Publications
| Title | Abstract | Year Filter | PMID(sorted descending) Filter |
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| 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 |
| metal ion roles and the movement of hydrogen during reaction catalyzed by d-xylose isomerase: a joint x-ray and neutron diffraction study. | conversion of aldo to keto sugars by the metalloenzyme d-xylose isomerase (xi) is a multistep reaction that involves hydrogen transfer. we have determined the structure of this enzyme by neutron diffraction in order to locate h atoms (or their isotope d). two studies are presented, one of xi containing cadmium and cyclic d-glucose (before sugar ring opening has occurred), and the other containing nickel and linear d-glucose (after ring opening has occurred but before isomerization). previously w ... | 2010 | 20541506 |
| crystal structure and ligand binding of the mid domain of a eukaryotic argonaute protein. | argonaute (ago) proteins are core components of rna-induced silencing complexes and have essential roles in rna-mediated gene silencing. they are characterized by a bilobal architecture, consisting of one lobe containing the amino-terminal and paz domains and another containing the mid and piwi domains. except for the paz domain, structural information on eukaryotic ago domains is not yet available. in this study, we report the crystal structure of the mid domain of the eukaryotic ago protein qd ... | 2010 | 20539312 |
| origin and evolution of the ribosome. | the modern ribosome was largely formed at the time of the last common ancestor, luca. hence its earliest origins likely lie in the rna world. central to its development were rnas that spawned the modern trnas and a symmetrical region deep within the large ribosomal rna, (rrna), where the peptidyl transferase reaction occurs. to understand pre-luca developments, it is argued that events that are coupled in time are especially useful if one can infer a likely order in which they occurred. using su ... | 2010 | 20534711 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| all things must pass: contrasts and commonalities in eukaryotic and bacterial mrna decay. | despite its universal importance for controlling gene expression, mrna degradation was initially thought to occur by disparate mechanisms in eukaryotes and bacteria. this conclusion was based on differences in the structures used by these organisms to protect mrna termini and in the rnases and modifying enzymes originally implicated in mrna decay. subsequent discoveries have identified several striking parallels between the cellular factors and molecular events that govern mrna degradation in th ... | 2010 | 20520623 |
| 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 |
| 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 |
| 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 |
| 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 |
| a novel atp-dependent conformation in p97 n-d1 fragment revealed by crystal structures of disease-related mutants. | mutations in p97, a major cytosolic aaa (atpases associated with a variety of cellular activities) chaperone, cause inclusion body myopathy associated with paget's disease of the bone and frontotemporal dementia (ibmpfd). ibmpfd mutants have single amino-acid substitutions at the interface between the n-terminal domain (n-domain) and the adjacent aaa domain (d1), resulting in a reduced affinity for adp. the structures of p97 n-d1 fragments bearing ibmpfd mutations adopt an atypical n-domain conf ... | 2010 | 20512113 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| lipoic acid metabolism in microbial pathogens. | lipoic acid [(r)-5-(1,2-dithiolan-3-yl)pentanoic acid] is an enzyme cofactor required for intermediate metabolism in free-living cells. lipoic acid was discovered nearly 60 years ago and was shown to be covalently attached to proteins in several multicomponent dehydrogenases. cells can acquire lipoate (the deprotonated charge form of lipoic acid that dominates at physiological ph) through either scavenging or de novo synthesis. microbial pathogens implement these basic lipoylation strategies wit ... | 2010 | 20508247 |
| 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 |
| iparts: an improved tool of pairwise alignment of rna tertiary structures. | iparts is an improved web server for aligning two rna 3d structures based on a structural alphabet (sa)-based approach. in particular, we first derive a ramachandran-like diagram of rnas by plotting nucleotides on a 2d axis using their two pseudo-torsion angles eta and . next, we apply the affinity propagation clustering algorithm to this eta- plot to obtain an sa of 23-nt conformations. we finally use this sa to transform rna 3d structures into 1d sequences of sa letters and continue to utilize ... | 2010 | 20507908 |
| 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 |
| structure and function of enzymes in heme biosynthesis. | tetrapyrroles like hemes, chlorophylls, and cobalamin are complex macrocycles which play essential roles in almost all living organisms. heme serves as prosthetic group of many proteins involved in fundamental biological processes like respiration, photosynthesis, and the metabolism and transport of oxygen. further, enzymes such as catalases, peroxidases, or cytochromes p450 rely on heme as essential cofactors. heme is synthesized in most organisms via a highly conserved biosynthetic route. in h ... | 2010 | 20506125 |
| alkyltransferase-like proteins: molecular switches between dna repair pathways. | alkyltransferase-like proteins (atls) play a role in the protection of cells from the biological effects of dna alkylation damage. although atls share functional motifs with the dna repair protein and cancer chemotherapy target o⁶-alkylguanine-dna alkyltransferase, they lack the reactive cysteine residue required for alkyltransferase activity, so its mechanism for cell protection was previously unknown. here we review recent advances in unraveling the enigmatic cellular protection provided by at ... | 2010 | 20502938 |
| 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 |
| 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 |
| 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 |
| structural signatures of antibiotic binding sites on the ribosome. | the ribosome represents a major target for antibacterial drugs. being a complex molecular machine, it offers many potential sites for functional interference. the high-resolution structures of ribosome in complex with various antibiotics provide a unique data set for understanding the universal features of drug-binding pockets on the ribosome. in this work, we have analyzed the structural and evolutionary properties of 65 antibiotic binding sites (abss) in the ribosome. we compared these sites t ... | 2010 | 20494981 |
| location of macular xanthophylls in the most vulnerable regions of photoreceptor outer-segment membranes. | lutein and zeaxanthin are two dietary carotenoids that compose the macular pigment of the primate retina. another carotenoid, meso-zeaxanthin, is formed from lutein in the retina. a membrane location is one possible site where these dipolar, terminally dihydroxylated carotenoids, named macular xanthophylls, are accumulated in the nerve fibers and photoreceptor outer segments. macular xanthophylls are oriented perpendicular to the membrane surface, which ensures their high solubility, stability, ... | 2010 | 20494651 |
| 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 |
| 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 |
| 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 |
| 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 |
| bioprocessing data for the production of marine enzymes. | this review is a synopsis of different bioprocess engineering approaches adopted for the production of marine enzymes. three major modes of operation: batch, fed-batch and continuous have been used for production of enzymes (such as protease, chitinase, agarase, peroxidase) mainly from marine bacteria and fungi on a laboratory bioreactor and pilot plant scales. submerged, immobilized and solid-state processes in batch mode were widely employed. the fed-batch process was also applied in several b ... | 2010 | 20479981 |
| 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 |
| a'-form rna helices are required for cytoplasmic mrna transport in drosophila. | microtubule-based mrna transport is widely used to restrict protein expression to specific regions in the cell and has important roles in defining cell polarity and axis determination as well as in neuronal function. however, the structural basis of recognition of cis-acting mrna localization signals by motor complexes is poorly understood. we have used nmr spectroscopy to describe the first tertiary structure to our knowledge of an rna element responsible for mrna transport. the drosophila mela ... | 2010 | 20473315 |
| the crystal structure of dynein intermediate chain-light chain roadblock complex gives new insights into dynein assembly. | the roadblock/lc7 dynein light chain is a ubiquitous component of all dyneins and is essential for many diverse processes including proper axonal transport and dendrite growth. in addition, lc7 functions in non-dynein transcriptional activation of the transforming growth factor-beta complex. crystal structures of drosophila melanogaster lc7 in the apo form and in complex with a segment of the disordered n-terminal domain of dynein intermediate chain (ic) provide the first definitive identificati ... | 2010 | 20472935 |
| 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 |
| invariant u2 snrna nucleotides form a stem loop to recognize the intron early in splicing. | u2 snrna-intron branchpoint pairing is a critical step in pre-mrna recognition by the splicing apparatus, but the mechanism by which these two rnas engage each other is unknown. here, we identify a u2 snrna structure, the branchpoint-interacting stem loop (bsl), which presents the u2 nucleotides that will contact the intron. we provide evidence that the bsl forms prior to interaction with the intron and is disrupted by the dexd/h protein prp5p during engagement of the snrna with the intron. in v ... | 2010 | 20471947 |
| 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 |
| 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 |
| two new families of the ftsz-tubulin protein superfamily implicated in membrane remodeling in diverse bacteria and archaea. | several recent discoveries reveal unexpected versatility of the bacterial and archaeal cytoskeleton systems that are involved in cell division and other processes based on membrane remodeling. here we apply methods for distant protein sequence similarity detection, phylogenetic approaches, and genome context analysis to described two previously unnoticed families of the ftsz-tubulin superfamily. one of these families is limited in its spread to proteobacteria whereas the other is represented in ... | 2010 | 20459678 |
| stepwise mechanism for transcription fidelity. | transcription is the first step of gene expression and is characterized by a high fidelity of rna synthesis. during transcription, the rna polymerase active centre discriminates against not just non-complementary ribo ntp substrates but also against complementary 2'- and 3'-deoxy ntps. a flexible domain of the rna polymerase active centre, the trigger loop, was shown to play an important role in this process, but the mechanisms of this participation remained elusive. | 2010 | 20459653 |
| 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 |
| 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 |
| 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 |
| sf1 and sf2 helicases: family matters. | helicases of the superfamily (sf) 1 and 2 are involved in virtually all aspects of rna and dna metabolism. sf1 and sf2 helicases share a catalytic core with high structural similarity, but different enzymes even within each sf perform a wide spectrum of distinct functions on diverse substrates. to rationalize similarities and differences between these helicases, we outline a classification based on protein families that are characterized by typical sequence, structural, and mechanistic features. ... | 2010 | 20456941 |
| 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 |
| 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 |
| 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 |
| 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 |
| a screen of chemical modifications identifies position-specific modification by una to most potently reduce sirna off-target effects. | small interfering rnas (sirnas) are now established as the preferred tool to inhibit gene function in mammalian cells yet trigger unintended gene silencing due to their inherent mirna-like behavior. such off-target effects are primarily mediated by the sequence-specific interaction between the sirna seed regions (position 2-8 of either sirna strand counting from the 5'-end) and complementary sequences in the 3'utr of (off-) targets. it was previously shown that chemical modification of sirnas ca ... | 2010 | 20453030 |
| 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 |
| 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 |
| sbspks: structure based sequence analysis of polyketide synthases. | polyketide synthases (pkss) catalyze biosynthesis of a diverse family of pharmaceutically important secondary metabolites. bioinformatics analysis of sequence and structural features of pks proteins plays a crucial role in discovery of new natural products by genome mining, as well as in design of novel secondary metabolites by biosynthetic engineering. the availability of the crystal structures of various pks catalytic and docking domains, and mammalian fatty acid synthase module prompted us to ... | 2010 | 20444870 |
| 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 |
| nanosecond time-resolved polarization spectroscopies: tools for probing protein reaction mechanisms. | polarization methods, introduced in the 1800s, offered one of the earliest ways to examine protein structure. since then, many other structure-sensitive probes have been developed, but circular dichroism (cd) remains a powerful technique because of its versatility and the specificity of protein structural information that can be explored. with improvements in time resolution, from millisecond to picosecond cd measurements, it has proven to be an important tool for studying the mechanism of foldi ... | 2010 | 20438842 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| structure and function of nematode rna-binding proteins. | rna-binding proteins are critical effectors of gene expression. they guide mrna localization, translation, and stability, and potentially play a role in regulating mrna synthesis. the structural basis for rna recognition by rna-binding proteins is the key to understand how they target specific transcripts for regulation. compared to other metazoans, nematode genomes contain a significant expansion in several rna-binding protein families, including pumilio-fbf (puf), ttp-like zinc finger (tzf), a ... | 2010 | 20418095 |
| 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 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 |
| 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 |
| 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 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 |
| 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 |
| mustang-mr structural sieving server: applications in protein structural analysis and crystallography. | a central tenet of structural biology is that related proteins of common function share structural similarity. this has key practical consequences for the derivation and analysis of protein structures, and is exploited by the process of "molecular sieving" whereby a common core is progressively distilled from a comparison of two or more protein structures. this paper reports a novel web server for "sieving" of protein structures, based on the multiple structural alignment program mustang. | 2010 | 20386610 |
| 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 |
| imprints of the genetic code in the ribosome. | the establishment of the genetic code remains elusive nearly five decades after the code was elucidated. the stereochemical hypothesis postulates that the code developed from interactions between nucleotides and amino acids, yet supporting evidence in a biological context is lacking. we show here that anticodons are selectively enriched near their respective amino acids in the ribosome, and that such enrichment is significantly correlated with the canonical code over random codes. ribosomal anti ... | 2010 | 20385807 |
| expression, purification and structural analysis of the pyrococcus abyssi rna binding protein pab1135. | abstract: | 2010 | 20380716 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| non-canonical dna transcription enzymes and the conservation of two-barrel rna polymerases. | dna transcription depends on multimeric rna polymerases that are exceptionally conserved in all cellular organisms, with an active site region of >500 amino acids mainly harboured by their rpb1 and rpb2 subunits. together with the distantly related eukaryotic rna-dependent polymerases involved in gene silencing, they form a monophyletic family of ribonucleotide polymerases with a similarly organized active site region based on two double-psi barrels. recent viral and phage genome sequencing have ... | 2010 | 20360047 |
| differences in the structure and dynamics of the apo- and palmitate-ligated forms of aedes aegypti sterol carrier protein 2 (aescp-2). | sterol carrier protein-2 (scp-2) is a nonspecific lipid-binding protein expressed ubiquitously in most organisms. knockdown of scp-2 expression in mosquitoes has been shown to result in high mortality in developing adults and significantly lowered fertility. thus, it is of interest to determine the structure of mosquito scp-2 and to identify its mechanism of lipid binding. we report here high quality three-dimensional solution structures of scp-2 from aedes aegypti determined by nmr spectroscopy ... | 2010 | 20356842 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| advances in nuclear magnetic resonance for drug discovery. | background: drug discovery is a complex and unpredictable endeavor with a high failure rate. current trends in the pharmaceutical industry have exasperated these challenges and are contributing to the dramatic decline in productivity observed over the last decade. the industrialization of science by forcing the drug discovery process to adhere to assembly-line protocols is imposing unnecessary restrictions, such as short project time-lines. recent advances in nuclear magnetic resonance are respo ... | 2009 | 20333269 |
| distinguishing microbial genome fragments based on their composition: evolutionary and comparative genomic perspectives. | it is well known that patterns of nucleotide composition vary within and among genomes, although the reasons why these variations exist are not completely understood. between-genome compositional variation has been exploited to assign environmental shotgun sequences to their most likely originating genomes, whereas within-genome variation has been used to identify recently acquired genetic material such as pathogenicity islands. recent sequence assignment techniques have achieved high levels of ... | 2010 | 20333228 |
| 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 |
| 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 |