Publications

TitleAbstractYear(sorted descending)
Filter
PMID
Filter
phylogenetic analysis of methanogens in the pig feces.in order to assess methanogen diversity in feces of pigs, archaeal 16s rrna gene clone libraries were constructed from feces of the pig. after the amplification by pcr using primers met86f and met1340r, equal quantities of pcr products from each of the five pigs were mixed together and used to construct the library. sequence analysis showed that the 74 clones were divided into ten phylotypes as defined by rflp analysis. phylogenetic analysis showed that three phylotypes were most closely affilia ...201121259005
crystal structure of bifunctional 5,10-methylenetetrahydrofolate dehydrogenase/cyclohydrolase from thermoplasma acidophilum.folate co-enzymes play a pivotal role in one-carbon transfer cellular processes. many eukaryotes encode the tri-functional tetrahydrofolate dehydrogenase/cyclohydrolase/synthetase (deh/cyc/syn) enzyme, which consists of a n-terminal bifunctional domain (deh/cyc) and a c-terminal monofunctional domain (syn). here, we report the first analogous archeal enzyme structures, for the bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase from thermoplasma acidophilum (tamthfdc) as the nati ...201121333632
atp binds to proteasomal atpases in pairs with distinct functional effects, implying an ordered reaction cycle.in the eukaryotic 26s proteasome, the 20s particle is regulated by six aaa atpase subunits and, in archaea, by a homologous ring complex, pan. to clarify the role of atp in proteolysis, we studied how nucleotides bind to pan. although pan has six identical subunits, it binds atps in pairs, and its subunits exhibit three conformational states with high, low, or no affinity for atp. when pan binds two atp?s molecules or two atp?s plus two adp molecules, it is maximally active in binding protein su ...201121335235
engineered thermoplasma acidophilum factor f3 mimics human aminopeptidase n (apn) as a target for anticancer drug development.human aminopeptidase n (hapn) is an appealing objective for the development of anti-cancer agents. the absence of mammalian apn experimental structure negatively impinges upon the progression of structure-based drug design. tricorn interacting factor f3 (factor f3) from thermoplasma acidophilum shares 33% sequence identity with hapn. engineered factor f3 with two point directed mutations resulted in a protein with an active site identical to hapn. in the present work, the engineered factor f3 ha ...201121493078
architectures of archaeal gins complexes, essential dna replication initiation factors.abstract: background: in the early stage of eukaryotic dna replication, the template dna is unwound by the mcm helicase, which is activated by forming a complex with the cdc45 and gins proteins. the eukaryotic gins forms a heterotetramer, comprising four types of subunits. on the other hand, the archaeal gins appears to be either a tetramer formed by two types of subunits in a 2:2 ratio (alpha2beta2) or a homotetramer of a single subunit (alpha4). due to the low sequence similarity between the a ...201121527023
crystallization and preliminary x-ray diffraction analysis of transaldolase from thermoplasma acidophilum.the metabolic enzyme transaldolase from thermoplasma acidophilum was recombinantly expressed in escherichia coli and could be crystallized in two polymorphic forms. crystals were grown by the hanging-drop vapour-diffusion method using peg 6000 as precipitant. native data sets for crystal forms 1 and 2 were collected in-house to resolutions of 3.0 and 2.7 å, respectively. crystal form 1 belonged to the orthorhombic space group c222(1) with five monomers per asymmetric unit and crystal form 2 belo ...201121543867
site-directed methyl group labeling as an nmr probe of structure and dynamics in supramolecular protein systems: applications to the proteasome and to the clpp protease.methyl groups are powerful reporters of structure, motion, and function in nmr studies of supramolecular protein assemblies. their utility can be hindered, however, by spectral overlap, difficulties with assignment or lack of probes in biologically important regions of the molecule studied. here we show that (13)ch(3)-s- labeling of cys side chains using (13)c-methyl-methanethiosulfonate ((13)c-mmts) (iupac name: methylsulfonylsulfanylmethane) provides a convenient probe of molecular structure a ...201121557628
crystal structure of the novel paia n-acetyltransferase from thermoplasma acidophilum involved in the negative control of sporulation and degradative enzyme production.gcn5-related n-acetyltransferases (gnats) are the most widely distributed acetyltransferase systems among all three domains of life. gnats appear to be involved in several key processes, including microbial antibiotic resistance, compacting eukaryotic dna, controlling gene expression, and protein synthesis. here, we report the crystal structure of a putative gnat ta0374 from thermoplasma acidophilum, a hyperacidophilic bacterium, that has been determined in an apo-form, in complex with its natur ...201121633970
the gins complex from the thermophilic archaeon, thermoplasma acidophilum may function as a homotetramer in dna replication.the eukaryotic gins heterotetramer, consisting of sld5, psf1, psf2, and psf3, participates in "cmg complex" formation with mini-chromosome maintenance (mcm) and cdc45 as a key component of a replicative helicase. there are only two homologs of the gins proteins in archaea, and these proteins, gins51 and gins23, form a heterotetrameric gins with a 2:2 molar ratio. the pyrococcus furiosus gins stimulates the atpase and helicase activities of its cognate mcm, whereas the sulfolobus solfataricus gin ...201121656171
uracil-dna glycosylase of thermoplasma acidophilumdirects long-patch base excision repair, which is promoted by deoxynucleoside triphosphates and atp/adp, into short-patch repair.hydrolytic deamination of cytosine to uracil in dna is increased in organisms adapted to high temperatures. hitherto, the uracil base excision repair (ber) pathway has only been described in two archaeons, the crenarchaeon pyrobaculum aerophilumand the euryarchaeon archaeoglobus fulgidus, which are hyperthermophiles and use single-nucleotide replacement. in the former the apurinic/apyrimidinic (ap) site intermediate is removed by the sequential action of a 5'-acting ap endonuclease and a 5'-deox ...201121665970
glucose sensing by electrogenerated chemiluminescence of glucose-dehydrogenase produced nadh on electrodeposited redox hydrogel.in this work, we report a new sensing approach based on electrogenerated chemiluminescence (ecl) in an electrodeposited redox hydrogel using glucose dehydrogenase as a model system. the ecl-hydrogel films were electrodeposited by potential cycling of a pbs solution containing [poly(4-vinylpyridine)ru(2,2'-bipyridine)(2)cl(-)](+/2+). the film was easily prepared in a rapid, reproducible and well-controlled one-step procedure. the deposited hydrogel film is permeable to water-soluble chemicals and ...201121733762
The catalytic core of an archaeal 2-oxoacid dehydrogenase multienzyme complex is a 42-mer protein assembly.The acyl-transferase (E2) enzyme forms the structural and catalytic core of the tripartite 2-oxoacid dehydrogenase multienzyme complexes of the central metabolic pathways. Although this family of multienzyme complexes share a common architecture, their E2 cores form homo-trimers that, depending on the source, further associate into either octahedral (24-mer) or icosahedral (60-mer) assemblies, as predicted by the principles of quasi-equivalence. In the crystal structure of the E2 core from Therm ...201122188654
column bioleaching of low-grade mining ore containing high level of smithsonite, talc, sphaerocobaltite and azurite.present work describes the bioleaching potential of metals from low-grade mining ore containing smithsonite, sphaerocobaltite, azurite and talc as main gangue minerals with adapted consortium of sulfobacillus thermosulfidooxidans strain-rdb and thermoplasma acidophilum. bioleaching potential improved markedly by added energy source, acid preleaching and adaptation of microbial consortium with mixed metal ions. during whole leaching period including acid preleaching stage of 960 h and bioleaching ...201121947702
The Streptomyces-produced antibiotic fosfomycin is a promiscuous substrate for Archaeal isopentenyl phosphate kinase.Isopentenyl phosphate kinase (IPK) catalyzes the phosphorylation of isopentenyl phosphate to form the isoprenoid precursor isopentenyl diphosphate (IPP) in the archaeal mevalonate pathway. This enzyme is highly homologous to fosfomycin kinase (FomA), an antibiotic resistance enzyme found in a few strains of Streptomyces and Pseudomonas whose mode of action is inactivation by phosphorylation. Superposition of Thermoplasma acidophilum (THA) IPK and FomA structures aligns their respective substrate ...201122148590
Functional and structural studies of the nucleotide excision repair helicase XPD suggest a polarity for DNA translocation.The XPD protein is a vital subunit of the general transcription factor TFIIH which is not only involved in transcription but is also an essential component of the eukaryotic nucleotide excision DNA repair (NER) pathway. XPD is a superfamily-2 5'-3' helicase containing an iron-sulphur cluster. Its helicase activity is indispensable for NER and it plays a role in the damage verification process. Here, we report the first structure of XPD from Thermoplasma acidophilum (taXPD) in complex with a shor ...201122081108
The structures of Thermoplasma volcanium phosphoribosyl pyrophosphate synthetase bound to ribose-5-phosphate and ATP analogs.Phosphoribosyl pyrophosphate (PRPP) synthetase catalyzes the transfer of the pyrophosphate group from ATP to ribose-5-phosphate (R5P) yielding PRPP and AMP. PRPP is an essential metabolite that plays a central role in cellular metabolism. The enzyme from a thermophilic archaeon Thermoplasma volcanium (Tv) was expressed in Escherichia coli, crystallized, and its X-ray molecular structure was determined in a complex with its substrate R5P and with substrate analogs ß,?-methylene ATP and ADP in two ...201121963988
twisted schiff base intermediates and substrate locale revise transaldolase mechanism.we examined the catalytic cycle of transaldolase (tal) from thermoplasma acidophilum by cryocrystallography and were able to structurally characterize--for the first time, to our knowledge--different genuine tal reaction intermediates. these include the schiff base adducts formed between the catalytic lysine and the donor ketose substrates fructose-6-phosphate and sedoheptulose-7-phosphate as well as the michaelis complex with acceptor aldose erythrose-4-phosphate. these structural snapshots nec ...201121857661
structural models for interactions between the 20s proteasome and its pan/19s activators.proteasome activity is regulated by sequestration of its proteolytic centers in a barrel-shaped structure that limits substrate access. substrates enter the proteasome by means of activator complexes that bind to the end rings of proteasome alpha subunits and induce opening of an axial entrance/exit pore. the pa26 activator binds in a pocket on the proteasome surface using main chain contacts of its c-terminal residues and uses an internal activation loop to trigger gate opening by repositioning ...201019889631
characterization of thermophilic archaeal isopentenyl phosphate kinases.archaea synthesize isopentenyl diphosphate (ipp) and dimethylallyl diphosphate (dmapp), the essential building blocks of isoprenoid compounds, from mevalonate (mva). however, an analysis of the genomes of several members of the archaea failed to identify genes for the enzymes required to convert phosphomevalonate (pm) to ipp in eukaryotes. the recent discovery of an isopentenyl kinase (ipk) in methanocaldococcus jannaschii (mj) suggests a new variation of the mva pathway where pm is decarboxylat ...201019928876
crystal structure and molecular modeling study of n-carbamoylsarcosine amidase ta0454 from thermoplasma acidophilum.a crystal structure of the putative n-carbamoylsarcosine amidase (cshase) ta0454 from thermoplasma acidophilum was solved by single-wavelength anomalous diffraction and refined at a resolution of 2.35a. cshases are involved in the degradation of creatinine. ta0454 shares a similar fold and a highly conserved c-d-k catalytic triad (cys123, asp9, and lys90) with the structures of three cysteine hydrolases (pdb codes 1nba, 1im5, and 2h0r). molecular dynamics (md) simulations of ta0454/n-carbamoylsa ...201019932181
structure and filament dynamics of the psk41 actin-like parm protein: implications for plasmid dna segregation.type ii plasmid partition systems utilize parm ntpases in coordination with a centromere-binding protein called parr to mediate accurate dna segregation, a process critical for plasmid retention. the staphylococcus aureus psk41 plasmid is a medically important plasmid that confers resistance to multiple antibiotics, disinfectants, and antiseptics. in the first step of partition, the psk41 parr binds its dna centromere to form a superhelical partition complex that recruits parm, which then mediat ...201020106979
a reported archaeal mechanosensitive channel is a structural homolog of marr-like transcriptional regulators.several archaeal mechanosensitive (ms) channels have been reported, including one from thermoplasma volcanium designated msctv. here, we report the crystal structure of msctv at 1.6-a resolution. unexpectedly, msctv was found to be a water-soluble protein exhibiting a winged helix-turn-helix (whth) motif, which is the signature of the marr (multiple antibiotic resistance regulator) family of transcriptional regulators. a cell-based osmotic downshock functional assay demonstrated that msctv was u ...201020162616
discovery of a putative acetoin dehydrogenase complex in the hyperthermophilic archaeon sulfolobus solfataricus.like many other aerobic archaea, the hyperthermophile sulfolobus solfataricus possesses a gene cluster encoding components of a putative 2-oxoacid dehydrogenase complex. in the current paper, we have cloned and expressed the first two genes of this cluster and demonstrate that the protein products form an alpha(2)beta(2) hetero-tetramer possessing the catalytic activity characteristic of the first component enzyme of an acetoin dehydrogenase multienzyme complex. this represents the first report ...201020171216
dynamic regulation of archaeal proteasome gate opening as studied by trosy nmr.the proteasome catalyzes the majority of protein degradation in the cell and plays an integral role in cellular homeostasis. control over proteolysis by the 20s core-particle (cp) proteasome is achieved by gated access of substrate; thus, an understanding of the molecular mechanism by which these gates regulate substrate entry is critical. we used methyl-transverse relaxation optimized nuclear magnetic resonance spectroscopy to show that the amino-terminal residues that compose the gates of the ...201020360109
x-ray structures of isopentenyl phosphate kinase.isoprenoid compounds are ubiquitous in nature, participating in important biological phenomena such as signal transduction, aerobic cellular respiration, photosynthesis, insect communication, and many others. they are derived from the 5-carbon isoprenoid substrates isopentenyl diphosphate (ipp) and its isomer dimethylallyl diphosphate (dmapp). in archaea and eukarya, these building blocks are synthesized via the mevalonate pathway. however, the genes required to convert mevalonate phosphate (mp) ...201020402538
molecular cloning and co-expression of thermoplasma volcanium proteasome subunit genes.in this study we describe, the construction of a co-expression vector allowing simultaneous production of thermoplasma volcanium 20s proteasome alpha- and beta-subunits in escherichia coli. this heterologous expression system provided high level production of fully active 20s proteasome that can be purified easily by using a conventional two-step chromatographic technique. the recombinant proteasome was purified to homogeneity 12-fold with a specific activity of 26.5 u/mg. sodium dodecyl sulfate ...201020460155
the xpd helicase: xpanding archaeal xpd structures to get a grip on human dna repair.xeroderma pigmentosum complementation group d protein (xpd) is an iron-sulfur cluster containing 5'-3' helicase and, in humans, part of the transcription factor tfiih. tfiih is involved in nucleotide excision repair as well as in transcription initiation. recently, three different groups have reported the structures of archaeal xpds. all structures revealed a four-domain organization with two reca-like domains, an arch domain and an iron-sulfur cluster domain. it was possible to rationalize seve ...201020482310
quantitative proteome and transcriptome analysis of the archaeon thermoplasma acidophilum cultured under aerobic and anaerobic conditions.a comparative proteome and transcriptome analysis of thermoplasma acidophilum cultured under aerobic and anaerobic conditions has been performed. one-thousand twenty-five proteins were identified covering 88% of the cytosolic proteome. using a label-free quantitation method, we found that approximately one-quarter of the identified proteome (263 proteins) were significantly induced (>2 fold) under anaerobic conditions. thirty-nine macromolecular complexes were identified, of which 28 were quanti ...201020669988
crystal structures of two archaeal pelotas reveal inter-domain structural plasticity.dom34 from saccharomyces cerevisiae is one of the key players in no-go mrna decay, a surveillance pathway by which an abnormal mrna stalled during translation is degraded by an endonucleolytic cleavage. its homologs called pelota are found in other species. we showed previously that s. cerevisiae dom34 (domain 1) has an endoribonuclease activity, which suggests its direct catalytic role in no-go decay. pelota from thermoplasma acidophilum and dom34 from s. cerevisiae have been structurally chara ...201020682285
(13)chd(2) methyl group probes of millisecond time scale exchange in proteins by (1)h relaxation dispersion: an application to proteasome gating residue dynamics.a pulse scheme is presented for quantifying millisecond time scale chemical exchange processes in proteins by measuring (1)h cpmg relaxation dispersion profiles of (13)chd(2) methyl groups. the use of (13)chd(2) isotopomers for (1)h methyl dispersion experiments eliminates problems with interconversion between differentially relaxing proton transitions that complicate the extraction of accurate exchange parameters when (13)ch(3) probes are used. good agreement is demonstrated between extracted c ...201020698653
insights into substrate specificity of geranylgeranyl reductases revealed by the structure of digeranylgeranylglycerophospholipid reductase, an essential enzyme in the biosynthesis of archaeal membrane lipids.archaeal membrane lipids consist of branched, saturated hydrocarbons distinct from those found in bacteria and eukaryotes. digeranylgeranylglycerophospholipid reductase (dggr) catalyzes the hydrogenation process that converts unsaturated 2,3-di-o-geranylgeranylglyceryl phosphate to saturated 2,3-di-o-phytanylglyceryl phosphate as a critical step in the biosynthesis of archaeal membrane lipids. the saturation of hydrocarbon chains confers the ability to resist hydrolysis and oxidation and helps a ...201020869368
structures of three members of pfam pf02663 (fmde) implicated in microbial methanogenesis reveal a conserved α+β core domain and an auxiliary c-terminal treble-clef zinc finger.examination of the genomic context for members of the fmde pfam family (pf02663), such as the protein encoded by the fmde gene from the methanogenic archaeon methanobacterium thermoautotrophicum, indicates that 13 of them are co-transcribed with genes encoding subunits of molybdenum formylmethanofuran dehydrogenase (ec 1.2.99.5), an enzyme that is involved in microbial methane production. here, the first crystal structures from pf02663 are described, representing two bacterial and one archaeal s ...201020944230
the proteasome antechamber maintains substrates in an unfolded state.eukaryotes and archaea use a protease called the proteasome that has an integral role in maintaining cellular function through the selective degradation of proteins. proteolysis occurs in a barrel-shaped 20s core particle, which in thermoplasma acidophilum is built from four stacked homoheptameric rings of subunits, α and β, arranged α(7)β(7)β(7)α(7) (ref. 5). these rings form three interconnected cavities, including a pair of antechambers (formed by α(7)β(7)) through which substrates are passed ...201020944750
indicators from archaeal secretomes.just as in the eukarya and the bacteria, members of the archaea need to export proteins beyond the cell membrane. this would be required to fulfill a variety of essential functions such as nutrient acquisition and biotransformations, maintenance of extracellular structures and more. apart from the eukarya and the bacteria however, members of the archaea share a number of unique characteristics. does this uniqueness extend to the protein secretion system? it was the objective of this study to ans ...201018407482
clioquinol inhibits the proteasome and displays preclinical activity in leukemia and myeloma. 200918754030
the stability of the archaeal hu histone-like dna-binding protein from thermoplasma volcanium.the complete genome analysis of the archaeon thermoplasma volcanium has revealed a gene assigned to encode the histone-like dna-binding protein hu. thermoplasma volcanium is a moderate thermophile growing around 60 degrees c and it is adaptable to aerobic and anaerobic environment and therefore it is unique as a candidate for the origin of eukaryotic nuclei in the endosymbiosis hypothesis. the hu protein is the major component of the bacterial nuclei and therefore it is an important protein to b ...200918818867
heterologous expression and characterization of an alcohol dehydrogenase from the archeon thermoplasma acidophilum.analysis of the thermoplasma acidophilum dsm 1728 genome identified two putative alcohol dehydrogenase (adh) open reading frames showing 50.4% identity against each other. the corresponding genes ta0841 and ta1316 encode proteins of 336 and 328 amino acids with molecular masses of 36.48 and 36.01 kda, respectively. the genes were expressed in escherichia coli and the recombinant enzymes were functionally assessed for activity. throughout the study only ta1316 adh resulted active in the oxidative ...200919058034
c-terminal tail derived from the neighboring subunit is critical for the activity of thermoplasma acidophilum d-aldohexose dehydrogenase.the d-aldohexose dehydrogenase from the thermoacidophilic archaeon thermoplasma acidophilum (aldt) is a homotetrameric enzyme that catalyzes the oxidation of several d-aldohexoses, especially d-mannose. aldt comprises a unique c-terminal tail motif (residues 247-255) that shuts the active-site pocket of the neighboring subunit. the functional role of the c-terminal tail of aldt has been investigated using mutational and crystallographic analyses. a total of four c-terminal deletion mutants (delt ...200919089950
adpase activity of recombinantly expressed thermotolerant atpases may be caused by copurification of adenylate kinase of escherichia coli.except for apyrases, atpases generally target only the gamma-phosphate of a nucleotide. some non-apyrase atpases from thermophilic microorganisms are reported to hydrolyze adp as well as atp, which has been described as a novel property of the atpases from extreme thermophiles. here, we describe an apparent adp hydrolysis by highly purified preparations of the aaa+ atpase ntrc1 from an extremely thermophilic bacterium, aquifex aeolicus. this activity is actually a combination of the activities o ...200919143839
domain architecture of the stator complex of the a1a0-atp synthase from thermoplasma acidophilum.a key structural element in the ion translocating f-, a-, and v-atpases is the peripheral stalk, an assembly of two polypeptides that provides a structural link between the atpase and ion channel domains. previously, we have characterized the peripheral stalk forming subunits e and h of the a-atpase from thermoplasma acidophilum and demonstrated that the two polypeptides interact to form a stable heterodimer with 1:1 stoichiometry (kish-trier, e., briere, l. k., dunn, s. d., and wilkens, s. (200 ...200919234304
the origins of phagocytosis and eukaryogenesis.phagocytosis, that is, engulfment of large particles by eukaryotic cells, is found in diverse organisms and is often thought to be central to the very origin of the eukaryotic cell, in particular, for the acquisition of bacterial endosymbionts including the ancestor of the mitochondrion.200919245710
microbial communities in acid mine drainage and their interaction with pyrite surface.microbes such as acidithiobacillus ferrooxidans and leptospirillum ferrooxidans have been investigated a lot, because of their important role in acid mine drainage (amd) generation. in this article, the composition of microbial communities in two amd samples was studied. a culture-independent 16s rdna-based cloning approach, restriction fragment length polymorphism has been used. the interaction between microbes and natural pyrite specimen surface was researched by scanning electrode microscopy ...200919319595
identifying catalytic residues in cpaf, a chlamydia-secreted protease.a secreted chlamydial protease designated cpaf (chlamydial protease/proteasome-like activity factor) degrades host proteins, enabling chlamydia to evade host defenses and replicate. the mechanistic details of cpaf action, however, remain obscure. we used a computational approach to search the protein databank for structures that are compatible with the cpaf amino acid sequence. the results reveal that cpaf possesses a fold similar to that of the catalytic domains of the tricorn protease from the ...200919388144
characterization of an acid-labile, thermostable beta-glycosidase from thermoplasma acidophilum.a recombinant putative beta-galactosidase from thermoplasma acidophilum was purified as a single 57 kda band of 82 u mg(-1). the molecular mass of the native enzyme was 114 kda as a dimer. maximum activity was observed at ph 6.0 and 90 degrees c. the enzyme was unstable below ph 6.0: at ph 6 its half-life at 75 degrees c was 28 days but at ph 4.5 was only 13 h. catalytic efficiencies decreased as p-nitrophenyl(pnp)-beta-d-fucopyranoside (1067) > pnp-beta-d-glucopyranoside (381) > pnp-beta-d-gala ...200919458917
the thermoplasma acidophilum lpla-lplb complex defines a new class of bipartite lipoate-protein ligases.lipoic acid is a covalently bound cofactor found throughout the domains of life that is required for aerobic metabolism of 2-oxoacids and for c(1) metabolism. utilization of exogenous lipoate is catalyzed by a ligation reaction that proceeds via a lipoyl-adenylate intermediate to attach the cofactor to the epsilon-amino group of a conserved lysine residue of protein lipoyl domains. the lipoyl ligases of demonstrated function have a large n-terminal catalytic domain and a small c-terminal accesso ...200919520844
importance of non-conserved distal carboxyl terminal amino acids in two peptidases belonging to the m1 family: thermoplasma acidophilum tricorn interacting factor f2 and escherichia coli peptidase n.enzymes belonging to the m1 family play important cellular roles and the key amino acids (aa) in the catalytic domain are conserved. however, c-terminal domain aa are highly variable and demonstrate distinct differences in organization. to address a functional role for the c-terminal domain, progressive deletions were generated in tricorn interacting factor f2 from thermoplasma acidophilum (f2) and peptidase n from escherichia coli (pepn). catalytic activity was partially reduced in pepn lacking ...200919527767
cloning and overexpression of a thermostable signal peptide peptidase (sppa) from thermoplasma volcanium gss1 in e. coli.in this study, a gene coding for thermophilic serine protease of the clpp class from the thermoacidophilic archaeon thermoplasma volcanium (tpv) was cloned and expressed in escherichia coli. the primary sequence and domain analysis of this enzyme showed similarities (50-60% similarity) to signal peptide peptidases (sppa) of bacteria and other archaea. an increase of about tenfold in the activity was achieved by overexpression of tpv sppa in e. coli, as detected by enzyme assays conducted using a ...200919557795
prevalence and molecular diversity of archaea in subgingival pockets of periodontitis patients.the aim of this study was to investigate the prevalence and molecular diversity of archaea in the subgingival crevices of patients with chronic periodontitis.200919572899
a unique lipoylation system in the archaea. lipoylation in thermoplasma acidophilum requires two proteins.members of the 2-oxoacid dehydrogenase multienzyme complex family play a key role in the pathways of central metabolism. post-translational lipoylation of the dihydrolipoyl acyltransferase component of these complexes is essential for their activity, the lipoyllysine moiety performing the transfer of substrates and intermediates between the different active sites within these multienzyme systems. we have previously shown that the thermophilic archaeon, thermoplasma acidophilum, has a four-gene c ...200919594830
size distribution of native cytosolic proteins of thermoplasma acidophilum.we used molecular sieve chromatography in combination with lc-ms/ms to identify protein complexes that can serve as templates in the template matching procedures of visual proteomics approaches. by this method the sample complexity was lowered sufficiently to identify 464 proteins and - on the basis of size distribution and bioinformatics analysis - 189 of them could be assigned as subunits of macromolecular complexes over the size of 300 kda. from these we purified six stable complexes of therm ...200919639595
the partial substrate dethiaacetyl-coenzyme a mimics all critical carbon acid reactions in the condensation half-reaction catalyzed by thermoplasma acidophilum citrate synthase.citrate synthase (cs) performs two half-reactions: the mechanistically intriguing condensation of acetyl-coa with oxaloacetate (oaa) to form citryl-coa and the subsequent, slower hydrolysis of citryl-coa that generally dominates steady-state kinetics. the condensation reaction requires the abstraction of a proton from the methyl carbon of acetyl-coa to generate a reactive enolate intermediate. the carbanion of that intermediate then attacks the oaa carbonyl to furnish citryl-coa, the initial pro ...200919645419
biochemical characterization of the minichromosome maintenance protein from the archaeon thermoplasma acidophilum.minichromosome maintenance (mcm) proteins are thought to function as the replicative helicases in archaea. studies have shown that the mcm complex from the thermoacidophilic euryarchaeon thermoplasma acidophilum (tamcm) has some properties not reported in other archaeal mcm helicases. here, the biochemical properties of the tamcm are studied. the protein binds single-stranded dna, has dna-dependent atpase activity and atp-dependent 3' --> 5' helicase activity. the optimal helicase conditions wit ...200919002376
a ppm-family protein phosphatase from the thermoacidophile thermoplasma volcanium hydrolyzes protein-bound phosphotyrosine.the genomes of virtually all free-living archaeons encode one or more deduced protein-serine/threonine/tyrosine kinases belonging to the so-called eukaryotic protein kinase superfamily. however, the distribution of their cognate protein-serine/threonine/phosphatases displays a mosaic pattern. thermoplasma volcanium is unique among the archaea inasmuch as it is the sole archaeon whose complement of deduced phosphoprotein phosphatases includes a member of the ppm-family of protein-serine/threonine ...200919039517
interaction of the thermoplasma acidophilum a1a0-atp synthase peripheral stalk with the catalytic domain.the peripheral stalk of the archaeal atp synthase (a1a0)-atp synthase is formed by the heterodimeric eh complex and is part of the stator domain, which counteracts the torque of rotational catalysis. here we used nuclear magnetic resonance spectroscopy to probe the interaction of the c-terminal domain of the eh heterodimer (e(ct1)h(ct)) with the n-terminal 23 residues of the b subunit (b(nt)). the data show a specific interaction of b(nt) peptide with 26 residues of the e(ct1)h(ct) domain, there ...200919720061
a potentially versatile nucleotide hydrolysis activity of group ii chaperonin monomers from thermoplasma acidophilum.compared to the group i chaperonins such as escherichia coli groel, which facilitate protein folding, many aspects of the functional mechanism of archaeal group ii chaperonins are still unclear. here, we show that monomeric forms of archaeal group ii chaperonin alpha and beta from thermoplasma acidophilum may be purified stably and that these monomers display a strong ampase activity in the presence of divalent ions, especially co(2+) ion, in addition to atpase and adpase activities. furthermore ...200919728744
bax1 is a novel endonuclease: implications for archaeal nucleotide excision repair.the helicases xpb and xpd are part of the tfiih complex, which mediates transcription initiation as well as eukaryotic nucleotide excision repair (ner). although there is no tfiih complex present in archaea, most species contain both xpb and xpd and serve as a model for their eukaryotic homologs. recently, a novel binding partner for xpb, bax1 (binds archeal xpb), was identified in archaea. to gain insights into its role in ner, bax1 from thermoplasma acidophilum was characterized. we identified ...200919759013
[evolution of prokaryotic cytoskeleton]. 200819044289
characterization of the cdc6 homologues from the euryarchaeon thermoplasma acidophilum.archaeal cell division cycle protein 6 (cdc6) homologues are thought to be involved in the initiation process of dna replication. in the present study, a biochemical characterization of the two cdc6 proteins from the archaeon thermoplasma acidophilum has been performed. both tacdc6-1 and tacdc6-2 behave as monomers in solution and both are abundantly expressed in vivo. further, tacdc6-1 shows strong ability to undergo autophosphorylation compared to tacdc6-2 and the autophosphorylation activity ...200819238189
structure of a haloacid dehalogenase superfamily phosphatase ph1421 from pyrococcus horikoshii ot3: oligomeric state and thermoadaptation mechanism.ph1421 from the hyperthermophilic archaeon pyrococcus horikoshii ot3 is a hypothetical protein belonging to the haloacid dehalogenase (had) superfamily. to gain insight into its biological function and thermostabilization mechanism, the crystal structure of ph1421 has been determined at 1.6 a resolution. the crystallographic asymmetric unit contains a homodimer. the monomeric protomer is composed of two distinct domains, a small cap domain and a large core domain, which agrees well with the typi ...200818931414
crystallization and preliminary x-ray analysis of the thermoplasma acidophilum 20s proteasome in complex with protein substrates.the 20s proteasome is a 700 kda barrel-shaped proteolytic complex that is traversed by an internal channel which widens into three cavities: two antechambers and one central chamber. entrance to the complex is restricted by the narrow opening of the channel, which only allows unfolded substrates to reach the active sites located within the central cavity. the x-ray structures of 20s proteasomes from different organisms with and without inhibitors bound have led to a detailed knowledge of their s ...200818931431
atomic structure of the keops complex: an ancient protein kinase-containing molecular machine.kae1 is a universally conserved atpase and part of the essential gene set in bacteria. in archaea and eukaryotes, kae1 is embedded within the protein kinase-containing keops complex. mutation of keops subunits in yeast leads to striking telomere and transcription defects, but the exact biochemical function of keops is not known. as a first step to elucidating its function, we solved the atomic structure of archaea-derived keops complexes involving kae1, bud32, pcc1, and cgi121 subunits. our stud ...200818951093
thermoplasma acidophilum cdc6 protein stimulates mcm helicase activity by regulating its atpase activity.the minichromosome maintenance (mcm) proteins are thought to function as the replicative helicases in archaea. in most archaeal species studied, the interaction between mcm and the initiator protein, cdc6, inhibits helicase activity. to date, the only exception is the helicase and cdc6 proteins from the archaeon thermoplasma acidophilum. it was previously shown that when the cdc6 protein interacts with mcm it substantially stimulates helicase activity. it is shown here that the mechanism by whic ...200818757887
biochemical and structural characterization of a novel family of cystathionine beta-synthase domain proteins fused to a zn ribbon-like domain.we have identified a novel family of proteins, in which the n-terminal cystathionine beta-synthase (cbs) domain is fused to the c-terminal zn ribbon domain. four proteins were overexpressed in escherichia coli and purified: ta0289 from thermoplasma acidophilum, tv1335 from thermoplasma volcanium, pf1953 from pyrococcus furiosus, and ph0267 from pyrococcus horikoshii. the purified proteins had a red/purple color in solution and an absorption spectrum typical of rubredoxins (rds). metal analysis o ...200818021800
the stator complex of the a1a0-atp synthase--structural characterization of the e and h subunits.archaeal atp synthase (a-atpase) is the functional homolog to the atp synthase found in bacteria, mitochondria and chloroplasts, but the enzyme is structurally more related to the proton-pumping vacuolar atpase found in the endomembrane system of eukaryotes. we have cloned, overexpressed and characterized the stator-forming subunits e and h of the a-atpase from the thermoacidophilic archaeon, thermoplasma acidophilum. size exclusion chromatography, cd, matrix-assisted laser desorption ionization ...200818036615
a thermoactive glucoamylase with biotechnological relevance from the thermoacidophilic euryarchaeon thermoplasma acidophilum.a gene encoding an intracellular glucoamylase was identified in the genome of the extreme thermoacidophilic archaeon thermoplasma acidophilum. the gene taga, consisting of 1,911 bp, was cloned and successfully expressed in escherichia coli. the recombinant protein was purified 22-fold to homogeneity using heat treatment, anion-exchange chromatography, and gel filtration. detailed analysis shows that the glucoamylase, with a molecular weight of 66 kda per subunit, is a homodimer in its active sta ...200818080814
functional characterization of the recombinant group ii chaperonin alpha from thermoplasma acidophilum.the functional characteristics of group ii chaperonins, especially those from archaea, have not been elucidated extensively. here, we performed a detailed functional characterization of recombinant chaperonin alpha subunits (16-mer) (ta-cpn alpha) from the thermophilic archaea thermoplasma acidophilum as a model protein of archaeal group ii chaperonins. recombinant ta-cpn alpha formed an oligomeric ring structure similar to that of native protein, and displayed an atp hydrolysis activity (optima ...200818174187
an oligonucleotide prokaryotic acidophile microarray: its validation and its use to monitor seasonal variations in extreme acidic environments with total environmental rna.an oligonucleotide microarray that monitors prokaryotic diversity in extremely acidic environments has been developed. the oligonucleotide probes target most known acidophilic microorganisms, including members of the nitrospira phylum, acidithiobacillus genus, acidobacteria, sulfur reducing bacteria, actinobacteria and archaea of the ferroplasma and thermoplasma genera. the probes were tested for their specificity against the corresponding type strain by microarray hybridization using pcr-amplif ...200818248453
structural insights into an equilibrium folding intermediate of an archaeal ankyrin repeat protein.repeat proteins are widespread in nature, with many of them functioning as binding molecules in protein-protein recognition. their simple structural architecture is used in biotechnology for generating proteins with high affinities to target proteins. recent folding studies of ankyrin repeat (ar) proteins revealed a new mechanism of protein folding. the formation of an intermediate state is rate limiting in the folding reaction, suggesting a scaffold function of this transient state for intrinsi ...200818305166
crystallization and preliminary x-ray diffraction analysis of 5,10- methylenetetrahydrofolate dehydrogenase/cyclohydrolase from thermoplasma acidophilum dsm 1728.the methylenetetrahydrofolate dehydrogenase/ cyclohydrolase (mthfdc) from the thermoacidophilic archaeon thermoplasma acidophilum is a 30.6 kda molecular-mass enzyme that sequentially catalyzes the conversion of formyltetrahydrofolate to methylenetetrahydrofolate, with a preference for nadp as a cofactor, rather than nad. in order to elucidate the functional and structural features of mthfdc from archaeons at a molecular level, it was overexpressed in escherichia coli and crystallized in the pre ...200818309272
mechanism of gate opening in the 20s proteasome by the proteasomal atpases.substrates enter the cylindrical 20s proteasome through a gated channel that is regulated by the atpases in the 19s regulatory particle in eukaryotes or the homologous pan atpase complex in archaea. these atpases contain a conserved c-terminal hydrophobic-tyrosine-x (hbyx) motif that triggers gate opening upon atp binding. using cryo-electron microscopy, we identified the sites in the archaeal 20s where pan's c-terminal residues bind and determined the structures of the gate in its closed and op ...200818471981
amino acid biases in the n- and c-termini of proteins are evolutionarily conserved and are conserved between functionally related proteins.analysis of the arabidopsis thaliana, saccharomyces cerevisiae, mus musculus, escherichia coli, bacillus subtilis, thermoplasma acidophilum, and sulfolobus tokodaii genomes demonstrate that many amino acid biases occur at the n- and c-termini of proteins, a statistically significant number of these biases are evolutionarily conserved, and these biases occur in amino acids beyond the first and last five amino acids. analyses designed to shed light on the mechanism causing amino acid biases sugges ...200818478318
culturable and molecular phylogenetic diversity of microorganisms in an open-dumped, extremely acidic pb/zn mine tailings.a combination of cultivation-based and molecular-based approaches was used to reveal the culturable and molecular diversity of the microbes inhabiting an open-dumped pb/zn mine tailings that was undergoing intensive acid generation (ph 1.9). culturable bacteria found in the extremely acidic mine tailings were acidithiobacillus ferrooxidans, leptospirillum ferriphilum, sulfobacillus thermotolerans and acidiphilium cryptum, where the number of acidophilic heterotrophs was ten times higher than tha ...200818512002
effects of ph and temperature on the composition of polar lipids in thermoplasma acidophilum ho-62.thermoplasma acidophilum ho-62 was grown at different phs and temperatures, and its polar lipid compositions were determined. although the number of cyclopentane rings in the caldarchaeol moiety increased when t. acidophilum was cultured at high temperature, the number decreased at low phs. glycolipids, phosphoglycolipids, and phospholipids were analyzed by high-performance liquid chromatography with an evaporative light-scattering detector. the amount of caldarchaeol with more than two sugar un ...200818539746
trosy-based nmr evidence for a novel class of 20s proteasome inhibitors.the proteasome plays a central role in maintaining cellular homeostasis, in controlling the cell cycle, in removing misfolded proteins that can be toxic, and in regulating the immune system. it is also an important target for novel anticancer drugs, such as bortezomib, a potent inhibitor that has been used successfully in the treatment of multiple myeloma. here, we show that the antimalaria drug chloroquine inhibits proteasome function in eukaryotic cell extracts and in preparations of purified ...200818540636
compositions and structures of archaeal communities in acid mineral bioleaching systems of dongxiang copper mine and yinshan lead-zinc mine, china.four samples were studied from four separated sites with heap leaching in the yinshan lead-zinc mine and the dongxiang copper mine in jiangxi province, china. the compositions and structures of archaeal communities in four sites were identified by a polymerase chain reaction-based cloning approach. a total of six operational taxonomic units (otus) was obtained from four samples. the highest percentage of overlapped otus was 88.9% between sites dx and d1. phylogenetic analysis revealed that archa ...200818592308
thioredoxin reductase from thermoplasma acidophilum: a new twist on redox regulation.thioredoxin reductases (trxrs) regulate the intracellular redox environment by using nadph to provide reducing equivalents for thioredoxins (trxs). here we present the cloning and biochemical characterization of a putative trxr (ta0984) and a putative trx (ta0866) from thermoplasma acidophilum. our data identify ta0866 as a trx through its capacity to reduce insulin and be reduced by escherichia coli trxr in a nadph-dependent manner. our data also establish ta0984 as a trxr due to its ability to ...200818717593
direct electrochemical analyses of a thermophilic thioredoxin reductase: interplay between conformational change and redox chemistry.thioredoxin reductases (trxrs) are flavin-containing dithioloxidoreductases that couple reduction equivalents from the soluble nad(p)h pool to the soluble protein thioredoxin (trx). previous crystallographic studies of the escherichia coli enzyme ( ectrxr) have shown that low molecular weight trxrs can adopt two distinct conformations: the first (fo) is required for the oxidation of the flavin cofactor and the generation of reduced trx; the second (fr) is adopted for the reduction of the flavin ...200818717594
the 2-oxoacid dehydrogenase multienzyme complex of haloferax volcanii.those aerobic archaea whose genomes have been sequenced possess four adjacent genes that, by sequence comparisons with bacteria and eukarya, appear to encode the component enzymes of a 2-oxoacid dehydrogenase multienzyme complex. however, no catalytic activity of any such complex has ever been detected in the archaea. in thermoplasma acidophilum, evidence has been presented that the heterologously expressed recombinant enzyme possesses activity with the branched chain 2-oxoacids and, to a lesser ...200817571210
characterization of cofactor-dependent and cofactor-independent phosphoglycerate mutases from archaea.phosphoglycerate mutases (pgm) catalyze the reversible conversion of 3-phosphoglycerate and 2-phosphoglycerate as part of glycolysis and gluconeogenesis. two structural and mechanistically unrelated types of pgms are known, a cofactor (2,3-bisphosphoglycerate)-dependent (dpgm) and a cofactor-independent enzyme (ipgm). here, we report the characterization of the first archaeal cofactor-dependent pgm from thermoplasma acidophilum, which is encoded by orf ta1347. this orf was cloned and expressed i ...200717576516
molecular architecture and divalent cation activation of tvok, a prokaryotic potassium channel.rck (regulator of conductance of potassium) domains form a family of ligand-binding domains found in many prokaryotic k+ channels and transport proteins. although many rck domains contain an apparent nucleotide binding motif, some are known instead to bind ca2+, which can then facilitate channel opening. here we report on the molecular architecture and ligand activation properties of an rck-containing potassium channel cloned from the prokaryote thermoplasma volcanium. this channel, called tvok, ...200717588939
solution structure of the hypothetical novel-fold protein ta0956 from thermoplasma acidophilum. 200717634985
solution structure of the hypothetical protein ta0095 from thermoplasma acidophilum: a novel superfamily with a two-layer sandwich architecture.ta0095 is a 96-residue hypothetical protein from thermoplasma acidophilum that exhibits no sequence similarity to any protein of known structure. also, ta0095 is a member of the cog4004 orthologous group of unknown function found in archaea bacteria. we determined its three-dimensional structure by nmr methods. the structure displays an alpha/beta two-layer sandwich architecture formed by three alpha-helices and five beta-strands following the order beta1-alpha1-beta2-beta3-beta4-beta5-alpha2-al ...200717766377
structural and mutational analysis of trna intron-splicing endonuclease from thermoplasma acidophilum dsm 1728: catalytic mechanism of trna intron-splicing endonucleases.in archaea, rna endonucleases that act specifically on rna with bulge-helix-bulge motifs play the main role in the recognition and excision of introns, while the eukaryal enzymes use a measuring mechanism to determine the positions of the universally positioned splice sites relative to the conserved domain of pre-trna. two crystallographic structures of trna intron-splicing endonuclease from thermoplasma acidophilum dsm 1728 (enda(ta)) have been solved to 2.5-a and 2.7-a resolution by molecular ...200717827289
structural and functional insights into dom34, a key component of no-go mrna decay.the yeast protein dom34 is a key component of no-go decay, by which mrnas with translational stalls are endonucleolytically cleaved and subsequently degraded. however, the identity of the endoribonuclease is unknown. homologs of dom34, called pelota, are broadly conserved in eukaryotes and archaea. to gain insights into the structure and function of dom34/pelota, we have determined the structure of pelota from thermoplasma acidophilum (ta pelota) and investigated the ribonuclease activity of dom ...200717889667
the 2-oxoacid dehydrogenase multi-enzyme complex of the archaeon thermoplasma acidophilum - recombinant expression, assembly and characterization.the aerobic archaea possess four closely spaced, adjacent genes that encode proteins showing significant sequence identities with the bacterial and eukaryal components comprising the 2-oxoacid dehydrogenase multi-enzyme complexes. however, catalytic activities of such complexes have never been detected in the archaea, although 2-oxoacid ferredoxin oxidoreductases that catalyze the equivalent metabolic reactions are present. in the current paper, we clone and express the four genes from the therm ...200717894823
microbial populations in acid mineral bioleaching systems of tong shankou copper mine, china.to understand the composition and structure of microbial communities in different acid mineral bioleaching systems, and to present a more complete picture of microbially mediated acid mine drainage production.200717897227
mucosal and systemic immune responses by intranasal immunization using archaeal lipid-adjuvanted vaccines.the utility of archaeal polar lipids as an adjuvant/delivery system for elicitation of antigen-specific mucosal immune responses in intranasally administered vaccines was investigated. although unilamellar archaeosomes (liposomes made from archaeal polar lipids) with encapsulated ovalbumin (ova/archaeosomes) induced anti-ova igg antibody responses in sera, they failed to induce anti-ova iga antibody responses at mucosal sites. however, the addition of cacl2 to convert ova/archaeosomes into an ar ...200717959279
thermogymnomonas acidicola gen. nov., sp. nov., a novel thermoacidophilic, cell wall-less archaeon in the order thermoplasmatales, isolated from a solfataric soil in hakone, japan.a novel thermoacidophilic, cell wall-less archaeon, strain ic-189t, was isolated from a solfataric field in ohwaku-dani, hakone, japan. the cells were irregular cocci, sometimes lobed, club-shaped or catenated, and were highly variable in size, ranging from 0.8 to 8.0 microm in diameter. the strain grew at temperatures in the range 38-68 degrees c (optimally at 60 degrees c) and at ph 1.8-4.0 (optimally at around ph 3.0). strain ic-189t was obligately aerobic and heterotrophic, requiring yeast e ...200717978217
structural insights into unique substrate selectivity of thermoplasma acidophilum d-aldohexose dehydrogenase.the d-aldohexose dehydrogenase from the thermoacidophilic archaea thermoplasma acidophilum (aldt) belongs to the short-chain dehydrogenase/reductase (sdr) superfamily and catalyzes the oxidation of several monosaccharides with a preference for nad(+) rather than nadp(+) as a cofactor. it has been found that aldt is a unique enzyme that exhibits the highest dehydrogenase activity against d-mannose. here, we describe the crystal structures of aldt in ligand-free form, in complex with nadh, and in ...200717300803
nmr structure of hypothetical protein ta0938 from thermoplasma acidophilum. 200717377985
phylogenomic analysis of proteins that are distinctive of archaea and its main subgroups and the origin of methanogenesis.the archaea are highly diverse in terms of their physiology, metabolism and ecology. presently, very few molecular characteristics are known that are uniquely shared by either all archaea or the different main groups within archaea. the evolutionary relationships among different groups within the euryarchaeota branch are also not clearly understood.200717394648
the n-terminal region is important for the nuclease activity and thermostability of the flap endonuclease-1 from sulfolobus tokodaii.this paper reports the biochemical properties of two types of recombinant flap endonuclease-1 (fen-1) proteins obtained from the thermophilic crenarchaeon, sulfolobus tokodaii strain 7. one of the two fen-1 proteins is a product of the gene with aug as the translational start codon (stos-fen-1), which is originally assigned in the database. the other is a product of the gene with a new aug start codon (stol-fen-1), which is inserted at 153 bases upstream of the original aug codon. although stol- ...200717420588
lateral diffusion coefficients of an eicosanyl-based bisglycerophosphocholine determined by pfg-nmr and frap.we report the lateral diffusion properties of 2,2'-di-o-decyl-3,3'-di-o-(eicosanyl)-bis-(rac-glycero)-1,1'-diphosphocholine (c20bas) using pulsed-field gradient nmr (pfg-nmr) and fluorescence recovery after photobleaching (frap). c20bas membranes display a melting transition at tm = 15.7 degrees c, as determined by differential scanning calorimetry and 31p nmr chemical shift anisotropy. the lateral diffusion coefficient of c20bas, as determined by pfg-nmr and frap, at 25 degrees c, were dpfg-nmr ...200717465580
molecular cloning and biochemical characterization of the first archaeal maltogenic amylase from the hyperthermophilic archaeon thermoplasma volcanium gss1.maltogenic amylases (maases), a subclass of cyclodextrin (cd)-hydrolyzing enzymes belonging to glycoside hydrolase family 13, have been studied extensively, but their physiological roles in microbes and evolutionary relationships with other amylolytic enzymes remain unclear. here, we report the biochemical properties of a thermostable archaeal maase from thermoplasma volcanium gss1 (tpma) for the first time. the primary structure and catalytic properties of tpma were similar to those of maases, ...200717468058
molecular diversity of methanogens in feedlot cattle from ontario and prince edward island, canada.the molecular diversity of rumen methanogens in feedlot cattle and the composition of the methanogen populations in these animals from two geographic locations were investigated using 16s rrna gene libraries prepared from pooled pcr products from 10 animals in ontario (127 clones) and 10 animals from prince edward island (114 clones). a total of 241 clones were examined, with methanobrevibacter ruminantium accounting for more than one-third (85 clones) of the clones identified. from these 241 cl ...200717483285
crystal structure of bovine lipoyltransferase in complex with lipoyl-amp.lipoic acid is an essential cofactor of the alpha-ketoacid dehydrogenase complexes and the glycine cleavage system. it is covalently attached to a specific lysine residue of the subunit of the complexes. the bovine lipoyltransferase (blt) catalyzes the lipoic acid attachment reaction using lipoyl-amp as a substrate, forming a lipoylated protein and amp. to gain insights into the reaction mechanism at the atomic level, we have determined the crystal structure of blt at 2.10 a resolution. unexpect ...200717570395
an extracellular--pepstatin insensitive acid protease produced by thermoplasma volcanium.in this study, some parameters for the production and caseinolytic activity of an extracellular thermostable acid protease from a thermoacidophilic archaeon thermoplasma volcanium were determined. the highest level of growth and enzyme production were detected at ph 3.0 over an incubation period of 192 h at 60 degrees c. the ph optimum for the acid protease activity was 3.0 and the enzyme was fairly stable over a broad ph range (ph 3.0-8.0). the temperature for maximum activity of the enzyme was ...200716386898
proteomics analysis of thermoplasma acidophilum with a focus on protein complexes.two-dimensional gel electrophoresis (2de) and maldi-tof ms were used to obtain a global view of the cytoplasmic proteins expressed by thermoplasma acidophilum. in addition, glycerol gradient ultracentrifugation coupled to 2de-maldi-tof ms analysis was used to identify subunits of macromolecular complexes. with the 2de proteomics approach, over 900 spots were resolved of which 271 proteins were identified. a significant number of these form macromolecular complexes, among them the ribosome, prote ...200717151018
an actin homolog of the archaeon thermoplasma acidophilum that retains the ancient characteristics of eukaryotic actin.actin, a central component of the eukaryotic cytoskeleton, plays a crucial role in determining cell shape in addition to several other functions. recently, the structure of the archaeal actin homolog ta0583, isolated from the archaeon thermoplasma acidophilum, which lacks a cell wall, was reported by roeben et al. (j. mol. biol. 358:145-156, 2006). here we show that ta0583 assembles into bundles of filaments similar to those formed by eukaryotic actin. specifically, ta0583 forms a helix with a f ...200717189356
quantitative dynamics and binding studies of the 20s proteasome by nmr.the machinery used by the cell to perform essential biological processes is made up of large molecular assemblies. one such complex, the proteasome, is the central molecular machine for removal of damaged and misfolded proteins from the cell. here we show that for the 670-kilodalton 20s proteasome core particle it is possible to overcome the molecular weight limitations that have traditionally hampered quantitative nuclear magnetic resonance (nmr) spectroscopy studies of such large systems. this ...200717237764
Displaying items 1 - 100 of 527