Publications
| Title | Abstract | Year Filter | PMID(sorted ascending) Filter |
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| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| quantifying the relationship between sequence and three-dimensional structure conservation in rna. | in recent years, the number of available rna structures has rapidly grown reflecting the increased interest on rna biology. similarly to the studies carried out two decades ago for proteins, which gave the fundamental grounds for developing comparative protein structure prediction methods, we are now able to quantify the relationship between sequence and structure conservation in rna. | 2010 | 20550657 |
| 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 |
| a structural database for k-turn motifs in rna. | the kink-turn (k-turn) is a common structural motif in rna that introduces a tight kink into the helical axis. k-turns play an important architectural role in rna structures and serve as binding sites for a number of proteins. we have created a database of known and postulated k-turn sequences and three-dimensional (3d) structures, available via the internet. this site provides (1) a database of sequence and structure, as a resource for the rna community, and (2) a tool to enable the manipulatio ... | 2010 | 20562215 |
| the transcription inhibitor lipiarmycin blocks dna fitting into the rna polymerase catalytic site. | worldwide spreading of drug-resistant pathogens makes mechanistic understanding of antibiotic action an urgent task. the macrocyclic antibiotic lipiarmycin (lpm), which is under development for clinical use, inhibits bacterial rna polymerase (rnap) by an unknown mechanism. using genetic and biochemical approaches, we show that lpm targets the sigma(70) subunit region 3.2 and the rnap beta' subunit switch-2 element, which controls the clamping of promoter dna in the rnap active-site cleft. lpm ab ... | 2010 | 20562828 |
| 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 |
| synchrotron x-ray-induced photoreduction of ferric myoglobin nitrite crystals gives the ferrous derivative with retention of the o-bonded nitrite ligand. | exposure of a single crystal of the nitrite adduct of ferric myoglobin (mb) at 100 k to high-intensity synchrotron x-ray radiation resulted in changes in the uv-vis spectrum that can be attributed to reduction of the ferric compound to the ferrous derivative. we employed correlated single-crystal spectroscopy with crystallography to further characterize this photoproduct. the 1.55 a resolution crystal structure of the photoproduct reveals retention of the o-binding mode for binding of nitrite to ... | 2010 | 20568729 |
| 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 |
| the genome sequence of the crenarchaeon acidilobus saccharovorans supports a new order, acidilobales, and suggests an important ecological role in terrestrial acidic hot springs. | acidilobus saccharovorans is an anaerobic, organotrophic, thermoacidophilic crenarchaeon isolated from a terrestrial hot spring. we report the complete genome sequence of a. saccharovorans, which has permitted the prediction of genes for embden-meyerhof and entner-doudoroff pathways and genes associated with the oxidative tricarboxylic acid cycle. the electron transfer chain is branched with two sites of proton translocation and is linked to the reduction of elemental sulfur and thiosulfate. the ... | 2010 | 20581186 |
| recognition of the amber uag stop codon by release factor rf1. | we report the crystal structure of a termination complex containing release factor rf1 bound to the 70s ribosome in response to an amber (uag) codon at 3.6-a resolution. the amber codon is recognized in the 30s subunit-decoding centre directly by conserved elements of domain 2 of rf1, including t186 of the pvt motif. together with earlier structures, the mechanisms of recognition of all three stop codons by release factors rf1 and rf2 can now be described. our structure confirms that the backbon ... | 2010 | 20588254 |
| using molecular dynamics to probe the structural basis for enhanced stability in thermal stable cytochromes p450. | high-temperature molecular dynamics (md) has been used to assess if md can be employed as a useful tool for probing the structural basis for enhanced stability in thermal stable cytochromes p450. cyp119, the most thermal stable p450 known, unfolds more slowly during 500 k md simulations than p450s that melt at lower temperatures, p450cam and p450cin. a comparison of the 500 k md trajectories shows that the cys ligand loop, a critically important structural feature just under the heme, in both p4 ... | 2010 | 20593793 |
| automatic structure classification of small proteins using random forest. | random forest, an ensemble based supervised machine learning algorithm, is used to predict the scop structural classification for a target structure, based on the similarity of its structural descriptors to those of a template structure with an equal number of secondary structure elements (sses). an initial assessment of random forest is carried out for domains consisting of three sses. the usability of random forest in classifying larger domains is demonstrated by applying it to domains consist ... | 2010 | 20594334 |
| p. aeruginosa pilt structures with and without nucleotide reveal a dynamic type iv pilus retraction motor. | type iv pili are bacterial extracellular filaments that can be retracted to create force and motility. retraction is accomplished by the motor protein pilt. crystal structures of pseudomonas aeruginosa pilt with and without bound beta,gamma-methyleneadenosine-5'-triphosphate have been solved at 2.6 a and 3.1 a resolution, respectively, revealing an interlocking hexamer formed by the action of a crystallographic 2-fold symmetry operator on three subunits in the asymmetric unit and held together b ... | 2010 | 20595000 |
| the architecture of rna polymerase fidelity. | the basis for transcriptional fidelity by rna polymerase is not understood, but the 'trigger loop', a conserved structural element that is rearranged in the presence of correct substrate nucleotides, is thought to be critical. a study just published in bmc biology sheds new light on the ways in which the trigger loop may promote selection of correct nucleotide triphosphate substrates. see research article http://www.biomedcentral.com/1741-7007/8/54. | 2010 | 20598112 |
| the ccmc:heme:ccme complex in heme trafficking and cytochrome c biosynthesis. | a superfamily of integral membrane proteins is characterized by a conserved tryptophan-rich region (called the wwd domain) in an external loop at the inner membrane surface. the three major members of this family (ccmc, ccmf, and ccsba) are each involved in cytochrome c biosynthesis, yet the function of the wwd domain is unknown. it has been hypothesized that the wwd domain binds heme to present it to an acceptor protein (apoccme for ccmc or apocytochrome c for ccmf and ccsba) such that the heme ... | 2010 | 20599545 |
| properties of the c-terminal tail of human mitochondrial inner membrane protein oxa1l and its interactions with mammalian mitochondrial ribosomes. | in humans the mitochondrial inner membrane protein oxa1l is involved in the biogenesis of membrane proteins and facilitates the insertion of both mitochondrial- and nuclear-encoded proteins from the mitochondrial matrix into the inner membrane. the c-terminal approximately 100-amino acid tail of oxa1l (oxa1l-ctt) binds to mitochondrial ribosomes and plays a role in the co-translational insertion of mitochondria-synthesized proteins into the inner membrane. contrary to suggestions made for yeast ... | 2010 | 20601428 |
| structure of an archaeal non-discriminating glutamyl-trna synthetase: a missing link in the evolution of gln-trnagln formation. | the molecular basis of the genetic code relies on the specific ligation of amino acids to their cognate trna molecules. however, two pathways exist for the formation of gln-trna(gln). the evolutionarily older indirect route utilizes a non-discriminating glutamyl-trna synthetase (nd-glurs) that can form both glu-trna(glu) and glu-trna(gln). the glu-trna(gln) is then converted to gln-trna(gln) by an amidotransferase. since the well-characterized bacterial nd-glurs enzymes recognize trna(glu) and t ... | 2010 | 20601684 |
| bacillus anthracis surface-layer proteins assemble by binding to the secondary cell wall polysaccharide in a manner that requires csab and tago. | bacillus anthracis, the causative agent of anthrax, requires surface (s)-layer proteins for the pathogenesis of infection. previous work characterized s-layer protein binding via the surface layer homology domain to a pyruvylated carbohydrate in the envelope of vegetative forms. the molecular identity of this carbohydrate and the mechanism of its display in the bacterial envelope are still unknown. analyzing acid-solubilized, purified carbohydrates by mass spectrometry and nmr spectroscopy, we i ... | 2010 | 20603129 |
| evolution of protein synthesis from an rna world. | because of the molecular complexity of the ribosome and protein synthesis, it is a challenge to imagine how translation could have evolved from a primitive rna world. two specific suggestions are made here to help to address this, involving separate evolution of the peptidyl transferase and decoding functions. first, it is proposed that translation originally arose not to synthesize functional proteins, but to provide simple (perhaps random) peptides that bound to rna, increasing its available s ... | 2012 | 20610545 |
| the subunit composition of mitochondrial nadh:ubiquinone oxidoreductase (complex i) from pichia pastoris. | respiratory complex i (nadh:quinone oxidoreductase) is an entry point to the electron transport chain in the mitochondria of many eukaryotes. it is a large, multisubunit enzyme with a hydrophilic domain in the matrix and a hydrophobic domain in the mitochondrial inner membrane. here we present a comprehensive analysis of the protein composition and post-translational modifications of complex i from pichia pastoris, using a combination of proteomic and bioinformatic approaches. forty-one subunits ... | 2010 | 20610779 |
| evolution and thermodynamics of the slow unfolding of hyperstable monomeric proteins. | the unfolding speed of some hyperthermophilic proteins is dramatically lower than that of their mesostable homologs. ribonuclease hii from the hyperthermophilic archaeon thermococcus kodakaraensis (tk-rnase hii) is stabilized by its remarkably slow unfolding rate, whereas rnase hi from the thermophilic bacterium thermus thermophilus (tt-rnase hi) unfolds rapidly, comparable with to that of rnase hi from escherichia coli (ec-rnase hi). | 2010 | 20615256 |
| glycosidic bond conformation preference plays a pivotal role in catalysis of rna pseudouridylation: a combined simulation and structural study. | the most abundant chemical modification on rna is isomerization of uridine (or pseudouridylation) catalyzed by pseudouridine synthases. the catalytic mechanism of this essential process remains largely speculative, partly due to lack of knowledge of the pre-reactive state that is important to the identification of reactive chemical moieties. in the present study, we showed, using orthogonal space random-walk free-energy simulation, that the pre-reactive states of uridine and its reactive derivat ... | 2010 | 20615421 |
| promoter melting triggered by bacterial rna polymerase occurs in three steps. | rna synthesis, carried out by dna-dependent rna polymerase (rnap) in a process called transcription, involves several stages. in bacteria, transcription initiation starts with promoter recognition and binding of rnap holoenzyme, resulting in the formation of the closed (r.p(c)) rnap-promoter dna complex. subsequently, a transition to the open r.p(o) complex occurs, characterized by separation of the promoter dna strands in an approximately 12 base-pair region to form the transcription bubble. us ... | 2010 | 20615963 |
| synthesis of glu-trna(gln) by engineered and natural aminoacyl-trna synthetases. | a protein engineering approach to delineating which distinct elements of homologous trna synthetase architectures are responsible for divergent rna-amino acid pairing specificities is described. previously, we constructed a hybrid enzyme in which 23 amino acids from the catalytic domain of escherichia coli glutaminyl-trna synthetase (glnrs) were replaced with the corresponding residues of human glutamyl-trna synthetase (glurs). the engineered hybrid (glnrs s1/l1/l2) synthesizes glu-trna(gln) mor ... | 2010 | 20617848 |
| a novel heme a insertion factor gene cotranscribes with the thermus thermophilus cytochrome ba3 oxidase locus. | studying the biogenesis of the thermus thermophilus cytochrome ba(3) oxidase, we analyze heme a cofactor insertion into this membrane protein complex. only three proteins linked to oxidase maturation have been described for this extreme thermophile, and in particular, no evidence for a canonical surf1 homologue, required for heme a insertion, is available from genome sequence data. here, we characterize the product of an open reading frame, cbax, in the operon encoding subunits of the ba(3)-type ... | 2010 | 20622059 |
| diversity of glycosyl hydrolases from cellulose-depleting communities enriched from casts of two earthworm species. | the guts and casts of earthworms contain microbial assemblages that process large amounts of organic polymeric substrates from plant litter and soil; however, the enzymatic potential of these microbial communities remains largely unexplored. in the present work, we retrieved carbohydrate-modifying enzymes through the activity screening of metagenomic fosmid libraries from cellulose-depleting microbial communities established with the fresh casts of two earthworm species, aporrectodea caliginosa ... | 2010 | 20622123 |
| temperature adaptation at homologous sites in proteins from nine thermophile-mesophile species pairs. | whether particular amino acids are favored by selection at high temperatures over others has long been an open question in protein evolution. one way to approach this question is to compare homologous sites in proteins from one thermophile and a closely related mesophile; asymmetrical substitution patterns have been taken as evidence for selection favoring certain amino acids over others. however, most pairs of prokaryotic species that differ in optimum temperature also differ in genome-wide gc ... | 2010 | 20624731 |
| structural studies of tri-functional human gart. | human purine de novo synthesis pathway contains several multi-functional enzymes, one of which, tri-functional gart, contains three enzymatic activities in a single polypeptide chain. we have solved structures of two domains bearing separate catalytic functions: glycinamide ribonucleotide synthetase and aminoimidazole ribonucleotide synthetase. structures are compared with those of homologous enzymes from prokaryotes and analyzed in terms of the catalytic mechanism. we also report small angle x- ... | 2010 | 20631005 |
| biosynthesis of compatible solutes in rhizobial strains isolated from phaseolus vulgaris nodules in tunisian fields. | associated with appropriate crop and soil management, inoculation of legumes with microbial biofertilizers can improve food legume yield and soil fertility and reduce pollution by inorganic fertilizers. rhizospheric bacteria are subjected to osmotic stress imposed by drought and/or nacl, two abiotic constraints frequently found in semi-arid lands. osmostress response in bacteria involves the accumulation of small organic compounds called compatible solutes. whereas most studies on rhizobial osmo ... | 2010 | 20633304 |
| definition and estimation of resolution in single-particle reconstructions. | in this paper, we review current practices for establishing the resolution in single-particle reconstructions. the classical raleigh criterion for the resolution is not applicable in this case, and the resolution is commonly defined by a consistency test, whereby the data set is randomly split in half and the two resulting reconstructions are then compared. such a procedure, however, may introduce statistical dependence between the two half-sets, which leads to a too optimistic resolution estima ... | 2010 | 20637413 |
| dynamics of secy translocons with translocation-defective mutations. | the secy/sec61 translocon complex, located in the endoplasmic reticulum membrane of eukaryotes (sec61) or the plasma membrane of prokaryotes (secy), mediates the transmembrane secretion or insertion of nascent proteins. mutations that permit the secretion of nascent proteins with defective signal sequences (prl-phenotype), or interfere with the transmembrane orientation of newly synthesized protein segments, can affect protein topogenesis. the crystallographic structure of secyebeta from methano ... | 2010 | 20637421 |
| functional analysis of thermus thermophilus transcription factor nusg. | transcription elongation factors from the nusg family are ubiquitous from bacteria to humans and play diverse roles in the regulation of gene expression. these proteins consist of at least two domains. the n-terminal domains directly bind to the largest, β' in bacteria, subunit of rna polymerase (rnap), whereas the c-terminal domains interact with other cellular components and serve as platforms for the assembly of large nucleoprotein complexes. escherichia coli nusg and its paralog rfah modify ... | 2010 | 20639538 |
| rosr (cg1324), a hydrogen peroxide-sensitive marr-type transcriptional regulator of corynebacterium glutamicum. | the cg1324 gene (rosr) of corynebacterium glutamicum encodes a marr-type transcriptional regulator. by a comparative transcriptome analysis with dna microarrays of a δrosr mutant and the wild type and subsequent emsas with purified rosr protein, direct target genes of rosr were identified. the narkghji operon, which encodes a nitrate/nitrite transporter and the dissimilatory nitrate reductase complex, was activated by rosr. all other target genes were repressed by rosr. they encode four putative ... | 2010 | 20643656 |
| a molecular clamp ensures allosteric coordination of peptidyltransfer and ligand binding to the ribosomal a-site. | although the ribosome is mainly comprised of rrna and many of its critical functions occur through rna-rna interactions, distinct domains of ribosomal proteins also participate in switching the ribosome between different conformational/functional states. prior studies demonstrated that two extended domains of ribosomal protein l3 form an allosteric switch between the pre- and post-translocational states. missing was an explanation for how the movements of these domains are communicated among the ... | 2010 | 20660012 |
| nmr structure of the let-7 mirna interacting with the site lcs1 of lin-41 mrna from caenorhabditis elegans. | we have determined the 3d structure of a 34-nt rna construct, herein named lcs1co, which mimics the interaction of let-7 microrna (mirna) to one of its complementary binding sites, lcs1, in the 3'-untranslated region of lin-41 mrna by solution-state nmr spectroscopy. let-7 mirnas control the timing of development of the nematode caenorhabditis elegans and are highly conserved in mammals. the sequence and structure of the two conserved let-7 complementary sites, lcs1 and lcs2, in the 3'-untransla ... | 2010 | 20660479 |
| mitochondrial enzyme rhodanese is essential for 5 s ribosomal rna import into human mitochondria. | 5 s rrna is an essential component of ribosomes. in eukaryotic cells, it is distinguished by particularly complex intracellular traffic, including nuclear export and re-import. the finding that in mammalian cells 5 s rrna can eventually escape its usual circuit toward nascent ribosomes to get imported into mitochondria has made the scheme more complex, and it has raised questions about both the mechanism of 5 s rrna mitochondrial targeting and its function inside the organelle. previously, we sh ... | 2010 | 20663881 |
| linkage isomerization in heme-nox compounds: understanding no, nitrite, and hyponitrite interactions with iron porphyrins. | nitric oxide (no) and its derivatives such as nitrite and hyponitrite are biologically important species of relevance to human health. much of their physiological relevance stems from their interactions with the iron centers in heme proteins. the chemical reactivities displayed by the heme-nox species (nox = no, nitrite, hyponitrite) are a function of the binding modes of the nox ligands. hence, an understanding of the types of binding modes extant in heme-nox compounds is important if we are to ... | 2010 | 20666385 |
| bioinspired heme, heme/nonheme diiron, heme/copper, and inorganic nox chemistry: *no((g)) oxidation, peroxynitrite-metal chemistry, and *no((g)) reductive coupling. | the focus of this forum article highlights work from our own laboratories and those of others in the area of biochemical and biologically inspired inorganic chemistry dealing with nitric oxide [nitrogen monoxide, *no((g))] and its biological roles and reactions. the latter focus is on (i) oxidation of *no((g)) to nitrate by nitric oxide dioxygenases (nods) and (ii) reductive coupling of two molecules of *no((g)) to give n(2)o(g). in the former case, nods are described, and the highlighting of po ... | 2010 | 20666386 |
| interference with histidyl-trna synthetase by a crispr spacer sequence as a factor in the evolution of pelobacter carbinolicus. | pelobacter carbinolicus, a bacterium of the family geobacteraceae, cannot reduce fe(iii) directly or produce electricity like its relatives. how p. carbinolicus evolved is an intriguing problem. the genome of p. carbinolicus contains clustered regularly interspaced short palindromic repeats (crispr) separated by unique spacer sequences, which recent studies have shown to produce rna molecules that interfere with genes containing identical sequences. | 2010 | 20667132 |
| structures of membrane proteins. | in reviewing the structures of membrane proteins determined up to the end of 2009, we present in words and pictures the most informative examples from each family. we group the structures together according to their function and architecture to provide an overview of the major principles and variations on the most common themes. the first structures, determined 20 years ago, were those of naturally abundant proteins with limited conformational variability, and each membrane protein structure det ... | 2010 | 20667175 |
| the crystal structure of human transketolase and new insights into its mode of action. | the crystal structure of human transketolase (tkt), a thiamine diphosphate (thdp) and ca(2+)-dependent enzyme that catalyzes the interketol transfer between ketoses and aldoses as part of the pentose phosphate pathway, has been determined to 1.75 å resolution. the recombinantly produced protein crystallized in space group c2 containing one monomer in the asymmetric unit. two monomers form the homodimeric biological assembly with two identical active sites at the dimer interface. although the pro ... | 2010 | 20667822 |
| structural and functional characterization of salmonella enterica serovar typhimurium ycbl: an unusual type ii glyoxalase. | ycbl has been annotated as either a metallo-β-lactamase or glyoxalase ii (glx2), both members of the zinc metallohydrolase superfamily, that contains many enzymes with a diverse range of activities. here, we report crystallographic and biochemical data for salmonella enterica serovar typhimurium ycbl that establishes it as glx2, which differs in certain structural and functional properties compared with previously known examples. these features include the insertion of an α-helix after residue 8 ... | 2010 | 20669241 |