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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
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
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
structure of leishmania major methionyl-trna synthetase in complex with intermediate products methionyladenylate and pyrophosphate.leishmania parasites cause two million new cases of leishmaniasis each year with several hundreds of millions of people at risk. due to the paucity and shortcomings of available drugs, we have undertaken the crystal structure determination of a key enzyme from leishmania major in hopes of creating a platform for the rational design of new therapeutics. crystals of the catalytic core of methionyl-trna synthetase from l. major (lmmetrs) were obtained with the substrates mgatp and methionine presen ...201021144880
structure of leishmania major methionyl-trna synthetase in complex with intermediate products methionyladenylate and pyrophosphate.leishmania parasites cause two million new cases of leishmaniasis each year with several hundreds of millions of people at risk. due to the paucity and shortcomings of available drugs, we have undertaken the crystal structure determination of a key enzyme from leishmania major in hopes of creating a platform for the rational design of new therapeutics. crystals of the catalytic core of methionyl-trna synthetase from l. major (lmmetrs) were obtained with the substrates mgatp and methionine presen ...201021144880
electron cryomicroscopy structure of a membrane-anchored mitochondrial aaa protease.ftsh-related aaa proteases are conserved membrane-anchored, atp-dependent molecular machines, which mediate the processing and turnover of soluble and membrane-embedded proteins in eubacteria, mitochondria, and chloroplasts. homo- and hetero-oligomeric proteolytic complexes exist, which are composed of homologous subunits harboring an atpase domain of the aaa family and an h41 metallopeptidase domain. mutations in subunits of mitochondrial m-aaa proteases have been associated with different neur ...201021147776
electron cryomicroscopy structure of a membrane-anchored mitochondrial aaa protease.ftsh-related aaa proteases are conserved membrane-anchored, atp-dependent molecular machines, which mediate the processing and turnover of soluble and membrane-embedded proteins in eubacteria, mitochondria, and chloroplasts. homo- and hetero-oligomeric proteolytic complexes exist, which are composed of homologous subunits harboring an atpase domain of the aaa family and an h41 metallopeptidase domain. mutations in subunits of mitochondrial m-aaa proteases have been associated with different neur ...201021147776
phenotypic characterization of transgenic mice overexpressing neuregulin-1.neuregulin-1 (nrg1) is one of the susceptibility genes for schizophrenia and implicated in the neurotrophic regulation of gabaergic and dopaminergic neurons, myelination, and nmda receptor function. postmortem studies often indicate a pathologic association of increased nrg1 expression or signaling with this illness. however, the psychobehavioral implication of nrg1 signaling has mainly been investigated using hypomorphic mutant mice for individual nrg1 splice variants.201021151609
molecular dynamics of ribosomal elongation factors g and tu.translation on the ribosome is controlled by external factors. during polypeptide lengthening, elongation factors ef-tu and ef-g consecutively interact with the bacterial ribosome. ef-tu binds and delivers an aminoacyl-trna to the ribosomal a site and ef-g helps translocate the trnas between their binding sites after the peptide bond is formed. these processes occur at the expense of gtp. ef-tu:trna and ef-g are of similar shape, share a common binding site, and undergo large conformational chan ...201021152913
molecular dynamics of ribosomal elongation factors g and tu.translation on the ribosome is controlled by external factors. during polypeptide lengthening, elongation factors ef-tu and ef-g consecutively interact with the bacterial ribosome. ef-tu binds and delivers an aminoacyl-trna to the ribosomal a site and ef-g helps translocate the trnas between their binding sites after the peptide bond is formed. these processes occur at the expense of gtp. ef-tu:trna and ef-g are of similar shape, share a common binding site, and undergo large conformational chan ...201021152913
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
ribonucleotide reduction - horizontal transfer of a required function spans all three domains.ribonucleotide reduction is the only de novo pathway for synthesis of deoxyribonucleotides, the building blocks of dna. the reaction is catalysed by ribonucleotide reductases (rnrs), an ancient enzyme family comprised of three classes. each class has distinct operational constraints, and are broadly distributed across organisms from all three domains, though few class i rnrs have been identified in archaeal genomes, and classes ii and iii likewise appear rare across eukaryotes. in this study, we ...201021143941
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
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
filling the gap, evolutionarily conserved omp85 in plastids of chromalveolates.chromalveolates are a diverse group of protists that include many ecologically and medically relevant organisms such as diatoms and apicomplexan parasites. they possess plastids generally surrounded by four membranes, which evolved by engulfment of a red alga. today, most plastid proteins must be imported, but many aspects of protein import into complex plastids are still cryptic. in particular, how proteins cross the third outermost membrane has remained unexplained. we identified a protein in ...201020042599
filling the gap, evolutionarily conserved omp85 in plastids of chromalveolates.chromalveolates are a diverse group of protists that include many ecologically and medically relevant organisms such as diatoms and apicomplexan parasites. they possess plastids generally surrounded by four membranes, which evolved by engulfment of a red alga. today, most plastid proteins must be imported, but many aspects of protein import into complex plastids are still cryptic. in particular, how proteins cross the third outermost membrane has remained unexplained. we identified a protein in ...201020042599
prediction and analysis of the modular structure of cytochrome p450 monooxygenases.cytochrome p450 monooxygenases (cyps) form a vast and diverse family of highly variable sequences. they catalyze a wide variety of oxidative reactions and are therefore of great relevance in drug development and biotechnological applications. despite their differences in sequence and substrate specificity, the structures of cyps are highly similar. although being in research focus for years, factors mediating selectivity and activity remain vague.201020950472
mustang-mr structural sieving server: applications in protein structural analysis and crystallography.a central tenet of structural biology is that related proteins of common function share structural similarity. this has key practical consequences for the derivation and analysis of protein structures, and is exploited by the process of "molecular sieving" whereby a common core is progressively distilled from a comparison of two or more protein structures. this paper reports a novel web server for "sieving" of protein structures, based on the multiple structural alignment program mustang.201020386610
bioprocessing data for the production of marine enzymes.this review is a synopsis of different bioprocess engineering approaches adopted for the production of marine enzymes. three major modes of operation: batch, fed-batch and continuous have been used for production of enzymes (such as protease, chitinase, agarase, peroxidase) mainly from marine bacteria and fungi on a laboratory bioreactor and pilot plant scales. submerged, immobilized and solid-state processes in batch mode were widely employed. the fed-batch process was also applied in several b ...201020479981
structures of membrane proteins.in reviewing the structures of membrane proteins determined up to the end of 2009, we present in words and pictures the most informative examples from each family. we group the structures together according to their function and architecture to provide an overview of the major principles and variations on the most common themes. the first structures, determined 20 years ago, were those of naturally abundant proteins with limited conformational variability, and each membrane protein structure det ...201020667175
the nucleotide addition cycle of rna polymerase is controlled by two molecular hinges in the bridge helix domain.cellular rna polymerases (rnaps) are complex molecular machines that combine catalysis with concerted conformational changes in the active center. previous work showed that kinking of a hinge region near the c-terminus of the bridge helix (bh-h(c)) plays a critical role in controlling the catalytic rate.201021034443
the architecture of rna polymerase fidelity.the basis for transcriptional fidelity by rna polymerase is not understood, but the 'trigger loop', a conserved structural element that is rearranged in the presence of correct substrate nucleotides, is thought to be critical. a study just published in bmc biology sheds new light on the ways in which the trigger loop may promote selection of correct nucleotide triphosphate substrates. see research article http://www.biomedcentral.com/1741-7007/8/54.201020598112
modulation of rna polymerase activity through the trigger loop folding.folding of the trigger loop of rna polymerase promotes nucleotide addition through creating a closed, catalytically competent conformation of the active center. here, we discuss the impact of adjacent rna polymerase elements, including the f loop and the jaw domain, as well as external regulatory factors on the trigger loop folding and catalysis.201021326898
stepwise mechanism for transcription fidelity.transcription is the first step of gene expression and is characterized by a high fidelity of rna synthesis. during transcription, the rna polymerase active centre discriminates against not just non-complementary ribo ntp substrates but also against complementary 2'- and 3'-deoxy ntps. a flexible domain of the rna polymerase active centre, the trigger loop, was shown to play an important role in this process, but the mechanisms of this participation remained elusive.201020459653
non-canonical dna transcription enzymes and the conservation of two-barrel rna polymerases.dna transcription depends on multimeric rna polymerases that are exceptionally conserved in all cellular organisms, with an active site region of >500 amino acids mainly harboured by their rpb1 and rpb2 subunits. together with the distantly related eukaryotic rna-dependent polymerases involved in gene silencing, they form a monophyletic family of ribonucleotide polymerases with a similarly organized active site region based on two double-psi barrels. recent viral and phage genome sequencing have ...201020360047
the bridge helix of rna polymerase acts as a central nanomechanical switchboard for coordinating catalysis and substrate movement.the availability of in vitro assembly systems to produce recombinant archaeal rna polymerases (rnaps) offers one of the most powerful experimental tools for investigating the still relatively poorly understood molecular mechanisms underlying rnap function. over the last few years, we pioneered new robot-based high-throughput mutagenesis approaches to study structure/function relationships within various domains surrounding the catalytic center. the bridge helix domain, which appears in numerous ...201122312317
the bridge helix of rna polymerase acts as a central nanomechanical switchboard for coordinating catalysis and substrate movement.the availability of in vitro assembly systems to produce recombinant archaeal rna polymerases (rnaps) offers one of the most powerful experimental tools for investigating the still relatively poorly understood molecular mechanisms underlying rnap function. over the last few years, we pioneered new robot-based high-throughput mutagenesis approaches to study structure/function relationships within various domains surrounding the catalytic center. the bridge helix domain, which appears in numerous ...201122312317
transcription initiation factor dksa has diverse effects on rna chain elongation.bacterial transcription factors dksa and greb belong to a family of coiled-coil proteins that bind within the secondary channel of rna polymerase (rnap). these proteins display structural homology but play different regulatory roles. dksa disrupts rnap interactions with promoter dna and inhibits formation of initiation complexes, sensitizing rrna synthesis to changes in concentrations of ppgpp and ntps. gre proteins remodel the rnap active site and facilitate cleavage of the nascent rna in elong ...201122210857
transcription initiation factor dksa has diverse effects on rna chain elongation.bacterial transcription factors dksa and greb belong to a family of coiled-coil proteins that bind within the secondary channel of rna polymerase (rnap). these proteins display structural homology but play different regulatory roles. dksa disrupts rnap interactions with promoter dna and inhibits formation of initiation complexes, sensitizing rrna synthesis to changes in concentrations of ppgpp and ntps. gre proteins remodel the rnap active site and facilitate cleavage of the nascent rna in elong ...201122210857
the dna exonucleases of escherichia coli.dna exonucleases, enzymes that hydrolyze phosphodiester bonds in dna from a free end, play important cellular roles in dna repair, genetic recombination and mutation avoidance in all organisms. this article reviews the structure, biochemistry, and biological functions of the 17 exonucleases currently identified in the bacterium escherichia coli. these include the exonucleases associated with dna polymerases i (pola), ii (polb), and iii (dnaq/mutd); exonucleases i (xona/sbcb), iii (xtha), iv, vii ...201126442508
enzymatic synthesis of long double-stranded dna labeled with haloderivatives of nucleobases in a precisely pre-determined sequence.restriction endonucleases are widely applied in recombinant dna technology. among them, enzymes of class iis, which cleave dna beyond recognition sites, are especially useful. we use bsai enzyme for the pinpoint introduction of halogen nucleobases into dna. this has been done for the purpose of anticancer radio- and phototherapy that is our long-term objective.201121864341
genetic tool development underpins recent advances in thermophilic whole-cell biocatalysts.the environmental value of sustainably producing bioproducts from biomass is now widely appreciated, with a primary target being the economic production of fuels such as bioethanol from lignocellulose. the application of thermophilic prokaryotes is a rapidly developing niche in this field, driven by their known catabolic versatility with lignocellulose-derived carbohydrates. fundamental to the success of this work has been the development of reliable genetic and molecular systems. these technica ...201121310009
microbial ecology of the dark ocean above, at, and below the seafloor.the majority of life on earth--notably, microbial life--occurs in places that do not receive sunlight, with the habitats of the oceans being the largest of these reservoirs. sunlight penetrates only a few tens to hundreds of meters into the ocean, resulting in large-scale microbial ecosystems that function in the dark. our knowledge of microbial processes in the dark ocean-the aphotic pelagic ocean, sediments, oceanic crust, hydrothermal vents, etc.-has increased substantially in recent decades. ...201121646433
mechanism of bacterial transcription initiation: rna polymerase - promoter binding, isomerization to initiation-competent open complexes, and initiation of rna synthesis.initiation of rna synthesis from dna templates by rna polymerase (rnap) is a multi-step process, in which initial recognition of promoter dna by rnap triggers a series of conformational changes in both rnap and promoter dna. the bacterial rnap functions as a molecular isomerization machine, using binding free energy to remodel the initial recognition complex, placing downstream duplex dna in the active site cleft and then separating the nontemplate and template strands in the region surrounding ...201121371479
x-ray crystal structures elucidate the nucleotidyl transfer reaction of transcript initiation using two nucleotides.we have determined the x-ray crystal structures of the pre- and postcatalytic forms of the initiation complex of bacteriophage n4 rna polymerase that provide the complete set of atomic images depicting the process of transcript initiation by a single-subunit rna polymerase. as observed during t7 rna polymerase transcript elongation, substrate loading for the initiation process also drives a conformational change of the o-helix, but only the correct base pairing between the +2 substrate and dna b ...201121321236
seleno-detergent mad phasing of leukotriene c4 synthase in complex with dodecyl-β-d-selenomaltoside.dodecyl-β-d-selenomaltoside (seddm) is a seleno-detergent with a β-glycosidic seleno-ether in place of the ether moiety in dodecyl-β-d-maltoside. seleno-detergents are candidates for heavy-atom agents in experimental phasing of membrane proteins in protein crystallography. crystals of a nuclear membrane-embedded enzyme, leukotriene c(4) synthase (ltc(4)s), in complex with seddm were prepared and a multiwavelength anomalous diffraction (mad) experiment was performed. the seddm in the ltc(4)s crys ...201122139193
ucsf chimera, modeller, and imp: an integrated modeling system.structural modeling of macromolecular complexes greatly benefits from interactive visualization capabilities. here we present the integration of several modeling tools into ucsf chimera. these include comparative modeling by modeller, simultaneous fitting of multiple components into electron microscopy density maps by imp multifit, computing of small-angle x-ray scattering profiles and fitting of the corresponding experimental profile by imp foxs, and assessment of amino acid sidechain conformat ...201121963794
ucsf chimera, modeller, and imp: an integrated modeling system.structural modeling of macromolecular complexes greatly benefits from interactive visualization capabilities. here we present the integration of several modeling tools into ucsf chimera. these include comparative modeling by modeller, simultaneous fitting of multiple components into electron microscopy density maps by imp multifit, computing of small-angle x-ray scattering profiles and fitting of the corresponding experimental profile by imp foxs, and assessment of amino acid sidechain conformat ...201121963794
a bioinformatics classifier and database for heme-copper oxygen reductases.heme-copper oxygen reductases (hcos) are the last enzymatic complexes of most aerobic respiratory chains, reducing dioxygen to water and translocating up to four protons across the inner mitochondrial membrane (eukaryotes) or cytoplasmatic membrane (prokaryotes). the number of completely sequenced genomes is expanding exponentially, and concomitantly, the number and taxonomic distribution of hco sequences. these enzymes were initially classified into three different types being this classificati ...201121559461
bioinformatic analysis reveals high diversity of bacterial genes for laccase-like enzymes.fungal laccases have been used in various fields ranging from processes in wood and paper industries to environmental applications. although a few bacterial laccases have been characterized in recent years, prokaryotes have largely been neglected as a source of novel enzymes, in part due to the lack of knowledge about the diversity and distribution of laccases within bacteria. in this work genes for laccase-like enzymes were searched for in over 2,200 complete and draft bacterial genomes and fou ...201122022440
the fggy carbohydrate kinase family: insights into the evolution of functional specificities.function diversification in large protein families is a major mechanism driving expansion of cellular networks, providing organisms with new metabolic capabilities and thus adding to their evolutionary success. however, our understanding of the evolutionary mechanisms of functional diversity in such families is very limited, which, among many other reasons, is due to the lack of functionally well-characterized sets of proteins. here, using the fggy carbohydrate kinase family as an example, we bu ...201122215998
a pilot study of bacterial genes with disrupted orfs reveals a surprising profusion of protein sequence recoding mediated by ribosomal frameshifting and transcriptional realignment.bacterial genome annotations contain a number of coding sequences (cdss) that, in spite of reading frame disruptions, encode a single continuous polypeptide. such disruptions have different origins: sequencing errors, frameshift, or stop codon mutations, as well as instances of utilization of nontriplet decoding. we have extracted over 1,000 cdss with annotated disruptions and found that about 75% of them can be clustered into 64 groups based on sequence similarity. analysis of the clusters reve ...201121673094
new target for inhibition of bacterial rna polymerase: 'switch region'.a new drug target - the 'switch region' - has been identified within bacterial rna polymerase (rnap), the enzyme that mediates bacterial rna synthesis. the new target serves as the binding site for compounds that inhibit bacterial rna synthesis and kill bacteria. since the new target is present in most bacterial species, compounds that bind to the new target are active against a broad spectrum of bacterial species. since the new target is different from targets of other antibacterial agents, com ...201121862392
structure-based ligand design of novel bacterial rna polymerase inhibitors.bacterial rna polymerase (rnap) is essential for transcription and is an antibacterial target for small molecule inhibitors. the binding region of myxopyronin b (myxb), a bacterial rnap inhibitor, offers the possibility of new inhibitor design. the molecular design program sprout has been used in conjunction with the x-ray cocrystal structure of thermus thermophilus rnap with myxb to design novel inhibitors based on a substituted pyridyl-benzamide scaffold. a series of molecules, with molecular ...201124900260
defense islands in bacterial and archaeal genomes and prediction of novel defense systems.the arms race between cellular life forms and viruses is a major driving force of evolution. a substantial fraction of bacterial and archaeal genomes is dedicated to antivirus defense. we analyzed the distribution of defense genes and typical mobilome components (such as viral and transposon genes) in bacterial and archaeal genomes and demonstrated statistically significant clustering of antivirus defense systems and mobile genes and elements in genomic islands. the defense islands are enriched ...201121908672
the universally conserved prokaryotic gtpases.members of the large superclass of p-loop gtpases share a core domain with a conserved three-dimensional structure. in eukaryotes, these proteins are implicated in various crucial cellular processes, including translation, membrane trafficking, cell cycle progression, and membrane signaling. as targets of mutation and toxins, gtpases are involved in the pathogenesis of cancer and infectious diseases. in prokaryotes also, it is hard to overestimate the importance of gtpases in cell physiology. nu ...201121885683
the origin of a derived superkingdom: how a gram-positive bacterium crossed the desert to become an archaeon.the tree of life is usually rooted between archaea and bacteria. we have previously presented three arguments that support placing the root of the tree of life in bacteria. the data have been dismissed because those who support the canonical rooting between the prokaryotic superkingdoms cannot imagine how the vast divide between the prokaryotic superkingdoms could be crossed.201121356104
transcriptional regulation of central carbon and energy metabolism in bacteria by redox responsive repressor rex.redox-sensing repressor rex was previously implicated in the control of anaerobic respiration in response to the cellular nadh/nad(+) levels in gram-positive bacteria. we utilized the comparative genomics approach to infer candidate rex-binding dna motifs and assess the rex regulon content in 119 genomes from 11 taxonomic groups. both dna-binding and nad-sensing domains are broadly conserved in rex orthologs identified in the phyla firmicutes, thermotogales, actinobacteria, chloroflexi, deinococ ...201122210771
Mimivirus reveals Mre11/Rad50 fusion proteins with a sporadic distribution in eukaryotes, bacteria, viruses and plasmids.The Mre11/Rad50 complex and the homologous SbcD/SbcC complex in bacteria play crucial roles in the metabolism of DNA double-strand breaks, including DNA repair, genome replication, homologous recombination and non-homologous end-joining in cellular life forms and viruses. Here we investigated the amino acid sequence of the Mimivirus R555 gene product, originally annotated as a Rad50 homolog, and later shown to have close homologs in marine microbial metagenomes.201121899737
Post-translational modification by ß-lysylation is required for the activity of E. coli Elongation Factor P (EF-P).Bacterial elongation factor P (EF-P) is the ortholog of archaeal and eukaryotic initiation factor 5A (aIF5A and eIF5A). EF-P shares sequence homology and crystal structure with eIF5A, but unlike eIF5A, EF-P does not undergo hypusine modification. Recently, two bacterial genes, yjeA and yjeK, encoding truncated homologs of class II lysyl-tRNA synthetase and of lysine-2,3-aminomutase, respectively, have been implicated in the modification of EF-P to convert a specific lysine to a hypothetical ß- ...201122128152
Post-translational modification by ß-lysylation is required for the activity of E. coli Elongation Factor P (EF-P).Bacterial elongation factor P (EF-P) is the ortholog of archaeal and eukaryotic initiation factor 5A (aIF5A and eIF5A). EF-P shares sequence homology and crystal structure with eIF5A, but unlike eIF5A, EF-P does not undergo hypusine modification. Recently, two bacterial genes, yjeA and yjeK, encoding truncated homologs of class II lysyl-tRNA synthetase and of lysine-2,3-aminomutase, respectively, have been implicated in the modification of EF-P to convert a specific lysine to a hypothetical ß- ...201122128152
genomics of bacterial and archaeal viruses: dynamics within the prokaryotic virosphere.prokaryotes, bacteria and archaea, are the most abundant cellular organisms among those sharing the planet earth with human beings (among others). however, numerous ecological studies have revealed that it is actually prokaryotic viruses that predominate on our planet and outnumber their hosts by at least an order of magnitude. an understanding of how this viral domain is organized and what are the mechanisms governing its evolution is therefore of great interest and importance. the vast majorit ...201122126996
estimation of absolute protein quantities of unlabeled samples by selected reaction monitoring mass spectrometry.for many research questions in modern molecular and systems biology information about absolute protein quantities is imperative. these include, for example, kinetic modeling of processes, protein turnover determinations, stoichiometric investigations of protein complexes or quantitative comparisons of different proteins within one or across samples. to date, the vast majority of proteomic studies are limited to providing relative quantitative comparisons of protein levels between limited numbers ...201122101334
estimation of absolute protein quantities of unlabeled samples by selected reaction monitoring mass spectrometry.for many research questions in modern molecular and systems biology information about absolute protein quantities is imperative. these include, for example, kinetic modeling of processes, protein turnover determinations, stoichiometric investigations of protein complexes or quantitative comparisons of different proteins within one or across samples. to date, the vast majority of proteomic studies are limited to providing relative quantitative comparisons of protein levels between limited numbers ...201122101334
Biochemical and structural studies of the uncharacterized protein PA0743 from Pseudomonas aeruginosa revealed a NAD+-dependent L-serine dehydrogenase.The ß-hydroxyacid dehydrogenases form a large family of ubiquitous enzymes that catalyze oxidation of various ß-hydroxyacid substrates to corresponding semialdehydes. Several known enzymes include ß-hydroxyisobutyrate dehydrogenase, 6-phosphogluconate dehydrogenase, 2-(hydroxymethyl)glutarate dehydrogenase, and phenylserine dehydrogenase, but the vast majority of ß-hydroxyacid dehydrogenases remain uncharacterized. Here, we demonstrate that the predicted ß-hydroxyisobutyrate dehydrogenase PA0743 ...201122128181
Biochemical and structural studies of the uncharacterized protein PA0743 from Pseudomonas aeruginosa revealed a NAD+-dependent L-serine dehydrogenase.The ß-hydroxyacid dehydrogenases form a large family of ubiquitous enzymes that catalyze oxidation of various ß-hydroxyacid substrates to corresponding semialdehydes. Several known enzymes include ß-hydroxyisobutyrate dehydrogenase, 6-phosphogluconate dehydrogenase, 2-(hydroxymethyl)glutarate dehydrogenase, and phenylserine dehydrogenase, but the vast majority of ß-hydroxyacid dehydrogenases remain uncharacterized. Here, we demonstrate that the predicted ß-hydroxyisobutyrate dehydrogenase PA0743 ...201122128181
mass spectrometry of intact v-type atpases reveals bound lipids and the effects of nucleotide binding.the ability of electrospray to propel large viruses into a mass spectrometer is established and is rationalized by analogy to the atmospheric transmission of the common cold. much less clear is the fate of membrane-embedded molecular machines in the gas phase. here we show that rotary adenosine triphosphatases (atpases)/synthases from thermus thermophilus and enterococcus hirae can be maintained intact with membrane and soluble subunit interactions preserved in vacuum. mass spectra reveal subuni ...201122021858
translational diffusion of macromolecular assemblies measured using transverse-relaxation-optimized pulsed field gradient nmr.in structural biology, pulsed field gradient (pfg) nmr spectroscopy for the characterization of size and hydrodynamic parameters of macromolecular solutes has the advantage over other techniques that the measurements can be recorded with identical solution conditions as used for nmr structure determination or for crystallization trials. this paper describes two transverse-relaxation-optimized (tro) (15)n-filtered pfg stimulated-echo (ste) experiments for studies of macromolecular translational d ...201121919531
Comparative analyses of transport proteins encoded within the genomes of Mycobacterium tuberculosis and Mycobacterium leprae.The co-emergence of multidrug resistant pathogenic bacterial strains and the HIV pandemic has made tuberculosis a leading public health threat. The causative agent is Mycobacterium tuberculosis (Mtu), a facultative intracellular parasite. Mycobacterium leprae (Mle), a related organism that causes leprosy, is an obligate intracellular parasite. Given that different transporters are required for bacterial growth and persistence under a variety of growth conditions, we conducted comparative analyse ...201122179038
Comparative analyses of transport proteins encoded within the genomes of Mycobacterium tuberculosis and Mycobacterium leprae.The co-emergence of multidrug resistant pathogenic bacterial strains and the HIV pandemic has made tuberculosis a leading public health threat. The causative agent is Mycobacterium tuberculosis (Mtu), a facultative intracellular parasite. Mycobacterium leprae (Mle), a related organism that causes leprosy, is an obligate intracellular parasite. Given that different transporters are required for bacterial growth and persistence under a variety of growth conditions, we conducted comparative analyse ...201122179038
Structure and Function of the Small MutS-Related Domain.MutS family proteins are widely distributed in almost all organisms from bacteria to human and play central roles in various DNA transactions such as DNA mismatch repair and recombinational events. The small MutS-related (Smr) domain was originally found in the C-terminal domain of an antirecombination protein, MutS2, a member of the MutS family. MutS2 is thought to suppress homologous recombination by endonucleolytic resolution of early intermediates in the process. The endonuclease activity of ...201122091410
Probing conformational states of glutaryl-CoA dehydrogenase by fragment screening.Glutaric acidemia type 1 is an inherited metabolic disorder which can cause macrocephaly, muscular rigidity, spastic paralysis and other progressive movement disorders in humans. The defects in glutaryl-CoA dehydrogenase (GCDH) associated with this disease are thought to increase holoenzyme instability and reduce cofactor binding. Here, the first structural analysis of a GCDH enzyme in the absence of the cofactor flavin adenine dinucleotide (FAD) is reported. The apo structure of GCDH from Burkh ...201121904051
structural basis of free reduced flavin generation by flavin reductase from thermus thermophilus hb8.free reduced flavins are involved in a variety of biological functions. they are generated from nad(p)h by flavin reductase via co-factor flavin bound to the enzyme. although recent findings on the structure and function of flavin reductase provide new information about co-factor fad and substrate nad, there have been no reports on the substrate flavin binding site. here we report the structure of ttha0420 from thermus thermophilus hb8, which belongs to flavin reductase, and describe the dual bi ...201122052907
Molecular basis of dihydrouridine formation on tRNA.Dihydrouridine (D) is a highly conserved modified base found in tRNAs from all domains of life. Dihydrouridine synthase (Dus) catalyzes the D formation of tRNA through reduction of uracil base with flavin mononucleotide (FMN) as a cofactor. Here, we report the crystal structures of Thermus thermophilus Dus (TthDus), which is responsible for D formation at positions 20 and 20a, in complex with tRNA and with a short fragment of tRNA (D-loop). Dus interacts extensively with the D-arm and recognizes ...201122123979
Crystallization and preliminary X-ray crystallographic analysis of putative tRNA-modification enzymes from Pyrococcus furiosus and Thermus thermophilus.Methyltransferases form a major class of tRNA-modifying enzymes that are needed for the proper functioning of tRNA. Here, the expression, purification and crystallization of two related putative tRNA methyltransferases from two kingdoms of life are reported. The protein encoded by the gene pf1002 from the archaeon Pyrococcus furiosus was crystallized in the monoclinic space group P2(1). A complete data set was collected to 2.2 Å resolution. The protein encoded by the gene ttc1157 from the eubact ...201122102250
Ratiometric pulse-chase amidination mass spectrometry as a probe of biomolecular complex formation.Selective chemical modification of protein side chains coupled with mass spectrometry is often most informative when used to compare residue-specific reactivities in a number of functional states or macromolecular complexes. Herein, we develop ratiometric pulse-chase amidination mass spectrometry (rPAm-MS) as a site-specific probe of lysine reactivities at equilibrium using the Cu(I)-sensing repressor CsoR from Bacillus subtilis as a model system. CsoR in various allosteric states was reacted ...201122007758
type-2 isopentenyl diphosphate isomerase: evidence for a stepwise mechanism.isopentenyl diphosphate isomerase (idi) catalyzes the interconversion of isopentenyl diphosphate (ipp) and dimethylallyl diphosphate (dmapp). these two molecules are the building blocks for construction of isoprenoid carbon skeletons in nature. two structurally unrelated forms of idi are known. a variety of studies support a proton addition/proton elimination mechanism for both enzymes. during studies with thermus thermophilus idi-2, we discovered that the olefinic hydrogens of a vinyl thiomethy ...201122047048
adaptation to trna acceptor stem structure by flexible adjustment in the catalytic domain of class i trna synthetases.class i aminoacyl-trna synthetases (aarss) use a rossmann-fold domain to catalyze the synthesis of aminoacyl-trnas required for decoding genetic information. while the rossmann-fold domain is conserved in evolution, the acceptor stem near the aminoacylation site varies among trna substrates, raising the question of how the conserved protein fold adapts to rna sequence variations. of interest is the existence of an unpaired c-a mismatch at the 1-72 position unique to bacterial initiator trna(fmet ...201122184460
Structural analysis of the Ras-like G protein MglA and its cognate GAP MglB and implications for bacterial polarity.The bacterium Myxococcus xanthus uses a G protein cycle to dynamically regulate the leading/lagging pole polarity axis. The G protein MglA is regulated by its GTPase-activating protein (GAP) MglB, thus resembling Ras family proteins. Here, we show structurally and biochemically that MglA undergoes a dramatic, GDP-GTP-dependent conformational change involving a screw-type forward movement of the central ß2-strand, never observed in any other G protein. This movement and complex formation with Mgl ...201121847100
termination of protein synthesis in mammalian mitochondria.all mechanisms of protein synthesis can be considered in four stages: initiation, elongation, termination, and ribosome recycling. remarkable progress has been made in understanding how these processes are mediated in the cytosol of many species; however, details of organellar protein synthesis remain sketchy. this is an important omission, as defects in human mitochondrial translation are known to cause disease and may contribute to the aging process itself. in this minireview, we focus on the ...201121873426
structural basis for leucine-induced allosteric activation of glutamate dehydrogenase.glutamate dehydrogenase (gdh) catalyzes reversible conversion between glutamate and 2-oxoglutarate using nad(p)(h) as a coenzyme. although mammalian gdh is regulated by gtp through the antenna domain, little is known about the mechanism of allosteric activation by leucine. an extremely thermophilic bacterium, thermus thermophilus, possesses gdh with a unique subunit configuration composed of two different subunits, gdha (regulatory subunit) and gdhb (catalytic subunit). t. thermophilus gdh is un ...201121900230
crystal structure of the central axis df complex of the prokaryotic v-atpase.v-atpases function as atp-dependent ion pumps in various membrane systems of living organisms. atp hydrolysis causes rotation of the central rotor complex, which is composed of the central axis d subunit and a membrane c ring that are connected by f and d subunits. here we determined the crystal structure of the df complex of the prokaryotic v-atpase of enterococcus hirae at 2.0-å resolution. the structure of the d subunit comprised a long left-handed coiled coil with a unique short β-hairpin re ...201122114184
Crystal structure of the NurA-dAMP-Mn2+ complex.Generation of the 3' overhang is a critical event during homologous recombination (HR) repair of DNA double strand breaks. A 5'-3' nuclease, NurA, plays an important role in generating 3' single-stranded DNA during archaeal HR, together with Mre11-Rad50 and HerA. We have determined the crystal structures of apo- and dAMP-Mn(2)(+)-bound NurA from Pyrococcus furiousus (Pf?NurA) to provide the basis for its cleavage mechanism. Pf?NurA forms a pyramid-shaped dimer containing a large central channel ...201122064858
Crystal structure of the NurA-dAMP-Mn2+ complex.Generation of the 3' overhang is a critical event during homologous recombination (HR) repair of DNA double strand breaks. A 5'-3' nuclease, NurA, plays an important role in generating 3' single-stranded DNA during archaeal HR, together with Mre11-Rad50 and HerA. We have determined the crystal structures of apo- and dAMP-Mn(2)(+)-bound NurA from Pyrococcus furiousus (Pf?NurA) to provide the basis for its cleavage mechanism. Pf?NurA forms a pyramid-shaped dimer containing a large central channel ...201122064858
structure and activity of the cas3 hd nuclease mj0384, an effector enzyme of the crispr interference.clustered regularly interspaced short palindromic repeats (crisprs) and cas proteins represent an adaptive microbial immunity system against viruses and plasmids. cas3 proteins have been proposed to play a key role in the crispr mechanism through the direct cleavage of invasive dna. here, we show that the cas3 hd domain protein mj0384 from methanocaldococcus jannaschii cleaves endonucleolytically and exonucleolytically (3'-5') single-stranded dnas and rnas, as well as 3'-flaps, splayed arms, and ...201122009198
Biogenesis of cbb(3)-type cytochrome c oxidase in Rhodobacter capsulatus.The cbb(3)-type cytochrome c oxidases (cbb(3)-Cox) constitute the second most abundant cytochrome c oxidase (Cox) group after the mitochondrial-like aa(3)-type Cox. They are present in bacteria only, and are considered to represent a primordial innovation in the domain of Eubacteria due to their phylogenetic distribution and their similarity to nitric oxide (NO) reductases. They are crucial for the onset of many anaerobic biological processes, such as anoxygenic photosynthesis or nitrogen fixati ...201122079199
Biogenesis of cbb(3)-type cytochrome c oxidase in Rhodobacter capsulatus.The cbb(3)-type cytochrome c oxidases (cbb(3)-Cox) constitute the second most abundant cytochrome c oxidase (Cox) group after the mitochondrial-like aa(3)-type Cox. They are present in bacteria only, and are considered to represent a primordial innovation in the domain of Eubacteria due to their phylogenetic distribution and their similarity to nitric oxide (NO) reductases. They are crucial for the onset of many anaerobic biological processes, such as anoxygenic photosynthesis or nitrogen fixati ...201122079199
Profile of Venkatraman Ramakrishnan. Interview by Prashant Nair. 201121914843
kinetic studies of the reactions of o(2) and no with reduced thermus thermophilus ba(3) and bovine aa(3) using photolabile carriers.the reactions of molecular oxygen (o(2)) and nitric oxide (no) with reduced thermus thermophilus (tt) ba(3) and bovine heart aa(3) were investigated by time-resolved optical absorption spectroscopy to establish possible relationships between the structural diversity of these enzymes and their reaction dynamics. to determine whether the photodissociated carbon monoxide (co) in the co flow-flash experiment affects the ligand binding dynamics, we monitored the reactions in the absence and presence ...201122201543
the structure of aquifex aeolicus ribosomal protein s8 reveals a unique subdomain that contributes to an extremely tight association with 16s rrna.the assembly of ribonucleoprotein complexes occurs under a broad range of conditions, but the principles that promote assembly and allow function at high temperature are poorly understood. the ribosomal protein s8 from aquifex aeolicus (as8) is unique in that there is a 41-residue insertion in the consensus s8 sequence. in addition, as8 exhibits an unusually high affinity for the 16s ribosomal rna, characterized by a picomolar dissociation constant that is approximately 26,000-fold tighter than ...201122079365
the structure of aquifex aeolicus ribosomal protein s8 reveals a unique subdomain that contributes to an extremely tight association with 16s rrna.the assembly of ribonucleoprotein complexes occurs under a broad range of conditions, but the principles that promote assembly and allow function at high temperature are poorly understood. the ribosomal protein s8 from aquifex aeolicus (as8) is unique in that there is a 41-residue insertion in the consensus s8 sequence. in addition, as8 exhibits an unusually high affinity for the 16s ribosomal rna, characterized by a picomolar dissociation constant that is approximately 26,000-fold tighter than ...201122079365
simultaneous polyhydroxyalkanoates and rhamnolipids production by thermus thermophilus hb8.abstract: the ability of thermus thermophilus hb8 to produce simultaneously two environmentally-friendly biodegradable products, polyhydroxyalkanoates (phas) and rhamnolipids (rls), using either sodium gluconate or glucose as sole carbon source, was demonstrated. the utilization of sodium gluconate resulted in higher levels of phas and rls production than when glucose was used as sole carbon source. the initial phosphate concentration (as po43-) influences both phas and rls productions that were ...201121906373
Properties and crystal structure of methylenetetrahydrofolate reductase from Thermus thermophilus HB8.Methylenetetrahydrofolate reductase (MTHFR) is one of the enzymes involved in homocysteine metabolism. Despite considerable genetic and clinical attention, the reaction mechanism and regulation of this enzyme are not fully understood because of difficult production and poor stability. While recombinant enzymes from thermophilic organisms are often stable and easy to prepare, properties of thermostable MTHFRs have not yet been reported.201121858212
bioinformatic analysis of leishmania donovani long-chain fatty acid-coa ligase as a novel drug target.fatty acyl-coa synthetase (fatty acid: coa ligase, amp-forming; (ec 6.2.1.3)) catalyzes the formation of fatty acyl-coa by a two-step process that proceeds through the hydrolysis of pyrophosphate. fatty acyl-coa represents bioactive compounds that are involved in protein transport, enzyme activation, protein acylation, cell signaling, and transcriptional control in addition to serving as substrates for beta oxidation and phospholipid biosynthesis. fatty acyl-coa synthetase occupies a pivotal rol ...201122091399
Mössbauer Spectroscopy on Respiratory Complex I: The Iron-Sulfur Cluster Ensemble in the NADH-Reduced Enzyme Is Partially Oxidized.In mitochondria, complex I (NADH:quinone oxidoreductase) couples electron transfer to proton translocation across an energy-transducing membrane. It contains a flavin mononucleotide to oxidize NADH, and an unusually long series of iron-sulfur (FeS) clusters that transfer the electrons to quinone. Understanding electron transfer in complex I requires spectroscopic and structural data to be combined to reveal the properties of individual clusters and of the ensemble. EPR studies on complex I from ...201122122402
Mössbauer Spectroscopy on Respiratory Complex I: The Iron-Sulfur Cluster Ensemble in the NADH-Reduced Enzyme Is Partially Oxidized.In mitochondria, complex I (NADH:quinone oxidoreductase) couples electron transfer to proton translocation across an energy-transducing membrane. It contains a flavin mononucleotide to oxidize NADH, and an unusually long series of iron-sulfur (FeS) clusters that transfer the electrons to quinone. Understanding electron transfer in complex I requires spectroscopic and structural data to be combined to reveal the properties of individual clusters and of the ensemble. EPR studies on complex I from ...201122122402
Histidine 66 in E. coli elongation factor Tu selectively stabilizes aminoacyl-tRNAs.The universally conserved H66 of Elongation Factor Tu stacks on the side chain of the esterified Phe of Phe-tRNA(Phe). The affinities of eight aminoacyl-tRNAs were differentially destabilized by the introduction of the H66A mutation into E. coli EF-Tu while Ala-tRNA(Ala) and Gly-tRNA(Gly) were unaffected. The H66F and H66W proteins each show a different pattern of binding of ten different aa-tRNAs, clearly showing that this position is critical in establishing the specificity of EF-Tu for differ ...201122105070
Histidine 66 in E. coli elongation factor Tu selectively stabilizes aminoacyl-tRNAs.The universally conserved H66 of Elongation Factor Tu stacks on the side chain of the esterified Phe of Phe-tRNA(Phe). The affinities of eight aminoacyl-tRNAs were differentially destabilized by the introduction of the H66A mutation into E. coli EF-Tu while Ala-tRNA(Ala) and Gly-tRNA(Gly) were unaffected. The H66F and H66W proteins each show a different pattern of binding of ten different aa-tRNAs, clearly showing that this position is critical in establishing the specificity of EF-Tu for differ ...201122105070
structures of domains i and iv from ybbr are representative of a widely distributed protein family.ybbr domains are widespread throughout eubacteria and are expressed as monomeric units, linked in tandem repeats or cotranslated with other domains. although the precise role of these domains remains undefined, the location of the multiple ybbr domain-encoding ybbr gene in the bacillus subtilis glmm operon and its previous identification as a substrate for a surfactin-type phosphopantetheinyl transferase suggests a role in cell growth, division, and virulence. to further characterize the ybbr do ...201121154411
structures of domains i and iv from ybbr are representative of a widely distributed protein family.ybbr domains are widespread throughout eubacteria and are expressed as monomeric units, linked in tandem repeats or cotranslated with other domains. although the precise role of these domains remains undefined, the location of the multiple ybbr domain-encoding ybbr gene in the bacillus subtilis glmm operon and its previous identification as a substrate for a surfactin-type phosphopantetheinyl transferase suggests a role in cell growth, division, and virulence. to further characterize the ybbr do ...201121154411
catalytic and non-catalytic roles for the mono-adp-ribosyltransferase arr in the mycobacterial dna damage response.recent evidence indicates that the mycobacterial response to dna double strand breaks (dsbs) differs substantially from previously characterized bacteria. these differences include the use of three dsb repair pathways (hr, nhej, ssa), and the card pathway, which integrates dna damage with transcription. here we identify a role for the mono-adp-ribosyltransferase arr in the mycobacterial dna damage response. arr is transcriptionally induced following dna damage and cellular stress. although arr i ...201121789183
"stealth" melanoma cells in histology-negative sentinel lymph nodes.a proportion of patients who develop regional and distant recurrences of melanoma after a pathologically negative sentinel lymph node (sn) biopsy are reported to have enhanced signals for melanoma-associated messenger ribonucleic acid (mrna) when sensitive molecular approaches such as reverse transcriptase polymerase chain reaction (rt-pcr) are used to evaluate their sn tissue. the significance of these findings remains controversial, because the cellular source of the augmented signals cannot b ...201121997686
Multifaceted SlyD from Helicobacter pylori: implication in [NiFe] hydrogenase maturation.SlyD belongs to the FK506-binding protein (FKBP) family with both peptidylprolyl isomerase (PPIase) and chaperone activities, and is considered to be a ubiquitous cytosolic protein-folding facilitator in bacteria. It possesses a histidine- and cysteine-rich C-terminus binding to selected divalent metal ions (e.g., Ni(2+), Zn(2+)), which is important for its involvement in the maturation processes of metalloenzymes. We have determined the solution structure of C-terminus-truncated SlyD from Helic ...201122045417
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