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dynamics of the base of ribosomal a-site finger revealed by molecular dynamics simulations and cryo-em.helix 38 (h38) of the large ribosomal subunit, with a length of 110 a, reaches the small subunit through intersubunit bridge b1a. previous cryo-em studies revealed that the tip of h38 moves by more than 10 a from the non-ratcheted to the ratcheted state of the ribosome while mutational studies implicated a key role of flexible h38 in attenuation of translocation and in dynamical signaling between ribosomal functional centers. we investigate a region including the elbow-shaped kink-turn (kt-38) i ...201019952067
mechanism of substrate recognition and insight into feedback inhibition of homocitrate synthase from thermus thermophilus.homocitrate synthase (hcs) catalyzes aldol-type condensation of acetyl coenzyme a (acetyl-coa) and alpha-ketoglutarate (alpha-kg) to synthesize homocitrate (hc), which is the first and committed step in the lysine biosynthetic pathway through alpha-aminoadipate. as known in most enzymes catalyzing the first reactions in amino acid biosynthetic pathways, hcs is regulated via feedback inhibition by the end product, lysine. here, we determined the crystal structures of hcs from thermus thermophilus ...201019996101
functional significance of eif5a and its hypusine modification in eukaryotes.the unusual basic amino acid, hypusine [n(epsilon)-(4-amino-2-hydroxybutyl)-lysine], is a modified lysine with the addition of the 4-aminobutyl moiety from the polyamine spermidine. this naturally occurring amino acid is a product of a unique posttranslational modification that occurs in only one cellular protein, eukaryotic translation initiation factor 5a (eif5a, eif-5a). hypusine is synthesized exclusively in this protein by two sequential enzymatic steps involving deoxyhypusine synthase (dhs ...201019997760
functional significance of eif5a and its hypusine modification in eukaryotes.the unusual basic amino acid, hypusine [n(epsilon)-(4-amino-2-hydroxybutyl)-lysine], is a modified lysine with the addition of the 4-aminobutyl moiety from the polyamine spermidine. this naturally occurring amino acid is a product of a unique posttranslational modification that occurs in only one cellular protein, eukaryotic translation initiation factor 5a (eif5a, eif-5a). hypusine is synthesized exclusively in this protein by two sequential enzymatic steps involving deoxyhypusine synthase (dhs ...201019997760
studies on the mechanism of p-hydroxyphenylacetate 3-hydroxylase from pseudomonas aeruginosa: a system composed of a small flavin reductase and a large flavin-dependent oxygenase.there are two known types of microbial two-component flavin-dependent monooxygenases that catalyze oxygenation of p-hydroxyphenylacetate (hpa), and they are distinguished by having structurally distinct reductases and oxygenases. this paper presents a detailed analysis of the properties of the enzyme from pseudomonas aeruginosa, an example of one group, and compares its properties to those published for the acinetobacter baumannii enzyme, an example of the alternative group. the reductase and ox ...201020000468
the pseudomonas aeruginosa magnesium transporter mgte inhibits transcription of the type iii secretion system.pseudomonas aeruginosa is an opportunistic pathogen that causes life-long pneumonia in individuals with cystic fibrosis (cf). these long-term infections are maintained by bacterial biofilm formation in the cf lung. we have recently developed a model of p. aeruginosa biofilm formation on cultured cf airway epithelial cells. using this model, we discovered that mutation of a putative magnesium transporter gene, called mgte, led to increased cytotoxicity of p. aeruginosa toward epithelial cells. th ...201020028803
the pseudomonas aeruginosa magnesium transporter mgte inhibits transcription of the type iii secretion system.pseudomonas aeruginosa is an opportunistic pathogen that causes life-long pneumonia in individuals with cystic fibrosis (cf). these long-term infections are maintained by bacterial biofilm formation in the cf lung. we have recently developed a model of p. aeruginosa biofilm formation on cultured cf airway epithelial cells. using this model, we discovered that mutation of a putative magnesium transporter gene, called mgte, led to increased cytotoxicity of p. aeruginosa toward epithelial cells. th ...201020028803
the oxidative dna glycosylases of mycobacterium tuberculosis exhibit different substrate preferences from their escherichia coli counterparts.the dna glycosylases that remove oxidized dna bases fall into two general families: the fpg/nei family and the nth superfamily. based on protein sequence alignments, we identified four putative fpg/nei family members, as well as a putative nth protein in mycobacterium tuberculosis h37rv. all four fpg/nei proteins were successfully overexpressed using a bicistronic vector created in our laboratory. the mtunth protein was also overexpressed in soluble form. the substrate specificities of the purif ...201020031487
the oxidative dna glycosylases of mycobacterium tuberculosis exhibit different substrate preferences from their escherichia coli counterparts.the dna glycosylases that remove oxidized dna bases fall into two general families: the fpg/nei family and the nth superfamily. based on protein sequence alignments, we identified four putative fpg/nei family members, as well as a putative nth protein in mycobacterium tuberculosis h37rv. all four fpg/nei proteins were successfully overexpressed using a bicistronic vector created in our laboratory. the mtunth protein was also overexpressed in soluble form. the substrate specificities of the purif ...201020031487
polymorphisms associated with resistance and cross-resistance to aminoglycosides and capreomycin in mycobacterium tuberculosis isolates from south korean patients with drug-resistant tuberculosis.the aminoglycosides streptomycin, amikacin, and kanamycin and the cyclic polypeptide capreomycin are all widely used in second-line therapy for patients who develop multidrug-resistant tuberculosis. we have characterized a set of 106 clinical isolates of mycobacterium tuberculosis using phenotypic drug susceptibility testing (dst) to determine the extent of resistance to each agent and cross-resistance between agents. these results were compared with polymorphisms in the dna sequences of ribosom ...201020032248
polymorphisms associated with resistance and cross-resistance to aminoglycosides and capreomycin in mycobacterium tuberculosis isolates from south korean patients with drug-resistant tuberculosis.the aminoglycosides streptomycin, amikacin, and kanamycin and the cyclic polypeptide capreomycin are all widely used in second-line therapy for patients who develop multidrug-resistant tuberculosis. we have characterized a set of 106 clinical isolates of mycobacterium tuberculosis using phenotypic drug susceptibility testing (dst) to determine the extent of resistance to each agent and cross-resistance between agents. these results were compared with polymorphisms in the dna sequences of ribosom ...201020032248
structural motifs of the bacterial ribosomal proteins s20, s18 and s16 that contact rrna present in the eukaryotic ribosomal proteins s25, s26 and s27a, respectively.the majority of constitutive proteins in the bacterial 30s ribosomal subunit have orthologues in eukarya and archaea. the eukaryotic counterparts for the remainder (s6, s16, s18 and s20) have not been identified. we assumed that amino acid residues in the ribosomal proteins that contact rrna are to be constrained in evolution and that the most highly conserved of them are those residues that are involved in forming the secondary protein structure. we aligned the sequences of the bacterial riboso ...201020034956
accommodation of tmrna-smpb into stalled ribosomes: a cryo-em study.in eubacteria, translation of defective messenger rnas (mrnas) produces truncated polypeptides that stall on the ribosome. a quality control mechanism referred to as trans-translation is performed by transfer-messenger rna (tmrna), a specialized rna acting as both a trna and an mrna, associated with small protein b (smpb). so far, a clear view of the structural movements of both the protein and rna necessary to perform accommodation is still lacking. by using a construct containing the trna-like ...201020038631
the adenosine wedge: a new structural motif in ribosomal rna.here, we present a new recurrent rna arrangement, the so-called adenosine wedge (a-wedge), which is found in three places of the ribosomal rna in both ribosomal subunits. the arrangement has a hierarchical structure, consisting of elements previously described as recurrent motifs, namely, the along-groove packing motif, the a-minor and the hook-turn. within the a-wedge, these elements are involved in different types of cause-effect relationships, providing together for the particular tertiary st ...201020038632
discovery of 3-formyl-tyrosine metabolites from pseudoalteromonas tunicata through heterologous expression.genome mining and identification of natural product gene clusters typically relies on the presence of canonical nonribosomal polypeptide synthetase (nrps) or polyketide synthase (pks) domains. recently, other condensation enzymes, such as the atp-grasp ligases, have been recognized as important players in natural product biosynthesis. in this study, sequence based searching for homologues of ddaf, the atp-grasp amide ligase from dapdiamide biosynthesis, led to the identification of a previously ...201020041686
discovery of 3-formyl-tyrosine metabolites from pseudoalteromonas tunicata through heterologous expression.genome mining and identification of natural product gene clusters typically relies on the presence of canonical nonribosomal polypeptide synthetase (nrps) or polyketide synthase (pks) domains. recently, other condensation enzymes, such as the atp-grasp ligases, have been recognized as important players in natural product biosynthesis. in this study, sequence based searching for homologues of ddaf, the atp-grasp amide ligase from dapdiamide biosynthesis, led to the identification of a previously ...201020041686
measurement and interpretation of 15n-1h residual dipolar couplings in larger proteins.a decade ago, dr. l.e. kay and co-workers described an ingenious hnco-based triple-resonance experiment from which several protein backbone rdcs can be measured simultaneously (yang et al. (1999) [1]). they implemented a j-scaling technique in the (15)n dimension of the 3d experiment to obtain the nh rdcs. we have used this idea to carry out j-scaling in a 2d (15)n-(1)h-trosy experiment and have found it to be an excellent method to obtain nh rdcs for larger proteins upto 70 kda, far superior to ...201020018538
measurement and interpretation of 15n-1h residual dipolar couplings in larger proteins.a decade ago, dr. l.e. kay and co-workers described an ingenious hnco-based triple-resonance experiment from which several protein backbone rdcs can be measured simultaneously (yang et al. (1999) [1]). they implemented a j-scaling technique in the (15)n dimension of the 3d experiment to obtain the nh rdcs. we have used this idea to carry out j-scaling in a 2d (15)n-(1)h-trosy experiment and have found it to be an excellent method to obtain nh rdcs for larger proteins upto 70 kda, far superior to ...201020018538
modifications of protein environment of the [2fe-2s] cluster of the bc1 complex: effects on the biophysical properties of the rieske iron-sulfur protein and on the kinetics of the complex.the rate-determining step in the overall turnover of the bc(1) complex is electron transfer from ubiquinol to the rieske iron-sulfur protein (isp) at the q(o)-site. structures of the isp from rhodobacter sphaeroides show that serine 154 and tyrosine 156 form h-bonds to s-1 of the [2fe-2s] cluster and to the sulfur atom of the cysteine liganding fe-1 of the cluster, respectively. these are responsible in part for the high potential (e(m)(,7) approximately 300 mv) and low pk(a) (7.6) of the isp, w ...201020023300
modifications of protein environment of the [2fe-2s] cluster of the bc1 complex: effects on the biophysical properties of the rieske iron-sulfur protein and on the kinetics of the complex.the rate-determining step in the overall turnover of the bc(1) complex is electron transfer from ubiquinol to the rieske iron-sulfur protein (isp) at the q(o)-site. structures of the isp from rhodobacter sphaeroides show that serine 154 and tyrosine 156 form h-bonds to s-1 of the [2fe-2s] cluster and to the sulfur atom of the cysteine liganding fe-1 of the cluster, respectively. these are responsible in part for the high potential (e(m)(,7) approximately 300 mv) and low pk(a) (7.6) of the isp, w ...201020023300
mapping of the signal peptide-binding domain of escherichia coli seca using förster resonance energy transfer.identification of the signal peptide-binding domain within seca atpase is an important goal for understanding the molecular basis of seca preprotein recognition as well as elucidating the chemo-mechanical cycle of this nanomotor during protein translocation. in this study, forster resonance energy transfer methodology was employed to map the location of the seca signal peptide-binding domain using a collection of functional monocysteine seca mutants and alkaline phosphatase signal peptides label ...201020025247
solution nmr structures of proteins vpa0419 from vibrio parahaemolyticus and yiis from shigella flexneri provide structural coverage for protein domain family pfam 04175. 201019927321
solution nmr structures of proteins vpa0419 from vibrio parahaemolyticus and yiis from shigella flexneri provide structural coverage for protein domain family pfam 04175. 201019927321
flexible recognition of the trna g18 methylation target site by trmh methyltransferase through first binding and induced fit processes.transfer rna (gm18) methyltransferase (trmh) catalyzes methyl transfer from s-adenosyl-l-methionine to a conserved g18 in trna. we investigated the recognition mechanism of thermus thermophilus trmh for its guanosine target. thirteen yeast trna(phe) mutant transcripts were prepared in which the modification site and/or other nucleotides in the d-loop were substituted by dg, inosine, or other nucleotides. we then conducted methyl transfer kinetic studies, gel shift assays, and inhibition experime ...201020053984
two new families of the ftsz-tubulin protein superfamily implicated in membrane remodeling in diverse bacteria and archaea.several recent discoveries reveal unexpected versatility of the bacterial and archaeal cytoskeleton systems that are involved in cell division and other processes based on membrane remodeling. here we apply methods for distant protein sequence similarity detection, phylogenetic approaches, and genome context analysis to described two previously unnoticed families of the ftsz-tubulin superfamily. one of these families is limited in its spread to proteobacteria whereas the other is represented in ...201020459678
card: a new rna polymerase modulator in mycobacteria.mycobacteria card is an essential rnap binding protein that regulates many transcripts including rrna. this article will review our present state of knowledge regarding card and compare the known functions of card with other rnap binding proteins in e. coli, emphasizing how this information can guide future investigations.201021326904
card: a new rna polymerase modulator in mycobacteria.mycobacteria card is an essential rnap binding protein that regulates many transcripts including rrna. this article will review our present state of knowledge regarding card and compare the known functions of card with other rnap binding proteins in e. coli, emphasizing how this information can guide future investigations.201021326904
lipoic acid metabolism in microbial pathogens.lipoic acid [(r)-5-(1,2-dithiolan-3-yl)pentanoic acid] is an enzyme cofactor required for intermediate metabolism in free-living cells. lipoic acid was discovered nearly 60 years ago and was shown to be covalently attached to proteins in several multicomponent dehydrogenases. cells can acquire lipoate (the deprotonated charge form of lipoic acid that dominates at physiological ph) through either scavenging or de novo synthesis. microbial pathogens implement these basic lipoylation strategies wit ...201020508247
the path to next generation biofuels: successes and challenges in the era of synthetic biology.volatility of oil prices along with major concerns about climate change, oil supply security and depleting reserves have sparked renewed interest in the production of fuels from renewable resources. recent advances in synthetic biology provide new tools for metabolic engineers to direct their strategies and construct optimal biocatalysts for the sustainable production of biofuels. metabolic engineering and synthetic biology efforts entailing the engineering of native and de novo pathways for con ...201020089184
superpose3d: a local structural comparison program that allows for user-defined structure representations.local structural comparison methods can be used to find structural similarities involving functional protein patches such as enzyme active sites and ligand binding sites. the outcome of such analyses is critically dependent on the representation used to describe the structure. indeed different categories of functional sites may require the comparison program to focus on different characteristics of the protein residues. we have therefore developed superpose3d, a novel structural comparison softw ...201020700534
distinguishing microbial genome fragments based on their composition: evolutionary and comparative genomic perspectives.it is well known that patterns of nucleotide composition vary within and among genomes, although the reasons why these variations exist are not completely understood. between-genome compositional variation has been exploited to assign environmental shotgun sequences to their most likely originating genomes, whereas within-genome variation has been used to identify recently acquired genetic material such as pathogenicity islands. recent sequence assignment techniques have achieved high levels of ...201020333228
complete genome sequence of meiothermus ruber type strain (21).meiothermus ruber (loginova et al. 1984) nobre et al. 1996 is the type species of the genus meiothermus. this thermophilic genus is of special interest, as its members share relatively low degrees of 16s rrna gene sequence similarity and constitute a separate evolutionary lineage from members of the genus thermus, from which they can generally be distinguished by their slightly lower temperature optima. the temperature related split is in accordance with the chemotaxonomic feature of the polar l ...201021304689
complete genome sequence of meiothermus silvanus type strain (vi-r2).meiothermus silvanus (tenreiro et al. 1995) nobre et al. 1996 belongs to a thermophilic genus whose members share relatively low degrees of 16s rrna gene sequence similarity. meiothermus constitutes an evolutionary lineage separate from members of the genus thermus, from which they can generally be distinguished by their slightly lower temperature optima. m. silvanus is of special interest as it causes colored biofilms in the paper making industry and may thus be of economic importance as a biof ...201021304690
complete genome sequence of archaeoglobus profundus type strain (av18).archaeoglobus profundus (burggraf et al. 1990) is a hyperthermophilic archaeon in the euryarchaeal class archaeoglobi, which is currently represented by the single family archaeoglobaceae, containing six validly named species and two strains ascribed to the genus 'geoglobus' which is taxonomically challenged as the corresponding type species has no validly published name. all members were isolated from marine hydrothermal habitats and are obligate anaerobes. here we describe the features of the ...201021304717
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
crystallization and preliminary x-ray crystallographic analysis of human quinolinate phosphoribosyltransferase.quinolinate phosphoribosyltransferase (qprtase) is a key nad-biosynthetic enzyme which catalyzes the transfer of quinolinic acid to 5-phosphoribosyl-1-pyrophosphate, yielding nicotinic acid mononucleotide. homo sapiens qprtase (hs-qprtase) appeared as a hexamer during purification and the protein was crystallized. diffraction data were collected and processed at 2.8 å resolution. native hs-qprtase crystals belonged to space group p2(1), with unit-cell parameters a=76.2, b=137.1, c=92.7 å, β=103. ...201021206019
crystallization and preliminary x-ray crystallographic analysis of human quinolinate phosphoribosyltransferase.quinolinate phosphoribosyltransferase (qprtase) is a key nad-biosynthetic enzyme which catalyzes the transfer of quinolinic acid to 5-phosphoribosyl-1-pyrophosphate, yielding nicotinic acid mononucleotide. homo sapiens qprtase (hs-qprtase) appeared as a hexamer during purification and the protein was crystallized. diffraction data were collected and processed at 2.8 å resolution. native hs-qprtase crystals belonged to space group p2(1), with unit-cell parameters a=76.2, b=137.1, c=92.7 å, β=103. ...201021206019
cloning, expression, crystallization and preliminary x-ray crystallographic analysis of the co-chaperonin xogroes from xanthomonas oryzae pv. oryzae.bacterial blight (bb), a devastating disease caused by xanthomonas oryzae pv. oryzae (xoo), causes serious production losses of rice in asian countries. protein misfolding may interfere with the function of proteins in all living cells and must be prevented to avoid cellular disaster. all cells naturally contain molecular chaperones that assist the unfolded proteins in folding into the native structure. one of the well characterized chaperone complexes is groel-groes. groel, which consists of tw ...201021206021
cloning, expression, crystallization and preliminary x-ray crystallographic analysis of the co-chaperonin xogroes from xanthomonas oryzae pv. oryzae.bacterial blight (bb), a devastating disease caused by xanthomonas oryzae pv. oryzae (xoo), causes serious production losses of rice in asian countries. protein misfolding may interfere with the function of proteins in all living cells and must be prevented to avoid cellular disaster. all cells naturally contain molecular chaperones that assist the unfolded proteins in folding into the native structure. one of the well characterized chaperone complexes is groel-groes. groel, which consists of tw ...201021206021
crystallization and preliminary x-ray analysis of isopentenyl diphosphate isomerase from methanocaldococcus jannaschii.type 2 isopentenyl diphosphate isomerase (idi-2) is a flavoprotein. recently, flavin has been proposed to play a role as a general acid-base catalyst with no redox role during the enzyme reaction. to clarify the detailed enzyme reaction mechanism of idi-2 and the unusual role of flavin, structural analysis of idi-2 from methanocaldococcus jannaschii (mjidi) was performed. recombinant mjidi was crystallized at 293 k using calcium acetate as a precipitant. the diffraction of the crystal extended t ...201021206036
crystallization and preliminary x-ray analysis of isopentenyl diphosphate isomerase from methanocaldococcus jannaschii.type 2 isopentenyl diphosphate isomerase (idi-2) is a flavoprotein. recently, flavin has been proposed to play a role as a general acid-base catalyst with no redox role during the enzyme reaction. to clarify the detailed enzyme reaction mechanism of idi-2 and the unusual role of flavin, structural analysis of idi-2 from methanocaldococcus jannaschii (mjidi) was performed. recombinant mjidi was crystallized at 293 k using calcium acetate as a precipitant. the diffraction of the crystal extended t ...201021206036
targeting the chromosome partitioning protein para in tuberculosis drug discovery.to identify inhibitors of the essential chromosome partitioning protein para that are active against mycobacterium tuberculosis.201020810423
template-directed ligation of tethered mononucleotides by t4 dna ligase for kinase ribozyme selection.in vitro selection of kinase ribozymes for small molecule metabolites, such as free nucleosides, will require partition systems that discriminate active from inactive rna species. while nucleic acid catalysis of phosphoryl transfer is well established for phosphorylation of 5' or 2' oh of oligonucleotide substrates, phosphorylation of diffusible small molecules has not been demonstrated.201020811490
protective role of catechin on d-galactosamine induced hepatotoxicity through a p53 dependent pathway.objective of this study was to obtain a better understanding of the mechanism responsible for the d-galactosamine (d-galn) induced hepatotoxicity and to study the effect of catechin against d-galn induced hepatotoxicity. catechin 50 and 100 mg/kg b.wt was administered for 1 week by oral route. liver damage was induced by intra-peritoneal administration of 400 mg/kg b.wt d-galactosamine on the last day of catechin treatment. at the end of treatment all animals were killed and liver enzyme levels ...201021966103
the structure of eukaryotic and prokaryotic complex i.the structures of the nadh dehydrogenases from bos taurus and aquifex aeolicus have been determined by 3d electron microscopy, and have been analyzed in comparison with the previously determined structure of complex i from yarrowia lipolytica. the results show a clearly preserved domain structure in the peripheral arm of complex i, which is similar in the bacterial and eukaryotic complex. the membrane arms of both eukaryotic complexes show a similar shape but also significant differences in dist ...201019732833
the structure of eukaryotic and prokaryotic complex i.the structures of the nadh dehydrogenases from bos taurus and aquifex aeolicus have been determined by 3d electron microscopy, and have been analyzed in comparison with the previously determined structure of complex i from yarrowia lipolytica. the results show a clearly preserved domain structure in the peripheral arm of complex i, which is similar in the bacterial and eukaryotic complex. the membrane arms of both eukaryotic complexes show a similar shape but also significant differences in dist ...201019732833
"hot standards" for the thermoacidophilic archaeon sulfolobus solfataricus.within the archaea, the thermoacidophilic crenarchaeote sulfolobus solfataricus has become an important model organism for physiology and biochemistry, comparative and functional genomics, as well as, more recently also for systems biology approaches. within the sulfolobus systems biology ("sulfosys")-project the effect of changing growth temperatures on a metabolic network is investigated at the systems level by integrating genomic, transcriptomic, proteomic, metabolomic and enzymatic informati ...201019802714
"hot standards" for the thermoacidophilic archaeon sulfolobus solfataricus.within the archaea, the thermoacidophilic crenarchaeote sulfolobus solfataricus has become an important model organism for physiology and biochemistry, comparative and functional genomics, as well as, more recently also for systems biology approaches. within the sulfolobus systems biology ("sulfosys")-project the effect of changing growth temperatures on a metabolic network is investigated at the systems level by integrating genomic, transcriptomic, proteomic, metabolomic and enzymatic informati ...201019802714
structural studies on cytosolic domain of magnesium transporter mgte from enterococcus faecalis. 201019787770
structure, expression, and function of kynurenine aminotransferases in human and rodent brains.kynurenine aminotransferases (kats) catalyze the synthesis of kynurenic acid (kyna), an endogenous antagonist of n-methyl-d: -aspartate and alpha 7-nicotinic acetylcholine receptors. abnormal kyna levels in human brains are implicated in the pathophysiology of schizophrenia, alzheimer's disease, and other neurological disorders. four kats have been reported in mammalian brains, kat i/glutamine transaminase k/cysteine conjugate beta-lyase 1, kat ii/aminoadipate aminotransferase, kat iii/cysteine ...201019826765
structure, expression, and function of kynurenine aminotransferases in human and rodent brains.kynurenine aminotransferases (kats) catalyze the synthesis of kynurenic acid (kyna), an endogenous antagonist of n-methyl-d: -aspartate and alpha 7-nicotinic acetylcholine receptors. abnormal kyna levels in human brains are implicated in the pathophysiology of schizophrenia, alzheimer's disease, and other neurological disorders. four kats have been reported in mammalian brains, kat i/glutamine transaminase k/cysteine conjugate beta-lyase 1, kat ii/aminoadipate aminotransferase, kat iii/cysteine ...201019826765
the crystal structure of the novobiocin biosynthetic enzyme novp: the first representative structure for the tylf o-methyltransferase superfamily.novp is an s-adenosyl-l-methionine-dependent o-methyltransferase that catalyzes the penultimate step in the biosynthesis of the aminocoumarin antibiotic novobiocin. specifically, it methylates at 4-oh of the noviose moiety, and the resultant methoxy group is important for the potency of the mature antibiotic: previous crystallographic studies have shown that this group interacts directly with the target enzyme dna gyrase, which is a validated drug target. we have determined the high-resolution c ...201019857499
the crystal structure of the novobiocin biosynthetic enzyme novp: the first representative structure for the tylf o-methyltransferase superfamily.novp is an s-adenosyl-l-methionine-dependent o-methyltransferase that catalyzes the penultimate step in the biosynthesis of the aminocoumarin antibiotic novobiocin. specifically, it methylates at 4-oh of the noviose moiety, and the resultant methoxy group is important for the potency of the mature antibiotic: previous crystallographic studies have shown that this group interacts directly with the target enzyme dna gyrase, which is a validated drug target. we have determined the high-resolution c ...201019857499
spermine synthase.spermine is present in many organisms including animals, plants, some fungi, some archaea, and some bacteria. it is synthesized by spermine synthase, a highly specific aminopropyltransferase. this review describes spermine synthase structure, genetics, and function. structural and biochemical studies reveal that human spermine synthase is an obligate dimer. each monomer contains a c-terminal domain where the active site is located, a central linking domain that also forms the lid of the catalyti ...201019859664
spermine synthase.spermine is present in many organisms including animals, plants, some fungi, some archaea, and some bacteria. it is synthesized by spermine synthase, a highly specific aminopropyltransferase. this review describes spermine synthase structure, genetics, and function. structural and biochemical studies reveal that human spermine synthase is an obligate dimer. each monomer contains a c-terminal domain where the active site is located, a central linking domain that also forms the lid of the catalyti ...201019859664
structural and dynamic features of the mutt protein in the recognition of nucleotides with the mutagenic 8-oxoguanine base.escherichia coli mutt hydrolyzes 8-oxo-dgtp to 8-oxo-dgmp, an event that can prevent the misincorporation of 8-oxoguanine opposite adenine in dna. of the several enzymes that recognize 8-oxoguanine, mutt exhibits high substrate specificity for 8-oxoguanine nucleotides; however, the structural basis for this specificity is unknown. the crystal structures of mutt in the apo and holo forms and in the binary and ternary forms complexed with the product 8-oxo-dgmp and 8-oxo-dgmp plus mn(2+), respecti ...201019864691
structural and dynamic features of the mutt protein in the recognition of nucleotides with the mutagenic 8-oxoguanine base.escherichia coli mutt hydrolyzes 8-oxo-dgtp to 8-oxo-dgmp, an event that can prevent the misincorporation of 8-oxoguanine opposite adenine in dna. of the several enzymes that recognize 8-oxoguanine, mutt exhibits high substrate specificity for 8-oxoguanine nucleotides; however, the structural basis for this specificity is unknown. the crystal structures of mutt in the apo and holo forms and in the binary and ternary forms complexed with the product 8-oxo-dgmp and 8-oxo-dgmp plus mn(2+), respecti ...201019864691
crystal structure of the aspartyl-trna synthetase from entamoeba histolytica.the crystal structure of the aspartyl-trna synthetase from the eukaryotic parasite entamoeba histolytica has been determined at 2.8aresolution. relative to homologous sequences, the e. histolytica protein contains a 43-residue insertion between the n-terminal anticodon binding domain and the c-terminal catalytic domain. the present structure reveals that this insertion extends an arm of the hinge region that has previously been shown to mediate interaction of aspartyl-trna synthetase with the co ...201019874856
crystal structure of the aspartyl-trna synthetase from entamoeba histolytica.the crystal structure of the aspartyl-trna synthetase from the eukaryotic parasite entamoeba histolytica has been determined at 2.8aresolution. relative to homologous sequences, the e. histolytica protein contains a 43-residue insertion between the n-terminal anticodon binding domain and the c-terminal catalytic domain. the present structure reveals that this insertion extends an arm of the hinge region that has previously been shown to mediate interaction of aspartyl-trna synthetase with the co ...201019874856
proteomics-based refinement of deinococcus deserti genome annotation reveals an unwonted use of non-canonical translation initiation codons.deinococcaceae are a family of extremely radiation-tolerant bacteria that are currently subjected to numerous studies aimed at understanding the molecular mechanisms for such radiotolerance. to achieve a comprehensive and accurate annotation of the deinococcus deserti genome, we performed an n terminus-oriented characterization of its proteome. for this, we used a labeling reagent, n-tris(2,4,6-trimethoxyphenyl)phosphonium acetyl succinimide, to selectively derivatize protein n termini. the larg ...201019875382
proteomics-based refinement of deinococcus deserti genome annotation reveals an unwonted use of non-canonical translation initiation codons.deinococcaceae are a family of extremely radiation-tolerant bacteria that are currently subjected to numerous studies aimed at understanding the molecular mechanisms for such radiotolerance. to achieve a comprehensive and accurate annotation of the deinococcus deserti genome, we performed an n terminus-oriented characterization of its proteome. for this, we used a labeling reagent, n-tris(2,4,6-trimethoxyphenyl)phosphonium acetyl succinimide, to selectively derivatize protein n termini. the larg ...201019875382
multifrequency epr studies of manganese catalases provide a complete description of proteinaceous nitrogen coordination.pulse electron paramagnetic resonance (epr) spectroscopy is employed at two very different excitation frequencies, 9.77 and 30.67 ghz, in the study of the nitrogen coordination environment of the mn(iii)mn(iv) state of the dimanganese-containing catalases from lactobacillus plantarum and thermus thermophilus. consistent with previous studies, the lower-frequency results reveal one unique histidine nitrogen-mn cluster interaction. for the first time, a second, more strongly hyperfine-coupled (14) ...201020055466
structure and ligand binding properties of the epoxidase component of styrene monooxygenase .styrene monooxygenase (smo) is a two-component flavoprotein monooxygenase that transforms styrene to styrene oxide in the first step of the styrene catabolic and detoxification pathway of pseudomonas putida s12. the crystal structure of the n-terminally histidine-tagged epoxidase component of this system, nsmoa, determined to 2.3 a resolution, indicates the enzyme exists as a homodimer in which each monomer forms two distinct domains. the overall architecture is most similar to that of p-hydroxy ...201020055497
crystallization and preliminary x-ray crystallographic analysis of dna gyrase gyrb subunit from xanthomonas oryzae pv. oryzae.dna gyrase is a type ii topoisomerase that is essential for chromosome segregation and cell division owing to its ability to modify the topological forms of bacterial dna. in this study, the n-terminal fragment of the gyrb subunit of dna gyrase from xanthomonas oryzae pv. oryzae was overexpressed in escherichia coli, purified and crystallized. diffraction data were collected to 2.10 a resolution using a synchrotron-radiation source. the crystal belonged to space group i4(1), with unit-cell param ...201020057069
crystallization and preliminary x-ray crystallographic analysis of dna gyrase gyrb subunit from xanthomonas oryzae pv. oryzae.dna gyrase is a type ii topoisomerase that is essential for chromosome segregation and cell division owing to its ability to modify the topological forms of bacterial dna. in this study, the n-terminal fragment of the gyrb subunit of dna gyrase from xanthomonas oryzae pv. oryzae was overexpressed in escherichia coli, purified and crystallized. diffraction data were collected to 2.10 a resolution using a synchrotron-radiation source. the crystal belonged to space group i4(1), with unit-cell param ...201020057069
crystallization and preliminary x-ray crystallographic analysis of thermus thermophilus transcription elongation complex bound to gfh1.rna polymerase (rnap) elongates rna by iterative nucleotide-addition cycles (nac). a specific structural state (or states) of rnap may be the target of transcription elongation factors. gfh1, a thermus thermophilus gre-family protein, inhibits nac. to elucidate which rnap structural state gfh1 associates with, the t. thermophilus rnap elongation complex (ec) was cocrystallized with gfh1. of the 70 dna/rna scaffolds tested, two (for ec1 and ec2) were successfully crystallized. in the presence of ...201020057074
role of copper ion in regulating ligand binding in a myoglobin-based cytochrome c oxidase model.cytochrome c oxidase (cco), the terminal enzyme in the mitochondrial respiratory chain, catalyzes the four-electron reduction of dioxygen to water in a binuclear center comprised of a high-spin heme (heme a(3)) and a copper atom (cu(b)) coordinated by three histidine residues. as a minimum model for cco, a mutant of sperm whale myoglobin, named cu(b)mb, has been engineered, in which a copper atom is held in the distal heme pocket by the native e7 histidine and two nonnative histidine residues. i ...201020070118
an active dimanganese(iii)-tyrosyl radical cofactor in escherichia coli class ib ribonucleotide reductase.escherichia coli class ib ribonucleotide reductase (rnr) converts nucleoside 5'-diphosphates to deoxynucleoside 5'-diphosphates and is expressed under iron-limited and oxidative stress conditions. this rnr is composed of two homodimeric subunits: alpha2 (nrde), where nucleotide reduction occurs, and beta2 (nrdf), which contains an unidentified metallocofactor that initiates nucleotide reduction. nrde and nrdf are found in an operon with nrdi, which encodes an unusual flavodoxin proposed to be in ...201020070127
predicting the pathway involved in post-translational modification of elongation factor p in a subset of bacterial species.background: the bacterial elongation factor p (ef-p) is strictly conserved in bacteria and essential for protein synthesis. it is homologous to the eukaryotic translation initiation factor 5a (eif5a). a highly conserved eif5a lysine is modified into an unusual amino acid derived from spermidine, hypusine. hypusine is absolutely required for eif5a's role in translation in saccharomyces cerevisiae. the homologous lysine of ef-p is also modified to a spermidine derivative in escherichia coli. howev ...201020070887
telomere-centromere-driven genomic instability contributes to karyotype evolution in a mouse model of melanoma.aneuploidy and chromosomal instability (cin) are hallmarks of most solid tumors. these alterations may result from inaccurate chromosomal segregation during mitosis, which can occur through several mechanisms including defective telomere metabolism, centrosome amplification, dysfunctional centromeres, and/or defective spindle checkpoint control. in this work, we used an in vitro murine melanoma model that uses a cellular adhesion blockade as a transforming factor to characterize telomeric and ce ...201020072649
the nd2 subunit is labeled by a photoaffinity analogue of asimicin, a potent complex i inhibitor.nadh:ubiquinone oxidoreductase (complex i) is the entry enzyme of mitochondrial oxidative phosphorylation. to obtain the structural information on inhibitor/quinone binding sites, we synthesized [3h]benzophenone-asimicin ([3h]bpa), a photoaffinity analogue of asimicin, which belongs to the acetogenin family known as the most potent complex i inhibitor. we found that [3h]bpa was photo-crosslinked to nd2, nd1 and nd5 subunits, by the three dimensional separation (blue-native/doubled sds-page) of [ ...201020074573
unique features of animal mitochondrial translation systems. the non-universal genetic code, unusual features of the translational apparatus and their relevance to human mitochondrial diseases.in animal mitochondria, several codons are non-universal and their meanings differ depending on the species. in addition, the trna structures that decipher codons are sometimes unusually truncated. these features seem to be related to the shortening of mitochondrial (mt) genomes, which occurred during the evolution of mitochondria. these organelles probably originated from the endosymbiosis of an aerobic eubacterium into an ancestral eukaryote. it is plausible that these events brought about the ...201020075606
structure of intact thermus thermophilus v-atpase by cryo-em reveals organization of the membrane-bound v(o) motor.the eubacterium thermus thermophilus uses a macromolecular assembly closely related to eukaryotic v-atpase to produce its supply of atp. this simplified v-atpase offers several advantages over eukaryotic v-atpases for structural analysis and investigation of the mechanism of the enzyme. here we report the structure of the complex at approximately 16 a resolution as determined by single particle electron cryomicroscopy (cryo-em). the resolution of the map and our use of cryo-em, rather than negat ...201020080582
temperature dependence of the flexibility of thermophilic and mesophilic flavoenzymes of the nitroreductase fold.a widely held hypothesis regarding the thermostability of thermophilic proteins states asserts that, at any given temperature, thermophilic proteins are more rigid than their mesophilic counterparts. many experimental and computational studies have addressed this question with conflicting results. here, we compare two homologous enzymes, one mesophilic (escherichia coli fmn-dependent nitroreductase; ntr) and one thermophilic (thermus thermophilus nadh oxidase; nox), by multiple molecular dynamic ...201020083491
properties of escherichia coli ef-tu mutants designed for fluorescence resonance energy transfer from trna molecules.here we describe the design, preparation and characterization of 10 ef-tu mutants of potential utility for the study of escherichia coli elongation factor tu (ef-tu) interaction with trna by a fluorescence resonance energy transfer assay. each mutant contains a single cysteine residue at positions in ef-tu that are proximal to trna sites within the aminoacyl-trna.ef-tu.gtp ternary complex that have previously been labeled with fluorophores. these positions fall in the 323-326 and 344-348 regions ...201020083494
new, closely related haloarchaeal viral elements with different nucleic acid types.during the search for haloarchaeal viruses, we isolated and characterized a new pleomorphic lipid-containing virus, haloarcula hispanica pleomorphic virus 1 (hhpv-1), that infects the halophilic archaeon haloarcula hispanica. the virus contains a circular double-stranded dna genome of 8,082 bp in size. the organization of the genome shows remarkable synteny and amino acid sequence similarity to the genome and predicted proteins of the halovirus hrpv-1, a pleomorphic single-stranded dna virus tha ...201020089654
structural basis for l-lysine feedback inhibition of homocitrate synthase.the alpha-aminoadipate pathway of lysine biosynthesis is modulated at the transcriptional and biochemical levels by feedback inhibition. the first enzyme in the alpha-aminoadipate pathway, homocitrate synthase (hcs), is the target of the feedback regulation and is strongly inhibited by l-lysine. here we report the structure of schizosaccharomyces pombe hcs (sphcs) in complex with l-lysine. the structure illustrates that the amino acid directly competes with the substrate 2-oxoglutarate for bindi ...201020089861
a major role of the recfor pathway in dna double-strand-break repair through esdsa in deinococcus radiodurans.in deinococcus radiodurans, the extreme resistance to dna-shattering treatments such as ionizing radiation or desiccation is correlated with its ability to reconstruct a functional genome from hundreds of chromosomal fragments. the rapid reconstitution of an intact genome is thought to occur through an extended synthesis-dependent strand annealing process (esdsa) followed by dna recombination. here, we investigated the role of key components of the recf pathway in esdsa in this organism naturall ...201020090937
the regulatory protein rraa modulates rna-binding and helicase activities of the e. coli rna degradosome.the escherichia coli endoribonuclease rnase e is an essential enzyme having key roles in mrna turnover and the processing of several structured rna precursors, and it provides the scaffold to assemble the multienzyme rna degradosome. the activity of rnase e is inhibited by the protein rraa, which can interact with the ribonuclease's degradosome-scaffolding domain. here, we report that rraa can bind to the rna helicase component of the degradosome (rhlb) and the two rna-binding sites in the degra ...201020106955
improving small-angle x-ray scattering data for structural analyses of the rna world.defining the shape, conformation, or assembly state of an rna in solution often requires multiple investigative tools ranging from nucleotide analog interference mapping to x-ray crystallography. a key addition to this toolbox is small-angle x-ray scattering (saxs). saxs provides direct structural information regarding the size, shape, and flexibility of the particle in solution and has proven powerful for analyses of rna structures with minimal requirements for sample concentration and volumes. ...201020106957
crystal structure of the first eubacterial mre11 nuclease reveals novel features that may discriminate substrates during dna repair.mre11 nuclease plays a central role in the repair of cytotoxic and mutagenic dna double-strand breaks. as x-ray structural information has been available only for the pyrococcus furiosus enzyme (pfmre11), the conserved and variable features of this nuclease across the domains of life have not been experimentally defined. our crystal structure and biochemical studies demonstrate that tm1635 from thermotoga maritima, originally annotated as a putative nuclease, is an mre11 endo/exonuclease (tmmre1 ...201020122942
crystallization and preliminary x-ray diffraction analyses of the homodimeric glycine decarboxylase (p-protein) from the cyanobacterium synechocystis sp. pcc 6803.glycine decarboxylase, or p-protein, is a major enzyme that is involved in the c(1) metabolism of all organisms and in the photorespiratory pathway of plants and cyanobacteria. the protein from synechocystis sp. pcc 6803 is a homodimer with a mass of 215 kda. recombinant glycine decarboxylase was expressed in escherichia coli and purified by metal-affinity, ion-exchange and gel-filtration chromatography. crystals of p-protein that diffracted to a resolution of 2.1 a were obtained using the hangi ...201020124719
identification of the tirandamycin biosynthetic gene cluster from streptomyces sp. 307-9.the structurally intriguing bicyclic ketal moiety of tirandamycin is common to several acyl-tetramic acid antibiotics, and is a key determinant of biological activity. we have identified the tirandamycin biosynthetic gene cluster from the environmental marine isolate streptomyces sp. 307-9, thus providing the first genetic insight into the biosynthesis of this natural product scaffold. sequence analysis revealed a hybrid polyketide synthase-nonribosomal peptide synthetase gene cluster with a col ...201020127927
structure of recj exonuclease defines its specificity for single-stranded dna.recj is a single-stranded dna (ssdna)-specific 5'-3' exonuclease that plays an important role in dna repair and recombination. to elucidate how recj achieves its high specificity for ssdna, we determined the entire structures of recj both in a ligand-free form and in a complex with mn(2+) or mg(2+) by x-ray crystallography. the entire recj consists of four domains that form a molecule with an o-like structure. one of two newly identified domains had structural similarities to an oligonucleotide/ ...201020129927
functional regions of the n-terminal domain of the antiterminator rfah.rfah is a bacterial elongation factor that increases expression of distal genes in several long, horizontally acquired operons. rfah is recruited to the transcription complex during rna chain elongation through specific interactions with a dna element called ops. following recruitment, rfah remains bound to rna polymerase (rnap) and acts as an antiterminator by reducing rnap pausing and termination at some factor-independent and rho-dependent signals. rfah consists of two domains connected by a ...201020132437
crystal structures of trypanosomal histidyl-trna synthetase illuminate differences between eukaryotic and prokaryotic homologs.crystal structures of histidyl-trna synthetase (hisrs) from the eukaryotic parasites trypanosoma brucei and trypanosoma cruzi provide a first structural view of a eukaryotic form of this enzyme and reveal differences from bacterial homologs. hisrss in general contain an extra domain inserted between conserved motifs 2 and 3 of the class ii aminoacyl-trna synthetase catalytic core. the current structures show that the three-dimensional topology of this domain is very different in bacterial and ar ...201020132829
crystal structure of the bifunctional proline utilization a flavoenzyme from bradyrhizobium japonicum.the bifunctional proline catabolic flavoenzyme, proline utilization a (puta), catalyzes the oxidation of proline to glutamate via the sequential activities of fad-dependent proline dehydrogenase (prodh) and nad(+)-dependent delta(1)-pyrroline-5-carboxylate dehydrogenase (p5cdh) domains. although structures for some of the domains of puta are known, a structure for the full-length protein has not previously been solved. here we report the 2.1 a resolution crystal structure of puta from bradyrhizo ...201020133651
muts and mutl are dispensable for maintenance of the genomic mutation rate in the halophilic archaeon halobacterium salinarum nrc-1.the genome of the halophilic archaeon halobacterium salinarum nrc-1 encodes for homologs of muts and mutl, which are key proteins of a dna mismatch repair pathway conserved in bacteria and eukarya. mismatch repair is essential for retaining the fidelity of genetic information and defects in this pathway result in the deleterious accumulation of mutations and in hereditary diseases in humans.201020140215
homopolymeric tracts represent a general regulatory mechanism in prokaryotes.while, traditionally, regulation of gene expression can be grouped into transcriptional, translational, and post-translational mechanisms, some mechanisms of rapid genetic variation can also contribute to regulation of gene expression, e.g., phase variation.201020144225
plasticity of the rna kink turn structural motif.the kink turn (k-turn) is an rna structural motif found in many biologically significant rnas. while most examples of the k-turn have a similar fold, the crystal structure of the azoarcus group i intron revealed a novel rna conformation, a reverse kink turn bent in the direction opposite that of a consensus k-turn. the reverse k-turn is bent toward the major grooves rather than the minor grooves of the flanking helices, yet the sequence differs from the k-turn consensus by only a single nucleoti ...201020145044
kinetic and structural characterization of human mortalin.human mortalin is an hsp70 chaperone that has been implicated in cancer, alzheimer's and parkinson's disease, and involvement has been suggested in cellular iron-sulfur cluster biosynthesis. however, study of this important human chaperone has been hampered by a lack of active material sufficient for biochemical characterization. herein, we report the successful purification and characterization of recombinant human mortalin in escherichia coli. the recombinant protein was expressed in the form ...201020152901
organization of the electron transfer chain to oxygen in the obligate human pathogen neisseria gonorrhoeae: roles for cytochromes c4 and c5, but not cytochrome c2, in oxygen reduction.although neisseria gonorrhoeae is a prolific source of eight c-type cytochromes, little is known about how its electron transfer pathways to oxygen are organized. in this study, the roles in the respiratory chain to oxygen of cytochromes c(2), c(4), and c(5), encoded by the genes ccca, cyca, and cycb, respectively, have been investigated. single mutations in genes for either cytochrome c(4) or c(5) resulted in an increased sensitivity to growth inhibition by excess oxygen and small decreases in ...201020154126
the structures of the anti-tuberculosis antibiotics viomycin and capreomycin bound to the 70s ribosome.viomycin and capreomycin belong to the tuberactinomycin family of antibiotics, which are among the most effective antibiotics against multidrug-resistant tuberculosis. here we present two crystal structures of the 70s ribosome in complex with three trnas and bound to either viomycin or capreomycin at 3.3- and 3.5-a resolution, respectively. both antibiotics bind to the same site on the ribosome, which lies at the interface between helix 44 of the small ribosomal subunit and helix 69 of the large ...201020154709
exit strategies for charged trna from glurs.for several class i aminoacyl-trna synthetases (aarss), the rate-determining step in aminoacylation is the dissociation of charged trna from the enzyme. in this study, the following factors affecting the release of the charged trna from aarss are computationally explored: the protonation states of amino acids and substrates present in the active site, and the presence and the absence of amp and elongation factor tu. through molecular modeling, internal pk(a) calculations, and molecular dynamics ...201020156451
multiple controls affect arsenite oxidase gene expression in herminiimonas arsenicoxydans.both the speciation and toxicity of arsenic are affected by bacterial transformations, i.e. oxidation, reduction or methylation. these transformations have a major impact on environmental contamination and more particularly on arsenic contamination of drinking water. herminiimonas arsenicoxydans has been isolated from an arsenic- contaminated environment and has developed various mechanisms for coping with arsenic, including the oxidation of as(iii) to as(v) as a detoxification mechanism.201020167112
increased incidence of rare codon clusters at 5' and 3' gene termini: implications for function.the process of translation can be affected by the use of rare versus common codons within the mrna transcript.201020167116
characterization of endott, a novel single-stranded dna-specific endonuclease from thermoanaerobacter tengcongensis.endott encoded by tte0829 of thermoanaerobacter tengcongensis binds and cleaves single-stranded (ss) and damaged double-stranded (ds) dna in vitro as well as binding dsdna. in the presence of a low concentration of nacl, endott cleaved ss regions of damaged dsdna efficiently but did not cleave dna that was entirely ss or ds. at high concentrations of nacl or mgcl(2) or atp, there was also specific cleavage of ssdna. this suggested a preference for ss/ds junctions to stimulate cleavage of the dna ...201020172959
interaction of an essential escherichia coli gtpase, der, with the 50s ribosome via the kh-like domain.der, an essential escherichia coli tandem gtpase, has been implicated in 50s subunit biogenesis. the rrmj gene encodes a methyltransferase that modifies the u2552 residue of 23s rrna, and its deletion causes a severe growth defect. peculiarly, overexpression of der suppresses growth impairment. in this study, using an rrmj-deletion strain, we demonstrated that two gtpase domains of der regulate its association with 50s subunit via the kh-like domain. we also identified a region of der that is cr ...201020172997
the structure of the peripheral stalk of thermus thermophilus h+-atpase/synthase.proton-translocating atpases are ubiquitous protein complexes that couple atp catalysis with proton translocation via a rotary catalytic mechanism. the peripheral stalks are essential components that counteract torque generated from proton translocation during atp synthesis or from atp hydrolysis during proton pumping. despite their essential role, the peripheral stalks are the least conserved component of the complexes, differing substantially between subtypes in composition and stoichiometry. ...201020173764
para2, a vibrio cholerae chromosome partitioning protein, forms left-handed helical filaments on dna.most bacterial chromosomes contain homologs of plasmid partitioning (par) loci. these loci encode atpases called para that are thought to contribute to the mechanical force required for chromosome and plasmid segregation. in vibrio cholerae, the chromosome ii (chrii) par locus is essential for chrii segregation. here, we found that purified para2 had atpase activities comparable to other para homologs, but, unlike many other para homologs, did not form high molecular weight complexes in the pres ...201020176965
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