assignments. we have performed a reannotation of 245 genomes using an updated version of eficaz, a highly precise method for enzyme function prediction.	2006	17166279
an inserted gly residue fine tunes dynamics between mesophilic and thermophilic ribonucleases h.	dynamic processes are inherent properties of proteins and are crucial for a wide range of biological functions. to address how changes in protein sequence and structure affect dynamic processes, a quantitative comparison of microsecond-to-microsecond time scale conformational changes, measured by solution nmr spectroscopy, within homologous mesophilic and thermophilic ribonuclease h (rnase h) enzymes is presented. kinetic transitions between the observed major state (high population) and alterna ...	2006	17088323
emergence of the universal genetic code imprinted in an rna record.	the molecular basis of the genetic code manifests itself in the interaction of the aminoacyl-trna synthetases and their cognate trnas. the fundamental biological question regarding these enzymes' role in the evolution of the genetic code remains open. here we probe this question in a system in which the same trna species is aminoacylated by two unrelated synthetases. should this trna possess major identity elements common to both enzymes, this would favor a scenario where the aminoacyl-trna synt ...	2006	17110438
time-dependent translational response of e. coli to excess zn(ii).	zinc homeostasis is not well understood beyond methods of import and export. in order to better understand zinc homeostasis in escherichia coli by identifying zn(ii)-responsive proteins, a proteomic approach was taken. through the use of two-dimensional gel electrophoresis, we were able to show that the levels of ompf, aspc, ycdo, eno, and cyse increased after 30 min of zn(ii) stress, while the levels of tig, tufa, sela, and leuc decreased relative to non-stressed controls. after 4 h of zn(ii) s ...	2006	17122063
biochemical characterisation of lign, an nad+-dependent dna ligase from the halophilic euryarchaeon haloferax volcanii that displays maximal in vitro activity at high salt concentrations.	dna ligases are required for dna strand joining in all forms of cellular life. nad+-dependent dna ligases are found primarily in eubacteria but also in some eukaryotic viruses, bacteriophage and archaea. among the archaeal nad+-dependent dna ligases is the lign enzyme of the halophilic euryarchaeon haloferax volcanii, the gene for which was apparently acquired by hfx. volcanii through lateral gene transfer (lgt) from a halophilic eubacterium. genetic studies show that the lgt-acquired lign enzym ...	2006	17132163
the precursor trna 3'-cca interaction with escherichia coli rnase p rna is essential for catalysis by rnase p in vivo.	the l15 region of escherichia coli rnase p rna forms two watson-crick base pairs with precursor trna 3'-cca termini (g292-c75 and g293-c74). here, we analyzed the phenotypes associated with disruption of the g292-c75 or g293-c74 pair in vivo. mutant rnase p rna alleles (rnpbc292 and rnpbc293) caused severe growth defects in the e. coli rnpb mutant strain dw2 and abolished growth in the newly constructed mutant strain bw, in which chromosomal rnpb expression strictly depended on the presence of a ...	2006	17135488
the structure of pyrococcus horikoshii 2'-5' rna ligase at 1.94 a resolution reveals a possible open form with a wider active-site cleft.	bacterial and archaeal 2'-5' rna ligases, members of the 2h phosphoesterase superfamily, catalyze the linkage of the 5' and 3' exons via a 2'-5'-phosphodiester bond during trna-precursor splicing. the crystal structure of the 2'-5' rna ligase ph0099 from pyrococcus horikoshii ot3 was solved at 1.94 a resolution (pdb code 1vgj). the molecule has a bilobal alpha+beta arrangement with two antiparallel beta-sheets constituting a v-shaped active-site cleft, as found in other members of the 2h phospho ...	2006	17142895
crystallization and preliminary x-ray analysis of a native human trna synthetase whose allelic variants are associated with charcot-marie-tooth disease.	glycyl-trna synthetase (glyrs) is one of a group of enzymes that catalyze the synthesis of aminoacyl-trnas for translation. mutations of human and mouse glyrss are causally associated with charcot-marie-tooth disease, the most common genetic disorder of the peripheral nervous system. as the first step towards a structure-function analysis of this disease, native human glyrs was expressed, purified and crystallized. the crystal belonged to space group p4(3)2(1)2 or its enantiomorphic space group ...	2006	17142907
biochemical and structural characterization of the secreted chorismate mutase (rv1885c) from mycobacterium tuberculosis h37rv: an *aroq enzyme not regulated by the aromatic amino acids.	the gene rv1885c from the genome of mycobacterium tuberculosis h37rv encodes a monofunctional and secreted chorismate mutase (mtcm) with a 33-amino-acid cleavable signal sequence; hence, it belongs to the aroq class of chorismate mutases. consistent with the heterologously expressed mtcm having periplasmic destination in escherichia coli and the absence of a discrete periplasmic compartment in m. tuberculosis, we show here that mtcm secretes into the culture filtrate of m. tuberculosis. *mtc ...	2006	17146044
evolutionary migration of a post-translationally modified active-site residue in the proton-pumping heme-copper oxygen reductases.	in the respiratory chains of aerobic organisms, oxygen reductase members of the heme-copper superfamily couple the reduction of o2 to proton pumping, generating an electrochemical gradient. there are three distinct families of heme-copper oxygen reductases: a, b, and c types. the a- and b-type oxygen reductases have an active-site tyrosine that forms a unique cross-linked histidine-tyrosine cofactor. in the c-type oxygen reductases (also called cbb3 oxidases), an analogous active-site tyrosine h ...	2006	17176062
effect of simulated microgravity on oxidation-sensitive gene expression in pc12 cells.	oxygen utilization by and oxygen dependence of cellular processes may be different in biological systems that are exposed to microgravity (micro-g). a baseline in which cellular changes in oxygen sensitive molecular processes occur during micro-g conditions would be important to pursue this question. the objective of this research is to analyze oxidation-sensitive gene expression in a model cell line [rat pheochromocytoma (pc12)] under simulated micro-g conditions. the pc12 cell line is well cha ...	2006	19081771
p-value based visualization of codon usage data.	two important and not yet solved problems in bacterial genome research are the identification of horizontally transferred genes and the prediction of gene expression levels. both problems can be addressed by multivariate analysis of codon usage data. in particular dimensionality reduction methods for visualization of multivariate data have shown to be effective tools for codon usage analysis. we here propose a multidimensional scaling approach using a novel similarity measure for codon usage tab ...	2006	16808834
phylogenomic analysis of the giy-yig nuclease superfamily.	the giy-yig domain was initially identified in homing endonucleases and later in other selfish mobile genetic elements (including restriction enzymes and non-ltr retrotransposons) and in enzymes involved in dna repair and recombination. however, to date no systematic search for novel members of the giy-yig superfamily or comparative analysis of these enzymes has been reported.	2006	16646971
a database of bacterial lipoproteins (dolop) with functional assignments to predicted lipoproteins.	lipid modification of the n-terminal cys residue (n-acyl-s-diacylglyceryl-cys) has been found to be an essential, ubiquitous, and unique bacterial posttranslational modification. such a modification allows anchoring of even highly hydrophilic proteins to the membrane which carry out a variety of functions important for bacteria, including pathogenesis. hence, being able to identify such proteins is of great value. to this end, we have created a comprehensive database of bacterial lipoproteins, c ...	2006	16585737
how phosphotransferase system-related protein phosphorylation regulates carbohydrate metabolism in bacteria.	the phosphoenolpyruvate(pep):carbohydrate phosphotransferase system (pts) is found only in bacteria, where it catalyzes the transport and phosphorylation of numerous monosaccharides, disaccharides, amino sugars, polyols, and other sugar derivatives. to carry out its catalytic function in sugar transport and phosphorylation, the pts uses pep as an energy source and phosphoryl donor. the phosphoryl group of pep is usually transferred via four distinct proteins (domains) to the transported sugar bo ...	2006	17158705
the tmrdb and srpdb resources.	maintained at the university of texas health science center at tyler, texas, the tmrna database (tmrdb) is accessible at the url http://psyche.uthct.edu/dbs/tmrdb/tmrdb.html with mirror sites located at auburn university, auburn, alabama (http://www.ag.auburn.edu/mirror/tmrdb/) and the royal veterinary and agricultural university, denmark (http://tmrdb.kvl.dk/). the signal recognition particle database (srpdb) at http://psyche.uthct.edu/dbs/srpdb/srpdb.html is mirrored at http://srpdb.kvl.dk/ an ...	2006	16381838
the tmrdb and srpdb resources.	maintained at the university of texas health science center at tyler, texas, the tmrna database (tmrdb) is accessible at the url http://psyche.uthct.edu/dbs/tmrdb/tmrdb.html with mirror sites located at auburn university, auburn, alabama (http://www.ag.auburn.edu/mirror/tmrdb/) and the royal veterinary and agricultural university, denmark (http://tmrdb.kvl.dk/). the signal recognition particle database (srpdb) at http://psyche.uthct.edu/dbs/srpdb/srpdb.html is mirrored at http://srpdb.kvl.dk/ an ...	2006	16381838
protrepeatsdb: a database of amino acid repeats in genomes.	genome wide and cross species comparisons of amino acid repeats is an intriguing problem in biology mainly due to the highly polymorphic nature and diverse functions of amino acid repeats. innate protein repeats constitute vital functional and structural regions in proteins. repeats are of great consequence in evolution of proteins, as evident from analysis of repeats in different organisms. in the post genomic era, availability of protein sequences encoded in different genomes provides a unique ...	2006	16827924
secretion by numbers: protein traffic in prokaryotes.	almost all aspects of protein traffic in bacteria were covered at the asm-fems meeting on the topic in iraklio, crete in may 2006. the studies presented ranged from mechanistic analysis of specific events leading proteins to their final destinations to the physiological roles of the targeted proteins. among the highlights from the meeting that are reviewed here are the molecular dynamics of seca protein, membrane protein insertion, type iii secretion needles and chaperones, type iv secretion, th ...	2006	17020575
the prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains.	ubiquitin (ub)-mediated signaling is one of the hallmarks of all eukaryotes. prokaryotic homologs of ub (this and moad) and e1 ligases have been studied in relation to sulfur incorporation reactions in thiamine and molybdenum/tungsten cofactor biosynthesis. however, there is no evidence for entire protein modification systems with ub-like proteins and deconjugation by deubiquitinating enzymes in prokaryotes. hence, the evolutionary assembly of the eukaryotic ub-signaling apparatus remains unclea ...	2006	16859499
the bacterial cytoskeleton.	in recent years it has been shown that bacteria contain a number of cytoskeletal structures. the bacterial cytoplasmic elements include homologs of the three major types of eukaryotic cytoskeletal proteins (actin, tubulin, and intermediate filament proteins) and a fourth group, the mind-para group, that appears to be unique to bacteria. the cytoskeletal structures play important roles in cell division, cell polarity, cell shape regulation, plasmid partition, and other functions. the proteins sel ...	2006	16959967
catalytic reduction of no to n2o by a designed heme copper center in myoglobin: implications for the role of metal ions.	the effects of metal ions on the reduction of nitric oxide (no) with a designed heme copper center in myoglobin (f43h/l29h sperm whale mb, cubmb) were investigated under reducing anaerobic conditions using uv-vis and epr spectroscopic techniques as well as gc/ms. in the presence of cu(i), catalytic reduction of no to n2o by cubmb was observed with turnover number of 2 mol no.mol cubmb-1.min-1, close to 3 mol no.mol enzyme-1.min-1 reported for the ba3 oxidases from t. thermophilus. formation of a ...	2006	16719438
energy transduction: proton transfer through the respiratory complexes.	a series of metalloprotein complexes embedded in a mitochondrial or bacterial membrane utilize electron transfer reactions to pump protons across the membrane and create an electrochemical potential (deltamuh+). current understanding of the principles of electron-driven proton transfer is discussed, mainly with respect to the wealth of knowledge available from studies of cytochrome c oxidase. structural, experimental, and theoretical evidence supports the model of long-distance proton transfer v ...	2006	16756489
participation of the trna a76 hydroxyl groups throughout translation.	the free 2'-3' cis-diol at the 3'-terminus of trna provides a unique juxtaposition of functional groups that play critical roles during protein synthesis. the translation process involves universally conserved chemistry at almost every stage of this multistep procedure, and the 2'- and 3'-ohs are in the immediate vicinity of chemistry at each step. the cis-diol contribution affects steps ranging from trna aminoacylation to peptide bond formation. the contributions have been studied in assays rel ...	2006	16681365
structural perspective on mutations affecting the function of multisubunit rna polymerases.	high-resolution crystallographic structures of multisubunit rna polymerases (rnaps) have increased our understanding of transcriptional mechanisms. based on a thorough review of the literature, we have compiled the mutations affecting the function of multisubunit rna polymerases, many of which having been generated and studied prior to the publication of the first high-resolution structure, and highlighted the positions of the altered amino acids in the structures of both the prokaryotic and euk ...	2006	16524917
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
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
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
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