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structural analysis of the extracellular entrance to the serotonin transporter permeation pathway.neurotransmitter transporters are responsible for removal of biogenic amine neurotransmitters after release into the synapse. these transporters are the targets for many clinically relevant drugs, such as antidepressants and psychostimulants. a high resolution crystal structure for the monoamine transporters has yet to be solved. we have developed a homology model for the serotonin transporter (sert) based on the crystal structure of the leucine transporter (leut(aa)) from aquifex aeolicus. the ...201020304925
inhibition of the fe(4)s(4)-cluster-containing protein isph (lytb): electron paramagnetic resonance, metallacycles, and mechanisms.we report the inhibition of the aquifex aeolicus isph enzyme (lytb, (e)-4-hydroxy-3-methyl-but-2-enyl diphosphate reductase, ec 1.17.1.2) by a series of diphosphates and bisphosphonates. the most active species was an alkynyl diphosphate having ic(50) = 0.45 microm (k(i) approximately 60 nm), which generated a very large change in the 9 ghz epr spectrum of the reduced protein. on the basis of previous work on organometallic complexes, together with computational docking and quantum chemical calc ...201020426416
membrane-bound hydrogenase i from the hyperthermophilic bacterium aquifex aeolicus: enzyme activation, redox intermediates and oxygen tolerance.the membrane-bound hydrogenase (hase i) of the hyperthermophilic bacterium aquifex aeolicus belongs to an intriguing class of redox enzymes that show enhanced thermostability and oxygen tolerance. protein film electrochemistry is employed here to portray the interaction of hase i with molecular oxygen and obtain an overall picture of the catalytic activity. fourier transform infrared (ftir) spectroscopy integrated with in situ electrochemistry is used to identify structural details of the [nife] ...201020441192
homology modelling of the gaba transporter and analysis of tiagabine binding.a homology model of the human gaba transporter (gat-1) based on the recently reported crystal structures of the bacterial leucine transporter from aquifex aeolicus (leut) was developed. the stability of the resulting model embedded in a membrane environment was analyzed by extensive molecular dynamics (md) simulations. based on docking studies and subsequent md simulations of three compounds, the endogenous ligand gaba and two potent inhibitors, (r)-nipecotic acid and the anti-epilepsy drug tiag ...201020491137
observation of a chemically labile, noncovalent enzyme intermediate in the reaction of metal-dependent aquifex pyrophilus kdo8ps by time-resolved mass spectrometry.the direct detection of intermediates in enzymatic reactions can yield important mechanistic insights but may be difficult due to short intermediate lifetimes and chemical instability. using a rapid-mixing device coupled with electrospray ionization time-of-flight mass spectrometry, the noncovalent hemiketal intermediate in the reaction of metal-dependent 3-deoxy-d-manno-octulosonate-8-phosphate (kdo8p) synthase from aquifex pyrophilus was observed in the millisecond time range. using single tur ...201020533322
post-transfer editing by a eukaryotic leucyl-trna synthetase resistant to the broad-spectrum drug an2690.some aarss (aminoacyl-trna synthetases) develop editing mechanisms to correct mis-charged trna. the cp1 (connective peptide 1) domain of leurs (leucyl-trna synthetase) contains the editing active site, which is the proven target for the broad-spectrum drug an2690 (5-fluoro-1,3-dihydro-1-hydroxy-2,1-benzoxaborole). the esi (eukarya-specific insertion 1) in the cp1 domain of glleurs (giardia lamblia leurs) has been identified. similar substitution with the esi from hsleurs (homo sapiens leurs) imp ...201020557293
crystal structures of bacillus subtilis lon protease.lon atp-dependent proteases are key components of the protein quality control systems of bacterial cells and eukaryotic organelles. eubacterial lon proteases contain an n-terminal domain, an atpase domain, and a protease domain, all in one polypeptide chain. the n-terminal domain is thought to be involved in substrate recognition, the atpase domain in substrate unfolding and translocation into the protease chamber, and the protease domain in the hydrolysis of polypeptides into small peptide frag ...201020600124
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
conformational flexibility of transmembrane helix vii of the human serotonin transporter impacts ion dependence and transport.the serotonin transporter (sert) regulates the serotonin concentration in the synapse and is a target of several antidepressant and psychostimulant drugs. previous work suggested that the middle transmembrane helices (tmhs) of the biogenic amine transporters (tmhs) play a role in substrate and ion recognition. we focused our present studies on exploring the role of tmh vii in transporter function and ion recognition. residues divergent between human sert and drosophila sert (hsert and dsert, res ...201020637736
new cultural approaches for microaerophilic hyperthermophiles.this article reports on a new culture system designed for studying the effects of nutritional factors on the growth of hyperthermophilic and chemolithotrophic microorganisms. the system comprises 5-l stainless steel jars, an automatic gas dispenser, propylene microplates, and a robotic platform. the culture system was validated using aquifex aeolicus, a hyperthermophilic, chemolithotrophic, and microaerophilic bacterium, which requires hydrogen, oxygen, co₂, and minerals for growth. we demonstra ...201120676678
characterizing a monotopic membrane enzyme. biochemical, enzymatic and crystallization studies on aquifex aeolicus sulfide:quinone oxidoreductase.monotopic membrane proteins are membrane proteins that interact with only one leaflet of the lipid bilayer and do not possess transmembrane spanning segments. they are endowed with important physiological functions but until now only few of them have been studied. here we present a detailed biochemical, enzymatic and crystallographic characterization of the monotopic membrane protein sulfide:quinone oxidoreductase. sulfide:quinone oxidoreductase is a ubiquitous enzyme involved in sulfide detoxif ...201020691146
crystal structures of glycinamide ribonucleotide synthetase, purd, from thermophilic eubacteria.glycinamide ribonucleotide synthetase (gar-syn, purd) catalyses the second reaction of the purine biosynthetic pathway; the conversion of phosphoribosylamine, glycine and atp to glycinamide ribonucleotide (gar), adp and pi. in the present study, crystal structures of gar-syn's from thermus thermophilus, geobacillus kaustophilus and aquifex aeolicus were determined in apo forms. crystal structures in ligand-bound forms were also determined for g. kaustophilus and a. aeolicus proteins. in general, ...201020716513
building arks for trna: structure and function of the arc1p family of non-catalytic trna-binding proteins.following the intricate architecture of the eukaryotic cell, protein synthesis involves formation of many macromolecular assemblies, some of which are composed by trna-aminoacylation enzymes. protein-protein and protein-trna interactions in these complexes can be facilitated by non-catalytic trna-binding proteins. this review focuses on the dissection of the molecular, structural and functional properties of a particular family of such proteins: yeast arc1p and its homologues in prokaryotes and ...201020728442
the oxygen-tolerant hydrogenase i from aquifex aeolicus weakly interacts with carbon monoxide: an electrochemical and time-resolved ftir study.the [nife] hydrogenase (hase i) involved in the aerobic respiration of the hyperthermophilic bacterium aquifex aeolicus shows increased oxygen tolerance and thermostability and can form very stable films on pyrolytic graphite electrodes. oxygen-tolerant enzymes, like the ones from a. aeolicus and ralstonia eutropha, are reported to be insensitive to co inhibition. this is in contrast to known and well-characterized (oxygen-sensitive) hydrogenases, for which carbon monoxide is a competitive inhib ...201020815411
the high-affinity binding site for tricyclic antidepressants resides in the outer vestibule of the serotonin transporter.the structure of the bacterial leucine transporter from aquifex aeolicus (leut(aa)) has been used as a model for mammalian na(+)/cl(-)-dependent transporters, in particular the serotonin transporter (sert). the crystal structure of leut(aa) liganded to tricyclic antidepressants predicts simultaneous binding of inhibitor and substrate. this is incompatible with the mutually competitive inhibition of substrates and inhibitors of sert. we explored the binding modes of tricyclic antidepressants by h ...201020829432
methionyl-trna synthetase from caenorhabditis elegans: a specific multidomain organization for convergent functional evolution.methionyl-trna synthetase (metrs) is a multidomain protein that specifically binds trnamet and catalyzes the synthesis of methionyl-trnamet. the minimal, core enzyme found in aquifex aeolicus is made of a catalytic domain, which catalyzes the aminoacylation reaction, and an anticodon-binding domain, which promotes trna-protein association. in eukaryotes, additional domains are appended in cis or in trans to the core enzyme and increase the stability of the trna-protein complexes. eventually, as ...201020954242
characterization of c- and n-terminal domains of aquifex aeolicus mutl endonuclease: n-terminal domain stimulates the endonuclease activity of c-terminal domain in a zinc-dependent manner.dna mmr (mismatch repair) is an excision repair system that removes mismatched bases generated primarily by failure of the 3'-5' proofreading activity associated with replicative dna polymerases. mutl proteins homologous to human pms2 are the endonucleases that introduce the entry point of the excision reaction. deficiency in pms2 function is one of the major etiologies of hereditary non-polyposis colorectal cancers in humans. although recent studies revealed that the ctd (c-terminal domain) of ...201120961292
structural origins of nitroxide side chain dynamics on membrane protein α-helical sites.understanding the structure and dynamics of membrane proteins in their native, hydrophobic environment is important to understanding how these proteins function. epr spectroscopy in combination with site-directed spin labeling (sdsl) can measure dynamics and structure of membrane proteins in their native lipid environment; however, until now the dynamics measured have been qualitative due to limited knowledge of the nitroxide spin label's intramolecular motion in the hydrophobic environment. alt ...201020964375
new functional sulfide oxidase-oxygen reductase supercomplex in the membrane of the hyperthermophilic bacterium aquifex aeolicus.aquifex aeolicus, a hyperthermophilic and microaerophilic bacterium, obtains energy for growth from inorganic compounds alone. it was previously proposed that one of the respiratory pathways in this organism consists of the electron transfer from hydrogen sulfide (h(2)s) to molecular oxygen. h(2)s is oxidized by the sulfide quinone reductase, a membrane-bound flavoenzyme, which reduces the quinone pool. we have purified and characterized a novel membrane-bound multienzyme supercomplex that bring ...201020971847
stabilization role of a phenothiazine derivative on the electrocatalytic oxidation of hydrogen via aquifex aeolicus hydrogenase at graphite membrane electrodes.the [nife] membrane-bound hydrogenase from the microaerophilic, hyperthermophilic aquifex aeolicus bacterium (aa hase) presents oxygen, carbon monoxide, and temperature resistances. since it oxidizes hydrogen with high turnover, this enzyme is thus of particular interest for biotechnological applications, such as biofuel cells. efficient immobilization of the enzyme onto electrodes is however a mandatory step. to gain further insight into the parameters governing the interfacial electron process ...201021043442
engagement of arginine finger to atp triggers large conformational changes in ntrc1 aaa+ atpase for remodeling bacterial rna polymerase.the ntrc-like aaa+ atpases control virulence and other important bacterial activities through delivering mechanical work to σ54-rna polymerase to activate transcription from σ54-dependent genes. we report the first crystal structure for such an atpase, ntrc1 of aquifex aeolicus, in which the catalytic arginine engages the γ-phosphate of atp. comparing the new structure with those previously known for apo and adp-bound states supports a rigid-body displacement model that is consistent with large- ...201021070941
a naturally chimeric type iia topoisomerase in aquifex aeolicus highlights an evolutionary path for the emergence of functional paralogs.bacteria frequently possess two type iia dna topoisomerases, gyrase and topo iv, which maintain chromosome topology by variously supercoiling, relaxing, and disentangling dna. dna recognition and functional output is thought to be controlled by the c-terminal domain (ctd) of the topoisomerase dna binding subunit (gyra/parc). the deeply rooted organism aquifex aeolicus encodes one type iia topoisomerase conflictingly categorized as either dna gyrase or topo iv. to resolve this enzyme's catalytic ...201021076033
assembling networks of microbial genomes using linear programming.microbial genomes exhibit complex sets of genetic affinities due to lateral genetic transfer. assessing the relative contributions of parent-to-offspring inheritance and gene sharing is a vital step in understanding the evolutionary origins and modern-day function of an organism, but recovering and showing these relationships is a challenging problem.201021092133
discovery of a minimal form of rnase p in pyrobaculum.rnase p rna is an ancient, nearly universal feature of life. as part of the ribonucleoprotein rnase p complex, the rna component catalyzes essential removal of 5' leaders in pre-trnas. in 2004, li and altman computationally identified the rnase p rna gene in all but three sequenced microbes: nanoarchaeum equitans, pyrobaculum aerophilum, and aquifex aeolicus (all hyperthermophiles) [li y, altman s (2004) rna 10:1533-1540]. a recent study concluded that n. equitans does not have or require rnase ...201021135215
characterization of aquifex aeolicus ribonuclease iii and the reactivity epitopes of its pre-ribosomal rna substrates.ribonuclease iii cleaves double-stranded (ds) structures in bacterial rnas and participates in diverse rna maturation and decay pathways. essential insight on the rnase iii mechanism of dsrna cleavage has been provided by crystallographic studies of the enzyme from the hyperthermophilic bacterium, aquifex aeolicus. however, the biochemical properties of a. aeolicus (aa)-rnase iii and the reactivity epitopes of its substrates are not known. the catalytic activity of purified recombinant aa-rnase ...201021138964
structure of leishmania major methionyl-trna synthetase in complex with intermediate products methionyladenylate and pyrophosphate.leishmania parasites cause two million new cases of leishmaniasis each year with several hundreds of millions of people at risk. due to the paucity and shortcomings of available drugs, we have undertaken the crystal structure determination of a key enzyme from leishmania major in hopes of creating a platform for the rational design of new therapeutics. crystals of the catalytic core of methionyl-trna synthetase from l. major (lmmetrs) were obtained with the substrates mgatp and methionine presen ...201021144880
original design of an oxygen-tolerant [nife] hydrogenase: major effect of a valine-to-cysteine mutation near the active site.hydrogenases are efficient biological catalysts of h(2) oxidation and production. most of them are inhibited by o(2), and a prerequisite for their use in biotechnological applications under air is to improve their oxygen tolerance. we have previously shown that exchanging the residue at position 74 in the large subunit of the oxygen-sensitive [nife] hydrogenase from desulfovibrio fructosovorans could impact the reaction of the enzyme with o(2) (dementin, s.; j. am. chem. soc. 2009, 131, 10156-10 ...201021175174
control of lipopolysaccharide biosynthesis by ftsh-mediated proteolysis of lpxc is conserved in enterobacteria but not in all gram-negative bacteria.despite the essential function of lipopolysaccharides (lps) in gram-negative bacteria, it is largely unknown how the exact amount of this molecule in the outer membrane is controlled. the first committed step in lps biosynthesis is catalyzed by the lpxc enzyme. in escherichia coli, the cellular concentration of lpxc is adjusted by the only essential protease in this organism, the membrane-anchored metalloprotease ftsh. turnover of e. coli lpxc requires a length- and sequence-specific c-terminal ...201021193611
crystal structures, dynamics and functional implications of molybdenum-cofactor biosynthesis protein moga from two thermophilic organisms.molybdenum-cofactor (moco) biosynthesis is an evolutionarily conserved pathway in almost all kingdoms of life, including humans. two proteins, moga and moea, catalyze the last step of this pathway in bacteria, whereas a single two-domain protein carries out catalysis in eukaryotes. here, three crystal structures of the moco-biosynthesis protein moga from the two thermophilic organisms thermus thermophilus (ttmoga; 1.64 å resolution, space group p2(1)) and aquifex aeolicus (aamoga; 1.70 å resolut ...201021206014
purification, crystallization and preliminary x-ray crystallographic analysis of the c-terminal cytoplasmic domain of flhb from aquifex aeolicus.flhb is a key protein in the regulation of protein export by the bacterial flagellar secretion system. it is composed of two domains: an n-terminal transmembrane domain and a c-terminal cytoplasmic domain (flhbc). here, the crystallization and preliminary crystallographic analysis of flhbc from aquifex aeolicus are reported. purified protein was crystallized using the vapour-diffusion technique. the crystals diffracted to 2.3 å resolution and belonged to space group c2, with unit-cell parameters ...201121301106
conferment of folding ability to a naturally unfolded apocytochrome c through introduction of hydrophobic amino acid residues.hyperthermophilic aquifex aeolicus cytochrome c(555) (aa c(555)) exceptionally folds even in the apo state, unlike general cytochromes c including mesophilic pseudomonas aeruginosa cytochrome c(551) (pa c(551)), which is structurally homologous to aa c(555) in the holo state. here we hypothesized that the exceptional apo aa c(555) folding can be attributed to nine hydrophobic amino acid residues and proved this using a pa c(551) variant (denoted as pa-nh) carrying the nine hydrophobic residues a ...201121329369
domain interactions of the transcription-translation coupling factor escherichia coli nusg are intermolecular and transient.the bacterial transcription factor nusg (n-utilization substance g) is suggested to act as a key coupling factor between transcription and translation [burmann, schweimer, luo, wahl, stitt, gottesman and rösch (2010) science 328, 501-504] and contributes to phage ?-mediated antitermination in escherichia coli that enables read-through of early transcription termination sites. e. coli nusg consists of two structurally and functionally distinct domains that are connected through a flexible linker. ...201121345171
characterization of a unique [fes] cluster in the electron transfer chain of the oxygen tolerant [nife] hydrogenase from aquifex aeolicus.iron-sulfur clusters are versatile electron transfer cofactors, ubiquitous in metalloenzymes such as hydrogenases. in the oxygen-tolerant hydrogenase i from aquifex aeolicus such electron "wires" form a relay to a diheme cytb, an integral part of a respiration pathway for the reduction of o(2) to water. amino acid sequence comparison with oxygen-sensitive hydrogenases showed conserved binding motifs for three iron-sulfur clusters, the nature and properties of which were unknown so far. electron ...201121444783
structural insight into the rotational switching mechanism of the bacterial flagellar motor.the bacterial flagellar motor can rotate either clockwise (cw) or counterclockwise (ccw). three flagellar proteins, flig, flim, and flin, are required for rapid switching between the cw and ccw directions. switching is achieved by a conformational change in flig induced by the binding of a chemotaxis signaling protein, phospho-chey, to flim and flin. flig consists of three domains, flig(n), flig(m), and flig(c), and forms a ring on the cytoplasmic face of the ms ring of the flagellar basal body. ...201121572987
molecular basis of the differential interaction with lithium of glycine transporters glyt1 and glyt2.j. neurochem. (2011) 10.1111/j.1471-4159.2011.07309.x abstract: glycine synaptic levels are controlled by glycine transporters (glyts) catalyzing na(+) /cl(-) /glycine cotransport. glyt1 displays a 2 : 1 : 1 stoichiometry and is the main regulator of extracellular glycine concentrations. the neuronal glyt2, with higher sodium coupling (3 : 1 : 1), supplies glycine to the pre-synaptic terminal to refill synaptic vesicles. in this work, using structural homology modelling and molecular dynamics si ...201121574997
survival of thermophilic and hyperthermophilic microorganisms after exposure to uv-c, ionizing radiation and desiccation.in this study, we investigated the ability of several (hyper-) thermophilic archaea and phylogenetically deep-branching thermophilic bacteria to survive high fluences of monochromatic uv-c (254 nm) and high doses of ionizing radiation, respectively. nine out of fourteen tested microorganisms showed a surprisingly high tolerance against ionizing radiation, and two species (aquifex pyrophilus and ignicoccus hospitalis) were even able to survive 20 kgy. therefore, these species had a comparable sur ...201121638055
The elusive third subunit IIa of the bacterial B-type oxidases: the enzyme from the hyperthermophile Aquifex aeolicus.The reduction of molecular oxygen to water is catalyzed by complicated membrane-bound metallo-enzymes containing variable numbers of subunits, called cytochrome c oxidases or quinol oxidases. We previously described the cytochrome c oxidase II from the hyperthermophilic bacterium Aquifex aeolicus as a ba(3)-type two-subunit (subunits I and II) enzyme and showed that it is included in a supercomplex involved in the sulfide-oxygen respiration pathway. It belongs to the B-family of the heme-copper ...201121738733
interconversion of functional motions between mesophilic and thermophilic adenylate kinases.dynamic properties are functionally important in many proteins, including the enzyme adenylate kinase (ak), for which the open/closed transition limits the rate of catalytic turnover. here, we compare our previously published coarse-grained (double-well go) simulation of mesophilic ak from e. coli (akmeso) to simulations of thermophilic ak from aquifex aeolicus (akthermo). in akthermo, as with akmeso, the lid domain prefers to close before the nmp domain in the presence of ligand, but lid rigid- ...201121779157
crystallization and preliminary x-ray analysis of a putative sensor histidine kinase domain: the c-terminal domain of hksp4 from aquifex aeolicus vf5.the histidine kinase domain of the cytoplasmic protein hksp4 from the hyperthermophilic bacterium aquifex aeolicus vf5, located in the c-terminal half of the protein, was expressed, purified and crystallized. diffraction-quality crystals were obtained in the presence of adenosine triphosphate (atp) or adenosine 5'-(ß,?-imido)triphosphate (amppnp) by the sitting-drop vapour-diffusion method using peg 3350 as the precipitant. the crystals obtained in the presence of atp and amppnp diffracted x-ray ...201121795799
crystal structure of prephenate dehydrogenase from streptococcus mutans.prephenate dehydrogenase (pdh) is a bacterial enzyme that catalyzes conversion of prephenate to 4-hydroxyphenylpyruvate through the oxidative decarboxylation pathway for tyrosine biosynthesis. this enzymatic pathway exists in prokaryotes but is absent in mammals, indicating that it is a potential target for the development of new antibiotics. the crystal structure of pdh from streptococcus mutans in a complex with nad(+) shows that the enzyme exists as a homo-dimer, each monomer consisting of tw ...201121798280
peripheral insertion modulates editing activity of the isolated cp1 domain of leucyl-trna synthetase.a large insertion domain called connective peptide 1 (cp1) present in class ia aminoacyl-trna synthetases is responsible for post-transfer editing. leucyl-trna synthetases (leurs) from aquifex aeolicus and giardia lamblia possess unique 20 and 59 amino acid insertions respectively within the cp1 that are crucial for editing activity. crystal structures of aaleurs-cp1 (2.4+à), glleurs-cp1 (2.6+à) and the insertion deletion mutant aaleurs-cp1-+ö20 (2.5+à) were solved to understand the role of thes ...201121819379
evidence for a two-metal-ion mechanism in the cytidyltransferase kdsb, an enzyme involved in lipopolysaccharide biosynthesis.lipopolysaccharide (lps) is located on the surface of gram-negative bacteria and is responsible for maintaining outer membrane stability, which is a prerequisite for cell survival. furthermore, it represents an important barrier against hostile environmental factors such as antimicrobial peptides and the complement cascade during gram-negative infections. the sugar 3-deoxy-d-manno-oct-2-ulosonic acid (kdo) is an integral part of lps and plays a key role in lps functionality. prior to its incorpo ...201121826242
substrate trna recognition mechanism of a multi-site-specific trna methyltransferase, aquifex aeolicus trm1, based on the x-ray crystal structure.archaeal and eukaryotic trna (n(2)-, n(2)-guanine) dimethyltransferase (trm1) produces n(2)-, n(2)-dimethylguanine at position 26 in trna. in contrast, trm1 from aquifex aeolicus, a hyper-thermophilic eubacterium, modifies g27 as well as g26. here, a gel-mobility shift assay revealed that the t-arm in trna is the binding site of a. aeolicus trm1. to address the multi-site specificity, we performed an x-ray crystal structure study. the overall structure of a. aeolicus trm1 is similar to that of a ...201121844194
Templates and models of monoamine transporter proteins.X-ray crystallography, structural bioinformatics and computational chemistry have become important techniques in the discovery and development of effective and safe new drugs. From a drug discovery point of view, membrane proteins are among the most interesting molecular targets, but the current knowledge about detailed 3D structures of membrane proteins is sparse. Homology modeling techniques may provide structural knowledge about membrane proteins and their interactions with drugs and other mo ...201121864275
NMR structure of an acyl-carrier protein from Borrelia burgdorferi.Nearly complete resonance assignment and the high-resolution NMR structure of the acyl-carrier protein from Borrelia burgdorferi, a target of the Seattle Structural Genomics Center for Infectious Disease (SSGCID) structure-determination pipeline, are reported. This protein was chosen as a potential target for drug-discovery efforts because of its involvement in fatty-acid biosynthesis, an essential metabolic pathway, in bacteria. It was possible to assign >98% of backbone resonances and >92% of ...201121904063
dna stretching by bacterial initiators promotes replication origin opening.many replication initiators form higher-order oligomers that process host replication origins to promote replisome formation. in addition to dedicated duplex-dna-binding domains, cellular initiators possess aaa+ (atpases associated with various cellular activities) elements that drive functions ranging from protein assembly to origin recognition. in bacteria, the aaa+ domain of the initiator dnaa has been proposed to assist in single-stranded dna formation during origin melting. here we show cry ...201121964332
the cphaii protein from aquifex aeolicus exhibits a metal-dependent phosphodiesterase activity.the cphaii protein from the hyperthermophile aquifex aeolicus shows the five conserved motifs of the metallo-β-lactamase (mbl) superfamily and presents 28% identity with the aeromonas hydrophila subclass b2 cpha mbl. the gene encoding cphaii was amplified by pcr from the a. aeolicus genomic dna and overexpressed in escherichia coli using a plex-based expression system. the recombinant cphaii protein was purified by a combination of heating (to denature e. coli proteins) and two steps of immobili ...201222009263
the structure of aquifex aeolicus ribosomal protein s8 reveals a unique subdomain that contributes to an extremely tight association with 16s rrna.the assembly of ribonucleoprotein complexes occurs under a broad range of conditions, but the principles that promote assembly and allow function at high temperature are poorly understood. the ribosomal protein s8 from aquifex aeolicus (as8) is unique in that there is a 41-residue insertion in the consensus s8 sequence. in addition, as8 exhibits an unusually high affinity for the 16s ribosomal rna, characterized by a picomolar dissociation constant that is approximately 26,000-fold tighter than ...201122079365
structural insights into the catalytic mechanism of escherichia coli selenophosphate synthetase.selenophosphate synthetase (sps) catalyzes the synthesis of selenophosphate, the selenium donor for the biosynthesis of selenocysteine and 2-selenouridine residues in seleno-trna. selenocysteine, known as the 21st amino acid, is then incorporated into proteins during translation to form selenoproteins which serve a variety of cellular processes. sps activity is dependent on both mg(2+) and k(+) and uses atp, selenide, and water to catalyze the formation of amp, orthophosphate, and selenophosphat ...201222081394
spectroscopic characterization of the key catalytic intermediate ni-c in the o2-tolerant [nife] hydrogenase i from aquifex aeolicus: evidence of a weakly bound hydride.ni-c in the o(2)-tolerant hydrogenase i from aquifex aeolicus binds a hydride weaker than that in o(2)-sensitive hydrogenases. this is in line with the enhanced light-sensitivity of ni-c, greater lability of the hydride complex and increased catalytic redox potentials relevant to bio-h(2) oxidation.201122143669
structures of leut in bicelles define conformation and substrate binding in a membrane-like context.neurotransmitter sodium symporters (nsss) catalyze the uptake of neurotransmitters into cells, terminating neurotransmission at chemical synapses. consistent with the role of nsss in the central nervous system, they are implicated in multiple diseases and disorders. leut, from aquifex aeolicus, is a prokaryotic ortholog of the nss family and has contributed to our understanding of the structure, mechanism and pharmacology of nsss. at present, however, the functional state of leut in crystals gro ...201222245965
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