Publications

structure of mycobacterium tuberculosis ruva, a protein involved in recombination.	the process of recombinational repair is crucial for maintaining genomic integrity and generating biological diversity. in association with ruvb and ruvc, ruva plays a central role in processing and resolving holliday junctions, which are a critical intermediate in homologous recombination. here, the cloning, purification and structure determination of the ruva protein from mycobacterium tuberculosis (mtruva) are reported. analysis of the structure and comparison with other known ruva proteins r ...	2006	16880543
peptide deformylase is a potential target for anti-helicobacter pylori drugs: reverse docking, enzymatic assay, and x-ray crystallography validation.	colonization of human stomach by the bacterium helicobacter pylori is a major causative factor for gastrointestinal illnesses and gastric cancer. however, the discovery of anti-h. pylori agents is a difficult task due to lack of mature protein targets. therefore, identifying new molecular targets for developing new drugs against h. pylori is obviously necessary. in this study, the in-house potential drug target database (pdtd, http://www.dddc.ac.cn/tarfisdock/) was searched by the reverse dockin ...	2006	16882991
a novel branching enzyme of the gh-57 family in the hyperthermophilic archaeon thermococcus kodakaraensis kod1.	branching enzyme (be) catalyzes formation of the branch points in glycogen and amylopectin by cleavage of the alpha-1,4 linkage and its subsequent transfer to the alpha-1,6 position. we have identified a novel be encoded by an uncharacterized open reading frame (tk1436) of the hyperthermophilic archaeon thermococcus kodakaraensis kod1. tk1436 encodes a conserved protein showing similarity to members of glycoside hydrolase family 57 (gh-57 family). at the c terminus of the tk1436 protein, two cop ...	2006	16885460
the essential gtpase yphc displays a major domain rearrangement associated with nucleotide binding.	the structure of a bacillus subtilis yphc/gdp complex shows that it contains two gtpase domains that pack against a central domain whose fold resembles that of an rna binding kh-domain. comparisons of this structure to that of a homologue in thermotoga maritima reveals a dramatic rearrangement in the position of the n-terminal gtpase domain with a shift of up to 60 a and the formation of a totally different interface to the central domain. this rearrangement appears to be triggered by conformati ...	2006	16894162
investigation of the mechanism of proton translocation by nadh:ubiquinone oxidoreductase (complex i) from bovine heart mitochondria: does the enzyme operate by a q-cycle mechanism?	complex i (nadh:ubiquinone oxidoreductase) is the first enzyme of the membrane-bound electron transport chain in mitochondria. it conserves energy, from the reduction of ubiquinone by nadh, as a protonmotive force across the inner membrane, but the mechanism of energy transduction is not known. the structure of the hydrophilic arm of thermophilic complex i supports the idea that proton translocation is driven at (or close to) the point of quinone reduction, rather than at the point of nadh oxida ...	2006	16895522
analyses of variant human papillomavirus type-16 e5 proteins for their ability to induce mitogenesis of murine fibroblasts.	human papillomavirus type 16 (hpv-16) e5 protein co-operates with epidermal growth factor to stimulate mitogenesis of murine fibroblasts. currently, little is known about which viral amino acids are involved in this process. using sequence variants of hpv-16 e5 we have investigated their effects upon e5 transcription, cell-cycling and cell-growth of murine fibroblasts.	2006	16899131
the structure and function of frataxin.	frataxin, a highly conserved protein found in prokaryotes and eukaryotes, is required for efficient regulation of cellular iron homeostasis. humans with a frataxin deficiency have the cardio- and neurodegenerative disorder friedreich's ataxia, commonly resulting from a gaa trinucleotide repeat expansion in the frataxin gene. while frataxin's specific function remains a point of controversy, the general consensus is that the protein assists in controlling cellular iron homeostasis by directly bin ...	2006	16911956
crystal structure of the moloney murine leukemia virus rnase h domain.	a crystallographic study of the moloney murine leukemia virus (mo-mlv) rnase h domain was performed to provide information about its structure and mechanism of action. these efforts resulted in the crystallization of a mutant mo-mlv rnase h lacking the putative helix c (deltac). the 1.6-angstroms resolution structure resembles the known structures of the human immunodeficiency virus type 1 (hiv-1) and escherichia coli rnase h. the structure revealed the coordination of a magnesium ion within the ...	2006	16912289
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
structural basis for topoisomerase vi inhibition by the anti-hsp90 drug radicicol.	members of the ghl atpase superfamily, including type ii topoisomerases, hsp90-class chaperones, and mutl, all share a common ghkl-type atp-binding fold and act as nucleotide-controlled 'molecular clamps'. these enzymes' atp-binding sites have proven to be rich drug targets, and certain inhibitors of type ii topoisomerases and hsp90 bind to this region and competitively inhibit these enzymes. recently, it was found that radicicol, a drug known to block hsp90 function, also inhibits the archaeal ...	2006	16920739
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
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
diverse bacterial genomes encode an operon of two genes, one of which is an unusual class-i release factor that potentially recognizes atypical mrna signals other than normal stop codons.	while all codons that specify amino acids are universally recognized by trna molecules, codons signaling termination of translation are recognized by proteins known as class-i release factors (rf). in most eukaryotes and archaea a single rf accomplishes termination at all three stop codons. in most bacteria, there are two rfs with overlapping specificity, rf1 recognizes ua(a/g) and rf2 recognizes u(a/g)a.	2006	16970810
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
oligomeric states of the seca and secyeg core components of the bacterial sec translocon.	many proteins synthesized in the cytoplasm ultimately function in non-cytoplasmic locations. in escherichia coli, the general secretory (sec) pathway transports the vast majority of these proteins. two fundamental components of the sec transport pathway are the secyeg heterotrimeric complex that forms the channel through the cytoplasmic membrane, and seca, the atpase that drives the preprotein to and across the membrane. this review focuses on what is known about the oligomeric states of these c ...	2007	17011510
oligomeric states of the seca and secyeg core components of the bacterial sec translocon.	many proteins synthesized in the cytoplasm ultimately function in non-cytoplasmic locations. in escherichia coli, the general secretory (sec) pathway transports the vast majority of these proteins. two fundamental components of the sec transport pathway are the secyeg heterotrimeric complex that forms the channel through the cytoplasmic membrane, and seca, the atpase that drives the preprotein to and across the membrane. this review focuses on what is known about the oligomeric states of these c ...	2007	17011510
the methanothermobacter thermautotrophicus exoiii homologue mth212 is a dna uridine endonuclease.	the genome of methanothermobacter thermautotrophicus, as a hitherto unique case, is apparently devoid of genes coding for general uracil dna glycosylases, the universal mediators of base excision repair following hydrolytic deamination of dna cytosine residues. we have now identified protein mth212, a member of the exoiii family of nucleases, as a possible initiator of dna uracil repair in this organism. this enzyme, in addition to bearing all the enzymological hallmarks of an exoiii homologue, ...	2006	17012282
an evolutionary 'intermediate state' of mitochondrial translation systems found in trichinella species of parasitic nematodes: co-evolution of trna and ef-tu.	ef-tu delivers aminoacyl-trnas to ribosomes in the translation system. however, unusual truncations found in some animal mitochondrial trnas seem to prevent recognition by a canonical ef-tu. we showed previously that the chromadorean nematode has two distinct ef-tus, one of which (ef-tu1) binds only to t-armless aminoacyl-trnas and the other (ef-tu2) binds to d-armless ser-trnas. neither of the ef-tus can bind to canonical cloverleaf trnas. in this study, by analyzing the translation system of e ...	2006	17012285
preparation, crystallization and preliminary x-ray analysis of protein ytlp from bacillus subtilis.	bacillus subtilis ytlp is a protein that is predicted to belong to the bacterial and archael 2'-5' rna-ligase family. it contains 183 residues and two copies of the hxtx sequence motif conserved among proteins belonging to this family. in order to determine the structure of ytlp and to compare it with the paralogue yjcg and identified 2'-5' rna ligases, the gene ytlp was amplified from b. subtilis genomic dna and cloned into expression vector pet-21a. the soluble protein was produced in escheric ...	2006	17012785
cloning, purification and preliminary crystallographic analysis of a putative pyridoxal kinase from bacillus subtilis.	pyridoxal kinases (pdxk) are able to catalyse the phosphorylation of three vitamin b(6) precursors, pyridoxal, pyridoxine and pyridoxamine, to their 5'-phosphates and play an important role in the vitamin b(6) salvage pathway. recently, the thid gene of bacillus subtilis was found to encode an enzyme which has the activity expected of a pyridoxal kinase despite its previous assignment as an hmpp kinase owing to higher sequence similarity. as such, this enzyme would appear to represent a new clas ...	2006	17012797
intrinsic and selected resistance to antibiotics binding the ribosome: analyses of brucella 23s rrn, l4, l22, ef-tu1, ef-tu2, efflux and phylogenetic implications.	brucella spp. are highly similar, having identical 16s rna. however, they have important phenotypic differences such as differential susceptibility to antibiotics binding the ribosome. neither the differential susceptibility nor its basis has been rigorously studied. differences found among other conserved ribosomal loci could further define the relationships among the classical brucella spp.	2006	17014718
a new paradigm: manganese superoxide dismutase influences the production of h2o2 in cells and thereby their biological state.	the principal source of hydrogen peroxide in mitochondria is thought to be from the dismutation of superoxide via the enzyme manganese superoxide dismutase (mnsod). however, the nature of the effect of sod on the cellular production of h(2)o(2) is not widely appreciated. the current paradigm is that the presence of sod results in a lower level of h(2)o(2) because it would prevent the non-enzymatic reactions of superoxide that form h(2)o(2). the goal of this work was to: a) demonstrate that sod c ...	2006	17015180
physiological analysis of the stringent response elicited in an extreme thermophilic bacterium, thermus thermophilus.	guanosine tetraphosphate (ppgpp) is a key mediator of stringent control, an adaptive response of bacteria to amino acid starvation, and has thus been termed a bacterial alarmone. previous x-ray crystallographic analysis has provided a structural basis for the transcriptional regulation of rna polymerase activity by ppgpp in the thermophilic bacterium thermus thermophilus. here we investigated the physiological basis of the stringent response by comparing the changes in intracellular ppgpp levels ...	2006	17015650
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
thermus thermophilus bacteriophage phiys40 genome and proteomic characterization of virions.	we determined the sequence of the 152,372 bp genome of phiys40, a lytic tailed bacteriophage of thermus thermophilus. the genome contains 170 putative open reading frames and three trna genes. functions for 25% of phiys40 gene products were predicted on the basis of similarity to proteins of known function from diverse phages and bacteria. phiys40 encodes a cluster of proteins involved in nucleotide salvage, such as flavin-dependent thymidylate synthase, thymidylate kinase, ribonucleotide reduct ...	2006	17027029
atomic force microscopy reveals dna bending during group ii intron ribonucleoprotein particle integration into double-stranded dna.	the mobile lactococcus lactis ll.ltrb group ii intron integrates into dna target sites by a mechanism in which the intron rna reverse splices into one dna strand while the intron-encoded protein uses a c-terminal dna endonuclease domain to cleave the opposite strand and then uses the cleaved 3' end to prime reverse transcription of the inserted intron rna. these reactions are mediated by an rnp particle that contains the intron-encoded protein and the excised intron lariat rna, with both the pro ...	2006	17029398
the key dna-binding residues in the c-terminal domain of mycobacterium tuberculosis dna gyrase a subunit (gyra).	as only the type ii topoisomerase is capable of introducing negative supercoiling, dna gyrase is involved in crucial cellular processes. although the other domains of dna gyrase are better understood, the mechanism of dna binding by the c-terminal domain of the dna gyrase a subunit (gyra-ctd) is less clear. here, we investigated the dna-binding sites in the gyra-ctd of mycobacterium tuberculosis gyrase through site-directed mutagenesis. the results show that y577, r691 and r745 are among the key ...	2006	17038336
structural basis for mrna and trna positioning on the ribosome.	protein synthesis requires the accurate positioning of mrna and trna in the peptidyl-trna site of the ribosome. here we describe x-ray crystal structures of the intact bacterial ribosome from escherichia coli in a complex with mrna and the anticodon stem-loop of p-site trna. at 3.5-a resolution, these structures reveal rearrangements in the intact ribosome that clamp p-site trna and mrna on the small ribosomal subunit. binding of the anticodon stem-loop of p-site trna to the ribosome is sufficie ...	2006	17038497
expression of the pyr operon of lactobacillus plantarum is regulated by inorganic carbon availability through a second regulator, pyrr2, homologous to the pyrimidine-dependent regulator pyrr1.	inorganic carbon (ic), such as bicarbonate or carbon dioxide, stimulates the growth of lactobacillus plantarum. at low ic levels, one-third of natural isolated l. plantarum strains are nutritionally dependent on exogenous arginine and pyrimidine, a phenotype previously defined as high-co2-requiring (hcr) prototrophy. ic enrichment significantly decreased the amounts of the enzymes in the pyrimidine biosynthetic pathway encoded by the pyrr1bcaa1ab1dfe operon, as demonstrated by proteomic analysis ...	2006	17041052
crystal structure of laao from calloselasma rhodostoma with an l-phenylalanine substrate: insights into structure and mechanism.	l-amino acid oxidase is a dimeric glycosylated flavoenzyme, a major constituent of the venom-from the snake calloselasma rhodostoma. the enzyme exhibits apoptosis inducing effects as well as antibacterial and anti-hiv activities. the structure of l-amino acid oxidase with its substrate (l-phenylalanine) has been refined to a resolution of 1.8 a. the complex structure reveals the substrate bound to the reduced flavin (fadred). alternative conformations for the key residues his223 and arg322 are e ...	2006	17046020
structure of electron transfer flavoprotein-ubiquinone oxidoreductase and electron transfer to the mitochondrial ubiquinone pool.	electron transfer flavoprotein-ubiquinone oxidoreductase (etf-qo) is a 4fe4s flavoprotein located in the inner mitochondrial membrane. it catalyzes ubiquinone (uq) reduction by etf, linking oxidation of fatty acids and some amino acids to the mitochondrial respiratory chain. deficiencies in etf or etf-qo result in multiple acyl-coa dehydrogenase deficiency, a human metabolic disease. crystal structures of etf-qo with and without bound uq were determined, and they are essentially identical. the m ...	2006	17050691
a novel single amino acid change in small subunit ribosomal protein s5 has profound effects on translational fidelity.	s5 is a small subunit ribosomal protein (r-protein) linked to the functional center of the 30s ribosomal subunit. in this study we have identified a unique amino acid mutation in escherichia coli s5 that produces spectinomycin-resistance and cold sensitivity. this mutation significantly alters cell growth, folding of 16s ribosomal rna, and translational fidelity. while translation initiation is not affected, both +1 and -1 frameshifting and nonsense suppression are greatly enhanced in the mutant ...	2006	17053085
bioinformatic, genetic, and biochemical evidence that some glycoside hydrolase family 42 beta-galactosidases are arabinogalactan type i oligomer hydrolases.	glycoside hydrolases are organized into glycoside hydrolase families (ghfs) and within this larger group, the beta-galactosidases are members of four families: 1, 2, 35, and 42. most genes encoding ghf 42 enzymes are from prokaryotes unlikely to encounter lactose, suggesting a different substrate for these enzymes. in search of this substrate, we analyzed genes neighboring ghf 42 genes in databases and detected an arrangement implying that these enzymes might hydrolyze oligosaccharides released ...	2006	17056685
coordinate expression of the acetyl coenzyme a carboxylase genes, accb and accc, is necessary for normal regulation of biotin synthesis in escherichia coli.	transcription of the biotin (bio) biosynthetic operon of escherichia coli is negatively regulated by the bira protein, an atypical repressor protein in that it is also an enzyme. the bira-catalyzed reaction involves the covalent attachment of biotin to accb, a subunit of acetyl coenzyme (acetyl-coa) carboxylase. the two functions of bira allow regulation of the bio operon to respond to the intracellular concentrations of both biotin and unbiotinylated accb. we report here that bio operon express ...	2007	17056747
coordinate expression of the acetyl coenzyme a carboxylase genes, accb and accc, is necessary for normal regulation of biotin synthesis in escherichia coli.	transcription of the biotin (bio) biosynthetic operon of escherichia coli is negatively regulated by the bira protein, an atypical repressor protein in that it is also an enzyme. the bira-catalyzed reaction involves the covalent attachment of biotin to accb, a subunit of acetyl coenzyme (acetyl-coa) carboxylase. the two functions of bira allow regulation of the bio operon to respond to the intracellular concentrations of both biotin and unbiotinylated accb. we report here that bio operon express ...	2007	17056747
identification of a histidine-tyrosine cross-link in the active site of the cbb3-type cytochrome c oxidase from rhodobacter sphaeroides.	the heme-copper oxidases constitute a superfamily of terminal dioxygen-reducing enzymes located in the inner mitochondrial or in the bacterial cell membrane. the presence of a mechanistically important covalent bond between a histidine ligand of the copper ion (cu(b)) in the active site and a generally conserved tyrosine residue nearby has been shown to exist in the canonical cytochrome c oxidases. however, according to sequence alignment studies, this critical tyrosine is missing from the subfa ...	2006	17060620
structural and biochemical characterization of human orphan dhrs10 reveals a novel cytosolic enzyme with steroid dehydrogenase activity.	to this day, a significant proportion of the human genome remains devoid of functional characterization. in this study, we present evidence that the previously functionally uncharacterized product of the human dhrs10 gene is endowed with 17beta-hsd (17beta-hydroxysteroid dehydrogenase) activity. 17beta-hsd enzymes are primarily involved in the metabolism of steroids at the c-17 position and also of other substrates such as fatty acids, prostaglandins and xenobiotics. in vitro, dhrs10 converts na ...	2007	17067289
characteristics of the nuclear (18s, 5.8s, 28s and 5s) and mitochondrial (12s and 16s) rrna genes of apis mellifera (insecta: hymenoptera): structure, organization, and retrotransposable elements.	as an accompanying manuscript to the release of the honey bee genome, we report the entire sequence of the nuclear (18s, 5.8s, 28s and 5s) and mitochondrial (12s and 16s) ribosomal rna (rrna)-encoding gene sequences (rdna) and related internally and externally transcribed spacer regions of apis mellifera (insecta: hymenoptera: apocrita). additionally, we predict secondary structures for the mature rrna molecules based on comparative sequence analyses with other arthropod taxa and reference to re ...	2006	17069639
biosynthesis of phosphoserine in the methanococcales.	methanococcus maripaludis and methanocaldococcus jannaschii produce cysteine for protein synthesis using a trna-dependent pathway. these methanogens charge trna(cys) with l-phosphoserine, which is also an intermediate in the predicted pathways for serine and cystathionine biosynthesis. to establish the mode of phosphoserine production in methanococcales, cell extracts of m. maripaludis were shown to have phosphoglycerate dehydrogenase and phosphoserine aminotransferase activities. the heterologo ...	2007	17071763
biosynthesis of phosphoserine in the methanococcales.	methanococcus maripaludis and methanocaldococcus jannaschii produce cysteine for protein synthesis using a trna-dependent pathway. these methanogens charge trna(cys) with l-phosphoserine, which is also an intermediate in the predicted pathways for serine and cystathionine biosynthesis. to establish the mode of phosphoserine production in methanococcales, cell extracts of m. maripaludis were shown to have phosphoglycerate dehydrogenase and phosphoserine aminotransferase activities. the heterologo ...	2007	17071763
crystallization, preliminary crystallographic analysis and phasing of the thiosulfate-binding protein soxy from chlorobium limicola f. thiosulfatophilum.	the 22 kda soxyz protein complex from the green sulfur bacterium chlorobium limicola f. thiosulfatophilum is a central player in the sulfur-oxidizing (sox) enzyme system of the organism by activating thiosulfate for oxidation by soxxa and soxb. it has been proposed that soxyz exists as a heterodimer or heterotetramer, but the properties and role of the individual components of the complex thus far remain unknown. here, the heterologous expression, purification, and the crystallization of stable ...	2006	17077486
overexpression, crystallization and preliminary x-ray crystallographic analysis of phosphopantetheine adenylyltransferase from enterococcus faecalis.	phosphopantetheine adenylyltransferase, an essential enzyme in the coenzyme a biosynthetic pathway, catalyzes the reversible transfer of an adenylyl group from atp to 4'-phosphopantetheine, yielding 3'-dephospho-coa and pyrophosphate. enterococcus faecalis ppat has been overexpressed in escherichia coli as a fusion with a c-terminal purification tag and crystallized at 297 k using a reservoir solution consisting of 0.1 m sodium hepes ph 7.5, 0.8 m sodium dihydrogen phosphate and 0.8 m potassium ...	2006	17077496
carotenoid biosynthesis in the primitive red alga cyanidioschyzon merolae.	cyanidioschyzon merolae is considered to be one of the most primitive of eukaryotic photosynthetic organisms. to obtain insights into the origin and evolution of the pathway of carotenoid biosynthesis in eukaryotic plants, the carotenoid content of c. merolae was ascertained, genes encoding enzymes of carotenoid biosynthesis in this unicellular red alga were identified, and the activities of two candidate pathway enzymes of particular interest, lycopene cyclase and beta-carotene hydroxylase, wer ...	2007	17085635
carotenoid biosynthesis in the primitive red alga cyanidioschyzon merolae.	cyanidioschyzon merolae is considered to be one of the most primitive of eukaryotic photosynthetic organisms. to obtain insights into the origin and evolution of the pathway of carotenoid biosynthesis in eukaryotic plants, the carotenoid content of c. merolae was ascertained, genes encoding enzymes of carotenoid biosynthesis in this unicellular red alga were identified, and the activities of two candidate pathway enzymes of particular interest, lycopene cyclase and beta-carotene hydroxylase, wer ...	2007	17085635
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
mechanism of template-independent nucleotide incorporation catalyzed by a template-dependent dna polymerase.	numerous template-dependent dna polymerases are capable of catalyzing template-independent nucleotide additions onto blunt-end dna. such non-canonical activity has been hypothesized to increase the genomic hypermutability of retroviruses including human immunodeficiency viruses. here, we employed pre-steady state kinetics and x-ray crystallography to establish a mechanism for blunt-end additions catalyzed by sulfolobus solfataricus dpo4. our kinetic studies indicated that the first blunt-end dat ...	2007	17095011
mechanism of template-independent nucleotide incorporation catalyzed by a template-dependent dna polymerase.	numerous template-dependent dna polymerases are capable of catalyzing template-independent nucleotide additions onto blunt-end dna. such non-canonical activity has been hypothesized to increase the genomic hypermutability of retroviruses including human immunodeficiency viruses. here, we employed pre-steady state kinetics and x-ray crystallography to establish a mechanism for blunt-end additions catalyzed by sulfolobus solfataricus dpo4. our kinetic studies indicated that the first blunt-end dat ...	2007	17095011
mutagenesis of rat acyl-coa synthetase 4 indicates amino acids that contribute to fatty acid binding.	although each of the five mammalian long-chain acyl-coa synthetases (acsl) can bind saturated and unsaturated fatty acids ranging from 12 to 22 carbons, acsl4 prefers longer chain polyunsaturated fatty acids. in order to gain a better understanding of acsl4 fatty acid binding, we based a mutagenesis approach on sequence alignments related to ttlc-facs crystallized from thermus thermophilus hb8. four residues selected for mutagenesis corresponded to residues in ttlc-facs that comprise the fatty a ...	2007	17110164
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
a thin-layer electrophoretic assay for asp-trnaasn/glu-trnagln amidotransferase.		2007	17113030
a thin-layer electrophoretic assay for asp-trnaasn/glu-trnagln amidotransferase.		2007	17113030
interpretation of electron density with stereographic roadmap projections.	the program rivem (radial interpretation of viral electron density maps) was developed to project density radially onto a sphere that is then presented as a stereographic diagram. this permits features resulting from an asymmetric reconstruction to be projected and positioned onto an icosahedral virus surface. the features that constitute the viral surface can also be simultaneously represented in terms of atoms, amino acid residues, potential charge distribution, and surface topology. the proce ...	2007	17116403
interpretation of electron density with stereographic roadmap projections.	the program rivem (radial interpretation of viral electron density maps) was developed to project density radially onto a sphere that is then presented as a stereographic diagram. this permits features resulting from an asymmetric reconstruction to be projected and positioned onto an icosahedral virus surface. the features that constitute the viral surface can also be simultaneously represented in terms of atoms, amino acid residues, potential charge distribution, and surface topology. the proce ...	2007	17116403
a structural model reveals energy transduction in dynein.	intracellular active transport is driven by atp-hydrolyzing motor proteins that move along cytoskeletal filaments. in particular, the microtubule-associated dynein motor is involved in the transport of organelles and vesicles, the maintenance of the golgi, and mitosis. however, unlike kinesin and myosin, the mechanism by which dynein converts chemical energy into mechanical force remains largely a mystery, due primarily to the lack of a high-resolution molecular structure. using homology modelin ...	2006	17121997
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
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 role of specific 2'-hydroxyl groups in the stabilization of the folded conformation of kink-turn rna.	the role of 2'-hydroxyl groups in stabilizing the tightly kinked geometry of the kink-turn (k-turn) has been investigated. individual 2'-oh groups have been removed by chemical synthesis, and the kinking of the rna has been studied by gel electrophoresis and fluorescence resonance energy transfer. the results have been analyzed by reference to a database of 11 different crystallographic structures of k-turns. the potential hydrogen bonds fall into several classes. the most important are those in ...	2007	17158708
infantile encephalopathy and defective mitochondrial dna translation in patients with mutations of mitochondrial elongation factors efg1 and eftu.	mitochondrial protein translation is a complex process performed within mitochondria by an apparatus composed of mitochondrial dna (mtdna)-encoded rnas and nuclear dna-encoded proteins. although the latter by far outnumber the former, the vast majority of mitochondrial translation defects in humans have been associated with mutations in rna-encoding mtdna genes, whereas mutations in protein-encoding nuclear genes have been identified in a handful of cases. genetic investigation involving patient ...	2007	17160893
infantile encephalopathy and defective mitochondrial dna translation in patients with mutations of mitochondrial elongation factors efg1 and eftu.	mitochondrial protein translation is a complex process performed within mitochondria by an apparatus composed of mitochondrial dna (mtdna)-encoded rnas and nuclear dna-encoded proteins. although the latter by far outnumber the former, the vast majority of mitochondrial translation defects in humans have been associated with mutations in rna-encoding mtdna genes, whereas mutations in protein-encoding nuclear genes have been identified in a handful of cases. genetic investigation involving patient ...	2007	17160893
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
loss of a universal trna feature.	trna(his) has thus far always been found with one of the most distinctive of trna features, an extra 5' nucleotide that is usually a guanylate. trna(his) genes in a disjoint alphaproteobacterial group comprising the rhizobiales, rhodobacterales, caulobacterales, parvularculales, and pelagibacter generally fail to encode this extra guanylate, unlike those of other alphaproteobacteria and bacteria in general. rather than adding an extra 5' guanylate posttranscriptionally as eukaryotes do, evidence ...	2007	17172343
loss of a universal trna feature.	trna(his) has thus far always been found with one of the most distinctive of trna features, an extra 5' nucleotide that is usually a guanylate. trna(his) genes in a disjoint alphaproteobacterial group comprising the rhizobiales, rhodobacterales, caulobacterales, parvularculales, and pelagibacter generally fail to encode this extra guanylate, unlike those of other alphaproteobacteria and bacteria in general. rather than adding an extra 5' guanylate posttranscriptionally as eukaryotes do, evidence ...	2007	17172343
x-ray crystal structure of mycobacterium tuberculosis beta-ketoacyl acyl carrier protein synthase ii (mtkasb).	mycolic acids are long chain alpha-alkyl branched, beta-hydroxy fatty acids that represent a characteristic component of the mycobacterium tuberculosis cell wall. through their covalent attachment to peptidoglycan via an arabinogalactan polysaccharide, they provide the basis for an essential outer envelope membrane. mycobacteria possess two fatty acid synthases (fas); fas-i carries out de novo synthesis of fatty acids while fas-ii is considered to elongate medium chain length fatty acyl primers ...	2007	17174327
x-ray crystal structure of mycobacterium tuberculosis beta-ketoacyl acyl carrier protein synthase ii (mtkasb).	mycolic acids are long chain alpha-alkyl branched, beta-hydroxy fatty acids that represent a characteristic component of the mycobacterium tuberculosis cell wall. through their covalent attachment to peptidoglycan via an arabinogalactan polysaccharide, they provide the basis for an essential outer envelope membrane. mycobacteria possess two fatty acid synthases (fas); fas-i carries out de novo synthesis of fatty acids while fas-ii is considered to elongate medium chain length fatty acyl primers ...	2007	17174327
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
scaffolding as an organizing principle in trans-translation. the roles of small protein b and ribosomal protein s1.	a eubacterial ribosome stalled on a defective mrna can be released through a quality control mechanism referred to as trans-translation, which depends on the coordinating binding actions of transfer-messenger rna, small protein b, and ribosome protein s1. by means of cryo-electron microscopy, we obtained a map of the complex composed of a stalled ribosome and small protein b, which appears near the decoding center. this result suggests that, when lacking a codon, the a-site on the small subunit ...	2007	17179154