Publications

structural dynamics of the aminoacylation and proofreading functional cycle of bacterial leucyl-trna synthetase.	leucyl-trna synthetase (leurs) produces error-free leucyl-trna(leu) by coordinating translocation of the 3' end of (mis-)charged trnas from its synthetic site to a separate proofreading site for editing. here we report cocrystal structures of the escherichia coli leurs-trna(leu) complex in the aminoacylation or editing conformations, showing that translocation involves correlated rotations of four flexibly linked leurs domains. this pivots the trna to guide its charged 3' end from the closed ami ...	2012	22683997
rational design and directed evolution of a bacterial-type glutaminyl-trna synthetase precursor.	protein biosynthesis requires aminoacyl-transfer rna (trna) synthetases to provide aminoacyl-trna substrates for the ribosome. most bacteria and all archaea lack a glutaminyl-trna synthetase (glnrs); instead, gln-trna(gln) is produced via an indirect pathway: a glutamyl-trna synthetase (glurs) first attaches glutamate (glu) to trna(gln), and an amidotransferase converts glu-trna(gln) to gln-trna(gln). the human pathogen helicobacter pylori encodes two glurs enzymes, with glurs2 specifically amin ...	2012	22661575
structure of escherichia coli aspartate α-decarboxylase asn72ala: probing the role of asn72 in pyruvoyl cofactor formation.	the crystal structure of the asn72ala site-directed mutant of escherichia coli aspartate α-decarboxylase (adc) has been determined at 1.7 å resolution. the refined structure is consistent with the presence of a hydrolysis product serine in the active site in place of the pyruvoyl group required for catalysis, which suggests that the role of asn72 is to protect the ester formed during adc activation from hydrolysis. in previously determined structures of activated adc, including the wild type and ...	2012	22505409
chemoinformatic identification of novel inhibitors against mycobacterium tuberculosis l-aspartate α-decarboxylase.	l-aspartate α-decarboxylase (adc) belongs to a class of pyruvoyl dependent enzymes and catalyzes the conversion of aspartate to β-alanine in the pantothenate pathway, which is critical for the growth of several micro-organisms, including mycobacterium tuberculosis (mtb). its presence only in micro-organisms, fungi and plants and its absence in animals, particularly human, make it a promising drug target. we have followed a chemoinformatics-based approach to identify potential drug-like inhibitor ...	2012	22470451
genetic recombination in bacillus subtilis: a division of labor between two single-strand dna-binding proteins.	we have investigated the structural, biochemical and cellular roles of the two single-stranded (ss) dna-binding proteins from bacillus subtilis, ssba and ssbb. during transformation, ssbb localizes at the dna entry pole where it binds and protects internalized ssdna. the 2.8-å resolution structure of ssbb bound to ssdna reveals a similar overall protein architecture and ssdna-binding surface to that of escherichia coli ssb. ssba, which binds ssdna with higher affinity than ssbb, co-assembles ont ...	2012	22373918
new insight into the transcarbamylase family: the structure of putrescine transcarbamylase, a key catalyst for fermentative utilization of agmatine.	transcarbamylases reversibly transfer a carbamyl group from carbamylphosphate (cp) to an amine. although aspartate transcarbamylase and ornithine transcarbamylase (otc) are well characterized, little was known about putrescine transcarbamylase (ptc), the enzyme that generates cp for atp production in the fermentative catabolism of agmatine. we demonstrate that ptc (from enterococcus faecalis), in addition to using putrescine, can utilize l-ornithine as a poor substrate. crystal structures at 2.5 ...	2012	22363663
substrate channeling in proline metabolism.	proline metabolism is an important pathway that has relevance in several cellular functions such as redox balance, apoptosis, and cell survival. results from different groups have indicated that substrate channeling of proline metabolic intermediates may be a critical mechanism. one intermediate is pyrroline-5-carboxylate (p5c), which upon hydrolysis opens to glutamic semialdehyde (gsa). recent structural and kinetic evidence indicate substrate channeling of p5c/gsa occurs in the proline catabol ...	2012	22201749
architecture and conservation of the bacterial dna replication machinery, an underexploited drug target.	new antibiotics with novel modes of action are required to combat the growing threat posed by multi-drug resistant bacteria. over the last decade, genome sequencing and other high-throughput techniques have provided tremendous insight into the molecular processes underlying cellular functions in a wide range of bacterial species. we can now use these data to assess the degree of conservation of certain aspects of bacterial physiology, to help choose the best cellular targets for development of n ...	2012	22206257
naxd is a deacetylase required for lipid a modification and francisella pathogenesis.	modification of specific gram-negative bacterial cell envelope components, such as capsule, o-antigen and lipid a, are often essential for the successful establishment of infection. francisella species express lipid a molecules with unique characteristics involved in circumventing host defences, which significantly contribute to their virulence. in this study, we show that naxd, a member of the highly conserved ydjc superfamily, is a deacetylase required for an important modification of the oute ...	2012	22966934
structure of ribose 5-phosphate isomerase from the probiotic bacterium lactobacillus salivarius ucc118.	the structure of ribose 5-phosphate isomerase from the probiotic bacterium lactobacillus salivarius ucc188 has been determined at 1.72 å resolution. the structure was solved by molecular replacement, which identified the functional homodimer in the asymmetric unit. despite only showing 57% sequence identity to its closest homologue, the structure adopted the typical α and β d-ribose 5-phosphate isomerase fold. comparison to other related structures revealed high homology in the active site, allo ...	2012	23192019
high-resolution structures of thermus thermophilus enoyl-acyl carrier protein reductase in the apo form, in complex with nad+ and in complex with nad+ and triclosan.	enoyl-acyl carrier protein reductase (enr; the product of the fabi gene) is an important enzyme that is involved in the type ii fatty-acid-synthesis pathway of bacteria, plants, apicomplexan protozoa and mitochondria. harmful pathogens such as mycobacterium tuberculosis and plasmodium falciparum use the type ii fatty-acid-synthesis system, but not mammals or fungi, which contain a type i fatty-acid-synthesis pathway consisting of one or two multifunctional enzymes. for this reason, specific inhi ...	2012	23027736
molecular evolution of hydrogen peroxide degrading enzymes.	for efficient removal of intra- and/or extracellular hydrogen peroxide by dismutation to harmless dioxygen and water (2h(2)o(2) → o(2) + 2h(2)o), nature designed three metalloenzyme families that differ in oligomeric organization, monomer architecture as well as active site geometry and catalytic residues. here we report on the updated reconstruction of the molecular phylogeny of these three gene families. ubiquitous typical (monofunctional) heme catalases are found in all domains of life showin ...	2012	22330759
glutamine versus ammonia utilization in the nad synthetase family.	nad is a ubiquitous and essential metabolic redox cofactor which also functions as a substrate in certain regulatory pathways. the last step of nad synthesis is the atp-dependent amidation of deamido-nad by nad synthetase (nads). members of the nads family are present in nearly all species across the three kingdoms of life. in eukaryotic nads, the core synthetase domain is fused with a nitrilase-like glutaminase domain supplying ammonia for the reaction. this two-domain nads arrangement enabling ...	2012	22720044
staphylococcus aureus fabi: inhibition, substrate recognition, and potential implications for in vivo essentiality.	methicillin-resistant staphylococcus aureus (mrsa) infections constitute a serious health threat worldwide, and novel antibiotics are therefore urgently needed. the enoyl-acp reductase (safabi) is essential for the s. aureus fatty acid biosynthesis and, hence, serves as an attractive drug target. we have obtained a series of snapshots of this enzyme that provide a mechanistic picture of ligand and inhibitor binding, including a dimer-tetramer transition combined with extensive conformational cha ...	2012	22579249
aggregate reactivation mediated by the hsp100 chaperones.	hsp100 family of molecular chaperones shows a unique capability to resolubilize and reactivate aggregated proteins. the hsp100-mediated protein disaggregation is linked to the activity of other chaperones from the hsp70 and hsp40 families. the best-studied members of the hsp100 family are the bacterial clpb and hsp104 from yeast. hsp100 chaperones are members of a large super-family of energy-driven conformational "machines" known as aaa+ atpases. this review describes the current mechanistic mo ...	2012	22306514
frequency, spectrum, and nonzero fitness costs of resistance to myxopyronin in staphylococcus aureus.	the antibiotic myxopyronin (myx) functions by inhibiting bacterial rna polymerase (rnap). the binding site on rnap for myx-the rnap "switch region sw1/sw2 subregion"-is different from the binding site on rnap for the rnap inhibitor currently used in broad-spectrum antibacterial therapy, rifampin (rif). here, we report the frequency, spectrum, and fitness costs of myx resistance in staphylococcus aureus. the resistance rate for myx is 4 × 10(-8) to 7 × 10(-8) per generation, which is equal within ...	2012	23006749
whole genome analysis of leptospira licerasiae provides insight into leptospiral evolution and pathogenicity.	the whole genome analysis of two strains of the first intermediately pathogenic leptospiral species to be sequenced (leptospira licerasiae strains var010 and mmd0835) provides insight into their pathogenic potential and deepens our understanding of leptospiral evolution. comparative analysis of eight leptospiral genomes shows the existence of a core leptospiral genome comprising 1547 genes and 452 conserved genes restricted to infectious species (including l. licerasiae) that are likely to be pa ...	2012	23145189
spectral identification of intermediates generated during the reaction of dioxygen with the wild-type and eq(i-286) mutant of rhodobacter sphaeroides cytochrome c oxidase.	cytochrome c oxidase from rhodobacter sphaeroides is frequently used to model the more complex mitochondrial enzyme. the o(2) reduction in both enzymes is generally described by a unidirectional mechanism involving the sequential formation of the ferrous-oxy complex (compound a), the p(r) state, the oxyferryl f form, and the oxidized state. in this study we investigated the reaction of dioxygen with the wild-type reduced r. sphaeroides cytochrome oxidase and the eq(i-286) mutant using the co flo ...	2012	23057757
roles of subunit nuok (nd4l) in the energy-transducing mechanism of escherichia coli ndh-1 (nadh:quinone oxidoreductase).	the bacterial h(+)-translocating nadh:quinone oxidoreductase (ndh-1) catalyzes electron transfer from nadh to quinone coupled with proton pumping across the cytoplasmic membrane. the nuok subunit (counterpart of the mitochondrial nd4l subunit) is one of the seven hydrophobic subunits in the membrane domain and bears three transmembrane segments (tm1-3). two glutamic residues located in the adjacent transmembrane helices of nuok are important for the energy coupled activity of ndh-1. in particula ...	2012	23105119
cell-free protein synthesis: the state of the art.	cell-free protein synthesis harnesses the synthetic power of biology, programming the ribosomal translational machinery of the cell to create macromolecular products. like pcr, which uses cellular replication machinery to create a dna amplifier, cell-free protein synthesis is emerging as a transformative technology with broad applications in protein engineering, biopharmaceutical development, and post-genomic research. by breaking free from the constraints of cell-based systems, it takes the nex ...	2012	23086573
cell-free protein synthesis: the state of the art.	cell-free protein synthesis harnesses the synthetic power of biology, programming the ribosomal translational machinery of the cell to create macromolecular products. like pcr, which uses cellular replication machinery to create a dna amplifier, cell-free protein synthesis is emerging as a transformative technology with broad applications in protein engineering, biopharmaceutical development, and post-genomic research. by breaking free from the constraints of cell-based systems, it takes the nex ...	2012	23086573
copper starvation-inducible protein for cytochrome oxidase biogenesis in bradyrhizobium japonicum.	microarray analysis of bradyrhizobium japonicum grown under copper limitation uncovered five genes named pcuabcde, which are co-transcribed and co-regulated as an operon. the predicted gene products are periplasmic proteins (pcua, pcuc, and pcud), a tonb-dependent outer membrane receptor (pcub), and a cytoplasmic membrane-integral protein (pcue). homologs of pcuc and pcue had been discovered in other bacteria, namely pcu(a)c and ycnj, where they play a role in cytochrome oxidase biogenesis and c ...	2012	23012364
spectroscopic and kinetic investigation of the fully reduced and mixed valence states of ba3-cytochrome c oxidase from thermus thermophilus: a fourier transform infrared (ftir) and time-resolved step-scan ftir study.	the complete understanding of a molecular mechanism of action requires the thermodynamic and kinetic characterization of different states and intermediates. cytochrome c oxidase reduces o(2) to h(2)o, a reaction coupled to proton translocation across the membrane. therefore, it is necessary to undertake a thorough characterization of the reduced form of the enzyme and the determination of the electron transfer processes and pathways between the redox-active centers. in this study fourier transfo ...	2012	22927441
a three-dimensional topology of complex i inferred from evolutionary correlations.	the quaternary structure of eukaryotic nadh:ubiquinone oxidoreductase (complex i), the largest complex of the oxidative phosphorylation, is still mostly unresolved. furthermore, it is unknown where transiently bound assembly factors interact with complex i. we therefore asked whether the evolution of complex i contains information about its 3d topology and the binding positions of its assembly factors. we approached these questions by correlating the evolutionary rates of eukaryotic complex i su ...	2012	22857522
structural determinants of the β-selectivity of a bacterial aminotransferase.	chiral β-amino acids occur as constituents of various natural and synthetic compounds with potentially useful bioactivities. the pyridoxal 5'-phosphate (plp)-dependent s-selective transaminase from mesorhizobium sp. strain luk (mesat) is a fold type i aminotransferase that can be used for the preparation of enantiopure β-phe and derivatives thereof. using x-ray crystallography, we solved structures of mesat in complex with (s)-β-phe, (r)-3-amino-5-methylhexanoic acid, 2-oxoglutarate, and the inh ...	2012	22745123
from static structure to living protein: computational analysis of cytochrome c oxidase main-chain flexibility.	crystallographic structure and deuterium accessibility comparisons of cco in different redox states have suggested conformational changes of mechanistic significance. to predict the intrinsic flexibility and low energy motions in cco, this work has analyzed available high-resolution crystallographic structures with proflex and elnémo computational methods. the results identify flexible regions and potential conformational changes in cco that correlate well with published structural and biochemic ...	2012	22824280
structure, function, and assembly of heme centers in mitochondrial respiratory complexes.	the sequential flow of electrons in the respiratory chain, from a low reduction potential substrate to o(2), is mediated by protein-bound redox cofactors. in mitochondria, hemes-together with flavin, iron-sulfur, and copper cofactors-mediate this multi-electron transfer. hemes, in three different forms, are used as a protein-bound prosthetic group in succinate dehydrogenase (complex ii), in bc(1) complex (complex iii) and in cytochrome c oxidase (complex iv). the exact function of heme b in comp ...	2012	22554985
mechanistic stoichiometry of proton translocation by cytochrome cbb3.	cytochrome cbb(3) belongs to the superfamily of respiratory heme-copper oxidases that couple the reduction of molecular oxygen to proton translocation across the bacterial or mitochondrial membrane. the cbb(3)-type enzymes are found only in bacteria, and are both structurally and functionally the most distant from their mitochondrial counterparts. the mechanistic h(+)/e(-) stoichiometry of proton translocation in these cbb(3)-type cytochrome c oxidases has remained controversial. a stoichiometri ...	2012	22529361
product-controlled steady-state kinetics between cytochrome aa(3) from rhodobacter sphaeroides and equine ferrocytochrome c analyzed by a novel spectrophotometric approach.	cytochrome c oxidase (cco) catalyzes the reduction of molecular oxygen to water using ferrocytochrome c (cyt c(2+)) as the electron donor. in this study, the oxidation of horse cyt c(2+) by cco from rhodobacter sphaeroides, was monitored using stopped-flow spectrophotometry. a novel analytic procedure was applied in which the spectra were deconvoluted into the reduced and oxidized forms of cyt c by a least-squares fitting method, yielding the reaction rates at various concentrations of cyt c(2+) ...	2012	22516686
electron transfer in subunit nuoi (tyky) of escherichia coli nadh:quinone oxidoreductase (ndh-1).	bacterial proton-translocating nadh:quinone oxidoreductase (ndh-1) consists of a peripheral and a membrane domain. the peripheral domain catalyzes the electron transfer from nadh to quinone through a chain of seven iron-sulfur (fe/s) clusters. subunit nuoi in the peripheral domain contains two [4fe-4s] clusters (n6a and n6b) and plays a role in bridging the electron transfer from cluster n5 to the terminal cluster n2. we constructed mutants for eight individual cys-coordinating fe/s clusters. wi ...	2012	22474289
exploring the proton pump and exit pathway for pumped protons in cytochrome ba3 from thermus thermophilus.	the heme-copper oxygen reductases are redox-driven proton pumps. in the current work, the effects of mutations in a proposed exit pathway for pumped protons are examined in the ba(3)-type oxygen reductase from thermus thermophilus, leading from the propionates of heme a(3) to the interface between subunits i and ii. recent studies have proposed important roles for his376 and asp372, both of which are hydrogen-bonded to propionate-a of heme a(3), and for glu126(ii) (subunit ii), which is hydrogen ...	2012	22431640
rna polymerase-promoter interactions determining different stability of the escherichia coli and thermus aquaticus transcription initiation complexes.	transcription initiation complexes formed by bacterial rna polymerases (rnaps) exhibit dramatic species-specific differences in stability, leading to different strategies of transcription regulation. the molecular basis for this diversity is unclear. promoter complexes formed by rnap from thermus aquaticus (taq) are considerably less stable than escherichia coli rnap promoter complexes, particularly at temperatures below 37°c. here, we used a fluorometric rnap molecular beacon assay to discern p ...	2012	23087380
interplay of dna repair with transcription: from structures to mechanisms.	many dna transactions are crucial for maintaining genomic integrity and faithful transfer of genetic information but remain poorly understood. an example is the interplay between nucleotide excision repair (ner) and transcription, also known as transcription-coupled dna repair (tcr). discovered decades ago, the mechanisms for tcr have remained elusive, not in small part due to the scarcity of structural studies of key players. here we summarize recent structural information on ner/tcr factors, f ...	2012	23084398
altered large-ring cyclodextrin product profile due to a mutation at tyr-172 in the amylomaltase of corynebacterium glutamicum.	corynebacterium glutamicum amylomaltase (cgam) catalyzes the formation of large-ring cyclodextrins (lr-cds) with a degree of polymerization of 19 and higher. the cloned cgam gene was ligated into the pet-17b vector and used to transform escherichia coli bl21(de3). site-directed mutagenesis of tyr-172 in cgam to alanine (y172a) was performed to determine its role in the control of lr-cd production. both the recombinant wild-type (wt) and y172a enzymes were purified to apparent homogeneity and cha ...	2012	22865069
basic mechanisms of rna polymerase ii activity and alteration of gene expression in saccharomyces cerevisiae.	transcription by rna polymerase ii (pol ii), and all rna polymerases for that matter, may be understood as comprising two cycles. the first cycle relates to the basic mechanism of the transcription process wherein pol ii must select the appropriate nucleoside triphosphate (ntp) substrate complementary to the dna template, catalyze phosphodiester bond formation, and translocate to the next position on the dna template. performing this cycle in an iterative fashion allows the synthesis of rna chai ...	2012	23022618
basic mechanisms of rna polymerase ii activity and alteration of gene expression in saccharomyces cerevisiae.	transcription by rna polymerase ii (pol ii), and all rna polymerases for that matter, may be understood as comprising two cycles. the first cycle relates to the basic mechanism of the transcription process wherein pol ii must select the appropriate nucleoside triphosphate (ntp) substrate complementary to the dna template, catalyze phosphodiester bond formation, and translocate to the next position on the dna template. performing this cycle in an iterative fashion allows the synthesis of rna chai ...	2012	23022618
dna stabilization at the bacillus subtilis polx core--a binding model to coordinate polymerase, ap-endonuclease and 3'-5' exonuclease activities.	family x dna polymerases (polxs) are involved in dna repair. their binding to gapped dnas relies on two conserved helix-hairpin-helix motifs, one located at the 8-kda domain and the other at the fingers subdomain. bacterial/archaeal polxs have a specifically conserved third helix-hairpin-helix motif (gfgxk) at the fingers subdomain whose putative role in dna binding had not been established. here, mutagenesis at the corresponding residues of bacillus subtilis polx (polxbs), gly130, gly132 and ly ...	2012	22844091
structural basis for translation termination by archaeal rf1 and gtp-bound ef1α complex.	when a stop codon appears at the ribosomal a site, the class i and ii release factors (rfs) terminate translation. in eukaryotes and archaea, the class i and ii rfs form a heterodimeric complex, and complete the overall translation termination process in a gtp-dependent manner. however, the structural mechanism of the translation termination by the class i and ii rf complex remains unresolved. in archaea, archaeal elongation factor 1 alpha (aef1α), a carrier gtpase for trna, acts as a class ii r ...	2012	22772989
draft genome sequence of thermus sp. strain rl, isolated from a hot water spring located atop the himalayan ranges at manikaran, india.	thermus sp. strain rl was isolated from a hot water spring (90°c to 98°c) at manikaran, himachal pradesh, india. here we report the draft genome sequence (20,36,600 bp) of this strain. the draft genome sequence consists of 17 contigs and 1,986 protein-coding sequences and has an average g+c content of 68.77%.	2012	22689228
distinct functions of regions 1.1 and 1.2 of rna polymerase σ subunits from escherichia coli and thermus aquaticus in transcription initiation.	rna polymerase (rnap) from thermophilic thermus aquaticus is characterized by higher temperature of promoter opening, lower promoter complex stability, and higher promoter escape efficiency than rnap from mesophilic escherichia coli. we demonstrate that these differences are in part explained by differences in the structures of the n-terminal regions 1.1 and 1.2 of the e. coli σ(70) and t. aquaticus σ(a) subunits. in particular, region 1.1 and, to a lesser extent, region 1.2 of the e. coli σ(70) ...	2012	22605342
closely related archaeal haloarcula hispanica icosahedral viruses hhiv-2 and sh1 have nonhomologous genes encoding host recognition functions.	studies on viral capsid architectures and coat protein folds have revealed the evolutionary lineages of viruses branching to all three domains of life. a widespread group of icosahedral tailless viruses, the prd1-adenovirus lineage, was the first to be established. a double β-barrel fold for a single major capsid protein is characteristic of these viruses. similar viruses carrying genes coding for two major capsid proteins with a more complex structure, such as thermus phage p23-77 and haloarcha ...	2012	22357274
characterization of multi-functional properties and conformational analysis of muts2 from thermotoga maritima msb8.	the muts2 homologues have received attention because of their unusual activities that differ from those of muts. in this work, we report on the functional characteristics and conformational diversities of thermotoga maritima muts2 (tmmuts2). various biochemical features of the protein were demonstrated via diverse techniques such as scanning probe microscopy (spm), atpase assays, analytical ultracentrifugation, dna binding assays, size chromatography, and limited proteolytic analysis. dimeric tm ...	2012	22545085
related bifunctional restriction endonuclease-methyltransferase triplets: tspdti, tth111ii/tthhb27i and tsoi with distinct specificities.	we previously defined a family of restriction endonucleases (reases) from thermus sp., which share common biochemical and biophysical features, such as the fusion of both the nuclease and methyltransferase (mtase) activities in a single polypeptide, cleavage at a distance from the recognition site, large molecular size, modulation of activity by s-adenosylmethionine (sam), and incomplete cleavage of the substrate dna. members include related thermophilic reases with five distinct specificities: ...	2012	22489904
a novel phage-encoded transcription antiterminator acts by suppressing bacterial rna polymerase pausing.	gp39, a small protein encoded by thermus thermophilus phage p23-45, specifically binds the host rna polymerase (rnap) and inhibits transcription initiation. here, we demonstrate that gp39 also acts as an antiterminator during transcription through intrinsic terminators. the antitermination activity of gp39 relies on its ability to suppress transcription pausing at poly(u) tracks. gp39 also accelerates transcription elongation by decreasing rnap pausing and backtracking but does not significantly ...	2012	22238378
crystal structures and molecular dynamics simulations of thermophilic malate dehydrogenase reveal critical loop motion for co-substrate binding.	malate dehydrogenase (mdh) catalyzes the conversion of oxaloacetate and malate by using the nad/nadh coenzyme system. the system is used as a conjugate for enzyme immunoassays of a wide variety of compounds, such as illegal drugs, drugs used in therapeutic applications and hormones. we elucidated the biochemical and structural features of mdh from thermus thermophilus (ttmdh) for use in various biotechnological applications. the biochemical characterization of recombinant ttmdh revealed greatly ...	2013	24386145
single molecule analysis of thermus thermophilus ssb protein dynamics on single-stranded dna.	single-stranded (ss) dna binding (ssb) proteins play central roles in dna replication, recombination and repair in all organisms. we previously showed that escherichia coli (eco) ssb, a homotetrameric bacterial ssb, undergoes not only rapid ssdna-binding mode transitions but also one-dimensional diffusion (or migration) while remaining bound to ssdna. whereas the majority of bacterial ssb family members function as homotetramers, dimeric ssb proteins were recently discovered in a distinct bacter ...	2013	24371279
single molecule analysis of thermus thermophilus ssb protein dynamics on single-stranded dna.	single-stranded (ss) dna binding (ssb) proteins play central roles in dna replication, recombination and repair in all organisms. we previously showed that escherichia coli (eco) ssb, a homotetrameric bacterial ssb, undergoes not only rapid ssdna-binding mode transitions but also one-dimensional diffusion (or migration) while remaining bound to ssdna. whereas the majority of bacterial ssb family members function as homotetramers, dimeric ssb proteins were recently discovered in a distinct bacter ...	2013	24371279
genetically encoded fluorescent indicator for imaging nad(+)/nadh ratio changes in different cellular compartments.	the ratio of nad(+)/nadh is a key indicator that reflects the overall redox state of the cells. until recently, there were no methods for real time nad(+)/nadh monitoring in living cells. genetically encoded fluorescent probes for nad(+)/nadh are fundamentally new approach for studying the nad(+)/nadh dynamics.	2013	24286672
genetically encoded fluorescent indicator for imaging nad(+)/nadh ratio changes in different cellular compartments.	the ratio of nad(+)/nadh is a key indicator that reflects the overall redox state of the cells. until recently, there were no methods for real time nad(+)/nadh monitoring in living cells. genetically encoded fluorescent probes for nad(+)/nadh are fundamentally new approach for studying the nad(+)/nadh dynamics.	2013	24286672
structure of escherichia coli rna polymerase holoenzyme at last.		2013	24272941
directed polymerase evolution.	polymerases evolved in nature to synthesize dna and rna, and they underlie the storage and flow of genetic information in all cells. the availability of these enzymes for use at the bench has driven a revolution in biotechnology and medicinal research; however, polymerases did not evolve to function efficiently under the conditions required for some applications and their high substrate fidelity precludes their use for most applications that involve modified substrates. to circumvent these limit ...	2013	24211837
directed polymerase evolution.	polymerases evolved in nature to synthesize dna and rna, and they underlie the storage and flow of genetic information in all cells. the availability of these enzymes for use at the bench has driven a revolution in biotechnology and medicinal research; however, polymerases did not evolve to function efficiently under the conditions required for some applications and their high substrate fidelity precludes their use for most applications that involve modified substrates. to circumvent these limit ...	2013	24211837
identification and characterization of a novel trehalose synthase gene derived from saline-alkali soil metagenomes.	a novel trehalose synthase (tres) gene was identified from a metagenomic library of saline-alkali soil by a simple activity-based screening system. sequence analysis revealed that tres encodes a protein of 552 amino acids, with a deduced molecular weight of 63.3 kda. after being overexpressed in escherichia coli and purified, the enzymatic properties of tres were investigated. the recombinant tres displayed its optimal activity at ph 9.0 and 45 °c, and the addition of most common metal ions (1 o ...	2013	24146994
interplay between the trigger loop and the f loop during rna polymerase catalysis.	the trigger loop (tl) in the rna polymerase (rnap) active center plays key roles in the reactions of nucleotide addition and rna cleavage catalyzed by rnap. the adjacent f loop (fl) was proposed to contribute to rnap catalysis by modulating structural changes in the tl. here, we investigate the interplay between these two elements during transcription by bacterial rnap. thermodynamic analysis of catalysis by rnap variants with mutations in the tl and fl suggests that the tl is the key element re ...	2013	24089145
interplay between the trigger loop and the f loop during rna polymerase catalysis.	the trigger loop (tl) in the rna polymerase (rnap) active center plays key roles in the reactions of nucleotide addition and rna cleavage catalyzed by rnap. the adjacent f loop (fl) was proposed to contribute to rnap catalysis by modulating structural changes in the tl. here, we investigate the interplay between these two elements during transcription by bacterial rnap. thermodynamic analysis of catalysis by rnap variants with mutations in the tl and fl suggests that the tl is the key element re ...	2013	24089145
effects of upconversion nanoparticles on polymerase chain reaction.	nanoparticles (nps) are attractive materials owing to their physical and electrochemical properties, which make them extremely useful in diagnostic applications. photon upconversion is the phenomenon where high-energy photons are emitted upon excitation of low-energy photons. nucleic acids detection based on upconversion nanoparticles (ucnps), which display a high signal-to-noise ratio and no photobleaching, has been widely applied. we evaluated whether ucnps can improve polymerase chain reactio ...	2013	24039935
exploration of deinococcus-thermus molecular diversity by novel group-specific pcr primers.	the deeply branching deinococcus-thermus lineage is recognized as one of the most extremophilic phylum of bacteria. in previous studies, the presence of deinococcus-related bacteria in the hot arid tunisian desert of tataouine was demonstrated through combined molecular and culture-based approaches. similarly, thermus-related bacteria have been detected in tunisian geothermal springs. the present work was conducted to explore the molecular diversity within the deinococcus-thermus phylum in these ...	2013	23996915
computational simulation strategies for analysis of multisubunit rna polymerases.		2013	23987500
incorporation of nucleoside probes opposite o⁶-methylguanine by sulfolobus solfataricus dna polymerase dpo4: importance of hydrogen bonding.	o⁶-methylguanine (o⁶-meg) is a mutagenic dna lesion, arising from the action of methylating agents on guanine (g) in dna. dpo4, an archaeal low-fidelity y-family dna polymerase involved in translesion dna synthesis (tls), is a model for studying how human y-family polymerases bypass dna adducts. previous work showed that dpo4-mediated dttp incorporation is favored opposite o⁶-meg rather than opposite g. however, factors influencing the preference of dpo4 to incorporate dttp opposite o⁶-meg are n ...	2013	23959784
tagetitoxin inhibits transcription by stabilizing pre-translocated state of the elongation complex.	transcription elongation consists of repetition of the nucleotide addition cycle: phosphodiester bond formation, translocation and binding of the next nucleotide. inhibitor of multi-subunit rna polymerase tagetitoxin (tgt) enigmatically slows down addition of nucleotides in a sequence-dependent manner, only at certain positions of the template. here, we show that tgt neither affects chemistry of rna synthesis nor induces backward translocation, nor competes with the nucleoside triphosphate (ntp) ...	2013	23935117
energetic and structural details of the trigger-loop closing transition in rna polymerase ii.	an evolutionarily conserved element in rna polymerase ii, the trigger loop (tl), has been suggested to play an important role in the elongation rate, fidelity of selection of the matched nucleoside triphosphate (ntp), catalysis of transcription elongation, and translocation in both eukaryotes and prokaryotes. in response to ntp binding, the tl undergoes large conformational changes to switch between distinct open and closed states to tighten the active site and avail catalysis. a computational s ...	2013	23931324
by ribosome possessed.		2013	23814064
x-ray crystal structures of the escherichia coli rna polymerase in complex with benzoxazinorifamycins.	rifampin, a semisynthetic rifamycin, is the cornerstone of current tuberculosis treatment. among many semisynthetic rifamycins, benzoxazinorifamycins have great potential for tb treatment due to their superior affinity for wild-type and rifampin-resistant mycobacterium tuberculosis rna polymerases and their reduced hepatic cyp450 induction activity. in this study, we have determined the crystal structures of the escherichia coli rna polymerase complexes with two benzoxazinorifamycins. the ansa-n ...	2013	23679862
the rna polymerase trigger loop functions in all three phases of the transcription cycle.	the trigger loop (tl) forms a conserved element in the rna polymerase active centre that functions in the elongation phase of transcription. here, we show that the tl also functions in transcription initiation and termination. using recombinant variants of rna polymerase from pyrococcus furiosus and a reconstituted transcription system, we demonstrate that the tl is essential for initial rna synthesis until a complete dna-rna hybrid is formed. the archaeal tl is further important for transcripti ...	2013	23737452
a structural role for the php domain in e. coli dna polymerase iii.	in addition to the core catalytic machinery, bacterial replicative dna polymerases contain a polymerase and histidinol phosphatase (php) domain whose function is not entirely understood. the php domains of some bacterial replicases are active metal-dependent nucleases that may play a role in proofreading. in e. coli dna polymerase iii, however, the php domain has lost several metal-coordinating residues and is likely to be catalytically inactive.	2013	23672456
a rex family transcriptional repressor influences h2o2 accumulation by enterococcus faecalis.	rex factors are bacterial transcription factors thought to respond to the cellular nad(+)/nadh ratio in order to modulate gene expression by differentially binding dna. to date, rex factors have been implicated in regulating genes of central metabolism, oxidative stress response, and biofilm formation. the genome of enterococcus faecalis, a low-gc gram-positive opportunistic pathogen, encodes ef2638, a putative rex factor. to study the role of e. faecalis rex, we purified ef2638 and evaluated it ...	2013	23417491
thermostable mismatch-recognizing protein muts suppresses nonspecific amplification during polymerase chain reaction (pcr).	polymerase chain reaction (pcr)-related technologies are hampered mainly by two types of error: nonspecific amplification and dna polymerase-generated mutations. here, we report that both errors can be suppressed by the addition of a dna mismatch-recognizing protein, muts, from a thermophilic bacterium. although it had been expected that muts has a potential to suppress polymerase-generated mutations, we unexpectedly found that it also reduced nonspecific amplification. on the basis of this find ...	2013	23519109
structure of the poliiiα-τc-dna complex suggests an atomic model of the replisome.	the c-terminal domain (ctd) of the τ subunit of the clamp loader (τc) binds to both the dnab helicase and the dna polymerase iii α subunit (poliiiα), and determines their relative positions and orientations on the leading and lagging strands. here, we present a 3.2 å resolution structure of thermus aquaticus poliiiα in complex with τc and a dna substrate. the structure reveals that the ctd of τc interacts with the ctd of poliiiα through its c-terminal helix and the adjacent loop. additionally, i ...	2013	23478062
x-ray crystal structure of escherichia coli rna polymerase σ70 holoenzyme.	escherichia coli rna polymerase (rnap) is the most studied bacterial rnap and has been used as the model rnap for screening and evaluating potential rnap-targeting antibiotics. however, the x-ray crystal structure of e. coli rnap has been limited to individual domains. here, i report the x-ray structure of the e. coli rnap σ(70) holoenzyme, which shows σ region 1.1 (σ1.1) and the α subunit c-terminal domain for the first time in the context of an intact rnap. σ1.1 is positioned at the rnap dna-b ...	2013	23389035
structural basis of transcriptional pausing in bacteria.	transcriptional pausing by multisubunit rna polymerases (rnaps) is a key mechanism for regulating gene expression in both prokaryotes and eukaryotes and is a prerequisite for transcription termination. pausing and termination states are thought to arise through a common, elemental pause state that is inhibitory for nucleotide addition. we report three crystal structures of thermus rnap elemental paused elongation complexes (epecs). the structures reveal the same relaxed, open-clamp rnap conforma ...	2013	23374340
whole genome sequencing of thermus oshimai jl-2 and thermus thermophilus jl-18, incomplete denitrifiers from the united states great basin.	the strains thermus oshimai jl-2 and thermus thermophilus jl-18 each have a circular chromosome, 2.07 mb and 1.9 mb in size, respectively, and each has two plasmids ranging from 0.27 mb to 57.2 kb. the megaplasmid of each strain contains a gene cluster for the reduction of nitrate to nitrous oxide, consistent with their incomplete denitrification phenotypes.	2013	23405355
density functional study for the bridged dinuclear center based on a high-resolution x-ray crystal structure of ba3 cytochrome c oxidase from thermus thermophilus.	strong electron density for a peroxide type dioxygen species bridging the fea3 and cub dinuclear center (dnc) was observed in the high-resolution (1.8 å) x-ray crystal structures (pdb entries 3s8g and 3s8f) of ba3 cytochrome c oxidase (cco) from thermus thermophilus. the crystals represent the as-isolated x-ray photoreduced cco structures. the bridging peroxide was proposed to arise from the recombination of two radiation-produced ho(•) radicals formed either very near to or even in the space be ...	2013	24262070
investigating the function of [2fe-2s] cluster n1a, the off-pathway cluster in complex i, by manipulating its reduction potential.	nadh:quinone oxidoreductase (complex i) couples nadh oxidation and quinone reduction to proton translocation across an energy-transducing membrane. all complexes i contain a flavin to oxidize nadh, seven iron-sulfur clusters to transfer electrons from the flavin to quinone and an eighth cluster (n1a) on the opposite side of the flavin. the role of cluster n1a is unknown, but escherichia coli complex i has an unusually high-potential cluster n1a and its reduced flavin produces h2o2, not superoxid ...	2013	23980528
molecular mechanism and physiological role of active-deactive transition of mitochondrial complex i.	the unique feature of mitochondrial complex i is the so-called a/d transition (active-deactive transition). the a-form catalyses rapid oxidation of nadh by ubiquinone (k ~104 min-1) and spontaneously converts into the d-form if the enzyme is idle at physiological temperatures. such deactivation occurs in vitro in the absence of substrates or in vivo during ischaemia, when the ubiquinone pool is reduced. the d-form can undergo reactivation given both nadh and ubiquinone availability during slow ( ...	2013	24059527
the nitric-oxide reductase from paracoccus denitrificans uses a single specific proton pathway.	the no reductase from paracoccus denitrificans reduces no to n2o (2no + 2h(+) + 2e(-) → n2o + h2o) with electrons donated by periplasmic cytochrome c (cytochrome c-dependent no reductase; cnor). cnors are members of the heme-copper oxidase superfamily of integral membrane proteins, comprising the o2-reducing, proton-pumping respiratory enzymes. in contrast, although no reduction is as exergonic as o2 reduction, there are no protons pumped in cnor, and in addition, protons needed for no reduction ...	2013	24014024
axial interactions in the mixed-valent cua active site and role of the axial methionine in electron transfer.	within cu-containing electron transfer active sites, the role of the axial ligand in type 1 sites is well defined, yet its role in the binuclear mixed-valent cua sites is less clear. recently, the mutation of the axial met to leu in a cua site engineered into azurin (cua az) was found to have a limited effect on e(0) relative to this mutation in blue copper (bc). detailed low-temperature absorption and magnetic circular dichroism, resonance raman, and electron paramagnetic resonance studies on c ...	2013	23964128
comparative genomics in acid mine drainage biofilm communities reveals metabolic and structural differentiation of co-occurring archaea.	metal sulfide mineral dissolution during bioleaching and acid mine drainage (amd) formation creates an environment that is inhospitable to most life. despite dominance by a small number of bacteria, amd microbial biofilm communities contain a notable variety of coexisting and closely related euryarchaea, most of which have defied cultivation efforts. for this reason, we used metagenomics to analyze variation in gene content that may contribute to niche differentiation among co-occurring amd arch ...	2013	23865623
characterization of the nitric oxide reductase from thermus thermophilus.	nitrous oxide (n2o) is a powerful greenhouse gas implicated in climate change. the dominant source of atmospheric n2o is incomplete biological dentrification, and the enzymes responsible for the release of n2o are no reductases. it was recently reported that ambient emissions of n2o from the great boiling spring in the united states great basin are high, and attributed to incomplete denitrification by thermus thermophilus and related bacterial species [hedlund bp, et al. (2011) geobiology 9(6)47 ...	2013	23858452
post-translational modifications near the quinone binding site of mammalian complex i.	complex i (nadh:ubiquinone oxidoreductase) in mammalian mitochondria is an l-shaped assembly of 44 protein subunits with one arm buried in the inner membrane of the mitochondrion and the orthogonal arm protruding about 100 å into the matrix. the protruding arm contains the binding sites for nadh, the primary acceptor of electrons flavin mononucleotide (fmn), and a chain of seven iron-sulfur clusters that carries the electrons one at a time from fmn to a coenzyme q molecule bound in the vicinity ...	2013	23836892
combined effect of loss of the caa3 oxidase and crp regulation drives shewanella to thrive in redox-stratified environments.	shewanella species are a group of facultative gram-negative microorganisms with remarkable respiration abilities that allow the use of a diverse array of terminal electron acceptors (ea). like most bacteria, s. oneidensis possesses multiple terminal oxidases, including two heme-copper oxidases (caa3- and cbb3-type) and a bd-type quinol oxidase. as aerobic respiration is energetically favored, mechanisms underlying the fact that these microorganisms thrive in redox-stratified environments remain ...	2013	23575370
semiquinone and cluster n6 signals in his-tagged proton-translocating nadh:ubiquinone oxidoreductase (complex i) from escherichia coli.	nadh:ubiquinone oxidoreductase (complex i) pumps protons across the membrane using downhill redox energy. the escherichia coli complex i consists of 13 different subunits named nuoa-n coded by the nuo operon. due to the low abundance of the protein and some difficulty with the genetic manipulation of its large ~15-kb operon, purification of e. coli complex i has been technically challenging. here, we generated a new strain in which a polyhistidine sequence was inserted upstream of nuoe in the op ...	2013	23543743
the mechanism of ubihydroquinone oxidation at the qo-site of the cytochrome bc1 complex.	1. recent results suggest that the major flux is carried by a monomeric function, not by an intermonomer electron flow. 2. the bifurcated reaction at the qo-site involves sequential partial processes, - a rate limiting first electron transfer generating a semiquinone (sq) intermediate, and a rapid second electron transfer in which the sq is oxidized by the low potential chain. 3. the rate constant for the first step in a strongly endergonic, proton-first-then-electron mechanism, is given by a ma ...	2013	23396004
etmb-rbf: discrimination of metal-binding sites in electron transporters based on rbf networks with pssm profiles and significant amino acid pairs.	cellular respiration is the process by which cells obtain energy from glucose and is a very important biological process in living cell. as cells do cellular respiration, they need a pathway to store and transport electrons, the electron transport chain. the function of the electron transport chain is to produce a trans-membrane proton electrochemical gradient as a result of oxidation-reduction reactions. in these oxidation-reduction reactions in electron transport chains, metal ions play very i ...	2013	23405059
ligand access to the active site in thermus thermophilus ba(3) and bovine heart aa(3) cytochrome oxidases.	knowledge of the structure and dynamics of the ligand channel(s) in heme-copper oxidases is critical for understanding how the protein environment modulates the functions of these enzymes. using photolabile no and o(2) carriers, we recently found that no and o(2) binding in thermus thermophilus (tt) ba(3) is ~10 times faster than in the bovine enzyme, indicating that inherent structural differences affect ligand access in these enzymes. using x-ray crystallography, time-resolved optical absorpti ...	2013	23282175
atypical features of thermus thermophilus succinate:quinone reductase.	the thermus thermophilus succinate:quinone reductase (sqr), serving as the respiratory complex ii, has been homologously produced under the control of a constitutive promoter and subsequently purified. the detailed biochemical characterization of the resulting wild type (wt-rcii) and his-tagged (rcii-his(8)-sdhb and rcii-sdhb-his(6)) complex ii variants showed the same properties as the native enzyme with respect to the subunit composition, redox cofactor content and sensitivity to the inhibitor ...	2013	23308253
integron gene cassettes: a repository of novel protein folds with distinct interaction sites.	mobile gene cassettes captured within integron arrays encompass a vast and diverse pool of genetic novelty. in most cases, functional annotation of gene cassettes directly recovered by cassette-pcr is obscured by their characteristically high sequence novelty. this inhibits identification of those specific functions or biological features that might constitute preferential factors for lateral gene transfer via the integron system. a structural genomics approach incorporating x-ray crystallograph ...	2013	23349695
initiation of mrna decay in bacteria.	the instability of messenger rna is fundamental to the control of gene expression. in bacteria, mrna degradation generally follows an "all-or-none" pattern. this implies that if control is to be efficient, it must occur at the initiating (and presumably rate-limiting) step of the degradation process. studies of e. coli and b. subtilis, species separated by 3 billion years of evolution, have revealed the principal and very disparate enzymes involved in this process in the two organisms. the early ...	2013	24064983
initiation of mrna decay in bacteria.	the instability of messenger rna is fundamental to the control of gene expression. in bacteria, mrna degradation generally follows an "all-or-none" pattern. this implies that if control is to be efficient, it must occur at the initiating (and presumably rate-limiting) step of the degradation process. studies of e. coli and b. subtilis, species separated by 3 billion years of evolution, have revealed the principal and very disparate enzymes involved in this process in the two organisms. the early ...	2013	24064983
detection, distribution and characterization of novel superoxide dismutases from yersinia enterocolitica biovar 1a.	superoxide dismutases (sods) cause dismutation of superoxide radicals to hydrogen peroxide and oxygen. besides protecting the cells against oxidative damage by endogenously generated oxygen radicals, sods play an important role in intraphagocytic survival of pathogenic bacteria. the complete genome sequences of yersinia enterocolitica strains show presence of three different sod genes. however, not much is known about the types of sods present in y. enterocolitica, their characteristics and role ...	2013	23704955
psychrophily and catalysis.	polar and other low temperature environments are characterized by a low content in energy and this factor has a strong incidence on living organisms which populate these rather common habitats. indeed, low temperatures have a negative effect on ectothermic populations since they can affect their growth, reaction rates of biochemical reactions, membrane permeability, diffusion rates, action potentials, protein folding, nucleic acids dynamics and other temperature-dependent biochemical processes. ...	2013	24832805
structures of protein-protein complexes involved in electron transfer.	electron transfer reactions are essential for life because they underpin oxidative phosphorylation and photosynthesis, processes leading to the generation of atp, and are involved in many reactions of intermediary metabolism. key to these roles is the formation of transient inter-protein electron transfer complexes. the structural basis for the control of specificity between partner proteins is lacking because these weak transient complexes have remained largely intractable for crystallographic ...	2013	23535590
type iv pili in gram-positive bacteria.	type iv pili (t4p) are surface-exposed fibers that mediate many functions in bacteria, including locomotion, adherence to host cells, dna uptake (competence), and protein secretion and that can act as nanowires carrying electric current. t4p are composed of a polymerized protein, pilin, and their assembly apparatuses share protein homologs with type ii secretion systems in eubacteria and the flagella of archaea. t4p are found throughout gram-negative bacterial families and have been studied most ...	2013	24006467
replacing sulfa drugs with novel dhps inhibitors.	more research effort needs to be invested in antimicrobial drug development to address the increasing threat of multidrug-resistant organisms. the enzyme dhps has been a validated drug target for over 70 years as the target for the highly successful sulfa drugs. the use of sulfa drugs has been compromised by the widespread presence of resistant organisms and the adverse side effects associated with their use. despite the large amount of structural information available for dhps, few recent publi ...	2013	23859210
systematic analysis of compositional order of proteins reveals new characteristics of biological functions and a universal correlate of macroevolution.	we present a novel analysis of compositional order (co) based on the occurrence of frequent amino-acid triplets (fts) that appear much more than random in protein sequences. the method captures all types of proteomic compositional order including single amino-acid runs, tandem repeats, periodic structure of motifs and otherwise low complexity amino-acid regions. we introduce new order measures, distinguishing between 'regularity', 'periodicity' and 'vocabulary', to quantify these phenomena and t ...	2013	24278003
molecular mechanisms of crispr-mediated microbial immunity.	bacteriophages (phages) infect bacteria in order to replicate and burst out of the host, killing the cell, when reproduction is completed. thus, from a bacterial perspective, phages pose a persistent lethal threat to bacterial populations. not surprisingly, bacteria evolved multiple defense barriers to interfere with nearly every step of phage life cycles. phages respond to this selection pressure by counter-evolving their genomes to evade bacterial resistance. the antagonistic interaction betwe ...	2013	23959171
molecular mechanisms of crispr-mediated microbial immunity.	bacteriophages (phages) infect bacteria in order to replicate and burst out of the host, killing the cell, when reproduction is completed. thus, from a bacterial perspective, phages pose a persistent lethal threat to bacterial populations. not surprisingly, bacteria evolved multiple defense barriers to interfere with nearly every step of phage life cycles. phages respond to this selection pressure by counter-evolving their genomes to evade bacterial resistance. the antagonistic interaction betwe ...	2013	23959171
angling for uniqueness in enzymatic preparation of glycosides.	in the early days of biocatalysis, limitations of an enzyme modeled the enzymatic applications; nowadays the enzyme can be engineered to be suitable for the process requirements. this is a general bird's-eye view and as such cannot be specific for articulated situations found in different classes of enzymes or for selected enzymatic processes. as far as the enzymatic preparation of glycosides is concerned, recent scientific literature is awash with examples of uniqueness related to the features ...	2013	24970171
in planta mutagenesis of src homology 3 domain-like fold of ndhs, a ferredoxin-binding subunit of the chloroplast nadh dehydrogenase-like complex in arabidopsis: a conserved arg-193 plays a critical role in ferredoxin binding.	chloroplast nadh dehydrogenase-like (ndh) complex mediates cyclic electron transport around photosystem i and chlororespiration in angiosperms. the src homology 3 domain (sh3)-like fold protein ndhs/crr31 is an ndh subunit that is necessary for high affinity binding of ferredoxin, indicating that chloroplast ndh functions as a ferredoxin:plastoquinone oxidoreductase. however, the mechanism of the interaction between ndhs and ferredoxin is unclear. in this study, we analyzed their interaction in ...	2013	24225949
a novel type of n-acetylglutamate synthase is involved in the first step of arginine biosynthesis in corynebacterium glutamicum.	arginine biosynthesis in corynebacterium glutamicum consists of eight enzymatic steps, starting with acetylation of glutamate, catalysed by n-acetylglutamate synthase (nags). there are different kinds of known nagss, for example, "classical" arga, bifunctional argj, argo, and s-nags. however, since c. glutamicum possesses a monofunctional argj, which catalyses only the fifth step of the arginine biosynthesis pathway, glutamate must be acetylated by an as of yet unknown nags gene.	2013	24138314
archaeal signal transduction: impact of protein phosphatase deletions on cell size, motility, and energy metabolism in sulfolobus acidocaldarius.	in this study, the in vitro and in vivo functions of the only two identified protein phosphatases, saci-ptp and saci-pp2a, in the crenarchaeal model organism sulfolobus acidocaldarius were investigated. biochemical characterization revealed that saci-ptp is a dual-specific phosphatase (against pser/pthr and ptyr), whereas saci-pp2a exhibited specific pser/pthr activity and inhibition by okadaic acid. deletion of saci_pp2a resulted in pronounced alterations in growth, cell shape and cell size, wh ...	2013	24078887