Publications

crystal structure and putative substrate identification for the entamoeba histolytica low molecular weight tyrosine phosphatase.	entamoeba histolytica is a eukaryotic intestinal parasite of humans, and is endemic in developing countries. we have characterized the e. histolytica putative low molecular weight protein tyrosine phosphatase (lmw-ptp). the structure for this amebic tyrosine phosphatase was solved, showing the ligand-induced conformational changes necessary for binding of substrate. in amebae, it was expressed at low but detectable levels as detected by immunoprecipitation followed by immunoblotting. a mutant lm ...	2014	24548880
the k-junction motif in rna structure.	the k-junction is a structural motif in rna comprising a three-way helical junction based upon kink turn (k-turn) architecture. a computer program written to examine relative helical orientation identified the three-way junction of the arabidopsis tpp riboswitch as an elaborated k-turn. the escherichia coli tpp riboswitch contains a related k-junction, and analysis of >11 000 sequences shows that the structure is common to these riboswitches. the k-junction exhibits all the key features of an n1 ...	2014	24531930
dna-guided dna interference by a prokaryotic argonaute.	rna interference is widely distributed in eukaryotes and has a variety of functions, including antiviral defence and gene regulation. all rna interference pathways use small single-stranded rna (ssrna) molecules that guide proteins of the argonaute (ago) family to complementary ssrna targets: rna-guided rna interference. the role of prokaryotic ago variants has remained elusive, although bioinformatics analysis has suggested their involvement in host defence. here we demonstrate that ago of the ...	2014	24531762
elements in nucleotide sensing and hydrolysis of the aaa+ disaggregation machine clpb: a structure-based mechanistic dissection of a molecular motor.	atpases of the aaa+ superfamily are large oligomeric molecular machines that remodel their substrates by converting the energy from atp hydrolysis into mechanical force. this study focuses on the molecular chaperone clpb, the bacterial homologue of hsp104, which reactivates aggregated proteins under cellular stress conditions. based on high-resolution crystal structures in different nucleotide states, mutational analysis and nucleotide-binding kinetics experiments, the atpase cycle of the c-term ...	2014	24531492
the putative trna 2-thiouridine synthetase ncs6 is an essential sulfur carrier in methanococcus maripaludis.	thiolation of carbon-2 of uridine located in the first position of the anticodons of trnauug(gln), trnauuc(glu), and trnauuu(lys) is a conserved rna modification event requiring the 2-thiouridine synthetase ncs6/ctu1 in archaea and eukaryotes. ncs6/ctu1 activates uridine by adenylation, but its role in sulfur transfer is unclear. here we show that mmp1356, the ncs6/ctu1 homolog in the archaeon methanococcus maripaludis, forms a persulfide enzyme adduct with an active site cysteine; this suggests ...	2014	24530533
crystal structure of cas9 in complex with guide rna and target dna.	the crispr-associated endonuclease cas9 can be targeted to specific genomic loci by single guide rnas (sgrnas). here, we report the crystal structure of streptococcus pyogenes cas9 in complex with sgrna and its target dna at 2.5 å resolution. the structure revealed a bilobed architecture composed of target recognition and nuclease lobes, accommodating the sgrna:dna heteroduplex in a positively charged groove at their interface. whereas the recognition lobe is essential for binding sgrna and dna, ...	2014	24529477
a new system for naming ribosomal proteins.	a system for naming ribosomal proteins is described that the authors intend to use in the future. they urge others to adopt it. the objective is to eliminate the confusion caused by the assignment of identical names to ribosomal proteins from different species that are unrelated in structure and function. in the system proposed here, homologous ribosomal proteins are assigned the same name, regardless of species. it is designed so that new names are similar enough to old names to be easily recog ...	2014	24524803
evolutionary insights about bacterial glxrs from whole genome analyses: is glurs2 a chimera?	evolutionary histories of glutamyl-trna synthetase (glurs) and glutaminyl-trna synthetase (glnrs) in bacteria are convoluted. after the divergence of eubacteria and eukarya, bacterial glurs glutamylated both trnagln and trnaglu until glnrs appeared by horizontal gene transfer (hgt) from eukaryotes or a duplicate copy of glurs (glurs2) that only glutamylates trnagln appeared. the current understanding is based on limited sequence data and not always compatible with available experimental results. ...	2014	24521160
using ¹⁵n-ammonium to characterise and map potassium binding sites in proteins by nmr spectroscopy.	a variety of enzymes are activated by the binding of potassium ions. the potassium binding sites of these enzymes are very specific, but ammonium ions can often replace potassium ions in vitro because of their similar ionic radii. in these cases, ammonium can be used as a proxy for potassium to characterise potassium binding sites in enzymes: the (1) h,(15) n spin-pair of enzyme-bound (15) nh4 (+) can be probed by (15) n-edited heteronuclear nmr experiments. here, we demonstrate the use of nmr s ...	2014	24520048
structural basis and target-specific modulation of adp sensing by the synechococcus elongatus pii signaling protein.	pii signaling proteins comprise one of the most versatile signaling devices in nature and have a highly conserved structure. in cyanobacteria, pipx and n-acetyl-l-glutamate kinase are receptors of pii signaling, and these interactions are modulated by adp, atp, and 2-oxoglutarate. these effector molecules bind interdependently to three anti-cooperative binding sites on the trimeric pii protein and thereby affect its structure. here we used the pii protein from synechococcus elongatus pcc 7942 to ...	2014	24519945
chlorite dismutases - a heme enzyme family for use in bioremediation and generation of molecular oxygen.	chlorite is a serious environmental concern, as rising concentrations of this harmful anthropogenic compound have been detected in groundwater, drinking water, and soil. chlorite dismutases (clds) are therefore important molecules in bioremediation as clds catalyze the degradation of chlorite to chloride and molecular oxygen. clds are heme b-containing oxidoreductases present in numerous bacterial and archaeal phyla. this review presents the phylogeny of functional clds and cld-like proteins, an ...	2014	24519858
the mtha mutation conferring low-level resistance to streptomycin enhances antibiotic production in bacillus subtilis by increasing the s-adenosylmethionine pool size.	certain str(r) mutations that confer low-level streptomycin resistance result in the overproduction of antibiotics by bacillus subtilis. using comparative genome-sequencing analysis, we successfully identified this novel mutation in b. subtilis as being located in the mtha gene, which encodes s-adenosylhomocysteine/methylthioadenosine nucleosidase, an enzyme involved in the s-adenosylmethionine (sam)-recycling pathways. transformation experiments showed that this mtha mutation was responsible fo ...	2014	24509311
fast proton-coupled electron transfer observed for a high-fidelity structural and functional [2fe-2s] rieske model.	rieske cofactors have a [2fe-2s] cluster with unique {his2cys2} ligation and distinct fe subsites. the histidine ligands are functionally relevant, since they allow for coupling of electron and proton transfer (pcet) during quinol oxidation in respiratory and photosynthetic et chains. here we present the highest fidelity synthetic analogue for the rieske [2fe-2s] cluster reported so far. this synthetic analogue 5(x-) emulates the heteroleptic {his2cys2} ligation of the [2fe-2s] core, and it also ...	2014	24506804
secondary structures of rrnas from all three domains of life.	accurate secondary structures are important for understanding ribosomes, which are extremely large and highly complex. using 3d structures of ribosomes as input, we have revised and corrected traditional secondary (2°) structures of rrnas. we identify helices by specific geometric and molecular interaction criteria, not by co-variation. the structural approach allows us to incorporate non-canonical base pairs on parity with watson-crick base pairs. the resulting rrna 2° structures are up-to-date ...	2014	24505437
structures of cas9 endonucleases reveal rna-mediated conformational activation.	type ii crispr (clustered regularly interspaced short palindromic repeats)-cas (crispr-associated) systems use an rna-guided dna endonuclease, cas9, to generate double-strand breaks in invasive dna during an adaptive bacterial immune response. cas9 has been harnessed as a powerful tool for genome editing and gene regulation in many eukaryotic organisms. we report 2.6 and 2.2 angstrom resolution crystal structures of two major cas9 enzyme subtypes, revealing the structural core shared by all cas9 ...	2014	24505130
the hica toxin from burkholderia pseudomallei has a role in persister cell formation.	ta (toxin-antitoxin) systems are widely distributed amongst bacteria and are associated with the formation of antibiotic tolerant (persister) cells that may have involvement in chronic and recurrent disease. we show that overexpression of the burkholderia pseudomallei hica toxin causes growth arrest and increases the number of persister cells tolerant to ciprofloxacin or ceftazidime. furthermore, our data show that persistence towards ciprofloxacin or ceftazidime can be differentially modulated ...	2014	24502667
structural studies of yeast δ(1)-pyrroline-5-carboxylate dehydrogenase (aldh4a1): active site flexibility and oligomeric state.	the proline catabolic enzyme δ(1)-pyrroline-5-carboxylate dehydrogenase (aldh4a1) catalyzes the nad(+)-dependent oxidation of γ-glutamate semialdehyde to l-glutamate. in saccharomyces cerevisiae, aldh4a1 is encoded by the put2 gene and known as put2p. here we report the steady-state kinetic parameters of the purified recombinant enzyme, two crystal structures of put2p, and the determination of the oligomeric state and quaternary structure from small-angle x-ray scattering and sedimentation veloc ...	2014	24502590
the dynamic nature of genomes across the tree of life.	genomes are dynamic in lineages across the tree of life. among bacteria and archaea, for example, dna content varies throughout life cycles, and nonbinary cell division in diverse lineages indicates the need for coordination of the inheritance of genomes. these observations contrast with the textbook view that bacterial and archaeal genomes are monoploid (i.e., single copied) and fixed both within species and throughout an individual's lifetime. here, we synthesize information on three aspects o ...	2014	24500971
coexistence of bacterial leucyl-trna synthetases with archaeal trna binding domains that distinguish trna(leu) in the archaeal mode.	leucyl-trna (transfer rna) synthetase (leurs) is a multi-domain enzyme, which is divided into bacterial and archaeal/eukaryotic types. in general, one specific leurs, the domains of which are of the same type, exists in a single cell compartment. however, some species, such as the haloalkaliphile natrialba magadii, encode two cytoplasmic leurss, nmleurs1 and nmleurs2, which are the first examples of naturally occurring chimeric enzymes with different domains of bacterial and archaeal types. furt ...	2014	24500203
in vitro assembly and activity of an archaeal crispr-cas type i-a cascade interference complex.	clustered regularly interspaced short palindromic repeats (crispr)-crispr-associated (cas) systems of type i use a cas ribonucleoprotein complex for antiviral defense (cascade) to mediate the targeting and degradation of foreign dna. to address molecular features of the archaeal type i-a cascade interference mechanism, we established the in vitro assembly of the thermoproteus tenax cascade from six recombinant cas proteins, synthetic crispr rnas (crrnas) and target dna fragments. rna-seq analyse ...	2014	24500198
global patterns of protein domain gain and loss in superkingdoms.	domains are modules within proteins that can fold and function independently and are evolutionarily conserved. here we compared the usage and distribution of protein domain families in the free-living proteomes of archaea, bacteria and eukarya and reconstructed species phylogenies while tracing the history of domain emergence and loss in proteomes. we show that both gains and losses of domains occurred frequently during proteome evolution. the rate of domain discovery increased approximately lin ...	2014	24499935
crystal structure of an (r)-selective ω-transaminase from aspergillus terreus.	chiral amines are important building blocks for the synthesis of pharmaceutical products, fine chemicals, and agrochemicals. ω-transaminases are able to directly synthesize enantiopure chiral amines by catalysing the transfer of an amino group from a primary amino donor to a carbonyl acceptor with pyridoxal 5'-phosphate (plp) as cofactor. in nature, (s)-selective amine transaminases are more abundant than the (r)-selective enzymes, and therefore more information concerning their structures is av ...	2014	24498081
recent advances in in vivo applications of intein-mediated protein splicing.	intein-mediated protein splicing has become an essential tool in modern biotechnology. fundamental progress in the structure and catalytic strategies of cis- and trans-splicing inteins has led to the development of modified inteins that promote efficient protein purification, ligation, modification and cyclization. recent work has extended these in vitro applications to the cell or to whole organisms. we review recent advances in intein-mediated protein expression and modification, post-translat ...	2014	24490831
natural competence and the evolution of dna uptake specificity.	many bacteria are naturally competent, able to actively transport environmental dna fragments across their cell envelope and into their cytoplasm. because incoming dna fragments can recombine with and replace homologous segments of the chromosome, competence provides cells with a potent mechanism of horizontal gene transfer as well as access to the nutrients in extracellular dna. this review starts with an introductory overview of competence and continues with a detailed consideration of the dna ...	2014	24488316
h(2)o(2) production in species of the lactobacillus acidophilus group: a central role for a novel nadh-dependent flavin reductase.	hydrogen peroxide production is a well-known trait of many bacterial species associated with the human body. in the presence of oxygen, the probiotic lactic acid bacterium lactobacillus johnsonii ncc 533 excretes up to 1 mm h(2)o(2), inducing growth stagnation and cell death. disruption of genes commonly assumed to be involved in h(2)o(2) production (e.g., pyruvate oxidase, nadh oxidase, and lactate oxidase) did not affect this. here we describe the purification of a novel nadh-dependent flavin ...	2014	24487531
s-layers: principles and applications.	monomolecular arrays of protein or glycoprotein subunits forming surface layers (s-layers) are one of the most commonly observed prokaryotic cell envelope components. s-layers are generally the most abundantly expressed proteins, have been observed in species of nearly every taxonomical group of walled bacteria, and represent an almost universal feature of archaeal envelopes. the isoporous lattices completely covering the cell surface provide organisms with various selection advantages including ...	2014	24483139
a bacteriophage transcription regulator inhibits bacterial transcription initiation by σ-factor displacement.	bacteriophages (phages) appropriate essential processes of bacterial hosts to benefit their own development. the multisubunit bacterial rna polymerase (rnap) enzyme, which catalyses dna transcription, is targeted by phage-encoded transcription regulators that selectively modulate its activity. here, we describe the structural and mechanistic basis for the inhibition of bacterial rnap by the transcription regulator p7 encoded by xanthomonas oryzae phage xp10. we reveal that p7 uses a two-step mec ...	2014	24482445
bioorganometallic chemistry with ispg and isph: structure, function, and inhibition of the [fe(4)s(4)] proteins involved in isoprenoid biosynthesis.	enzymes of the methylerythritol phosphate pathway of isoprenoid biosynthesis are attractive anti-infective drug targets. the last two enzymes of this pathway, ispg and isph, are [fe4 s4 ] proteins that are not produced by humans and catalyze 2 h(+) / 2 e(-) reductions with novel mechanisms. in this review, we summarize recent advances in structural, mechanistic, and inhibitory studies of these two enzymes. in particular, mechanistic proposals involving bioorganometallic intermediates are present ...	2014	24481599
discovery and characterization of ionic liquid-tolerant thermophilic cellulases from a switchgrass-adapted microbial community.	the development of advanced biofuels from lignocellulosic biomass will require the use of both efficient pretreatment methods and new biomass-deconstructing enzyme cocktails to generate sugars from lignocellulosic substrates. certain ionic liquids (ils) have emerged as a promising class of compounds for biomass pretreatment and have been demonstrated to reduce the recalcitrance of biomass for enzymatic hydrolysis. however, current commercial cellulase cocktails are strongly inhibited by most of ...	2014	24479406
the omega subunit of the rna polymerase core directs transcription efficiency in cyanobacteria.	the eubacterial rna polymerase core, a transcription machinery performing dna-dependent rna polymerization, consists of two α subunits and β, β' and ω subunits. an additional σ subunit is recruited for promoter recognition and transcription initiation. cyanobacteria, a group of eubacteria characterized by oxygenic photosynthesis, have a unique composition of the rna polymerase (rnap) core due to splitting of the β' subunit to n-terminal γ and c-terminal β' subunits. the physiological roles of th ...	2014	24476911
radical s-adenosylmethionine enzymes.		2014	24476342
crystal structure of e. coli arginyl-trna synthetase and ligand binding studies revealed key residues in arginine recognition.	the arginyl-trna synthetase (argrs) catalyzes the esterification reaction between l-arginine and its cognate trna(arg). previously reported structures of argrs shed considerable light on the trna recognition mechanism, while the aspect of amino acid binding in argrs remains largely unexplored. here we report the first crystal structure of e. coli argrs (eargrs) complexed with l-arginine, and a series of mutational studies using isothermal titration calorimetry (itc). combined with previously rep ...	2014	24474195
4'-o-substitutions determine selectivity of aminoglycoside antibiotics.	clinical use of 2-deoxystreptamine aminoglycoside antibiotics, which target the bacterial ribosome, is compromised by adverse effects related to limited drug selectivity. here we present a series of 4',6'-o-acetal and 4'-o-ether modifications on glucopyranosyl ring i of aminoglycosides. chemical modifications were guided by measuring interactions between the compounds synthesized and ribosomes harbouring single point mutations in the drug-binding site, resulting in aminoglycosides that interact ...	2014	24473108
binding of copper and silver to single-site variants of peptidylglycine monooxygenase reveals the structure and chemistry of the individual metal centers.	peptidylglycine monooxygenase (phm) catalyzes the final step in the biosynthesis of amidated peptides that serve as important signaling molecules in numerous endocrine pathways. the catalytic mechanism has attracted much attention because of a number of unique attributes, including the presence of a pair of uncoupled copper centers separated by 11 å (termed cuh and cum), an unusual cu(i)smet interaction at the oxygen binding m-site, and the postulated cu(ii)-superoxo intermediate. understanding ...	2014	24471980
the mononuclear molybdenum enzymes.		2014	24467397
a biochemical approach to study the role of the terminal oxidases in aerobic respiration in shewanella oneidensis mr-1.	the genome of the facultative anaerobic γ-proteobacterium shewanella oneidensis mr-1 encodes for three terminal oxidases: a bd-type quinol oxidase and two heme-copper oxidases, a a-type cytochrome c oxidase and a cbb 3-type oxidase. in this study, we used a biochemical approach and directly measured oxidase activities coupled to mass-spectrometry analysis to investigate the physiological role of the three terminal oxidases under aerobic and microaerobic conditions. our data revealed that the cbb ...	2014	24466040
structural basis of thermal stability of the tungsten cofactor synthesis protein moab from pyrococcus furiosus.	molybdenum and tungsten cofactors share a similar pterin-based scaffold, which hosts an ene-dithiolate function being essential for the coordination of either molybdenum or tungsten. the biosynthesis of both cofactors involves a multistep pathway, which ends with the activation of the metal binding pterin (mpt) by adenylylation before the respective metal is incorporated. in the hyperthermophilic organism pyrococcus furiosus, the hexameric protein moab (pfumoab) has been shown to catalyse mpt-ad ...	2014	24465852
a complex of cas proteins 5, 6, and 7 is required for the biogenesis and stability of clustered regularly interspaced short palindromic repeats (crispr)-derived rnas (crrnas) in haloferax volcanii.	the clustered regularly interspaced short palindromic repeats/crispr-associated (crispr-cas) system is a prokaryotic defense mechanism against foreign genetic elements. a plethora of crispr-cas versions exist, with more than 40 different cas protein families and several different molecular approaches to fight the invading dna. one of the key players in the system is the crispr-derived rna (crrna), which directs the invader-degrading cas protein complex to the invader. the crispr-cas types i and ...	2014	24459147
folding a stable rna pseudoknot through rearrangement of two hairpin structures.	folding messenger rna into specific structures is a common regulatory mechanism involved in translation. in escherichia coli, the operator of the rpso gene transcript folds into a pseudoknot or double-hairpin conformation. s15, the gene product, binds only to the pseudoknot, thereby repressing its own synthesis when it is present in excess in the cell. the two rna conformations have been proposed to exist in equilibrium. however, it remained unclear how structural changes can be achieved between ...	2014	24459133
the moxr atpase rava and its cofactor viaa interact with the nadh:ubiquinone oxidoreductase i in escherichia coli.	moxr atpases are widespread throughout bacteria and archaea. the experimental evidence to date suggests that these proteins have chaperone-like roles in facilitating the maturation of dedicated protein complexes that are functionally diverse. in escherichia coli, the moxr atpase rava and its putative cofactor viaa are found to exist in early stationary-phase cells at 37 °c at low levels of about 350 and 90 molecules per cell, respectively. both proteins are predominantly localized to the cytopla ...	2014	24454883
structural and functional analyses of a sterol carrier protein in spodoptera litura.	in insects, cholesterol is one of the membrane components in cells and a precursor of ecdysteroid biosynthesis. because insects lack two key enzymes, squalene synthase and lanosterol synthase, in the cholesterol biosynthesis pathway, they cannot autonomously synthesize cholesterol de novo from simple compounds and therefore have to obtain sterols from their diet. sterol carrier protein (scp) is a cholesterol-binding protein responsible for cholesterol absorption and transport.	2014	24454688
distinct functions of the rna polymerase σ subunit region 3.2 in rna priming and promoter escape.	the σ subunit of bacterial rna polymerase (rnap) has been implicated in all steps of transcription initiation, including promoter recognition and opening, priming of rna synthesis, abortive initiation and promoter escape. the post-promoter-recognition σ functions were proposed to depend on its conserved region σ3.2 that directly contacts promoter dna immediately upstream of the rnap active centre and occupies the rna exit path. analysis of the transcription effects of substitutions and deletions ...	2014	24452800
characterization of cleavage intermediate and star sites of rm.tth111ii.	tth111ii is a thermostable type iigs restriction enzyme that recognizes dna sites caarca (r = a or g) and cleaves downstream at n11/n9. here, the tth111iirm gene was cloned and expressed in e. coli, and tth111ii was purified. the purified enzyme contains internally-bound s-adenosylmethionine (sam). when the internal sam was removed, the endonuclease activity was stimulated by adding sam or its analog sinefungin. the cleavage intermediate is mostly top-strand nicked dna on a single-site plasmid. ...	2014	24452415
a highly divergent archaeo-eukaryotic primase from the thermococcus nautilus plasmid, ptn2.	we report the characterization of a dna primase/polymerase protein (polptn2) encoded by the ptn2 plasmid from thermococcus nautilus. sequence analysis revealed that this protein corresponds to a fusion between an n-terminal domain homologous to the small catalytic subunit pris of heterodimeric archaeal and eukaryotic primases (aep) and a c-terminal domain related to their large regulatory subunit pril. this unique domain configuration is not found in other virus- and plasmid-encoded primases in ...	2014	24445805
parallel pathways for nitrite reduction during anaerobic growth in thermus thermophilus.	respiratory reduction of nitrate and nitrite is encoded in thermus thermophilus by the respective transferable gene clusters. nitrate is reduced by a heterotetrameric nitrate reductase (nar) encoded along transporters and regulatory signal transduction systems within the nitrate respiration conjugative element (nce). the nitrite respiration cluster (nic) encodes homologues of nitrite reductase (nir) and nitric oxide reductase (nor). the expression and role of the nirsjm genes in nitrite respirat ...	2014	24443532
trna anticodon shifts in eukaryotic genomes.	embedded in the sequence of each transfer rna are elements that promote specific interactions with its cognate aminoacyl trna-synthetase. although many such "identity elements" are known, their detection is difficult since they rely on unique structural signatures and the combinatorial action of multiple elements spread throughout the trna molecule. since the anticodon is often a major identity determinant itself, it is possible to switch between certain trna functional types by means of anticod ...	2014	24442610
halorhabdus tiamatea: proteogenomics and glycosidase activity measurements identify the first cultivated euryarchaeon from a deep-sea anoxic brine lake as potential polysaccharide degrader.	euryarchaea from the genus halorhabdus have been found in hypersaline habitats worldwide, yet are represented by only two isolates: halorhabdus utahensis ax-2(t) from the shallow great salt lake of utah, and halorhabdus tiamatea sarl4b(t) from the shaban deep-sea hypersaline anoxic lake (dhal) in the red sea. we sequenced the h. tiamatea genome to elucidate its niche adaptations. among sequenced archaea, h. tiamatea features the highest number of glycoside hydrolases, the majority of which were ...	2014	24428220
measurement of the intrinsic variability within protein crystals: implications for sample-evaluation and data-collection strategies.	the advent of micro-focused x-ray beams has led to the development of a number of advanced methods of sample evaluation and data collection. in particular, multiple-position data-collection and helical oscillation strategies are now becoming commonplace in order to alleviate the problems associated with radiation damage. however, intra-crystal and inter-crystal variation means that it is not always obvious on which crystals or on which region or regions of a crystal these protocols should be per ...	2013	24419635
measurement of the intrinsic variability within protein crystals: implications for sample-evaluation and data-collection strategies.	the advent of micro-focused x-ray beams has led to the development of a number of advanced methods of sample evaluation and data collection. in particular, multiple-position data-collection and helical oscillation strategies are now becoming commonplace in order to alleviate the problems associated with radiation damage. however, intra-crystal and inter-crystal variation means that it is not always obvious on which crystals or on which region or regions of a crystal these protocols should be per ...	2013	24419635
lysine carboxylation: unveiling a spontaneous post-translational modification.	the carboxylation of lysine residues is a post-translational modification (ptm) that plays a critical role in the catalytic mechanisms of several important enzymes. it occurs spontaneously under certain physicochemical conditions, but is difficult to detect experimentally. its full impact is unknown. in this work, the signature microenvironment of lysine-carboxylation sites has been characterized. in addition, a computational method called predictor of lysine carboxylation (prelyscar) for the de ...	2013	24419378
lysine carboxylation: unveiling a spontaneous post-translational modification.	the carboxylation of lysine residues is a post-translational modification (ptm) that plays a critical role in the catalytic mechanisms of several important enzymes. it occurs spontaneously under certain physicochemical conditions, but is difficult to detect experimentally. its full impact is unknown. in this work, the signature microenvironment of lysine-carboxylation sites has been characterized. in addition, a computational method called predictor of lysine carboxylation (prelyscar) for the de ...	2013	24419378
an archaeal glutamate decarboxylase homolog functions as an aspartate decarboxylase and is involved in β-alanine and coenzyme a biosynthesis.	β-alanine is a precursor for coenzyme a (coa) biosynthesis and is a substrate for the bacterial/eukaryotic pantothenate synthetase and archaeal phosphopantothenate synthetase. β-alanine is synthesized through various enzymes/pathways in bacteria and eukaryotes, including the direct decarboxylation of asp by aspartate 1-decarboxylase (adc), the degradation of pyrimidine, or the oxidation of polyamines. however, in most archaea, homologs of these enzymes are not present; thus, the mechanisms of β- ...	2014	24415726
the isolated carboxy-terminal domain of human mitochondrial leucyl-trna synthetase rescues the pathological phenotype of mitochondrial trna mutations in human cells.	mitochondrial (mt) diseases are multisystem disorders due to mutations in nuclear or mtdna genes. among the latter, more than 50% are located in transfer rna (trna) genes and are responsible for a wide range of syndromes, for which no effective treatment is available at present. we show that three human mt aminoacyl-trna syntethases, namely leucyl-, valyl-, and isoleucyl-trna synthetase are able to improve both viability and bioenergetic proficiency of human transmitochondrial cybrid cells carry ...	2014	24413190
crystal structures of ispf from plasmodium falciparum and burkholderia cenocepacia: comparisons inform antimicrobial drug target assessment.	2c-methyl-d-erythritol-2,4-cyclodiphosphate synthase (ispf) catalyzes the conversion of 4-diphosphocytidyl-2c-methyl-d-erythritol-2-phosphate to 2c-methyl-d-erythritol-2,4-cyclodiphosphate and cytidine monophosphate in production of isoprenoid-precursors via the methylerythritol phosphate biosynthetic pathway. ispf is found in the protozoan plasmodium falciparum, a parasite that causes cerebral malaria, as well as in many gram-negative bacteria such as burkholderia cenocepacia. ispf represents a ...	2014	24410837
context of action of proline dehydrogenase (prodh) in the hypersensitive response of arabidopsis.	proline (pro) dehydrogenase (prodh) potentiates the oxidative burst and cell death of the plant hypersensitive response (hr) by mechanisms not yet elucidated. prodh converts pro into ∆1 pyrroline-5-carboxylate (p5c) and can act together with p5c dehydrogenase (p5cdh) to produce glu, or with p5c reductase (p5cr) to regenerate pro and thus stimulate the pro/p5c cycle. to better understand the effects of prodh in hr, we studied the enzyme at three stages of the defense response differing in their r ...	2014	24410747
crystal structures and kinetic properties of enoyl-acyl carrier protein reductase i from candidatus liberibacter asiaticus.	huanglongbing (hlb) is a destructive citrus disease. the leading cause of hlb is candidatus liberibacter asiaticus. fatty acid biosynthesis is essential for bacterial viability and has been validated as a target for the discovery of novel antibacterial agents. enoyl-acyl carrier protein reductase (also called enr or fabi and a product of the fabi gene) is an enzyme required in a critical step of bacterial fatty acid biosynthesis and has attracted attention as a target of novel antimicrobial agen ...	2014	24407918
mutant lv(476-7)aa of a-subunit of enterococcus hirae v1-atpase: high affinity of a3b3 complex to df axis and low atpase activity.	vacuolar atpase (v-atpase) of enterococcus hirae is composed of a soluble functional domain v1 (a3b3df) and an integral membrane domain vo (ac), where v1 and vo domains are connected by a central stalk, composed of d-, f-, and d-subunits; and two peripheral stalks (e- and g-subunits). we identified 120 interacting residues of a3b3 heterohexamer with d-subunit in df heterodimer in the crystal structures of a3b3 and a3b3df. in our previous study, we reported 10 mutants of e. hirae v1-atpase, which ...	2013	24404436
mlh1-mlh3, a meiotic crossover and dna mismatch repair factor, is a msh2-msh3-stimulated endonuclease.	crossing over between homologous chromosomes is initiated in meiotic prophase in most sexually reproducing organisms by the appearance of programmed double strand breaks throughout the genome. in saccharomyces cerevisiae the double-strand breaks are resected to form three prime single-strand tails that primarily invade complementary sequences in unbroken homologs. these invasion intermediates are converted into double holliday junctions and then resolved into crossovers that facilitate homolog s ...	2014	24403070
charge segregation and low hydrophobicity are key features of ribosomal proteins from different organisms.	ribosomes are large and highly charged macromolecular complexes consisting of rna and proteins. here, we address the electrostatic and nonpolar properties of ribosomal proteins that are important for ribosome assembly and interaction with other cellular components and may influence protein folding on the ribosome. we examined 50 s ribosomal subunits from 10 species and found a clear distinction between the net charge of ribosomal proteins from halophilic and non-halophilic organisms. we found th ...	2014	24398678
dynamic protein ligand interactions--insights from ms.	proteins undergo dynamic interactions with carbohydrates, lipids and nucleotides to form catalytic cores, fine-tuned for different cellular actions. the study of dynamic interactions between proteins and their cognate ligands is therefore fundamental to the understanding of biological systems. during the last two decades ms, and its associated techniques, has become accepted as a method for the study of protein-ligand interactions, not only for covalent complexes, where the use of ms is well est ...	2014	24393119
redox specificity of 2-hydroxyacid-coupled nad(+)/nadh dehydrogenases: a study exploiting "reactive" arginine as a reporter of protein electrostatics.	with "reactive" arginine as a kinetic reporter, 2-hydroxyacid dehydrogenases are assessed in basis of their specialization as nad(+)-reducing or nadh-oxidizing enzymes. specifically, m4 and h4 lactate dehydrogenases (ldhs) and cytoplasmic and mitochondrial malate dehydrogenases (mdhs) are compared to assess if their coenzyme specificity may involve electrostatics of cationic or neutral nicotinamide structure as the basis. the enzymes from diverse eukaryote and prokaryote sources thus are assesse ...	2013	24391777
comea is essential for the transfer of external dna into the periplasm in naturally transformable vibrio cholerae cells.	the dna uptake of naturally competent bacteria has been attributed to the action of dna uptake machineries resembling type iv pilus complexes. however, the protein(s) for pulling the dna across the outer membrane of gram-negative bacteria remain speculative. here we show that the competence protein comea binds incoming dna in the periplasm of naturally competent vibrio cholerae cells thereby promoting dna uptake, possibly through ratcheting and entropic forces associated with comea binding. usin ...	2014	24391524
crystal structures and molecular dynamics simulations of thermophilic malate dehydrogenase reveal critical loop motion for co-substrate binding.	malate dehydrogenase (mdh) catalyzes the conversion of oxaloacetate and malate by using the nad/nadh coenzyme system. the system is used as a conjugate for enzyme immunoassays of a wide variety of compounds, such as illegal drugs, drugs used in therapeutic applications and hormones. we elucidated the biochemical and structural features of mdh from thermus thermophilus (ttmdh) for use in various biotechnological applications. the biochemical characterization of recombinant ttmdh revealed greatly ...	2013	24386145
significance of neuropilin-1 expression in acute myeloid leukemia.	neuropilin-1 is a vascular endothelial growth factor receptor that acts as a mediator of angiogenesis. its importance in hematological malignancies such as acute myeloid leukemia (aml) remains to be elucidated. the aim of this study was to evaluate the significance of neuropilin-1 expression in aml patients by both flow cytometry and real-time polymerase chain reaction (pcr) in regard to its diagnostic and prognostic values.	2013	24385810
new mini- zincin structures provide a minimal scaffold for members of this metallopeptidase superfamily.	the acel_2062 protein from acidothermus cellulolyticus is a protein of unknown function. initial sequence analysis predicted that it was a metallopeptidase from the presence of a motif conserved amongst the asp-zincins, which are peptidases that contain a single, catalytic zinc ion ligated by the histidines and aspartic acid within the motif (hexxhxxgxxd). the acel_2062 protein was chosen by the joint center for structural genomics for crystal structure determination to explore novel protein seq ...	2014	24383880
genomics of kpc-producing klebsiella pneumoniae sequence type 512 clone highlights the role of ramr and ribosomal s10 protein mutations in conferring tigecycline resistance.	full genome sequences were determined for five klebsiella pneumoniae strains belonging to the sequence type 512 (st512) clone, producing kpc-3. three strains were resistant to tigecycline, one showed an intermediate phenotype, and one was susceptible. comparative analysis performed using the genome of the susceptible strain as a reference sequence identified genetic differences possibly associated with resistance to tigecycline. results demonstrated that mutations in the ramr gene occurred in tw ...	2014	24379204
structure-based cleavage mechanism of thermus thermophilus argonaute dna guide strand-mediated dna target cleavage.	we report on crystal structures of ternary thermus thermophilus argonaute (ttago) complexes with 5'-phosphorylated guide dna and a series of dna targets. these ternary complex structures of cleavage-incompatible, cleavage-compatible, and postcleavage states solved at improved resolution up to 2.2 å have provided molecular insights into the orchestrated positioning of catalytic residues, a pair of mg(2+) cations, and the putative water nucleophile positioned for in-line attack on the cleavable ph ...	2013	24374628
structure-based cleavage mechanism of thermus thermophilus argonaute dna guide strand-mediated dna target cleavage.	we report on crystal structures of ternary thermus thermophilus argonaute (ttago) complexes with 5'-phosphorylated guide dna and a series of dna targets. these ternary complex structures of cleavage-incompatible, cleavage-compatible, and postcleavage states solved at improved resolution up to 2.2 å have provided molecular insights into the orchestrated positioning of catalytic residues, a pair of mg(2+) cations, and the putative water nucleophile positioned for in-line attack on the cleavable ph ...	2013	24374628
single molecule analysis of thermus thermophilus ssb protein dynamics on single-stranded dna.	single-stranded (ss) dna binding (ssb) proteins play central roles in dna replication, recombination and repair in all organisms. we previously showed that escherichia coli (eco) ssb, a homotetrameric bacterial ssb, undergoes not only rapid ssdna-binding mode transitions but also one-dimensional diffusion (or migration) while remaining bound to ssdna. whereas the majority of bacterial ssb family members function as homotetramers, dimeric ssb proteins were recently discovered in a distinct bacter ...	2013	24371279
single molecule analysis of thermus thermophilus ssb protein dynamics on single-stranded dna.	single-stranded (ss) dna binding (ssb) proteins play central roles in dna replication, recombination and repair in all organisms. we previously showed that escherichia coli (eco) ssb, a homotetrameric bacterial ssb, undergoes not only rapid ssdna-binding mode transitions but also one-dimensional diffusion (or migration) while remaining bound to ssdna. whereas the majority of bacterial ssb family members function as homotetramers, dimeric ssb proteins were recently discovered in a distinct bacter ...	2013	24371279
distinct trna recognition strategies used by a homologous family of editing domains prevent mistranslation.	errors in protein synthesis due to mispairing of amino acids with trnas jeopardize cell viability. several checkpoints to prevent formation of ala- and cys-trna(pro) have been described, including the ala-specific editing domain (ins) of most bacterial prolyl-trna synthetases (prorss) and an autonomous single-domain ins homolog, ybak, which clears cys-trna(pro) in trans. in many species where prors lacks an ins domain, proxp-ala, another single-domain ins-like protein, is responsible for editing ...	2013	24371276
distinct trna recognition strategies used by a homologous family of editing domains prevent mistranslation.	errors in protein synthesis due to mispairing of amino acids with trnas jeopardize cell viability. several checkpoints to prevent formation of ala- and cys-trna(pro) have been described, including the ala-specific editing domain (ins) of most bacterial prolyl-trna synthetases (prorss) and an autonomous single-domain ins homolog, ybak, which clears cys-trna(pro) in trans. in many species where prors lacks an ins domain, proxp-ala, another single-domain ins-like protein, is responsible for editing ...	2013	24371276
active site plasticity enables metal-dependent tuning of cas5d nuclease activity in crispr-cas type i-c system.	clustered regularly interspaced short palindromic repeat (crispr) in association with crispr-associated (cas) proteins constitutes a formidable defense system against mobile genetic elements in prokaryotes. in type i-c, the ribonucleoprotein surveillance complex comprises only three cas proteins, namely, cas5d, csd1 and csd2. unlike type i-e that uses cse3/case for metal-independent crispr rna maturation, type i-c that lacks this deputes cas5d to process the pre-crrna. here, we report the promis ...	2013	24371266
active site plasticity enables metal-dependent tuning of cas5d nuclease activity in crispr-cas type i-c system.	clustered regularly interspaced short palindromic repeat (crispr) in association with crispr-associated (cas) proteins constitutes a formidable defense system against mobile genetic elements in prokaryotes. in type i-c, the ribonucleoprotein surveillance complex comprises only three cas proteins, namely, cas5d, csd1 and csd2. unlike type i-e that uses cse3/case for metal-independent crispr rna maturation, type i-c that lacks this deputes cas5d to process the pre-crrna. here, we report the promis ...	2013	24371266
biosynthesis of rare hexoses using microorganisms and related enzymes.	rare sugars, referred to as monosaccharides and their derivatives that rarely exist in nature, can be applied in many areas ranging from foodstuffs to pharmaceutical and nutrition industry, or as starting materials for various natural products and drug candidates. unfortunately, an important factor restricting the utilization of rare sugars is their limited availability, resulting from limited synthetic methods. nowadays, microbial and enzymatic transformations have become a very powerful tool i ...	2013	24367410
functional characterization of osmotically inducible protein c (mg_427) from mycoplasma genitalium.	mycoplasma genitalium is the smallest self-replicating bacterium and an important human pathogen responsible for a range of urogenital infections and pathologies. due to its limited genome size, many genes conserved in other bacteria are missing in m. genitalium. genes encoding catalase and superoxide dismutase are absent, and how this pathogen overcomes oxidative stress remains poorly understood. in this study, we characterized mg_427, a homolog of the conserved osmc, which encodes hydroperoxid ...	2014	24363346
sequence, structure, and stacking: specifics of trna anchoring to the t box riboswitch.	the term riboswitch usually refers to small molecule sensing regulatory modules in the 5' untranslated regions of a mrna. they are typically comprised of separate ligand binding and regulatory domains. the t box riboswitch is unique from other identified riboswitches because its effector is an essential macromolecule, trna. it senses the aminoacylation state of trna to regulate genes involved in a variety of functions relating to amino acid metabolism and trna aminoacylation. t box riboswitches ...	2013	24356646
an unusual mechanism for ef-tu activation during tmrna-mediated ribosome rescue.	in bacteria, ribosomes stalled on truncated mrnas are rescued by transfer-messenger rna (tmrna) and its protein partner smpb. acting like trna, the aminoacyl-tmrna/smpb complex is delivered to the ribosomal a site by ef-tu and accepts the transfer of the nascent polypeptide. although smpb binding within the decoding center is clearly critical for licensing tmrna entry into the ribosome, it is not known how activation of ef-tu occurs in the absence of a codon-anticodon interaction. a recent cryst ...	2014	24345396
timmdc1/c3orf1 functions as a membrane-embedded mitochondrial complex i assembly factor through association with the mcia complex.	complex i (ci) of the electron transport chain, a large membrane-embedded nadh dehydrogenase, couples electron transfer to the release of protons into the mitochondrial inner membrane space to promote atp production through atp synthase. in addition to being a central conduit for atp production, ci activity has been linked to neurodegenerative disorders, including parkinson's disease. ci is built in a stepwise fashion through the actions of several assembly factors. we employed interaction prote ...	2014	24344204
antibiotic streptolydigin requires noncatalytic mg2+ for binding to rna polymerase.	multisubunit rna polymerase, an enzyme that accomplishes transcription in all living organisms, is a potent target for antibiotics. the antibiotic streptolydigin inhibits rna polymerase by sequestering the active center in a catalytically inactive conformation. here, we show that binding of streptolydigin to rna polymerase strictly depends on a noncatalytic magnesium ion which is likely chelated by the aspartate of the bridge helix of the active center. substitutions of this aspartate may explai ...	2014	24342645
asymmetric chromosome segregation in xanthomonas citri ssp. citri.	this study was intended to characterize the chromosome segregation process of xanthomonas citri ssp. citri (xac) by investigating the functionality of the parb factor encoded on its chromosome, and its requirement for cell viability and virulence. using tap tagging we show that parb is expressed in xac. disruption of parb increased the cell doubling time and precluded the ability of xac to colonize the host citrus. moreover, xac mutant cells expressing only truncated forms of parb exhibited the ...	2013	24339434
asymmetric chromosome segregation in xanthomonas citri ssp. citri.	this study was intended to characterize the chromosome segregation process of xanthomonas citri ssp. citri (xac) by investigating the functionality of the parb factor encoded on its chromosome, and its requirement for cell viability and virulence. using tap tagging we show that parb is expressed in xac. disruption of parb increased the cell doubling time and precluded the ability of xac to colonize the host citrus. moreover, xac mutant cells expressing only truncated forms of parb exhibited the ...	2013	24339434
mechanisms of allosteric activation and inhibition of the deoxyribonucleoside triphosphate triphosphohydrolase from enterococcus faecalis.	ef1143 from enterococcus faecalis, a life-threatening pathogen that is resistant to common antibiotics, is a homo-tetrameric deoxyribonucleoside triphosphate (dntp) triphosphohydrolase (dntpase), converting dntps into the deoxyribonucleosides and triphosphate. the dntpase activity of ef1143 is regulated by canonical dntps, which simultaneously act as substrates and activity modulators. previous crystal structures of apo-ef1143 and the protein bound to both dgtp and datp suggested allosteric regu ...	2013	24338016
mechanisms of allosteric activation and inhibition of the deoxyribonucleoside triphosphate triphosphohydrolase from enterococcus faecalis.	ef1143 from enterococcus faecalis, a life-threatening pathogen that is resistant to common antibiotics, is a homo-tetrameric deoxyribonucleoside triphosphate (dntp) triphosphohydrolase (dntpase), converting dntps into the deoxyribonucleosides and triphosphate. the dntpase activity of ef1143 is regulated by canonical dntps, which simultaneously act as substrates and activity modulators. previous crystal structures of apo-ef1143 and the protein bound to both dgtp and datp suggested allosteric regu ...	2013	24338016
functional domains of the 50s subunit mature late in the assembly process.	despite the identification of many factors that facilitate ribosome assembly, the molecular mechanisms by which they drive ribosome biogenesis are poorly understood. here, we analyze the late stages of assembly of the 50s subunit using bacillus subtilis cells depleted of rbga, a highly conserved gtpase. we found that rbga-depleted cells accumulate late assembly intermediates bearing sub-stoichiometric quantities of ribosomal proteins l16, l27, l28, l33a, l35 and l36. using a novel pulse labeling ...	2013	24335279
functional domains of the 50s subunit mature late in the assembly process.	despite the identification of many factors that facilitate ribosome assembly, the molecular mechanisms by which they drive ribosome biogenesis are poorly understood. here, we analyze the late stages of assembly of the 50s subunit using bacillus subtilis cells depleted of rbga, a highly conserved gtpase. we found that rbga-depleted cells accumulate late assembly intermediates bearing sub-stoichiometric quantities of ribosomal proteins l16, l27, l28, l33a, l35 and l36. using a novel pulse labeling ...	2013	24335279
identification of a selective polymerase enables detection of n(6)-methyladenosine in rna.	n(6)-methyladenosine (m(6)a) is the most abundant mrna modification and has important links to human health. while recent studies have successfully identified thousands of mammalian rna transcripts containing the modification, it is extremely difficult to identify the exact location of any specific m(6)a. here we have identified a polymerase with reverse transcriptase activity (from thermus thermophilus) that is selective by up to 18-fold for incorporation of thymidine opposite unmodified a over ...	2013	24328136
allosteric regulation in phosphofructokinase from the extreme thermophile thermus thermophilus.	an investigation into the kinetics and regulatory properties of the type-1 phosphofructokinase (pfk) from the extreme thermophile thermus thermophilus (ttpfk) reveals an enzyme that is inhibited by pep and activated by adp by modifying the affinity exhibited for the substrate fructose 6-phosphate (fru-6-p) in a manner analogous to other prokaryotic pfks. however, ttpfk binds both of these allosteric ligands significantly more tightly than other bacterial pfks while effecting a substantially more ...	2013	24328040
allosteric regulation in phosphofructokinase from the extreme thermophile thermus thermophilus.	an investigation into the kinetics and regulatory properties of the type-1 phosphofructokinase (pfk) from the extreme thermophile thermus thermophilus (ttpfk) reveals an enzyme that is inhibited by pep and activated by adp by modifying the affinity exhibited for the substrate fructose 6-phosphate (fru-6-p) in a manner analogous to other prokaryotic pfks. however, ttpfk binds both of these allosteric ligands significantly more tightly than other bacterial pfks while effecting a substantially more ...	2013	24328040
redox regulation of the calvin-benson cycle: something old, something new.	reversible redox post-translational modifications such as oxido-reduction of disulfide bonds, s-nitrosylation, and s-glutathionylation, play a prominent role in the regulation of cell metabolism and signaling in all organisms. these modifications are mainly controlled by members of the thioredoxin and glutaredoxin families. early studies in photosynthetic organisms have identified the calvin-benson cycle, the photosynthetic pathway responsible for carbon assimilation, as a redox regulated proces ...	2013	24324475
structure of the ribosome with elongation factor g trapped in the pretranslocation state.	during protein synthesis, trnas and their associated mrna codons move sequentially on the ribosome from the a (aminoacyl) site to the p (peptidyl) site to the e (exit) site in a process catalyzed by a universally conserved ribosome-dependent gtpase [elongation factor g (ef-g) in prokaryotes and elongation factor 2 (ef-2) in eukaryotes]. although the high-resolution structure of ef-g bound to the posttranslocation ribosome has been determined, the pretranslocation conformation of the ribosome bou ...	2013	24324137
identification of residues required for stalled-ribosome rescue in the codon-independent release factor yaej.	the yaej protein is a codon-independent release factor with peptidyl-trna hydrolysis (pth) activity, and functions as a stalled-ribosome rescue factor in escherichia coli. to identify residues required for yaej function, we performed mutational analysis for in vitro pth activity towards rescue of ribosomes stalled on a non-stop mrna, and for ribosome-binding efficiency. we focused on residues conserved among bacterial yaej proteins. additionally, we determined the solution structure of the ggq d ...	2013	24322300
identification of residues required for stalled-ribosome rescue in the codon-independent release factor yaej.	the yaej protein is a codon-independent release factor with peptidyl-trna hydrolysis (pth) activity, and functions as a stalled-ribosome rescue factor in escherichia coli. to identify residues required for yaej function, we performed mutational analysis for in vitro pth activity towards rescue of ribosomes stalled on a non-stop mrna, and for ribosome-binding efficiency. we focused on residues conserved among bacterial yaej proteins. additionally, we determined the solution structure of the ggq d ...	2013	24322300
metagenomics and novel gene discovery: promise and potential for novel therapeutics.	metagenomics provides a means of assessing the total genetic pool of all the microbes in a particular environment, in a culture-independent manner. it has revealed unprecedented diversity in microbial community composition, which is further reflected in the encoded functional diversity of the genomes, a large proportion of which consists of novel genes. herein, we review both sequence-based and functional metagenomic methods to uncover novel genes and outline some of the associated problems of e ...	2013	24317337
metagenomics and novel gene discovery: promise and potential for novel therapeutics.	metagenomics provides a means of assessing the total genetic pool of all the microbes in a particular environment, in a culture-independent manner. it has revealed unprecedented diversity in microbial community composition, which is further reflected in the encoded functional diversity of the genomes, a large proportion of which consists of novel genes. herein, we review both sequence-based and functional metagenomic methods to uncover novel genes and outline some of the associated problems of e ...	2013	24317337
cloning, expression, purification, crystallization and preliminary x-ray studies of argininosuccinate lyase (rv1659) from mycobacterium tuberculosis.	the last enzyme in the arginine-biosynthesis pathway, argininosuccinate lyase, from mycobacterium tuberculosis has been cloned, expressed, purified and crystallized, and preliminary x-ray studies have been carried out on the crystals. the his-tagged tetrameric enzyme with a subunit molecular weight of 50.9 kda crystallized with two tetramers in the asymmetric unit of the orthorhombic unit cell, space group p2(1)2(1)2(1). molecular-replacement calculations and self-rotation calculations confirmed ...	2013	24316845
purification, crystallization and preliminary x-ray studies of mbtn (rv1346) from mycobacterium tuberculosis.	in mycobacterium tuberculosis, the protein mbtn (rv1346) catalyzes the formation of a double bond in the fatty-acyl moiety of the siderophore mycobactin, which is used by this organism to acquire essential iron. mbtn is homologous to acyl-coa dehydrogenases, whose general role is to catalyze the α,β-dehydrogenation of fatty-acyl-coa conjugates. mycobactins, however, contain a long unsaturated fatty-acid chain with an unusual cis double bond conjugated to the carbonyl group of the mycobactin core ...	2013	24316828
posttranscriptional rna modifications: playing metabolic games in a cell's chemical legoland.	nature combines existing biochemical building blocks, at times with subtlety of purpose. rna modifications are a prime example of this, where standard rna nucleosides are decorated with chemical groups and building blocks that we recall from our basic biochemistry lectures. the result: a wealth of chemical diversity whose full biological relevance has remained elusive despite being public knowledge for some time. here, we highlight several modifications that, because of their chemical intricacy, ...	2013	24315934
posttranscriptional rna modifications: playing metabolic games in a cell's chemical legoland.	nature combines existing biochemical building blocks, at times with subtlety of purpose. rna modifications are a prime example of this, where standard rna nucleosides are decorated with chemical groups and building blocks that we recall from our basic biochemistry lectures. the result: a wealth of chemical diversity whose full biological relevance has remained elusive despite being public knowledge for some time. here, we highlight several modifications that, because of their chemical intricacy, ...	2013	24315934
the mononuclear metal center of type-i dihydroorotase from aquifex aeolicus.	dihydroorotase (dho) is a zinc metalloenzyme, although the number of active site zinc ions has been controversial. e. coli dho was initially thought to have a mononuclear metal center, but the subsequent x-ray structure clearly showed two zinc ions, α and β, at the catalytic site. aquifex aeolicus dho, is a dodecamer comprised of six dho and six aspartate transcarbamoylase (atc) subunits. the isolated dho monomer, which lacks catalytic activity, has an intact α-site and conserved β-site ligands, ...	2013	24314009