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cadaverine covalently linked to peptidoglycan is required for interaction between the peptidoglycan and the periplasm-exposed s-layer-homologous domain of major outer membrane protein mep45 in selenomonas ruminantium.the peptidoglycan of selenomonas ruminantium is covalently bound to cadaverine (pg-cadaverine), which likely plays a significant role in maintaining the integrity of the cell surface structure. the outer membrane of this bacterium contains a 45-kda major protein (mep45) that is a putative peptidoglycan-associated protein. in this report, we determined the nucleotide sequence of the mep45 gene and investigated the relationship between pg-cadaverine, mep45, and the cell surface structure. amino ac ...201020851903
bioenergetic cost of making an adenosine triphosphate molecule in animal mitochondria.the catalytic domain of the f-atpase in mitochondria protrudes into the matrix of the organelle, and is attached to the membrane domain by central and peripheral stalks. energy for the synthesis of atp from adp and phosphate is provided by the transmembrane proton-motive-force across the inner membrane, generated by respiration. the proton-motive force is coupled mechanically to atp synthesis by the rotation at about 100 times per second of the central stalk and an attached ring of c-subunits in ...201020847295
structural and kinetic characterization of 4-hydroxy-4-methyl-2-oxoglutarate/4-carboxy-4-hydroxy-2-oxoadipate aldolase, a protocatechuate degradation enzyme evolutionarily convergent with the hpai and dmpg pyruvate aldolases.4-hydroxy-4-methyl-2-oxoglutarate/4-carboxy-4-hydroxy-2-oxoadipate (hmg/cha) aldolase from pseudomonas putida f1 catalyzes the last step of the bacterial protocatechuate 4,5-cleavage pathway. the preferred substrates of the enzyme are 2-keto-4-hydroxy acids with a 4-carboxylate substitution. the enzyme also exhibits oxaloacetate decarboxylation and pyruvate α-proton exchange activity. sodium oxalate is a competitive inhibitor of the aldolase reaction. the ph dependence of k(cat)/k(m) and k(cat) ...201020843800
comparative study of three commonly used continuous deterministic methods for modeling gene regulation networks.a gene-regulatory network (grn) refers to dna segments that interact through their rna and protein products and thereby govern the rates at which genes are transcribed. creating accurate dynamic models of grns is gaining importance in biomedical research and development. to improve our understanding of continuous deterministic modeling methods employed to construct dynamic grn models, we have carried out a comprehensive comparative study of three commonly used systems of ordinary differential eq ...201020840745
small-molecule antioxidant proteome-shields in deinococcus radiodurans.for deinococcus radiodurans and other bacteria which are extremely resistant to ionizing radiation, ultraviolet radiation, and desiccation, a mechanistic link exists between resistance, manganese accumulation, and protein protection. we show that ultrafiltered, protein-free preparations of d. radiodurans cell extracts prevent protein oxidation at massive doses of ionizing radiation. in contrast, ultrafiltrates from ionizing radiation-sensitive bacteria were not protective. the d. radiodurans ult ...201020838443
inhibition of osteoclast bone resorption by disrupting vacuolar h+-atpase a3-b2 subunit interaction.vacuolar h(+)-atpases (v-atpases) are highly expressed in ruffled borders of bone-resorbing osteoclasts, where they play a crucial role in skeletal remodeling. to discover protein-protein interactions with the a subunit in mammalian v-atpases, a gal4 activation domain fusion library was constructed from an in vitro osteoclast model, receptor activator of nf-κb ligand-differentiated raw 264.7 cells. this library was screened with a bait construct consisting of a gal4 binding domain fused to the n ...201020837476
structural and biochemical studies of a fluoroacetyl-coa-specific thioesterase reveal a molecular basis for fluorine selectivity.we have initiated a broad-based program aimed at understanding the molecular basis of fluorine specificity in enzymatic systems, and in this context, we report crystallographic and biochemical studies on a fluoroacetyl-coenzyme a (coa) specific thioesterase (flk) from streptomyces cattleya. our data establish that flk is competent to protect its host from fluoroacetate toxicity in vivo and demonstrate a 10(6)-fold discrimination between fluoroacetyl-coa (k(cat)/k(m) = 5 × 10⁷ m⁻¹ s⁻¹) and acetyl ...201020836570
molecular modeling study for interaction between bacillus subtilis obg and nucleotides.the bacterial obg proteins (spo0b-associated gtp-binding protein) belong to the subfamily of p-loop gtpase proteins that contain two equally and highly conserved domains, a c-terminal gtp binding domain and an n-terminal glycine-rich domain which is referred as the "obg fold" and now it is considered as one of the new targets for antibacterial drug. when the obg protein is associated with gtp, it becomes activated, because conformation of obg fold changes due to the structural changes of gtpase ...201020830302
sequence- and structure-specific rna processing by a crispr endonuclease.many bacteria and archaea contain clustered regularly interspaced short palindromic repeats (crisprs) that confer resistance to invasive genetic elements. central to this immune system is the production of crispr-derived rnas (crrnas) after transcription of the crispr locus. here, we identify the endoribonuclease (csy4) responsible for crispr transcript (pre-crrna) processing in pseudomonas aeruginosa. a 1.8 angstrom crystal structure of csy4 bound to its cognate rna reveals that csy4 makes sequ ...201020829488
the membrane subunit nuol(nd5) is involved in the indirect proton pumping mechanism of escherichia coli complex i.complex i pumps protons across the membrane by using downhill redox energy. here, to investigate the proton pumping mechanism by complex i, we focused on the largest transmembrane subunit nuol (escherichia coli nd5 homolog). nuol/nd5 is believed to have h(+) translocation site(s), because of a high sequence similarity to multi-subunit na(+)/h(+) antiporters. we mutated thirteen highly conserved residues between nuol/nd5 and mrpa of na(+)/h(+) antiporters in the chromosomal nuol gene. the dnadh o ...201020826797
crystallization and preliminary x-ray crystallographic study of genx, a lysyl-trna synthetase paralogue from escherichia coli, in complex with translation elongation factor p.genx, a lysyl-trna synthetase paralogue from escherichia coli, was overexpressed in e. coli, purified by three chromatographic steps and cocrystallized with a lysyl adenylate analogue (lysams) by the hanging-drop vapour-diffusion method using peg 4000 as a precipitant. the genx-lysams crystals belonged to the triclinic space group p1, with unit-cell parameters a=54.80, b=69.15, c=94.08 a, alpha=95.47, beta=106.51, gamma=90.46 degrees, and diffracted to 1.9 a resolution. furthermore, genx was coc ...201020823541
bacteria, yeast, worms, and flies: exploiting simple model organisms to investigate human mitochondrial diseases.the extensive conservation of mitochondrial structure, composition, and function across evolution offers a unique opportunity to expand our understanding of human mitochondrial biology and disease. by investigating the biology of much simpler model organisms, it is often possible to answer questions that are unreachable at the clinical level. here, we review the relative utility of four different model organisms, namely the bacterium escherichia coli, the yeast saccharomyces cerevisiae, the nema ...201020818735
a new hypothesis on the simultaneous direct and indirect proton pump mechanisms in nadh-quinone oxidoreductase (complex i).recently, sazanov's group reported the x-ray structure of whole complex i [nature, 465, 441 (2010)], which presented a strong clue for a "piston-like" structure as a key element in an "indirect" proton pump. we have studied the nuol subunit which has a high sequence similarity to na(+)/h(+) antiporters, as do the nuom and n subunits. we constructed 27 site-directed nuol mutants. our data suggest that the h(+)/e(-) stoichiometry seems to have decreased from (4h(+)/2e(-)) in the wild-type to appro ...201020816962
structural biology of redox partner interactions in p450cam monooxygenase: a fresh look at an old system.the p450cam monooxygenase system consists of three separate proteins: the fad-containing, nadh-dependent oxidoreductase (putidaredoxin reductase or pdr), cytochrome p450cam and the 2fe2s ferredoxin (putidaredoxin or pdx), which transfers electrons from pdr to p450cam. over the past few years our lab has focused on the interaction between these redox components. it has been known for some time that pdx can serve as an effector in addition to its electron shuttle role. the binding of pdx to p450ca ...201120816746
structural biology of redox partner interactions in p450cam monooxygenase: a fresh look at an old system.the p450cam monooxygenase system consists of three separate proteins: the fad-containing, nadh-dependent oxidoreductase (putidaredoxin reductase or pdr), cytochrome p450cam and the 2fe2s ferredoxin (putidaredoxin or pdx), which transfers electrons from pdr to p450cam. over the past few years our lab has focused on the interaction between these redox components. it has been known for some time that pdx can serve as an effector in addition to its electron shuttle role. the binding of pdx to p450ca ...201120816746
rna helicases at work: binding and rearranging.rna helicases are ubiquitous, highly conserved enzymes that participate in nearly all aspects of rna metabolism. these proteins bind or remodel rna or rna-protein complexes in an atp-dependent fashion. how rna helicases physically perform their cellular tasks has been a longstanding question, but in recent years, intriguing models have started to link structure, mechanism and biological function for some rna helicases. this review outlines our current view on major structural and mechanistic the ...201120813532
template-directed ligation of tethered mononucleotides by t4 dna ligase for kinase ribozyme selection.in vitro selection of kinase ribozymes for small molecule metabolites, such as free nucleosides, will require partition systems that discriminate active from inactive rna species. while nucleic acid catalysis of phosphoryl transfer is well established for phosphorylation of 5' or 2' oh of oligonucleotide substrates, phosphorylation of diffusible small molecules has not been demonstrated.201020811490
mathematics, thermodynamics, and modeling to address ten common misconceptions about protein structure, folding, and stability.to fully understand the roles proteins play in cellular processes, students need to grasp complex ideas about protein structure, folding, and stability. our current understanding of these topics is based on mathematical models and experimental data. however, protein structure, folding, and stability are often introduced as descriptive, qualitative phenomena in undergraduate classes. in the process of learning about these topics, students often form incorrect ideas. for example, by learning about ...201020810950
ancestral roles of small rnas: an ago-centric perspective.rnai has existed at least since the divergence of prokaryotes and eukaryotes. this collection of pathways responds to a diversity of "abberant" rnas and generally silences or eliminates genes sharing sequence content with the silencing trigger. in the canonical pathway, double-stranded rnas are processed into small rnas, which guide effector complexes to their targets by complementary base pairing. many alternative routes from silencing trigger to small rna are continuously being uncovered. thou ...201120810548
targeting the chromosome partitioning protein para in tuberculosis drug discovery.to identify inhibitors of the essential chromosome partitioning protein para that are active against mycobacterium tuberculosis.201020810423
modular pathways for editing non-cognate amino acids by human cytoplasmic leucyl-trna synthetase.to prevent potential errors in protein synthesis, some aminoacyl-transfer rna (trna) synthetases have evolved editing mechanisms to hydrolyze misactivated amino acids (pre-transfer editing) or misacylated trnas (post-transfer editing). class ia leucyl-trna synthetase (leurs) may misactivate various natural and non-protein amino acids and then mischarge trna(leu). it is known that the fidelity of prokaryotic leurs depends on multiple editing pathways to clear the incorrect intermediates and produ ...201120805241
modular pathways for editing non-cognate amino acids by human cytoplasmic leucyl-trna synthetase.to prevent potential errors in protein synthesis, some aminoacyl-transfer rna (trna) synthetases have evolved editing mechanisms to hydrolyze misactivated amino acids (pre-transfer editing) or misacylated trnas (post-transfer editing). class ia leucyl-trna synthetase (leurs) may misactivate various natural and non-protein amino acids and then mischarge trna(leu). it is known that the fidelity of prokaryotic leurs depends on multiple editing pathways to clear the incorrect intermediates and produ ...201120805241
binding of the dimeric deinococcus radiodurans single-stranded dna binding protein to single-stranded dna.deinococcus radiodurans single-stranded (ss) dna binding protein (drssb) originates from a radiation-resistant bacterium and participates in dna recombination, replication, and repair. although it functions as a homodimer, it contains four dna binding domains (ob-folds) and thus is structurally similar to the escherichia coli ssb (ecossb) homotetramer. we examined the equilibrium binding of drssb to ssdna for comparison with that of ecossb. we find that the occluded site size of drssb on poly(dt ...201020795631
n-terminal fusion of a hyperthermophilic chitin-binding domain to xylose isomerase from thermotoga neapolitana enhances kinetics and thermostability of both free and immobilized enzymes.immobilization of a thermostable d-xylose isomerase (ec 5.3.1.5) from thermotoga neapolitana 5068 (tnxi) on chitin beads was accomplished via a n-terminal fusion with a chitin-binding domain (cbd) from a hyperthermophilic chitinase produced by pyrococcus furiosus (pf1233) to create a fusion protein (cbd-tnxi). the turnover numbers for glucose to fructose conversion for both unbound and immobilized cbd-tnxi were greater than the wild-type enzyme: k(cat) (min(-1)) was approximately 1,000, 3,800, a ...201020730758
a polyhedron made of trnas.supramolecular assembly is a powerful strategy used by nature to build nanoscale architectures with predefined sizes and shapes. with synthetic systems, however, numerous challenges remain to be solved before precise control over the synthesis, folding and assembly of rationally designed three-dimensional nano-objects made of rna can be achieved. here, using the transfer rna molecule as a structural building block, we report the design, efficient synthesis and structural characterization of stab ...201020729899
molecular basis of vancomycin dependence in vana-type staphylococcus aureus vrsa-9.the vancomycin-resistant staphylococcus aureus vrsa-9 clinical isolate was partially dependent on glycopeptide for growth. the responsible vana operon had the same organization as that of tn1546 and was located on a plasmid. the chromosomal d-ala:d-ala ligase (ddl) gene had two point mutations that led to q260k and a283e substitutions, resulting in a 200-fold decrease in enzymatic activity compared to that of the wild-type strain vrsa-6. to gain insight into the mechanism of enzyme impairment, w ...201020729361
an extreme thermophile, thermus thermophilus, is a polyploid bacterium.an extremely thermophilic bacterium, thermus thermophilus hb8, is one of the model organisms for systems biology. its genome consists of a chromosome (1.85 mb), a megaplasmid (0.26 mb) designated ptt27, and a plasmid (9.3 kb) designated ptt8, and the complete sequence is available. we show here that t. thermophilus is a polyploid organism, harboring multiple genomic copies in a cell. in the case of the hb8 strain, the copy number of the chromosome was estimated to be four or five, and the copy n ...201020729360
a mutation within the β subunit of escherichia coli rna polymerase impairs transcription from bacteriophage t4 middle promoters.during infection of escherichia coli, bacteriophage t4 usurps the host transcriptional machinery, redirecting it to the expression of early, middle, and late phage genes. middle genes, whose expression begins about 1 min postinfection, are transcribed both from the extension of early rna into middle genes and by the activation of t4 middle promoters. middle-promoter activation requires the t4 transcriptional activator mota and coactivator asia, which are known to interact with σ(70), the specifi ...201020729353
multifactorial determinants of protein expression in prokaryotic open reading frames.a quantitative description of the relationship between protein expression levels and open reading frame (orf) nucleotide sequences is important for understanding natural systems, designing synthetic systems, and optimizing heterologous expression. codon identity, mrna secondary structure, and nucleotide composition within orfs markedly influence expression levels. bioinformatic analysis of orf sequences in 816 bacterial genomes revealed that these features show distinct regional trends. to inves ...201020727358
dna mismatch repair in eukaryotes and bacteria.dna mismatch repair (mmr) corrects mismatched base pairs mainly caused by dna replication errors. the fundamental mechanisms and proteins involved in the early reactions of mmr are highly conserved in almost all organisms ranging from bacteria to human. the significance of this repair system is also indicated by the fact that defects in mmr cause human hereditary nonpolyposis colon cancers as well as sporadic tumors. to date, 2 types of mmrs are known: the human type and escherichia coli type. t ...201020725617
single molecule transcription profiling with afm.established techniques for global gene expression profiling, such as microarrays, face fundamental sensitivity constraints. due to greatly increasing interest in examining minute samples from micro-dissected tissues, including single cells, unorthodox approaches, including molecular nanotechnologies, are being explored in this application. here, we examine the use of single molecule, ordered restriction mapping, combined with afm, to measure gene transcription levels from very low abundance samp ...200720721301
crystal structure of a transfer-ribonucleoprotein particle that promotes asparagine formation.four out of the 22 aminoacyl-trnas (aa-trnas) are systematically or alternatively synthesized by an indirect, two-step route requiring an initial mischarging of the trna followed by trna-dependent conversion of the non-cognate amino acid. during trna-dependent asparagine formation, trna(asn) promotes assembly of a ribonucleoprotein particle called transamidosome that allows channelling of the aa-trna from non-discriminating aspartyl-trna synthetase active site to the gatcab amidotransferase site ...201020717102
the diheme cytochrome c(4) from vibrio cholerae is a natural electron donor to the respiratory cbb(3) oxygen reductase.the respiratory chain of vibrio cholerae contains three bd-type quinol oxygen reductases as well as one cbb(3) oxygen reductase. the cbb(3) oxygen reductase has been previously isolated and characterized; however, the natural mobile electron donor(s) that shuttles electrons between the bc(1) complex and the cbb(3) oxygen reductase is not known. the most likely candidates are the diheme cytochrome c(4) and monoheme cytochrome c(5), which have been previously shown to be present in the periplasm o ...201020715760
a flexible loop in yeast ribosomal protein l11 coordinates p-site trna binding.high-resolution structures reveal that yeast ribosomal protein l11 and its bacterial/archael homologs called l5 contain a highly conserved, basically charged internal loop that interacts with the peptidyl-transfer rna (trna) t-loop. we call this the l11 'p-site loop'. chemical protection of wild-type ribosome shows that that the p-site loop is inherently flexible, i.e. it is extended into the ribosomal p-site when this is unoccupied by trna, while it is retracted into the terminal loop of 25s rr ...201020705654
structural basis for the bacterial transcription-repair coupling factor/rna polymerase interaction.the transcription-repair coupling factor (trcf, the product of the mfd gene) is a widely conserved bacterial protein that mediates transcription-coupled dna repair. trcf uses its atp-dependent dna translocase activity to remove transcription complexes stalled at sites of dna damage, and stimulates repair by recruiting components of the nucleotide excision repair pathway to the site. a protein/protein interaction between trcf and the β-subunit of rna polymerase (rnap) is essential for trcf functi ...201020702425
superpose3d: a local structural comparison program that allows for user-defined structure representations.local structural comparison methods can be used to find structural similarities involving functional protein patches such as enzyme active sites and ligand binding sites. the outcome of such analyses is critically dependent on the representation used to describe the structure. indeed different categories of functional sites may require the comparison program to focus on different characteristics of the protein residues. we have therefore developed superpose3d, a novel structural comparison softw ...201020700534
yeast 18 s rrna is directly involved in the ribosomal response to stringent aug selection during translation initiation.in eukaryotes, the 40 s ribosomal subunit serves as the platform of initiation factor assembly, to place itself precisely on the aug start codon. structural arrangement of the 18 s rrna determines the overall shape of the 40 s subunit. here, we present genetic evaluation of yeast 18 s rrna function using 10 point mutations altering the polysome profile. all the mutants reduce the abundance of the mutant 40 s, making it limiting for translation initiation. two of the isolated mutations, g875a, al ...201020699223
mutations in 23s rrna at the peptidyl transferase center and their relationship to linezolid binding and cross-resistance.the oxazolidinone antibiotic linezolid targets the peptidyl transferase center (ptc) on the bacterial ribosome. thirteen single and four double 23s rrna mutations were introduced into a mycobacterium smegmatis strain with a single rrna operon. converting bacterial base identity by single mutations at positions 2032, 2453, and 2499 to human cytosolic base identity did not confer significantly reduced susceptibility to linezolid. the largest decrease in linezolid susceptibility for any of the intr ...201020696869
rnamotifscan: automatic identification of rna structural motifs using secondary structural alignment.recent studies have shown that rna structural motifs play essential roles in rna folding and interaction with other molecules. computational identification and analysis of rna structural motifs remains a challenging task. existing motif identification methods based on 3d structure may not properly compare motifs with high structural variations. other structural motif identification methods consider only nested canonical base-pairing structures and cannot be used to identify complex rna structura ...201020696653
structures of hypoxanthine-guanine phosphoribosyltransferase (ttha0220) from thermus thermophilus hb8.hypoxanthine-guanine phosphoribosyltransferase (hgprtase), which is a key enzyme in the purine-salvage pathway, catalyzes the synthesis of imp or gmp from alpha-d-phosphoribosyl-1-pyrophosphate and hypoxanthine or guanine, respectively. structures of hgprtase from thermus thermophilus hb8 in the unliganded form, in complex with imp and in complex with gmp have been determined at 2.1, 1.9 and 2.2 a resolution, respectively. the overall fold of the imp complex was similar to that of the unliganded ...201020693661
the role of l1 stalk-trna interaction in the ribosome elongation cycle.the ribosomal l1 stalk is a mobile structure implicated in directing trna movement during translocation through the ribosome. this article investigates three aspects of l1 stalk-trna interaction. first, by combining data from cryo electron microscopy, x-ray crystallography, and molecular dynamics simulations through the molecular dynamics flexible fitting method, we obtained atomic models of different trnas occupying the hybrid p/e state interacting with the l1 stalk. these models confirm the as ...201020691699
structural and functional studies of wlba: a dehydrogenase involved in the biosynthesis of 2,3-diacetamido-2,3-dideoxy-d-mannuronic acid .2,3-diacetamido-2,3-dideoxy-d-mannuronic acid (mannac3naca) is an unusual dideoxy sugar first identified nearly 30 years ago in the lipopolysaccharide of pseudomonas aeruginosa o:3a,d. it has since been observed in other organisms, including bordetella pertussis, the causative agent of whooping cough. five enzymes are required for the biosynthesis of udp-mannac3naca starting from udp-n-acetyl-d-glucosamine. here we describe a structural study of wlba, the nad-dependent dehydrogenase that catalyz ...201020690587
three distinct peptides from the n domain of translation termination factor erf1 surround stop codon in the ribosome.to study positioning of the polypeptide release factor erf1 toward a stop signal in the ribosomal decoding site, we applied photoactivatable mrna analogs, derivatives of oligoribonucleotides. the human erf1 peptides cross-linked to these short mrnas were identified. cross-linkers on the guanines at the second, third, and fourth stop signal positions modified fragment 31-33, and to lesser extent amino acids within region 121-131 (the "yxcxxxf loop") in the n domain. hence, both regions are involv ...201020688868
mechanism of microrna-target interaction: molecular dynamics simulations and thermodynamics analysis.micrornas (mirnas) are endogenously produced approximately 21-nt riboregulators that associate with argonaute (ago) proteins to direct mrna cleavage or repress the translation of complementary rnas. capturing the molecular mechanisms of mirna interacting with its target will not only reinforce the understanding of underlying rna interference but also fuel the design of more effective small-interfering rna strands. to address this, in the present work the rna-bound (ago-mirna, ago-mirna-target) a ...201020686687
origin of light-induced spin-correlated radical pairs in cryptochrome.blue-light excitation of cryptochromes and homologues uniformly triggers electron transfer (et) from the protein surface to the flavin adenine dinucleotide (fad) cofactor. a cascade of three conserved tryptophan residues has been considered to be critically involved in this photoreaction. if the fad is initially in its fully oxidized (diamagnetic) redox state, light-induced et via the tryptophan triad generates a series of short-lived spin-correlated radical pairs comprising an fad radical and a ...201020684534
electron cryomicroscopy of membrane proteins: specimen preparation for two-dimensional crystals and single particles.membrane protein structure and function can be studied by two powerful and highly complementary electron cryomicroscopy (cryo-em) methods: electron crystallography of two-dimensional (2d) crystals and single particle analysis of detergent-solubilized protein complexes. to obtain the highest-possible resolution data from membrane proteins, whether prepared as 2d crystals or single particles, cryo-em samples must be vitrified with great care. grid preparation for cryo-em of 2d crystals is possible ...201020678942
electron cryomicroscopy of membrane proteins: specimen preparation for two-dimensional crystals and single particles.membrane protein structure and function can be studied by two powerful and highly complementary electron cryomicroscopy (cryo-em) methods: electron crystallography of two-dimensional (2d) crystals and single particle analysis of detergent-solubilized protein complexes. to obtain the highest-possible resolution data from membrane proteins, whether prepared as 2d crystals or single particles, cryo-em samples must be vitrified with great care. grid preparation for cryo-em of 2d crystals is possible ...201020678942
functional role of thr-312 and thr-315 in the proton-transfer pathway in ba3 cytochrome c oxidase from thermus thermophilus.cytochrome ba(3) from thermus thermophilus is a member of the family of b-type heme-copper oxidases, which have a low degree of sequence homology to the well-studied mitochondrial-like a-type enzymes. recently, it was suggested that the ba(3) oxidase has only one pathway for the delivery of protons to the active site and that this pathway is spatially analogous to the k-pathway in the a-type oxidases [chang, h.-y., et al. (2009) proc. natl. acad. sci. u.s.a. 106, 16169-16173]. this suggested pat ...201020677778
dual biosynthesis pathway for longer-chain polyamines in the hyperthermophilic archaeon thermococcus kodakarensis.long-chain and/or branched-chain polyamines are unique polycations found in thermophiles. cytoplasmic polyamines were analyzed for cells cultivated at various growth temperatures in the hyperthermophilic archaeon thermococcus kodakarensis. spermidine [34] and n4-aminopropylspermine [3(3)43] were identified as major polyamines at 60°c, and the amounts of n4-aminopropylspermine [3(3)43] increased as the growth temperature rose. to identify genes involved in polyamine biosynthesis, a gene disruptio ...201020675472
poxa, yjek, and elongation factor p coordinately modulate virulence and drug resistance in salmonella enterica.we report an interaction between poxa, encoding a paralog of lysyl trna-synthetase, and the closely linked yjek gene, encoding a putative 2,3-beta-lysine aminomutase, that is critical for virulence and stress resistance in salmonella enterica. salmonella poxa and yjek mutants share extensive phenotypic pleiotropy, including attenuated virulence in mice, an increased ability to respire under nutrient-limiting conditions, hypersusceptibility to a variety of diverse growth inhibitors, and altered e ...201020670890
insights into the nitric oxide reductase mechanism of flavodiiron proteins from a flavin-free enzyme.flavodiiron proteins (fdps) catalyze reductive scavenging of dioxygen and nitric oxide in air-sensitive microorganisms. fdps contain a distinctive non-heme diiron/flavin mononucleotide (fmn) active site. alternative mechanisms for the nitric oxide reductase (nor) activity consisting of either protonation of a diiron-bridging hyponitrite or "super-reduction" of a diferrous-dinitrosyl by the proximal fmnh(2) in the rate-determining step have been proposed. to test these alternative mechanisms, we ...201020669924
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 ...201020669241
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 ...201020667822
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 ...201020667175
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.201020667132
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 ...201020666386
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 ...201020666385
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 ...201020663881
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 ...201020660479
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 ...201020660012
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 ...201020643656
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 ...201020639538
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 ...201020637421
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 ...201020637413
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 ...201020633304
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- ...201020631005
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 ...201020624731
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 ...201020622123
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 ...201020622059
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 ...201020617848
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 ...201020615963
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 ...201020615421
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).201020615256
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 ...201020610779
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 ...201220610545
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 ...201020603129
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 ...201020601684
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 ...201020601428
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 ...201020599545
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/1741-7007/8/54.201020598112
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 ...201020595000
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 ...201020594334
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 ...201020593793
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 ...201020588254
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 ...201020581186
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 ...201020575532
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 ...201020573954
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 ...201020573952
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 ...201020571080
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, ...201020568735
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 ...201020568729
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 ...201020564035
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 ...201020562828
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 ...201020562215
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 ...201020560533
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 ...201020558725
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 ...201020558545
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.201020550657
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 ...201020543819
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 ...201020543190
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