Publications

deep phylogeny--how a tree can help characterize early life on earth.	the darwinian concept of biological evolution assumes that life on earth shares a common ancestor. the diversification of this common ancestor through speciation events and vertical transmission of genetic material implies that the classification of life can be illustrated in a tree-like manner, commonly referred to as the tree of life. this article describes features of the tree of life, such as how the tree has been both pruned and become bushier throughout the past century as our knowledge of ...	2010	20182607
structural and biochemical bases for the redox sensitivity of mycobacterium tuberculosis rsla.	an effective transcriptional response to redox stimuli is of particular importance for mycobacterium tuberculosis, as it adapts to the environment of host alveoli and macrophages. the m. tuberculosis sigma factor sigma(l) regulates the expression of genes involved in cell-wall and polyketide syntheses. sigma(l) interacts with the cytosolic anti-sigma domain of a membrane-associated protein, rsla. here we demonstrate that rsla binds zn(2+) and can sequester sigma(l) in a reducing environment. in ...	2010	20184899
a functional peptidyl-trna hydrolase, ict1, has been recruited into the human mitochondrial ribosome.	bioinformatic analysis classifies the human protein encoded by immature colon carcinoma transcript-1 (ict1) as one of a family of four putative mitochondrial translation release factors. however, this has not been supported by any experimental evidence. as only a single member of this family, mtrf1a, is required to terminate the synthesis of all 13 mitochondrially encoded polypeptides, the true physiological function of ict1 was unclear. here, we report that ict1 is an essential mitochondrial pr ...	2010	20186120
bacterial lifestyle in a deep-sea hydrothermal vent chimney revealed by the genome sequence of the thermophilic bacterium deferribacter desulfuricans ssm1.	the complete genome sequence of the thermophilic sulphur-reducing bacterium, deferribacter desulfuricans smm1, isolated from a hydrothermal vent chimney has been determined. the genome comprises a single circular chromosome of 2,234,389 bp and a megaplasmid of 308,544 bp. many genes encoded in the genome are most similar to the genes of sulphur- or sulphate-reducing bacterial species within deltaproteobacteria. the reconstructed central metabolisms showed a heterotrophic lifestyle primarily driv ...	2010	20189949
partial steps of charge translocation in the nonpumping n139l mutant of rhodobacter sphaeroides cytochrome c oxidase with a blocked d-channel.	the n139l substitution in the d-channel of cytochrome oxidase from rhodobacter sphaeroides results in an approximately 15-fold decrease in the turnover number and a loss of proton pumping. time-resolved absorption and electrometric assays of the f --> o transition in the n139l mutant oxidase result in three major findings. (1) oxidation of the reduced enzyme by o(2) shows approximately 200-fold inhibition of the f --> o step (k approximately 2 s(-1) at ph 8) which is not compatible with enzyme t ...	2010	20192226
evolution and multifarious horizontal transfer of an alternative biosynthetic pathway for the alternative polyamine sym-homospermidine.	polyamines are small flexible organic polycations found in almost all cells. they likely existed in the last universal common ancestor of all extant life, and yet relatively little is understood about their biological function, especially in bacteria and archaea. unlike eukaryotes, where the predominant polyamine is spermidine, bacteria may contain instead an alternative polyamine, sym-homospermidine. we demonstrate that homospermidine synthase (hss) has evolved vertically, primarily in the alph ...	2010	20194510
the crystal structure of unmodified trnaphe from escherichia coli.	post-transcriptional nucleoside modifications fine-tune the biophysical and biochemical properties of transfer rna (trna) so that it is optimized for participation in cellular processes. here we report the crystal structure of unmodified trna(phe) from escherichia coli at a resolution of 3 a. we show that in the absence of modifications the overall fold of the trna is essentially the same as that of mature trna. however, there are a number of significant structural differences, such as rearrange ...	2010	20203084
the structure of dinb from geobacillus stearothermophilus: a representative of a unique four-helix-bundle superfamily.	the crystal structure of the dinb gene product from geobacillus stearothermophilus (gsdinb) is reported at 2.5 a resolution. the dinb gene is one of the dna-damage-induced genes and the corresponding protein, dinb, is the founding member of a pfam family with no known function. the protein contains a four-helix up-down-down-up bundle that has previously been described in the literature in three disparate proteins: the enzyme mdmpi (mycothiol-dependent maleylpyruvate isomerase), yfit and ttha0303 ...	2010	20208147
crystallization and preliminary x-ray studies of ferredoxin-nadp+ oxidoreductase encoded by bacillus subtilis yumc.	ferredoxin-nadp(+) oxidoreductase encoded by bacillus subtilis yumc has been purified and successfully crystallized in complex with nadp(+) in two forms. diffraction data from crystals of these two forms were collected at resolutions of 1.8 and 1.9 a. the former belonged to space group p2(1)2(1)2, with unit-cell parameters a = 63.90, b = 135.72, c = 39.19 a, and the latter to space group c2, with unit-cell parameters a = 207.47, b = 64.85, c = 61.12 a, beta = 105.82 degrees. the initial structur ...	2010	20208166
crystallization and preliminary x-ray crystallographic study of phosphoglucose isomerase from plasmodium falciparum.	phosphoglucose isomerase (pgi) is a key enzyme in glycolysis and glycogenesis that catalyses the interconversion of glucose 6-phosphate (g6p) and fructose 6-phosphate (f6p). for crystallographic studies, pgi from the human malaria parasite plasmodium falciparum (pfpgi) was overproduced in escherichia coli, purified and crystallized using the hanging-drop vapour-diffusion method. x-ray diffraction data to 1.5 a resolution were collected from an orthorhombic crystal form belonging to space group p ...	2010	20208175
isolation and purification of thermus thermophilus hpab by a crystallization approach.	the oxygenase hpab is a component of the 4-hydroxyphenylacetate 3-monooxygenase enzyme that is responsible for the hydroxylation of 4-hydroxyphenylacetate. it utilizes molecular oxygen and a reduced flavin, which is provided by hpac, the second component of the enzyme. while isolating integral membrane respiratory complexes from thermus thermophilus, microcrystals of hpab were formed. further purification of the enzyme was achieved by repetitive crystallization. subsequently, well shaped single ...	2010	20208179
structural basis of o6-alkylguanine recognition by a bacterial alkyltransferase-like dna repair protein.	alkyltransferase-like proteins (atls) are a novel class of dna repair proteins related to o(6)-alkylguanine-dna alkyltransferases (agts) that tightly bind alkylated dna and shunt the damaged dna into the nucleotide excision repair pathway. here, we present the first structure of a bacterial atl, from vibrio parahaemolyticus (vpatl). we demonstrate that vpatl adopts an agt-like fold and that the protein is capable of tightly binding to o(6)-methylguanine-containing dna and disrupting its repair b ...	2010	20212037
dynamic effects of cofactors and dna on the oligomeric state of human mitochondrial dna helicase.	we examined the effects of cofactors and dna on the stability, oligomeric state and conformation of the human mitochondrial dna helicase. we demonstrate that low salt conditions result in protein aggregation that may cause dissociation of oligomeric structure. the low salt sensitivity of the mitochondrial dna helicase is mitigated by the presence of magnesium, nucleotide, and increased temperature. electron microscopic and glutaraldehyde cross-linking analyses provide the first evidence of a hep ...	2010	20212038
potassium-activated gtpase reaction in the g protein-coupled ferrous iron transporter b.	feob is a prokaryotic membrane protein responsible for the import of ferrous iron (fe(2+)). a defining feature of feob is that it includes an n-terminal 30-kda soluble domain with gtpase activity, which is required for iron transport. however, the low intrinsic gtp hydrolysis rate of this domain appears to be too slow for feob either to function as a channel or to possess an active fe(2+) membrane transport mechanism. here, we present crystal structures of the soluble domain of feob from strepto ...	2010	20220129
dewetting transitions in protein cavities.	in a previous analysis of the solvation of protein active sites, a drying transition was observed in the narrow hydrophobic binding cavity of cox-2. with the use of a crude metric that often seems able to discriminate those protein cavities that dry from those that do not, we made an extensive search of the pdb, and identified five other proteins that, in molecular dynamics simulations, undergo drying transitions in their active sites. because such cavities need not desolvate before binding hydr ...	2010	20225258
how to slice: snapshots of argonaute in action.	abstract: argonaute is the principal protein component of the mechanisms of rna silencing, providing anchor sites for the small guide rna strand and the 'slicer' activity for cleavage of target mrnas or short passenger rna strands. argonaute is the core constituent of the silencing effector complexes risc (rna-induced silencing complex) and the rits complex (rna-induced initiation of transcriptional gene silencing complex), interacting directly or indirectly with dicer proteins, r2d2/loquacious/ ...	2010	20226069
sesaw: balancing sequence and structural information in protein functional mapping.	motivation: functional similarity between proteins is evident at both the sequence and structure levels. sesaw is a web-based program for identifying functionally or evolutionarily conserved motifs in protein structures by locating sequence and structural similarities, and quantifying these at the level of individual residues. results can be visualized in 2d, as annotated alignments, or in 3d, as structural superpositions. an example is given for both an experimentally determined query structure ...	2010	20299324
crystal structure and functional insight of hp0420-homolog from helicobacter felis.	helicobacter pylori infect more than half of the world's population and are considered a cause of peptic ulcer disease and gastric cancer. recently, hypothetical gene hp0421 was identified in h. pylori as a cholesterol alpha-glucosyltransferase, which is required to synthesize cholesteryl glucosides, essential cell wall components of the bacteria. in the same gene-cluster, hp0420 was co-identified, whose function remains unknown. here we report the crystal structure of hp0420-homolog of h. felis ...	2010	20302842
blocking the k-pathway still allows rapid one-electron reduction of the binuclear center during the anaerobic reduction of the aa3-type cytochrome c oxidase from rhodobacter sphaeroides.	the k-pathway is one of the two proton-input channels required for function of cytochrome c oxidase. in the rhodobacter sphaeroides cytochrome c oxidase, the k-channel starts at glu101 in subunit ii, which is at the surface of the protein exposed to the cytoplasm, and runs to tyr288 at the heme a3/cub active site. mutations of conserved, polar residues within the k-channel block or inhibit steady state oxidase activity. a large body of research has demonstrated that the k-channel is required to ...	2010	20307488
disparate pathways for the biogenesis of cytochrome oxidases in bradyrhizobium japonicum.	this work addresses the biogenesis of heme-copper terminal oxidases in bradyrhizobium japonicum, the nitrogen-fixing root nodule symbiont of soybean. b. japonicum has four quinol oxidases and four cytochrome oxidases. the latter include the aa(3)- and cbb(3)-type oxidases. although both have a cu(b) center in subunit i, the subunit ii proteins differ in having either a cu(a) center (in aa(3)) or a covalently bound heme c (in cbb(3)). two biogenesis factors were genetically studied here, the peri ...	2010	20335176
conserved properties of polypeptide transport-associated (potra) domains derived from cyanobacterial omp85.	proteins of the omp85 family are conserved in all kingdoms of life. they mediate protein transport across or protein insertion into membranes and reside in the outer membranes of gram-negative bacteria, mitochondria, and chloroplasts. omp85 proteins contain a c-terminal transmembrane beta-barrel and a soluble n terminus with a varying number of polypeptide-transport-associated or potra domains. here we investigate omp85 from the cyanobacterium anabaena sp. pcc 7120. the crystallographic three-di ...	2010	20348103
a low affinity ground state conformation for the dynein microtubule binding domain.	dynein interacts with microtubules through a dedicated binding domain that is dynamically controlled to achieve high or low affinity, depending on the state of nucleotide bound in a distant catalytic pocket. the active sites for microtubule binding and atp hydrolysis communicate via conformational changes transduced through a approximately 10-nm length antiparallel coiled-coil stalk, which connects the binding domain to the roughly 300-kda motor core. recently, an x-ray structure of the murine c ...	2010	20351100
identification of a tsetse fly salivary protein with dual inhibitory action on human platelet aggregation.	tsetse flies (glossina sp.), the african trypanosome vectors, rely on anti-hemostatic compounds for efficient blood feeding. despite their medical importance, very few salivary proteins have been characterized and functionally annotated.	2010	20351782
structural analysis of thermus thermophilus hb27 mannosyl-3-phosphoglycerate synthase provides evidence for a second catalytic metal ion and new insight into the retaining mechanism of glycosyltransferases.	mannosyl-3-phosphoglycerate synthase is a glycosyltransferase involved in the two-step synthetic pathway of mannosylglycerate, a compatible solute that accumulates in response to salt and/or heat stresses in many microorganisms thriving in hot environments. the three-dimensional structure of mannosyl-3-phosphoglycerate synthase from thermus thermophilus hb27 in its binary complex form, with gdp-alpha-d-mannose and mg(2+), shows a second metal binding site, about 6 a away from the mannose moiety. ...	2010	20356840
oligomeric interfaces under the lens: gemini.	the assembly of subunits in protein oligomers is an important topic to study as a vast number of proteins exists as stable or transient oligomer and because it is a mechanism used by some protein oligomers for killing cells (e.g., perforin from the human immune system, pore-forming toxins from bacteria, phage, amoeba, protein misfolding diseases, etc.). only a few of the amino acids that constitute a protein oligomer seem to regulate the capacity of the protein to assemble (to form interfaces), ...	2010	20360856
evaluation of lysine biosynthesis as an antifungal drug target: biochemical characterization of aspergillus fumigatus homocitrate synthase and virulence studies.	aspergillus fumigatus is the main cause of severe invasive aspergillosis. to combat this life-threatening infection, only limited numbers of antifungals are available. the fungal alpha-aminoadipate pathway, which is essential for lysine biosynthesis, has been suggested as a potential antifungal drug target. here we reanalyzed the role of this pathway for establishment of invasive aspergillosis in murine models. we selected the first pathway-specific enzyme, homocitrate synthase (hcsa), for bioch ...	2010	20363898
structural and functional characterization of an rnase hi domain from the bifunctional protein rv2228c from mycobacterium tuberculosis.	the open reading frame rv2228c from mycobacterium tuberculosis is predicted to encode a protein composed of two domains, each with individual functions, annotated through sequence similarity searches. the n-terminal domain is homologous with prokaryotic and eukaryotic rnase h domains and the c-terminal domain with alpha-ribazole phosphatase (cobc). the n-terminal domain of rv2228c (rv2228c/n) and the full-length protein were expressed as fusions with maltose binding protein (mbp). rv2228c/n was ...	2010	20363939
x-ray structure determination of the glycine cleavage system protein h of mycobacterium tuberculosis using an inverse compton synchrotron x-ray source.	structural genomics discovery projects require ready access to both x-ray diffraction and nmr spectroscopy which support the collection of experimental data needed to solve large numbers of novel protein structures. the most productive x-ray crystal structure determination laboratories make extensive use of tunable synchrotron x-ray light to solve novel structures by anomalous diffraction methods. this requires that frozen cryo-protected crystals be shipped to large multi acre synchrotron facili ...	2010	20364333
cdnl, a member of the large card-like family of bacterial proteins, is vital for myxococcus xanthus and differs functionally from the global transcriptional regulator card.	card, a global transcriptional regulator in myxococcus xanthus, interacts with carg via cardnter, its n-terminal domain, and with dna via a eukaryotic hmga-type c-terminal domain. genomic analysis reveals a large number of standalone proteins resembling cardnter. these constitute, together with the rna polymerase (rnap) interacting domain, rid, of transcription-repair coupling factors, the card_trcf protein family. we show that one such cardnter-like protein, m. xanthus cdnl, cannot functionally ...	2010	20371514
redox sensing by a rex-family repressor is involved in the regulation of anaerobic gene expression in staphylococcus aureus.	an alignment of upstream regions of anaerobically induced genes in staphylococcus aureus revealed the presence of an inverted repeat, corresponding to rex binding sites in streptomyces coelicolor. gel shift experiments of selected upstream regions demonstrated that the redox-sensing regulator rex of s. aureus binds to this inverted repeat. the binding sequence--ttgtgaaw(4)ttcacaa--is highly conserved in s. aureus. rex binding to this sequence leads to the repression of genes located downstream. ...	2010	20374494
euryarchaeal beta-casp proteins with homology to bacterial rnase j have 5'- to 3'-exoribonuclease activity.	in the archaea only a handful of ribonucleases involved in rna processing and degradation have been characterized. one potential group of archaeal ribonucleases are homologues of the bacterial rnase j family, which have a beta-casp metallo-beta-lactamase fold. here we show that beta-casp proteins encoded in the genomes of the hyperthermophilic euryarchaeota pyrococcus abyssi and thermococcus kodakaraensis are processive exoribonucleases with a 5' end dependence and a 5' to 3' directionality. we ...	2010	20375016
expression, purification and structural analysis of the pyrococcus abyssi rna binding protein pab1135.	abstract:	2010	20380716
ampn-ampg operon is essential for expression of l1 and l2 beta-lactamases in stenotrophomonas maltophilia.	ampg is an inner membrane permease which transports products of murein sacculus degradation from the periplasm into the cytosol in gram-negative bacteria. this process is linked to induction of the chromosomal ampc beta-lactamase gene in some members of the enterobacteriaceae and in pseudomonas aeruginosa. in this study, the ampg homologue of stenotrophomonas maltophilia kj was analyzed. the ampg homologue and its upstream ampn gene form an operon and are cotranscribed under the control of the p ...	2010	20385866
structure of a virulence regulatory factor cvfb reveals a novel winged helix rna binding module.	cvfb is a conserved regulatory protein important for the virulence of staphylococcus aureus. we show here that cvfb binds rna. the crystal structure of the cvfb ortholog from streptococcus pneumoniae at 1.4 a resolution reveals a unique rna binding protein that is formed from a concatenation of well-known structural modules that bind nucleic acids: three consecutive s1 rna binding domains and a winged helix (wh) domain. the third s1 and the wh domains are required for cooperative rna binding and ...	2010	20399190
a unique group of virus-related, genome-integrating elements found solely in the bacterial family thermaceae and the archaeal family halobacteriaceae.	viruses sh1 and p23-77, infecting archaeal haloarcula species and bacterial thermus species, respectively, were recently designated to form a novel viral lineage. in this study, the lineage is expanded to archaeal halomicrobium and bacterial meiothermus species by analysis of five genome-integrated elements that share the core genes with these viruses.	2010	20400546
cryoem structure of hsp104 and its mechanistic implication for protein disaggregation.	hsp104 is a ring-forming aaa+ machine that recognizes both aggregated proteins and prion-fibrils as substrates and, together with the hsp70 system, remodels substrates in an atp-dependent manner. whereas the ability to disaggregate proteins is dependent on the hsp104 m-domain, the location of the m-domain is controversial and its exact function remains unknown. here we present cryoem structures of two hsp104 variants in both crosslinked and noncrosslinked form, in addition to the structure of a ...	2010	20404203
a nonheme high-spin ferrous pool in mitochondria isolated from fermenting saccharomyces cerevisiae.	mössbauer spectroscopy was used to detect pools of fe in mitochondria from fermenting yeast cells, including those consisting of nonheme high-spin (hs) fe(ii) species, fe(iii) nanoparticles, and mononuclear hs fe(iii) species. at issue was whether these species were located within mitochondria or on their exterior. none could be removed by washing mitochondria extensively with ethylene glycol tetraacetic acid or bathophenanthroline sulfonate (bps), fe(ii) chelators that do not appear to penetrat ...	2010	20408527
a bacterial antirepressor with sh3 domain topology mimics operator dna in sequestering the repressor dna recognition helix.	direct targeting of critical dna-binding elements of a repressor by its cognate antirepressor is an effective means to sequester the repressor and remove a transcription initiation block. structural descriptions for this, though often proposed for bacterial and phage repressor-antirepressor systems, are unavailable. here, we describe the structural and functional basis of how the myxococcus xanthus cars antirepressor recognizes and neutralizes its cognate repressors to turn on a photo-inducible ...	2010	20410074
helix-hairpin-helix protein mj1434 from methanocaldococcus jannaschii and endoiv homologue ttc0482 from thermus thermophilus hb27 do not process dna uracil residues.	the mutagenic threat of hydrolytic dna cytosine deamination is met mostly by uracil dna glycosylases (udg) initiating base excision repair. however, several sequenced genomes of archaeal organisms are devoid of genes coding for homologues of the otherwise ubiquitous udg superfamily of proteins. previously, two possible solutions to this problem were offered by (i) a report of a newly discovered family of uracil dna glycosylases exemplified by mj1434, a protein found in the hyperthermophilic arch ...	2010	20410075
a selection that reports on protein-protein interactions within a thermophilic bacterium.	many proteins can be split into fragments that exhibit enhanced function upon fusion to interacting proteins. while this strategy has been widely used to create protein-fragment complementation assays (pcas) for discovering protein-protein interactions within mesophilic organisms, similar assays have not yet been developed for studying natural and engineered protein complexes at the temperatures where thermophilic microbes grow. we describe the development of a selection for protein-protein inte ...	2010	20418388
methanococci use the diaminopimelate aminotransferase (dapl) pathway for lysine biosynthesis.	the pathway of lysine biosynthesis in the methanococci has not been identified previously. a variant of the diaminopimelic acid (dap) pathway uses diaminopimelate aminotransferase (dapl) to catalyze the direct conversion of tetrahydrodipicolinate (thdpa) to ll-dap. recently, the enzyme dapl (mth52) was identified in methanothermobacter thermautotrophicus and shown to belong to the dapl1 group. although the methanococcus maripaludis genome lacks a gene that can be unambiguously assigned a dapl fu ...	2010	20418392
diversity of 16s rrna genes within individual prokaryotic genomes.	analysis of intragenomic variation of 16s rrna genes is a unique approach to examining the concept of ribosomal constraints on rrna genes; the degree of variation is an important parameter to consider for estimation of the diversity of a complex microbiome in the recently initiated human microbiome project (http://nihroadmap.nih.gov/hmp). the current genbank database has a collection of 883 prokaryotic genomes representing 568 unique species, of which 425 species contained 2 to 15 copies of 16s ...	2010	20418441
bioinformatic, structural, and functional analyses support release factor-like mtrf1 as a protein able to decode nonstandard stop codons beginning with adenine in vertebrate mitochondria.	vertebrate mitochondria use stop codons uaa and uag decoded by the release factor (rf) mtrf1l and two reassigned arginine codons, aga and agg. a second highly conserved rf-like factor, mtrf1, which evolved from a gene duplication of an ancestral mitochondrial rf1 and not a rf2, is a good candidate for recognizing the nonstandard codons. mtrf1 differs from other rfs by having insertions in the two external loops important for stop codon recognition (tip of helix alpha5 and recognition loop) and b ...	2010	20421313
structure of the 70s ribosome bound to release factor 2 and a substrate analog provides insights into catalysis of peptide release.	we report the crystal structure of release factor 2 bound to ribosome with an aminoacyl trna substrate analog at the ribosomal p site, at 3.1 a resolution. the structure shows that upon stop-codon recognition, the universally conserved ggq motif packs tightly into the peptidyl transferase center. nucleotide a2602 of 23s rrna, implicated in peptide release, packs with the ggq motif in release factor 2. the ribose of a76 of the peptidyl-trna adopts the c2'-endo conformation, and the 2' hydroxyl of ...	2010	20421507
the small subunit arob of arsenite oxidase: lessons on the [2fe-2s] rieske protein superfamily.	here, we describe the characterization of the [2fe-2s] clusters of arsenite oxidases from rhizobium sp. nt-26 and ralstonia sp. 22. both reduced rieske proteins feature epr signals similar to their homologs from rieske-cyt b complexes, with g values at 2.027, 1.88, and 1.77. redox titrations in a range of ph values showed that both [2fe-2s] centers have constant e(m) values up to ph 8 at approximately +210 mv. above this ph value, the e(m) values of both centers are ph-dependent, similar to what ...	2010	20421651
structural basis for the activity and substrate specificity of fluoroacetyl-coa thioesterase flk.	the thioesterase flk from the fluoroacetate-producing streptomyces cattleya catalyzes the hydrolysis of fluoroacetyl-coenzyme a. this provides an effective self-defense mechanism, preventing any fluoroacetyl-coenzyme a formed from being further metabolized to 4-hydroxy-trans-aconitate, a lethal inhibitor of the tricarboxylic acid cycle. remarkably, flk does not accept acetyl-coenzyme a as a substrate. crystal structure analysis shows that flk forms a dimer, in which each subunit adopts a hot dog ...	2010	20430898
molecular structure of wlbb, a bacterial n-acetyltransferase involved in the biosynthesis of 2,3-diacetamido-2,3-dideoxy-d-mannuronic acid .	the pathogenic bacteria pseudomonas aeruginosa and bordetella pertussis contain in their outer membranes the rare sugar 2,3-diacetamido-2,3-dideoxy-d-mannuronic acid. five enzymes are required for the biosynthesis of this sugar starting from udp-n-acetylglucosamine. one of these, referred to as wlbb, is an n-acetyltransferase that converts udp-2-acetamido-3-amino-2,3-dideoxy-d-glucuronic acid (udp-glcnac3na) to udp-2,3-diacetamido-2,3-dideoxy-d-glucuronic acid (udp-glcnac3naca). here we report t ...	2010	20433200
analysis of the functional consequences of lethal mutations in mitochondrial translational elongation factors.	mammalian mitochondria synthesize a set of thirteen proteins that are essential for energy generation via oxidative phosphorylation. the genes for all of the factors required for synthesis of the mitochondrially encoded proteins are located in the nuclear genome. a number of disease-causing mutations have been identified in these genes. in this manuscript, we have elucidated the mechanisms of translational failure for two disease states characterized by lethal mutations in mitochondrial elongati ...	2010	20435138
an unconventional copper protein required for cytochrome c oxidase respiratory function under extreme acidic conditions.	very little is known about the processes used by acidophile organisms to preserve stability and function of respiratory pathways. here, we reveal a potential strategy of these organisms for protecting and keeping functional key enzymes under extreme conditions. using acidithiobacillus ferrooxidans, we have identified a protein belonging to a new cupredoxin subfamily, acop, for "acidophile cco partner," which is required for the cytochrome c oxidase (cco) function. we show that it is a multifunct ...	2010	20442397
regulation and isoform function of the v-atpases.	the vacuolar (h(+))-atpases are atp-dependent proton pumps that acidify intracellular compartments and, in some cases, transport protons across the plasma membrane of eukaryotic cells. intracellular v-atpases play an important role in normal physiological processes such as receptor-mediated endocytosis, intracellular membrane trafficking, pro-hormone processing, protein degradation, and the coupled uptake of small molecules, such as neurotransmitters. they also function in the entry of various p ...	2010	20450191
purification and characterization of put1p from saccharomyces cerevisiae.	in saccharomyces cerevisiae, the put1 and put2 genes are required for the conversion of proline to glutamate. the put1 gene encodes put1p, a proline dehydrogenase (prodh) enzyme localized in the mitochondrion. put1p was expressed and purified from escherichia coli and shown to have a uv-visible absorption spectrum that is typical of a bound flavin cofactor. a k(m) value of 36 mm proline and a k(cat)=27 s(-1) were determined for put1p using an artificial electron acceptor. put1p also exhibited hi ...	2010	20450881
identification of a novel arsenite oxidase gene, arxa, in the haloalkaliphilic, arsenite-oxidizing bacterium alkalilimnicola ehrlichii strain mlhe-1.	although arsenic is highly toxic to most organisms, certain prokaryotes are known to grow on and respire toxic metalloids of arsenic (i.e., arsenate and arsenite). two enzymes are known to be required for this arsenic-based metabolism: (i) the arsenate respiratory reductase (arra) and (ii) arsenite oxidase (aoxb). both catalytic enzymes contain molybdopterin cofactors and form distinct phylogenetic clades (arra and aoxb) within the dimethyl sulfoxide (dmso) reductase family of enzymes. here we r ...	2010	20453090
the hyperthermophilic euryarchaeon archaeoglobus fulgidus repairs uracil by single-nucleotide replacement.	hydrolytic deamination of cytosine to uracil in cellular dna is a major source of c-to-t transition mutations if uracil is not repaired by the dna base excision repair (ber) pathway. since deamination increases rapidly with temperature, hyperthermophiles, in particular, are expected to succumb to such damage. there has been only one report of crenarchaeotic ber showing strong similarities to that in most eukaryotes and bacteria for hyperthermophilic archaea. here we report a different type of be ...	2010	20453094
cracking pre-40s ribosomal subunit structure by systematic analyses of rna-protein cross-linking.	understanding of eukaryotic ribosome synthesis has been slowed by a lack of structural data for the pre-ribosomal particles. we report rrna-binding sites for six late-acting 40s ribosome synthesis factors, three of which cluster around the 3' end of the 18s rrna in model 3d structures. enp1 and ltv1 were previously implicated in 'beak' structure formation during 40s maturation--and their binding sites indicate direct functions. the kinase rio2, putative gtpase tsr1 and dimethylase dim1 bind sequ ...	2010	20453830
mechanisms of the hsp70 chaperone system.	molecular chaperones of the hsp70 family have diverse functions in cells. they assist the folding of newly synthesized and stress-denatured proteins, as well as the import of proteins into organelles, and the dissociation of aggregated proteins. the well-conserved hsp70 chaperones are atp dependent: binding and hydrolysis of atp regulates their interactions with unfolded polypeptide substrates, and atpase cycling is necessary for their function. all cellular functions of hsp70 chaperones use the ...	2010	20453930
a novel single-stranded dna-specific 3'-5' exonuclease, thermus thermophilus exonuclease i, is involved in several dna repair pathways.	single-stranded dna (ssdna)-specific exonucleases (ssexos) are expected to be involved in a variety of dna repair pathways corresponding to their cleavage polarities; however, the relationship between the cleavage polarity and the respective dna repair pathways is only partially understood. to understand the cellular function of ssexos in dna repair better, genes encoding ssexos were disrupted in thermus thermophilus hb8 that seems to have only a single set of 5'-3' and 3'-5' ssexos unlike other ...	2010	20457749
multiple roles of the rna polymerase {beta}' sw2 region in transcription initiation, promoter escape, and rna elongation.	interactions of rna polymerase (rnap) with nucleic acids must be tightly controlled to ensure precise and processive rna synthesis. the rnap β'-subunit switch-2 (sw2) region is part of a protein network that connects the clamp domain with the rnap body and mediates opening and closing of the active center cleft. sw2 interacts with the template dna near the rnap active center and is a target for antibiotics that block dna melting during initiation. here, we show that substitutions of a conserved ...	2010	20457751
the archaeal transamidosome for rna-dependent glutamine biosynthesis.	archaea make glutaminyl-trna (gln-trna(gln)) in a two-step process; a non-discriminating glutamyl-trna synthetase (nd-glurs) forms glu-trna(gln), while the heterodimeric amidotransferase gatde converts this mischarged trna to gln-trna(gln). many prokaryotes synthesize asparaginyl-trna (asn-trna(asn)) in a similar manner using a non-discriminating aspartyl-trna synthetase (nd-asprs) and the heterotrimeric amidotransferase gatcab. the transamidosome, a complex of trna synthetase, amidotransferase ...	2010	20457752
kinetic and structural characterization of a heterohexamer 4-oxalocrotonate tautomerase from chloroflexus aurantiacus j-10-fl: implications for functional and structural diversity in the tautomerase superfamily .	4-oxalocrotonate tautomerase (4-ot) isozymes play prominent roles in the bacterial utilization of aromatic hydrocarbons as sole carbon sources. these enzymes catalyze the conversion of 2-hydroxy-2,4-hexadienedioate (or 2-hydroxymuconate) to 2-oxo-3-hexenedioate, where pro-1 functions as a general base and shuttles a proton from the 2-hydroxyl group of the substrate to the c-5 position of the product. 4-ot, a homohexamer from pseudomonas putida mt-2, is the most extensively studied 4-ot isozyme a ...	2010	20465238
mass spectrometry defines the stoichiometry of ribosomal stalk complexes across the phylogenetic tree.	the ribosomal stalk complex plays a crucial role in delivering translation factors to the catalytic site of the ribosome. it has a very similar architecture in all cells, although the protein components in bacteria are unrelated to those in archaea and eukaryotes. here we used mass spectrometry to investigate ribosomal stalk complexes from bacteria, eukaryotes, and archaea in situ on the ribosome. specifically we targeted ribosomes with different optimal growth temperatures. our results showed t ...	2010	20467040
natural competence in thermoanaerobacter and thermoanaerobacterium species.	low-g+c thermophilic obligate anaerobes in the class clostridia are considered among the bacteria most resistant to genetic engineering due to the difficulty of introducing foreign dna, thus limiting the ability to study and exploit their native hydrolytic and fermentative capabilities. here, we report evidence of natural genetic competence in 13 thermoanaerobacter and thermoanaerobacterium strains previously believed to be difficult to transform or genetically recalcitrant. in thermoanaerobacte ...	2010	20472726
conformational coupling, bridge helix dynamics and active site dehydration in catalysis by rna polymerase.	molecular dynamics simulation of thermus thermophilus (tt) rna polymerase (rnap) in a catalytic conformation demonstrates that the active site dnmp-ntp base pair must be substantially dehydrated to support full active site closing and optimum conditions for phosphodiester bond synthesis. in silico mutant beta r428a rnap, which was designed based on substitutions at the homologous position (rpb2 r512) of saccharomyces cerevisiae (sc) rnap ii, was used as a reference structure to compare to tt rna ...	2010	20478425
binding of a small molecule at a protein-protein interface regulates the chaperone activity of hsp70-hsp40.	heat shock protein 70 (hsp70) is a highly conserved molecular chaperone that plays multiple roles in protein homeostasis. in these various tasks, the activity of hsp70 is shaped by interactions with co-chaperones, such as hsp40. the hsp40 family of co-chaperones binds to hsp70 through a conserved j-domain, and these factors stimulate atpase and protein-folding activity. using chemical screens, we identified a compound, 115-7c, which acts as an artificial co-chaperone for hsp70. specifically, the ...	2010	20481474
thermal stability, ph dependence and inhibition of four murine kynurenine aminotransferases.	kynurenine aminotransferase (kat) catalyzes the transamination of kynunrenine to kynurenic acid (kyna). kyna is a neuroactive compound and functions as an antagonist of alpha7-nicotinic acetylcholine receptors and is the only known endogenous antagonist of n-methyl-d-aspartate receptors. four kat enzymes, kat i/glutamine transaminase k/cysteine conjugate beta-lyase 1, kat ii/aminoadipate aminotransferase, kat iii/cysteine conjugate beta-lyase 2, and kat iv/glutamic-oxaloacetic transaminase 2/mit ...	2010	20482848
insights into the hyperthermostability and unusual region-specificity of archaeal pyrococcus abyssi trna m1a57/58 methyltransferase.	the s-adenosyl-l-methionine dependent methylation of adenine 58 in the t-loop of trnas is essential for cell growth in yeast or for adaptation to high temperatures in thermophilic organisms. in contrast to bacterial and eukaryotic trna m(1)a58 methyltransferases that are site-specific, the homologous archaeal enzyme from pyrococcus abyssi catalyzes the formation of m(1)a also at the adjacent position 57, m(1)a57 being a precursor of 1-methylinosine. we report here the crystal structure of p. aby ...	2010	20483913
identification of residual structure in the unfolded state of ribonuclease h1 from the moderately thermophilic chlorobium tepidum: comparison with thermophilic and mesophilic homologues.	ribonucleases h from organisms that grow at different temperatures demonstrate a variable change in heat capacity upon unfolding (deltac degrees (p)) [ratcliff, k., et al. (2009) biochemistry 48, 5890-5898]. this deltac degrees (p) has been shown to correlate with a tolerance to higher temperatures and residual structure in the unfolded state of the thermophilic proteins. in the rnase h from thermus thermophilus, the low deltac degrees (p) has been shown to arise from the same region as the fold ...	2010	20491485
nmr investigations of the rieske protein from thermus thermophilus support a coupled proton and electron transfer mechanism.	the rieske protein component of the cytochrome bc complex contains a [2fe-2s] cluster ligated by two cysteines and two histidines. we report here the pk(a) values of each of the imidazole rings of the two ligating histidines (his134 and his154) in the oxidized and reduced states of the rieske protein from thermus thermophilus (ttrp) as determined by nmr spectroscopy. knowledge of these pk(a) values is of critical interest because of their pertinence to the mechanism of electron and proton transf ...	2010	20496909
rna polymerase mutations that facilitate replication progression in the rep uvrd recf mutant lacking two accessory replicative helicases.	we observed that cells lacking rep and uvrd, two replication accessory helicases, and the recombination protein recf are cryo-sensitive on rich medium. we isolated five mutations that suppress this luria-bertani (lb)-cryo-sensitivity and show that they map in the genes encoding the rna polymerase subunits rpob and rpoc. these rpob (d444g, h447r and n518d) and rpoc mutants (h113r and p451l) were characterized. rpob(h447r) and rpob(d444g) prevent activation of the prrn core promoter in rich medium ...	2010	20497334
the qrc membrane complex, related to the alternative complex iii, is a menaquinone reductase involved in sulfate respiration.	biological sulfate reduction is a process with high environmental significance due to its major contribution to the carbon and sulfur cycles in anaerobic environments. however, the respiratory chain of sulfate-reducing bacteria is still poorly understood. here we describe a new respiratory complex that was isolated as a major protein present in the membranes of desulfovibrio vulgaris hildenborough. the complex, which was named qrc, is the first representative of a new family of redox complexes. ...	2010	20498375
thioesterases: a new perspective based on their primary and tertiary structures.	thioesterases (tes) are classified into ec 3.1.2.1 through ec 3.1.2.27 based on their activities on different substrates, with many remaining unclassified (ec 3.1.2.-). analysis of primary and tertiary structures of known tes casts a new light on this enzyme group. we used strong primary sequence conservation based on experimentally proved proteins as the main criterion, followed by verification with tertiary structure superpositions, mechanisms, and catalytic residue positions, to accurately de ...	2010	20506386
molecular dynamics simulations suggest that rna three-way junctions can act as flexible rna structural elements in the ribosome.	we present extensive explicit solvent molecular dynamics analysis of three rna three-way junctions (3wjs) from the large ribosomal subunit: the 3wj formed by helices 90-92 (h90-h92) of 23s rrna; the 3wj formed by h42-h44 organizing the gtpase associated center (gac) of 23s rrna; and the 3wj of 5s rrna. h92 near the peptidyl transferase center binds the 3'-cca end of amino-acylated trna. the gac binds protein factors and stimulates gtp hydrolysis driving protein synthesis. the 5s rrna binds the c ...	2010	20507916
essential biological processes of an emerging pathogen: dna replication, transcription, and cell division in acinetobacter spp.	within the last 15 years, members of the bacterial genus acinetobacter have risen from relative obscurity to be among the most important sources of hospital-acquired infections. the driving force for this has been the remarkable ability of these organisms to acquire antibiotic resistance determinants, with some strains now showing resistance to every antibiotic in clinical use. there is an urgent need for new antibacterial compounds to combat the threat imposed by acinetobacter spp. and other in ...	2010	20508250
a cytochrome c fusion protein domain for convenient detection, quantification, and enhanced production of membrane proteins in escherichia coli--expression and characterization of cytochrome-tagged complex i subunits.	overproduction of membrane proteins can be a cumbersome task, particularly if high yields are desirable. nadh:quinone oxidoreductase (complex i) contains several very large membrane-spanning protein subunits that hitherto have been impossible to express individually in any appreciable amounts in escherichia coli. the polypeptides contain no prosthetic groups and are poorly antigenic, making optimization of protein production a challenging task. in this work, the c-terminal ends of the complex i ...	2010	20509166
transcriptional control by two leucine-responsive regulatory proteins in halobacterium salinarum r1.	archaea combine bacterial-as well as eukaryotic-like features to regulate cellular processes. halobacterium salinarum r1 encodes eight leucine-responsive regulatory protein (lrp)-homologues. the function of two of them, irp (oe3923f) and lrpa1 (oe2621r), were analyzed by gene deletion and overexpression, including genome scale impacts using microarrays.	2010	20509863
deletion of switch 3 results in an archaeal rna polymerase that is defective in transcript elongation.	switch 3 is a polypeptide loop conserved in all multisubunit dna-dependent rna polymerases (rnaps) that extends into the main cleft of the rnap and contacts each base in a nascent transcript as that base is released from the internal dna-rna hybrid. plasmids have been constructed and transformed into thermococcus kodakaraensis, which direct the constitutive synthesis of the archaeal rnap subunit rpob with an n-terminal his(6) tag and the switch 3 loop either intact (wild-type) or deleted (deltas ...	2010	20511223
remembering malcolm j. casadaban.	malcolm j. casadaban died on 13 september 2009 from an infection and was found to have a weakened strain of the bacterium yersinia pestis in his blood. this tragic event took the life of one of the most creative and influential geneticists of our time. in the late 1970s and '80s, malcolm invented novel approaches which changed the way many of us did science. jon beckwith, tom silhavy, and olaf schneewind have chronicled his scientific life from graduate school to his death and give us insight in ...	2010	20511498
free zinc ions outside a narrow concentration range are toxic to a variety of cells in vitro.	the zinc(ii) ion has recently been implicated in a number of novel functions and pathologies in loci as diverse as the brain, retina, small intestine, prostate, heart, pancreas, and immune system. zinc ions are a required nutrient but elevated concentrations are known to kill cells in vitro. paradoxical observations regarding zinc's effects have appeared frequently in the literature, and often their physiological relevance is unclear. we found that for pc-12, hela and ht-29 cell lines as well as ...	2010	20511678
cell surface display of chimeric glycoproteins via the s-layer of paenibacillus alvei.	the gram-positive, mesophilic bacterium paenibacillus alvei ccm 2051(t) possesses a two-dimensional crystalline protein surface layer (s-layer) with oblique lattice symmetry composed of a single type of o-glycoprotein species. herein, we describe a strategy for nanopatterned in vivo cell surface co-display of peptide and glycan epitopes based on this s-layer glycoprotein self-assembly system. the open reading frame of the corresponding structural gene spaa codes for a protein of 983 amino acids, ...	2010	20513375
the structure of phaz7 at atomic (1.2 a) resolution reveals details of the active site and suggests a substrate-binding mode.	poly-(r)-hydroxyalkanoates (phas) are bacterial polyesters that are degraded by a group of enzymes known as pha depolymerases. paucimonas lemoignei phaz7 depolymerase is the only extracellular depolymerase that has been described as being active towards amorphous phas. a previously determined crystal structure of phaz7 revealed an alpha/beta-hydrolase fold and a ser-his-asp catalytic triad. in order to address questions regarding the catalytic mechanism and substrate binding, the atomic resoluti ...	2010	20516591
crystallization and preliminary x-ray diffraction analysis of various enzyme-substrate complexes of isopropylmalate dehydrogenase from thermus thermophilus.	the thermus thermophilus 3-isopropylmalate dehydrogenase (tt-ipmdh) enzyme catalyses the penultimate step of the leucine-biosynthesis pathway. it converts (2r,3s)-3-isopropylmalate to (2s)-2-isopropyl-3-oxosuccinate in the presence of divalent mg(2+) or mn(2+) and with the help of nad(+). in order to elucidate the detailed structural and functional mode of the enzymatic reaction, crystals of tt-ipmdh were grown in the presence of various combinations of substrate and/or cofactors. here, the crys ...	2010	20516614
structural characterization of tartrate dehydrogenase: a versatile enzyme catalyzing multiple reactions.	the first structure of an nad-dependent tartrate dehydrogenase (tdh) has been solved to 2 a resolution by single anomalous diffraction (sad) phasing as a complex with the intermediate analog oxalate, mg(2+) and nadh. this tdh structure from pseudomonas putida has a similar overall fold and domain organization to other structurally characterized members of the hydroxy-acid dehydrogenase family. however, there are considerable differences between tdh and these functionally related enzymes in the r ...	2010	20516620
crystal structures of the apo and atp bound mycobacterium tuberculosis nitrogen regulatory pii protein.	pii constitutes a family of signal transduction proteins that act as nitrogen sensors in microorganisms and plants. mycobacterium tuberculosis (mtb) has a single homologue of pii whose precise role has as yet not been explored. we have solved the crystal structures of the mtb pii protein in its apo and atp bound forms to 1.4 and 2.4 a resolutions, respectively. the protein forms a trimeric assembly in the crystal lattice and folds similarly to the other pii family proteins. the mtb pii:atp binar ...	2010	20521335
three-dimensional structure of beta-cell-specific zinc transporter, znt-8, predicted from the type 2 diabetes-associated gene variant slc30a8 r325w.	abstract:	2010	20525392
redesign, reconstruction, and directed extension of the brevibacterium linens c40 carotenoid pathway in escherichia coli.	in this study, the carotenoid biosynthetic pathways of brevibacterium linens dsmz 20426 were reconstructed, redesigned, and extended with additional carotenoid-modifying enzymes of other sources in a heterologous host escherichia coli. the modular lycopene pathway synthesized an unexpected carotenoid structure, 3,4-didehydrolycopene, as well as lycopene. extension of the novel 3,4-didehydrolycopene pathway with the mutant pantoea lycopene cyclase crty(2) and the rhodobacter spheroidene monooxyge ...	2010	20525861
crystal structure of arginase from plasmodium falciparum and implications for l-arginine depletion in malarial infection .	the 2.15 a resolution crystal structure of arginase from plasmodium falciparum, the parasite that causes cerebral malaria, is reported in complex with the boronic acid inhibitor 2(s)-amino-6-boronohexanoic acid (abh) (k(d) = 11 microm). this is the first crystal structure of a parasitic arginase. various protein constructs were explored to identify an optimally active enzyme form for inhibition and structural studies and to probe the structure and function of two polypeptide insertions unique to ...	2010	20527960
domain characterization and interaction of the yeast vacuolar atpase subunit c with the peripheral stator stalk subunits e and g.	the proton pumping activity of the eukaryotic vacuolar atpase (v-atpase) is regulated by a unique mechanism that involves reversible enzyme dissociation. in yeast, under conditions of nutrient depletion, the soluble catalytic v(1) sector disengages from the membrane integral v(o), and at the same time, both functional units are silenced. notably, during enzyme dissociation, a single v(1) subunit, c, is released into the cytosol. the affinities of the other v(1) and v(o) subunits for subunit c ar ...	2010	20529855
central role of the rna polymerase trigger loop in intrinsic rna hydrolysis.	the active center of rna polymerase can hydrolyze phosphodiester bonds in nascent rna, a reaction thought to be important for proofreading of transcription. the reaction proceeds via a general two mg(2+) mechanism and is assisted by the 3' end nucleotide of the transcript. here, by using thermus aquaticus rna polymerase, we show that the reaction also requires the flexible domain of the active center, the trigger loop (tl). we show that the invariant histidine (beta' his1242) of the tl is essent ...	2010	20534498
organometallic mechanism of action and inhibition of the 4fe-4s isoprenoid biosynthesis protein gcpe (ispg).	we report the results of a series of chemical, epr, endor, and hyscore spectroscopic investigations of the mechanism of action (and inhibition) of gcpe, e-1-hydroxy-2-methyl-but-2-enyl-4-diphosphate (hmbpp) synthase, also known as ispg, an fe(4)s(4) cluster-containing protein. we find that the epoxide of hmbpp when reduced by gcpe generates the same transient epr species as observed on addition of the substrate, 2-c-methyl-d-erythritol-2, 4-cyclo-diphosphate. endor and hyscore spectra of these t ...	2010	20534554
redox status affects the catalytic activity of glutamyl-trna synthetase.	glutamyl-trna synthetases (glurs) provide glu-trna for different processes including protein synthesis, glutamine transamidation and tetrapyrrole biosynthesis. many organisms contain multiple glurss, but whether these duplications solely broaden trna specificity or also play additional roles in tetrapyrrole biosynthesis is not known. previous studies have shown that glurs1, one of two glurss from the extremophile acidithiobacillus ferrooxidans, is inactivated when intracellular heme is elevated ...	2010	20541532
discovery and characterization of hemq: an essential heme biosynthetic pathway component.	here we identify a previously undescribed protein, hemq, that is required for heme synthesis in gram-positive bacteria. we have characterized hemq from bacillus subtilis and a number of actinobacteria. hemq is a multimeric heme-binding protein. spectroscopic studies indicate that this heme is high spin ferric iron and is ligated by a conserved histidine with the sixth coordination site available for binding a small molecule. the presence of hemq along with the terminal two pathway enzymes, proto ...	2010	20543190
regulation of dynamic polarity switching in bacteria by a ras-like g-protein and its cognate gap.	the rod-shaped cells of the bacterium myxococcus xanthus move uni-directionally and occasionally undergo reversals during which the leading/lagging polarity axis is inverted. cellular reversals depend on pole-to-pole relocation of motility proteins that localize to the cell poles between reversals. we show that mgla is a ras-like g-protein and acts as a nucleotide-dependent molecular switch to regulate motility and that mglb represents a novel gtpase-activating protein (gap) family and is the co ...	2010	20543819
multi-site-specific 16s rrna methyltransferase rsmf from thermus thermophilus.	cells devote a significant effort toward the production of multiple modified nucleotides in rrnas, which fine tune the ribosome function. here, we report that two methyltransferases, rsmb and rsmf, are responsible for all four 5-methylcytidine (m(5)c) modifications in 16s rrna of thermus thermophilus. like escherichia coli rsmb, t. thermophilus rsmb produces m(5)c967. in contrast to e. coli rsmf, which introduces a single m(5)c1407 modification, t. thermophilus rsmf modifies three positions, gen ...	2010	20558545
the multifunctional pe_pgrs11 protein from mycobacterium tuberculosis plays a role in regulating resistance to oxidative stress.	mycobacterium tuberculosis utilizes unique strategies to survive amid the hostile environment of infected host cells. infection-specific expression of a unique mycobacterial cell surface antigen that could modulate key signaling cascades can act as a key survival strategy in curtailing host effector responses like oxidative stress. we demonstrate here that hypothetical pe_pgrs11 orf encodes a functional phosphoglycerate mutase. the transcriptional analysis revealed that pe_pgrs11 is a hypoxia-re ...	2010	20558725
type ii isopentenyl diphosphate isomerase: probing the mechanism with alkyne/allene diphosphate substrate analogues.	isopentenyl diphosphate isomerase (idi) catalyzes the interconversion of isopentenyl diphosphate (ipp) and dimethylallyl diphosphate (dmapp), the basic five-carbon building blocks of isoprenoid molecules. two structurally unrelated classes of idis are known. type i ipp isomerase (idi-1) utilizes a divalent metal in a protonation-deprotonation reaction. in contrast, the type ii enzyme (idi-2) requires reduced flavin, raising the possibility that the reaction catalyzed by idi-2 involves the net ad ...	2010	20560533
design and use of peptide-based antibodies decreasing superoxide production by mitochondrial complex i and complex ii.	mitochondria are the major source of reactive oxygen species. both complex i and complex ii mediate o(2) (*-) production in mitochondria and host reactive protein thiols. to explore the functions of the specific domains involved in the redox modifications of complexes i and ii, various peptide-based antibodies were generated against these complexes, and their inhibitory effects were subsequently measured. the redox domains involved in s-glutathionylation and nitration, as well as the binding mot ...	2010	20564035
cation selectivity by the cora mg2+ channel requires a fully hydrated cation.	the cora mg(2+) channel is the primary uptake system in about half of all bacteria and archaea. however, the basis for its mg(2+) selectivity is unknown. previous data suggested that cora binds a fully hydrated mg(2+) ion, unlike other ion channels. the crystal structure of thermotoga maritima cora shows a homopentamer with two transmembrane segments per monomer connected by a short periplasmic loop. this highly conserved loop, (281)efmpelkws(289) in salmonella enterica serovar typhimurium cora, ...	2010	20568735
single-stranded dna binding protein from human malarial parasite plasmodium falciparum is encoded in the nucleus and targeted to the apicoplast.	apicoplast, an essential organelle of human malaria parasite plasmodium falciparum contains a ∼35 kb circular genome and is a possible target for therapy. proteins required for the replication and maintenance of the apicoplast dna are not clearly known. here we report the presence of single-stranded dna binding protein (ssb) in p falciparum. pfssb is targeted to the apicoplast and it binds to apicoplast dna. a strong ssdna binding activity specific to ssb was also detected in p. falciparum lysat ...	2010	20571080
mechanism of concerted inhibition of alpha2beta2-type hetero-oligomeric aspartate kinase from corynebacterium glutamicum.	aspartate kinase (ak) is the first and committed enzyme of the biosynthetic pathway producing aspartate family amino acids, lysine, threonine, and methionine. ak from corynebacterium glutamicum (cgak), a bacterium used for industrial fermentation of amino acids, including glutamate and lysine, is inhibited by lysine and threonine in a concerted manner. to elucidate the mechanism of this unique regulation in cgak, we determined the crystal structures in several forms: an inhibitory form complexed ...	2010	20573952
structural insights into the catalytic mechanism of bacterial guanosine-diphospho-d-mannose pyrophosphorylase and its regulation by divalent ions.	gmp catalyzes the formation of gdp-man, a fundamental precursor for protein glycosylation and bacterial cell wall and capsular polysaccharide biosynthesis. crystal structures of gmp from the thermophilic bacterium thermotoga maritima in the apo form, in complex with the substrates mannose-1-phosphate or gtp and bound with the end product gdp-man in the presence of the essential divalent cation mg(2+), were solved in the 2.1-2.8 a resolution range. the t. maritima gmp molecule is organized in two ...	2010	20573954
functional and structural impact of target uridine substitutions on the h/aca ribonucleoprotein particle pseudouridine synthase.	box h/aca ribonucleoprotein protein particles catalyze the majority of pseudouridylation in functional rna. different from stand alone pseudouridine synthases, the rnp pseudouridine synthase comprises multiple protein subunits and an rna subunit. previous studies showed that each subunit, regardless its location, is sensitive to the step of subunit placement at the catalytic center and potentially to the reaction status of the substrate. here we describe the impact of chemical substitutions of t ...	2010	20575532