Publications

recognition of trnagln by helicobacter pylori glurs2--a trnagln-specific glutamyl-trna synthetase.	accurate aminoacylation of trnas by the aminoacyl-trna synthetases (aarss) plays a critical role in protein translation. however, some of the aarss are missing in many microorganisms. helicobacter pylori does not have a glutaminyl-trna synthetase (glnrs) but has two divergent glutamyl-trna synthetases: glurs1 and glurs2. like a canonical glurs, glurs1 aminoacylates trna(glu1) and trna(glu2). in contrast, glurs2 only misacylates trna(gln) to form glu-trna(gln). it is not clear how glurs2 achieves ...	2009	19755501
demonstration and characterization of the heterodimerization of znt5 and znt6 in the early secretory pathway.	the majority of cdf/znt zinc transporters form homo-oligomers. however, znt5, znt6, and their orthologues form hetero-oligomers in the early secretory pathway where they load zinc onto zinc-requiring enzymes and maintain secretory pathway functions. the details of this hetero-oligomerization remain to be elucidated, and much more is known about homo-oligomerization that occurs in other cdf/znt family proteins. here, we addressed this issue using co-immunoprecipitation experiments, mutagenesis, a ...	2009	19759014
the schizosaccharomyces pombe hsp104 disaggregase is unable to propagate the [psi] prion.	the molecular chaperone hsp104 is a crucial factor in the acquisition of thermotolerance in yeast. under stress conditions, the disaggregase activity of hsp104 facilitates the reactivation of misfolded proteins. hsp104 is also involved in the propagation of fungal prions. for instance, the well-characterized [psi(+)] prion of saccharomyces cerevisiae does not propagate in deltahsp104 cells or in cells overexpressing hsp104. in this study, we characterized the functional homolog of hsp104 from sc ...	2009	19759825
exploring conformational modes of macromolecular assemblies by multiparticle cryo-em.	single particle cryo-electron microscopy (cryo-em) is a technique aimed at structure determination of large macromolecular complexes in their unconstrained, physiological conditions. the power of the method has been demonstrated in selected studies where for highly symmetric molecules the resolution attained permitted backbone tracing. however, most molecular complexes appear to exhibit intrinsic conformational variability necessary to perform their functions. therefore, it is now increasingly r ...	2009	19767196
zinc-independent folate biosynthesis: genetic, biochemical, and structural investigations reveal new metal dependence for gtp cyclohydrolase ib.	gtp cyclohydrolase i (gcyh-i) is an essential zn(2+)-dependent enzyme that catalyzes the first step of the de novo folate biosynthetic pathway in bacteria and plants, the 7-deazapurine biosynthetic pathway in bacteria and archaea, and the biopterin pathway in mammals. we recently reported the discovery of a new prokaryotic-specific gcyh-i (gcyh-ib) that displays no sequence identity to the canonical enzyme and is present in approximately 25% of bacteria, the majority of which lack the canonical ...	2009	19767425
structure of d-alanine-d-alanine ligase from thermus thermophilus hb8: cumulative conformational change and enzyme-ligand interactions.	d-alanine-d-alanine ligase (ddl) is one of the key enzymes in peptidoglycan biosynthesis and is an important target for drug discovery. the enzyme catalyzes the condensation of two d-ala molecules using atp to produce d-ala-d-ala, which is the terminal peptide of a peptidoglycan monomer. the structures of five forms of the enzyme from thermus thermophilus hb8 (ttddl) were determined: unliganded ttddl (2.3 a resolution), ttddl-adenylyl imidodiphosphate (2.6 a), ttddl-adp (2.2 a), ttddl-adp-d-ala ...	2009	19770507
effects of protein subunits removal on the computed motions of partial 30s structures of the ribosome.	the anisotropic network model (anm) is used to study motions of the 30s small ribosomal subunit. the effect of the absence of certain subunits on the motions of the remaining partial structures was investigated by removing one protein, pairs of proteins and selected sets of proteins at a time. our results show that the removal of some proteins doesn't change the large-scale dynamics of the partial structures, but the removal of certain subunits does cause significant changes in motion of the rem ...	2008	19771145
crystal structure and functional analysis of homocitrate synthase, an essential enzyme in lysine biosynthesis.	homocitrate synthase (hcs) catalyzes the first and committed step in lysine biosynthesis in many fungi and certain archaea and is a potential target for antifungal drugs. here we report the crystal structure of the hcs apoenzyme from schizosaccharomyces pombe and two distinct structures of the enzyme in complex with the substrate 2-oxoglutarate (2-og). the structures reveal that hcs forms an intertwined homodimer stabilized by domain-swapping between the n- and c-terminal domains of each monomer ...	2009	19776021
adenosine triphosphate stimulates aquifex aeolicus mutl endonuclease activity.	background: human pms2 (hpms2) homologues act to nick 5' and 3' to misincorporated nucleotides during mismatch repair in organisms that lack muth. mn(++) was previously found to stimulate the endonuclease activity of these homologues. atp was required for the nicking activity of hpms2 and ypms1, but was reported to inhibit bacterial mutl proteins from thermus thermophilus and aquifex aeolicus that displayed homology to hpms2. mutational analysis has identified the dqha(x)(2)e(x)(4)e motif presen ...	2009	19777055
increased expression of the oxidative pentose phosphate pathway and gluconeogenesis in anaerobically growing xylose-utilizing saccharomyces cerevisiae.	fermentation of xylose to ethanol has been achieved in s. cerevisiae by genetic engineering. xylose utilization is however slow compared to glucose, and during anaerobic conditions addition of glucose has been necessary for cellular growth. in the current study, the xylose-utilizing strain tmb 3415 was employed to investigate differences between anaerobic utilization of glucose and xylose. this strain carried a xylose reductase (xyl1 k270r) engineered for increased nadh utilization and was capab ...	2009	19778438
inter-subunit interaction and quaternary rearrangement defined by the central stalk of prokaryotic v1-atpase.	v-type atpases (v-atpases) are categorized as rotary atp synthase/atpase complexes. the v-atpases are distinct from f-atpases in terms of their rotation scheme, architecture and subunit composition. however, there is no detailed structural information on v-atpases despite the abundant biochemical and biophysical research. here, we report a crystallographic study of v1-atpase, from thermus thermophilus, which is a soluble component consisting of a, b, d and f subunits. the structure at 4.5 a reso ...	2009	19779483
ion-induced folding of a kink turn that departs from the conventional sequence.	kink turns (k-turns) are important structural motifs that create a sharp axial bend in rna. most conform to a consensus in which a three-nucleotide bulge is followed by consecutive ga and ag base pairs, and when these ga pairs are modified in vitro this generally leads to a failure to adopt the k-turn conformation. kt-23 in the 30s ribosomal subunit of thermus thermophilus is a rare exception in which the bulge-distal ag pair is replaced by a non-watson-crick a*u pair. in the context of the ...	2009	19783814
recode-2: new design, new search tools, and many more genes.	'recoding' is a term used to describe non-standard read-out of the genetic code, and encompasses such phenomena as programmed ribosomal frameshifting, stop codon readthrough, selenocysteine insertion and translational bypassing. although only a small proportion of genes utilize recoding in protein synthesis, accurate annotation of 'recoded' genes lags far behind annotation of 'standard' genes. in order to address this issue, provide a service to researchers in the field, and offer training data ...	2009	19783826
recode-2: new design, new search tools, and many more genes.	'recoding' is a term used to describe non-standard read-out of the genetic code, and encompasses such phenomena as programmed ribosomal frameshifting, stop codon readthrough, selenocysteine insertion and translational bypassing. although only a small proportion of genes utilize recoding in protein synthesis, accurate annotation of 'recoded' genes lags far behind annotation of 'standard' genes. in order to address this issue, provide a service to researchers in the field, and offer training data ...	2009	19783826
tuning the properties of the bacterial membrane with aminoacylated phosphatidylglycerol.	the bacterial envelope is a semi-permeable barrier that protects the cell from the hostilities of the environment. to survive the ever-changing conditions of their surroundings, bacteria need to rapidly adjust the biochemical properties of their cellular envelope. amino acid (aa) addition to phosphatidylglycerol (pg) of the membrane is one of the mechanisms used by bacteria to lower the net negative charge of their cellular envelope, thereby decreasing its affinity for several antibacterial agen ...	2009	19787708
structural studies on cytosolic domain of magnesium transporter mgte from enterococcus faecalis.		2010	19787770
redox characterization of the fes protein mitoneet and impact of thiazolidinedione drug binding.	mitoneet is a small mitochondrial protein that has been identified recently as a target for the thiazolidinedione (tzd) class of diabetes drugs. mitoneet also binds a unique three-cys- and one-his-ligated [corrected] [2fe-2s] cluster. here we use protein film voltammetry (pfv) as a means to probe the redox properties of mitoneet and demonstrate the direct impact of tzd drug binding upon the redox chemistry of the fes cluster. when tzds bind, the midpoint potential at ph 7 is lowered by more than ...	2009	19791753
mg(2+)-dependent gating of bacterial mgte channel underlies mg(2+) homeostasis.	the mgte family of mg(2+) transporters is ubiquitously distributed in all phylogenetic domains. recent crystal structures of the full-length mgte and of its cytosolic domain in the presence and absence of mg(2+) suggested a mg(2+)-homeostasis mechanism, in which the mgte cytosolic domain acts as a 'mg(2+) sensor' to regulate the gating of the ion-conducting pore in response to the intracellular mg(2+) concentration. however, complementary functional analyses to confirm the proposed model have be ...	2009	19798051
crystal structure of ynje from escherichia coli, a sulfurtransferase with three rhodanese domains.	rhodaneses/sulfurtransferases are ubiquitous enzymes that catalyze the transfer of sulfane sulfur from a donor molecule to a thiophilic acceptor via an active site cysteine that is modified to a persulfide during the reaction. here, we present the first crystal structure of a triple-domain rhodanese-like protein, namely ynje from escherichia coli, in two states where its active site cysteine is either unmodified or present as a persulfide. compared to well-characterized tandem domain rhodaneses, ...	2009	19798741
multiple biochemical and morphological factors underlie the production of methylketones in tomato trichomes.	genetic analysis of interspecific populations derived from crosses between the wild tomato species solanum habrochaites f. sp. glabratum, which synthesizes and accumulates insecticidal methylketones (mk), mostly 2-undecanone and 2-tridecanone, in glandular trichomes, and cultivated tomato (solanum lycopersicum), which does not, demonstrated that several genetic loci contribute to mk metabolism in the wild species. a strong correlation was found between the shape of the glandular trichomes and th ...	2009	19801397
"hot standards" for the thermoacidophilic archaeon sulfolobus solfataricus.	within the archaea, the thermoacidophilic crenarchaeote sulfolobus solfataricus has become an important model organism for physiology and biochemistry, comparative and functional genomics, as well as, more recently also for systems biology approaches. within the sulfolobus systems biology ("sulfosys")-project the effect of changing growth temperatures on a metabolic network is investigated at the systems level by integrating genomic, transcriptomic, proteomic, metabolomic and enzymatic informati ...	2010	19802714
"hot standards" for the thermoacidophilic archaeon sulfolobus solfataricus.	within the archaea, the thermoacidophilic crenarchaeote sulfolobus solfataricus has become an important model organism for physiology and biochemistry, comparative and functional genomics, as well as, more recently also for systems biology approaches. within the sulfolobus systems biology ("sulfosys")-project the effect of changing growth temperatures on a metabolic network is investigated at the systems level by integrating genomic, transcriptomic, proteomic, metabolomic and enzymatic informati ...	2010	19802714
two-dimensional pulsed electron spin resonance characterization of 15n-labeled archaeal rieske-type ferredoxin.	two-dimensional electron spin-echo envelope modulation (eseem) analysis of the uniformly (15)n-labeled archaeal rieske-type [2fe-2s] ferredoxin (arf) from sulfolobus solfataricus p1 has been conducted in comparison with the previously characterized high-potential protein homologs. major differences among these proteins were found in the hyperfine sublevel correlation (hyscore) lineshapes and intensities of the signals in the (++) quadrant, which are contributed from weakly coupled (non-coordinat ...	2009	19804777
the cytochrome ba3 oxygen reductase from thermus thermophilus uses a single input channel for proton delivery to the active site and for proton pumping.	the heme-copper oxygen reductases are redox-driven proton pumps that generate a proton motive force in both prokaryotes and mitochondria. these enzymes have been divided into 3 evolutionarily related groups: the a-, b- and c-families. most experimental work on proton-pumping mechanisms has been performed with members of the a-family. these enzymes require 2 proton input pathways (d- and k-channels) to transfer protons used for oxygen reduction chemistry and for proton pumping, with the d-channel ...	2009	19805275
structure of a trna-dependent kinase essential for selenocysteine decoding.	compared to bacteria, archaea and eukaryotes employ an additional enzyme for the biosynthesis of selenocysteine (sec), the 21(st) natural amino acid (aa). an essential rna-dependent kinase, o-phosphoseryl-trna(sec) kinase (pstk), converts seryl-trna(sec) to o-phosphoseryl-trna(sec), the immediate precursor of selenocysteinyl-trna(sec). the sequence of methanocaldococcus jannaschii pstk (mjpstk) suggests an n-terminal kinase domain (177 aa) followed by a presumed trna binding region (75 aa). the ...	2009	19805283
knowledge-based instantiation of full atomic detail into coarse-grain rna 3d structural models.	the recent development of methods for modeling rna 3d structures using coarse-grain approaches creates a need to bridge low- and high-resolution modeling methods. although they contain topological information, coarse-grain models lack atomic detail, which limits their utility for some applications.	2009	19812110
estimating the fraction of non-coding rnas in mammalian transcriptomes.	recent studies of mammalian transcriptomes have identified numerous rna transcripts that do not code for proteins; their identity, however, is largely unknown. here we explore an approach based on sequence randomness patterns to discern different rna classes. the relative z-score we use helps identify the known ncrna class from the genome, intergene and intron classes. this leads us to a fractional ncrna measure of putative ncrna datasets which we model as a mixture of genuine ncrnas and other t ...	2008	19812767
features of subunit nuom (nd4) in escherichia coli ndh-1: topology and implication of conserved glu144 for coupling site 1.	the bacterial h(+)-pumping nadh-quinone oxidoreductase (ndh-1) is an l-shaped membrane-bound enzymatic complex. escherichia coli ndh-1 is composed of 13 subunits (nuoa-n). nuom (nd4) subunit is one of the hydrophobic subunits that constitute the membrane arm of ndh-1 and was predicted to bear 14 helices. we attempted to clarify the membrane topology of nuom by the introduction of histidine tags into different positions by chromosomal site-directed mutagenesis. from the data, we propose a topolog ...	2009	19815558
acyl-coa synthesis, lipid metabolism and lipotoxicity.	although the underlying causes of insulin resistance have not been completely delineated, in most analyses, a recurring theme is dysfunctional metabolism of fatty acids. because the conversion of fatty acids to activated acyl-coas is the first and essential step in the metabolism of long-chain fatty acid metabolism, interest has grown in the synthesis of acyl-coas, their contribution to the formation of signaling molecules like ceramide and diacylglycerol, and their direct effects on cell functi ...	2009	19818872
acyl-coa synthesis, lipid metabolism and lipotoxicity.	although the underlying causes of insulin resistance have not been completely delineated, in most analyses, a recurring theme is dysfunctional metabolism of fatty acids. because the conversion of fatty acids to activated acyl-coas is the first and essential step in the metabolism of long-chain fatty acid metabolism, interest has grown in the synthesis of acyl-coas, their contribution to the formation of signaling molecules like ceramide and diacylglycerol, and their direct effects on cell functi ...	2009	19818872
structural insights into rna processing by the human risc-loading complex.	targeted gene silencing by rna interference (rnai) requires loading of a short guide rna (small interfering rna (sirna) or microrna (mirna)) onto an argonaute protein to form the functional center of an rna-induced silencing complex (risc). in humans, argonaute2 (ago2) assembles with the guide rna-generating enzyme dicer and the rna-binding protein trbp to form a risc-loading complex (rlc), which is necessary for efficient transfer of nascent sirnas and mirnas from dicer to ago2. here, using sin ...	2009	19820710
multistart simulated annealing refinement of the crystal structure of the 70s ribosome.	a macromolecular x-ray crystal structure is usually represented as a single static model with a single set of temperature factors representing a simple approximation of motion and disorder of the structure. multiconformer representations of small proteins have been shown to better describe anisotropic motion and disorder and improve the quality of their electron density maps. here, we apply multistart simulated annealing crystallographic refinement to a 70s ribosome-rf1 translation termination c ...	2009	19822758
structure, expression, and function of kynurenine aminotransferases in human and rodent brains.	kynurenine aminotransferases (kats) catalyze the synthesis of kynurenic acid (kyna), an endogenous antagonist of n-methyl-d: -aspartate and alpha 7-nicotinic acetylcholine receptors. abnormal kyna levels in human brains are implicated in the pathophysiology of schizophrenia, alzheimer's disease, and other neurological disorders. four kats have been reported in mammalian brains, kat i/glutamine transaminase k/cysteine conjugate beta-lyase 1, kat ii/aminoadipate aminotransferase, kat iii/cysteine ...	2010	19826765
structure, expression, and function of kynurenine aminotransferases in human and rodent brains.	kynurenine aminotransferases (kats) catalyze the synthesis of kynurenic acid (kyna), an endogenous antagonist of n-methyl-d: -aspartate and alpha 7-nicotinic acetylcholine receptors. abnormal kyna levels in human brains are implicated in the pathophysiology of schizophrenia, alzheimer's disease, and other neurological disorders. four kats have been reported in mammalian brains, kat i/glutamine transaminase k/cysteine conjugate beta-lyase 1, kat ii/aminoadipate aminotransferase, kat iii/cysteine ...	2010	19826765
polyamines: ubiquitous polycations with unique roles in growth and stress responses.	polyamines are small polycationic molecules found ubiquitously in all organisms and function in a wide variety of biological processes. in the past decade, molecular and genetic studies using mutants and transgenic plants with an altered activity of enzymes involved in polyamine biosynthesis have contributed much to a better understanding of the biological functions of polyamines in plants.	2009	19828463
polyamines: ubiquitous polycations with unique roles in growth and stress responses.	polyamines are small polycationic molecules found ubiquitously in all organisms and function in a wide variety of biological processes. in the past decade, molecular and genetic studies using mutants and transgenic plants with an altered activity of enzymes involved in polyamine biosynthesis have contributed much to a better understanding of the biological functions of polyamines in plants.	2009	19828463
the structure of the ribosome with elongation factor g trapped in the posttranslocational state.	elongation factor g (ef-g) is a guanosine triphosphatase (gtpase) that plays a crucial role in the translocation of transfer rnas (trnas) and messenger rna (mrna) during translation by the ribosome. we report a crystal structure refined to 3.6 angstrom resolution of the ribosome trapped with ef-g in the posttranslocational state using the antibiotic fusidic acid. fusidic acid traps ef-g in a conformation intermediate between the guanosine triphosphate and guanosine diphosphate forms. the interac ...	2009	19833919
the crystal structure of the ribosome bound to ef-tu and aminoacyl-trna.	the ribosome selects a correct transfer rna (trna) for each amino acid added to the polypeptide chain, as directed by messenger rna. aminoacyl-trna is delivered to the ribosome by elongation factor tu (ef-tu), which hydrolyzes guanosine triphosphate (gtp) and releases trna in response to codon recognition. the signaling pathway that leads to gtp hydrolysis upon codon recognition is critical to accurate decoding. here we present the crystal structure of the ribosome complexed with ef-tu and amino ...	2009	19833920
v for victory--a v1-atpase structure revealed.		2009	19834508
production of cell-cell signalling molecules by bacteria isolated from human chronic wounds.	to (i) identify chronic wound bacteria and to test their ability to produce acyl-homoserine-lactones (ahls) and autoinducer-2 (ai-2) cell-cell signalling molecules and (ii) determine whether chronic wound debridement samples might contain these molecules.	2010	19840177
production of cell-cell signalling molecules by bacteria isolated from human chronic wounds.	to (i) identify chronic wound bacteria and to test their ability to produce acyl-homoserine-lactones (ahls) and autoinducer-2 (ai-2) cell-cell signalling molecules and (ii) determine whether chronic wound debridement samples might contain these molecules.	2010	19840177
crystal structure of the atpase domain of the human aaa+ protein paraplegin/spg7.	paraplegin is an m-aaa protease of the mitochondrial inner membrane that is linked to hereditary spastic paraplegias. the gene encodes an ftsh-homology protease domain in tandem with an aaa+ homology atpase domain. the protein is believed to form a hexamer that uses atpase-driven conformational changes in its aaa-domain to deliver substrate peptides to its protease domain. we present the crystal structure of the aaa-domain of human paraplegin bound to adp at 2.2 a. this enables assignment of the ...	2009	19841671
marine-derived metabolites of s-adenosylmethionine as templates for new anti-infectives.	s-adenosylmethionine (adomet) is a key biochemical co-factor whose proximate metabolites include methylated macromolecules (e.g., nucleic acids, proteins, phospholipids), methylated small molecules (e.g., sterols, biogenic amines), polyamines (e.g., spermidine, spermine), ethylene, and n-acyl-homoserine lactones. marine organisms produce numerous adomet metabolites whose novel structures can be regarded as lead compounds for anti-infective drug design.	2009	19841722
yeast aep3p is an accessory factor in initiation of mitochondrial translation.	initiation of protein synthesis in mitochondria and chloroplasts normally uses a formylated initiator methionyl-trna (fmet-trna(f)(met)). however, mitochondrial protein synthesis in saccharomyces cerevisiae can initiate with nonformylated met-trna(f)(met), as demonstrated in yeast mutants in which the nuclear gene encoding mitochondrial methionyl-trna formyltransferase (fmt1) has been deleted. the role of formylation of the initiator trna is not known, but in vitro formylation increases binding ...	2009	19843529
the structure of staphylococcus aureus phosphopantetheine adenylyltransferase in complex with 3'-phosphoadenosine 5'-phosphosulfate reveals a new ligand-binding mode.	bacterial phosphopantetheine adenylyltransferase (ppat) catalyzes the penultimate step in the coenzyme a (coa) biosynthetic pathway. it catalyzes the reversible transfer of an adenylyl group from atp to 4'-phosphopantetheine (ppant) to form dephospho-coa (dpcoa) and pyrophosphate. previous structural studies have revealed how several ligands are recognized by bacterial ppats. atp, adp, ppant and dpcoa bind to the same binding site in a highly similar manner, while coa binds to a partially overla ...	2009	19851003
crystallization and preliminary x-ray analysis of mannosyl-3-phosphoglycerate synthase from thermus thermophilus hb27.	mannosylglycerate (mg) is a compatible solute that is widespread in marine organisms that are adapted to hot environments, with its intracellular pool generally increasing in response to osmotic stress. these observations suggest that mg plays a relevant role in osmoadaptation and thermoadaptation. the pathways for the synthesis of mg have been characterized in a number of thermophilic and hyperthermophilic organisms. mannosyl-3-phosphoglycerate synthase (mpgs) is a key enzyme in the biosynthesi ...	2009	19851010
'rna walk' a novel approach to study rna-rna interactions between a small rna and its target.	in this study we describe a novel method to investigate the rna-rna interactions between a small rna and its target that we termed 'rna walk'. the method is based on uv-induced amt cross-linking in vivo followed by affinity selection of the hybrid molecules and mapping the intermolecular adducts by rt-pcr or real-time pcr. domains carrying the cross-linked adducts fail to efficiently amplify by pcr compared with non-cross-linked domains. this method was calibrated and used to study the interacti ...	2009	19854950
'rna walk' a novel approach to study rna-rna interactions between a small rna and its target.	in this study we describe a novel method to investigate the rna-rna interactions between a small rna and its target that we termed 'rna walk'. the method is based on uv-induced amt cross-linking in vivo followed by affinity selection of the hybrid molecules and mapping the intermolecular adducts by rt-pcr or real-time pcr. domains carrying the cross-linked adducts fail to efficiently amplify by pcr compared with non-cross-linked domains. this method was calibrated and used to study the interacti ...	2009	19854950
allosteric control of catalysis by the f loop of rna polymerase.	bacterial rna polymerases (rnaps) undergo coordinated conformational changes during catalysis. in particular, concerted folding of the trigger loop and rearrangements of the bridge helix at the rnap active center have been implicated in nucleotide addition and rnap translocation. at moderate temperatures, the rate of catalysis by rnap from thermophilic thermus aquaticus is dramatically reduced compared with its closest mesophilic relative, deinococcus radiodurans. here, we show that a part of th ...	2009	19855007
the crystal structure of the novobiocin biosynthetic enzyme novp: the first representative structure for the tylf o-methyltransferase superfamily.	novp is an s-adenosyl-l-methionine-dependent o-methyltransferase that catalyzes the penultimate step in the biosynthesis of the aminocoumarin antibiotic novobiocin. specifically, it methylates at 4-oh of the noviose moiety, and the resultant methoxy group is important for the potency of the mature antibiotic: previous crystallographic studies have shown that this group interacts directly with the target enzyme dna gyrase, which is a validated drug target. we have determined the high-resolution c ...	2010	19857499
the crystal structure of the novobiocin biosynthetic enzyme novp: the first representative structure for the tylf o-methyltransferase superfamily.	novp is an s-adenosyl-l-methionine-dependent o-methyltransferase that catalyzes the penultimate step in the biosynthesis of the aminocoumarin antibiotic novobiocin. specifically, it methylates at 4-oh of the noviose moiety, and the resultant methoxy group is important for the potency of the mature antibiotic: previous crystallographic studies have shown that this group interacts directly with the target enzyme dna gyrase, which is a validated drug target. we have determined the high-resolution c ...	2010	19857499
spermine synthase.	spermine is present in many organisms including animals, plants, some fungi, some archaea, and some bacteria. it is synthesized by spermine synthase, a highly specific aminopropyltransferase. this review describes spermine synthase structure, genetics, and function. structural and biochemical studies reveal that human spermine synthase is an obligate dimer. each monomer contains a c-terminal domain where the active site is located, a central linking domain that also forms the lid of the catalyti ...	2010	19859664
spermine synthase.	spermine is present in many organisms including animals, plants, some fungi, some archaea, and some bacteria. it is synthesized by spermine synthase, a highly specific aminopropyltransferase. this review describes spermine synthase structure, genetics, and function. structural and biochemical studies reveal that human spermine synthase is an obligate dimer. each monomer contains a c-terminal domain where the active site is located, a central linking domain that also forms the lid of the catalyti ...	2010	19859664
pharmacological targeting of the hsp70 chaperone.	the molecular chaperone, heat shock protein 70 (hsp70), acts at multiple steps in a protein's life cycle, including during the processes of folding, trafficking, remodeling and degradation. to accomplish these various tasks, the activity of hsp70 is shaped by a host of co-chaperones, which bind to the core chaperone and influence its functions. genetic studies have strongly linked hsp70 and its co-chaperones to numerous diseases, including cancer, neurodegeneration and microbial pathogenesis, ye ...	2009	19860737
structural and dynamic features of the mutt protein in the recognition of nucleotides with the mutagenic 8-oxoguanine base.	escherichia coli mutt hydrolyzes 8-oxo-dgtp to 8-oxo-dgmp, an event that can prevent the misincorporation of 8-oxoguanine opposite adenine in dna. of the several enzymes that recognize 8-oxoguanine, mutt exhibits high substrate specificity for 8-oxoguanine nucleotides; however, the structural basis for this specificity is unknown. the crystal structures of mutt in the apo and holo forms and in the binary and ternary forms complexed with the product 8-oxo-dgmp and 8-oxo-dgmp plus mn(2+), respecti ...	2010	19864691
structural and dynamic features of the mutt protein in the recognition of nucleotides with the mutagenic 8-oxoguanine base.	escherichia coli mutt hydrolyzes 8-oxo-dgtp to 8-oxo-dgmp, an event that can prevent the misincorporation of 8-oxoguanine opposite adenine in dna. of the several enzymes that recognize 8-oxoguanine, mutt exhibits high substrate specificity for 8-oxoguanine nucleotides; however, the structural basis for this specificity is unknown. the crystal structures of mutt in the apo and holo forms and in the binary and ternary forms complexed with the product 8-oxo-dgmp and 8-oxo-dgmp plus mn(2+), respecti ...	2010	19864691
kinetics of stop codon recognition by release factor 1.	recognition of stop codons by class i release factors is a fundamental step in the termination phase of protein synthesis. since premature termination is costly to the cell, release factors have to efficiently discriminate between stop and sense codons. to understand the mechanism of discrimination between stop and sense codons, we developed a new, pre-steady state kinetic assay to monitor the interaction of rf1 with the ribosome. our results show that rf1 associates with similar association rat ...	2009	19874047
crystal structure of the aspartyl-trna synthetase from entamoeba histolytica.	the crystal structure of the aspartyl-trna synthetase from the eukaryotic parasite entamoeba histolytica has been determined at 2.8aresolution. relative to homologous sequences, the e. histolytica protein contains a 43-residue insertion between the n-terminal anticodon binding domain and the c-terminal catalytic domain. the present structure reveals that this insertion extends an arm of the hinge region that has previously been shown to mediate interaction of aspartyl-trna synthetase with the co ...	2010	19874856
crystal structure of the aspartyl-trna synthetase from entamoeba histolytica.	the crystal structure of the aspartyl-trna synthetase from the eukaryotic parasite entamoeba histolytica has been determined at 2.8aresolution. relative to homologous sequences, the e. histolytica protein contains a 43-residue insertion between the n-terminal anticodon binding domain and the c-terminal catalytic domain. the present structure reveals that this insertion extends an arm of the hinge region that has previously been shown to mediate interaction of aspartyl-trna synthetase with the co ...	2010	19874856
proteomics-based refinement of deinococcus deserti genome annotation reveals an unwonted use of non-canonical translation initiation codons.	deinococcaceae are a family of extremely radiation-tolerant bacteria that are currently subjected to numerous studies aimed at understanding the molecular mechanisms for such radiotolerance. to achieve a comprehensive and accurate annotation of the deinococcus deserti genome, we performed an n terminus-oriented characterization of its proteome. for this, we used a labeling reagent, n-tris(2,4,6-trimethoxyphenyl)phosphonium acetyl succinimide, to selectively derivatize protein n termini. the larg ...	2010	19875382
proteomics-based refinement of deinococcus deserti genome annotation reveals an unwonted use of non-canonical translation initiation codons.	deinococcaceae are a family of extremely radiation-tolerant bacteria that are currently subjected to numerous studies aimed at understanding the molecular mechanisms for such radiotolerance. to achieve a comprehensive and accurate annotation of the deinococcus deserti genome, we performed an n terminus-oriented characterization of its proteome. for this, we used a labeling reagent, n-tris(2,4,6-trimethoxyphenyl)phosphonium acetyl succinimide, to selectively derivatize protein n termini. the larg ...	2010	19875382
the role of upf0157 in the folding of m. tuberculosis dephosphocoenzyme a kinase and the regulation of the latter by ctp.	targeting the biosynthetic pathway of coenzyme a (coa) for drug development will compromise multiple cellular functions of the tubercular pathogen simultaneously. structural divergence in the organization of the penultimate and final enzymes of coa biosynthesis in the host and pathogen and the differences in their regulation mark out the final enzyme, dephosphocoenzyme a kinase (coae) as a potential drug target.	2009	19876400
isolation and characterization of tirandamycins from a marine-derived streptomyces sp.	the novel dienoyl tetramic acids tirandamycin c (1) and tirandamycin d (2) with activity against vancomycin-resistant enterococcus faecalis were isolated from the marine environmental isolate streptomyces sp. 307-9, which also produces the previously identified compounds tirandamycins a (3) and b (4). spectroscopic analysis of 1 and 2 indicated structural similarity to 3 and 4, with differences only in the pattern of pendant oxygenation on the bicyclic ketal system. the isolation of these putati ...	2009	19883065
atp-induced conformational changes in hsp70: molecular dynamics and experimental validation of an in silico predicted conformation.	the 70 kda heat shock proteins (hsp70s) play important roles in preventing the misfolding of proteins and repairing damage under stress by coupling atp binding and hydrolysis to protein substrate release and binding, respectively. atp binding is believed to induce closing of the hsp70 nucleotide binding domain (nbd) around the nucleotide. we report here a combined computational-experimental study of this open-closed transition. all-atom molecular dynamics simulations were performed for isolated ...	2009	19883127
macromolecular micromovements: how rna polymerase translocates.	multi-subunit dna-dependent rna polymerases synthesize rna molecules thousands of nucleotides long. the reiterative reaction of nucleotide condensation occurs at rates of tens of nucleotides per second, invariably linked to the translocation of the enzyme along the dna template, or threading of the dna and the nascent rna molecule through the enzyme. reiteration of the nucleotide addition/translocation cycle without dissociation from the dna and rna requires both isomorphic and metamorphic confo ...	2009	19889534
direct evidence for nitrogen ligation to the high stability semiquinone intermediate in escherichia coli nitrate reductase a.	the membrane-bound heterotrimeric nitrate reductase a (narghi) catalyzes the oxidation of quinols in the cytoplasmic membrane of escherichia coli and reduces nitrate to nitrite in the cytoplasm. the enzyme strongly stabilizes a menasemiquinone intermediate at a quinol oxidation site (q(d)) located in the vicinity of the distal heme b(d). here molecular details of the interaction between the semiquinone radical and the protein environment have been provided using advanced multifrequency pulsed ep ...	2010	19892705
direct evidence for nitrogen ligation to the high stability semiquinone intermediate in escherichia coli nitrate reductase a.	the membrane-bound heterotrimeric nitrate reductase a (narghi) catalyzes the oxidation of quinols in the cytoplasmic membrane of escherichia coli and reduces nitrate to nitrite in the cytoplasm. the enzyme strongly stabilizes a menasemiquinone intermediate at a quinol oxidation site (q(d)) located in the vicinity of the distal heme b(d). here molecular details of the interaction between the semiquinone radical and the protein environment have been provided using advanced multifrequency pulsed ep ...	2010	19892705
molecular evolution of multisubunit rna polymerases: structural analysis.	comprehensive multiple sequence alignments of the multisubunit dna-dependent rna polymerase (rnap) large subunits, including the bacterial beta and beta' subunits and their homologs from archaebacterial rnaps, eukaryotic rnaps i-iii, nuclear-cytoplasmic large double-stranded dna virus rnaps, and plant plastid rnaps, were created [lane, w. j. and darst, s. a. (2009). molecular evolution of multisubunit rna polymerases: sequence analysis. in press]. the alignments were used to delineate sequence r ...	2010	19895816
molecular evolution of multisubunit rna polymerases: structural analysis.	comprehensive multiple sequence alignments of the multisubunit dna-dependent rna polymerase (rnap) large subunits, including the bacterial beta and beta' subunits and their homologs from archaebacterial rnaps, eukaryotic rnaps i-iii, nuclear-cytoplasmic large double-stranded dna virus rnaps, and plant plastid rnaps, were created [lane, w. j. and darst, s. a. (2009). molecular evolution of multisubunit rna polymerases: sequence analysis. in press]. the alignments were used to delineate sequence r ...	2010	19895816
molecular evolution of multisubunit rna polymerases: sequence analysis.	transcription in all cellular organisms is performed by multisubunit, dna-dependent rna polymerases that synthesize rna from dna templates. previous sequence and structural studies have elucidated the importance of shared regions common to all multisubunit rna polymerases. in addition, rna polymerases contain multiple lineage-specific domain insertions involved in protein-protein and protein-nucleic acid interactions. we have created comprehensive multiple sequence alignments using all available ...	2009	19895820
molecular evolution of multisubunit rna polymerases: sequence analysis.	transcription in all cellular organisms is performed by multisubunit, dna-dependent rna polymerases that synthesize rna from dna templates. previous sequence and structural studies have elucidated the importance of shared regions common to all multisubunit rna polymerases. in addition, rna polymerases contain multiple lineage-specific domain insertions involved in protein-protein and protein-nucleic acid interactions. we have created comprehensive multiple sequence alignments using all available ...	2009	19895820
function-biased choice of additives for optimization of protein crystallization - the case of the putative thioesterase pa5185 from pseudomonas aeruginosa pao1.	the crystal structure of pa5185, a putative thioesterase from pseudomonas aeruginosa strain pao1, was solved using multi-wavelength anomalous diffraction to 2.4 a. analysis of the structure and information about the putative function of the protein were used to optimize crystallization conditions. the crystal growth was optimized by applying additives with chemical similarity to a fragment of a putative pa5185 substrate (coa or its derivative). using new crystallization conditions containing thi ...	2008	19898606
trnas: cellular barcodes for amino acids.	the role of trna in translating the genetic code has received considerable attention over the last 50 years, and we now know in great detail how particular amino acids are specifically selected and brought to the ribosome in response to the corresponding mrna codon. over the same period, it has also become increasingly clear that the ribosome is not the only destination to which trnas deliver amino acids, with processes ranging from lipid modification to antibiotic biosynthesis all using aminoac ...	2010	19903480
cryptochromes--a potential magnetoreceptor: what do we know and what do we want to know?	cryptochromes have been suggested to be the primary magnetoreceptor molecules underlying light-dependent magnetic compass detection in migratory birds. here we review and evaluate (i) what is known about these candidate magnetoreceptor molecules, (ii) what characteristics cryptochrome molecules must fulfil to possibly underlie light-dependent, radical pair based magnetoreception, (iii) what evidence supports the involvement of cryptochromes in magnetoreception, and (iv) what needs to be addresse ...	2009	19906675
cryptochromes--a potential magnetoreceptor: what do we know and what do we want to know?	cryptochromes have been suggested to be the primary magnetoreceptor molecules underlying light-dependent magnetic compass detection in migratory birds. here we review and evaluate (i) what is known about these candidate magnetoreceptor molecules, (ii) what characteristics cryptochrome molecules must fulfil to possibly underlie light-dependent, radical pair based magnetoreception, (iii) what evidence supports the involvement of cryptochromes in magnetoreception, and (iv) what needs to be addresse ...	2009	19906675
two distinct regions in staphylococcus aureus gatcab guarantee accurate trna recognition.	in many prokaryotes the biosynthesis of the amide aminoacyl-trnas, gln-trna(gln) and asn-trna(asn), proceeds by an indirect route in which mischarged glu-trna(gln) or asp-trna(asn) is amidated to the correct aminoacyl-trna catalyzed by a trna-dependent amidotransferase (adt). two types of adts exist: bacteria, archaea and organelles possess heterotrimeric gatcab, while heterodimeric gatde occurs exclusively in archaea. bacterial gatcab and gatde recognize the first base pair of the acceptor stem ...	2010	19906721
two distinct regions in staphylococcus aureus gatcab guarantee accurate trna recognition.	in many prokaryotes the biosynthesis of the amide aminoacyl-trnas, gln-trna(gln) and asn-trna(asn), proceeds by an indirect route in which mischarged glu-trna(gln) or asp-trna(asn) is amidated to the correct aminoacyl-trna catalyzed by a trna-dependent amidotransferase (adt). two types of adts exist: bacteria, archaea and organelles possess heterotrimeric gatcab, while heterodimeric gatde occurs exclusively in archaea. bacterial gatcab and gatde recognize the first base pair of the acceptor stem ...	2010	19906721
crystal and solution structures of a prokaryotic m16b peptidase: an open and shut case.	the m16 family of zinc peptidases comprises a pair of homologous domains that form two halves of a "clam-shell" surrounding the active site. the m16a and m16c subfamilies form one class ("peptidasomes"): they degrade 30-70 residue peptides, and adopt both open and closed conformations. the eukaryotic m16b subfamily forms a second class ("processing proteases"): they adopt a single partly-open conformation that enables them to cleave signal sequences from larger proteins. here, we report the solu ...	2009	19913481
characterization of chlorophenol 4-monooxygenase (tftd) and nadh:fad oxidoreductase (tftc) of burkholderia cepacia ac1100.	burkholderia cepacia ac1100 completely degrades 2,4,5-trichlorophenol, in which an fadh(2)-dependent monooxygenase (tftd) and an nadh:fad oxidoreductase (tftc) catalyze the initial steps. tftd oxidizes 2,4,5-trichlorophenol (2,4,5-tcp) to 2,5-dichloro-p-benzoquinone, which is chemically reduced to 2,5-dichloro-p-hydroquinone (2,5-dichq). then, tftd oxidizes the latter to 5-chloro-2-hydroxy-p-benzoquinone. in those processes, tftc provides all the required fadh(2). we have determined the crystal ...	2010	19915006
characterization of chlorophenol 4-monooxygenase (tftd) and nadh:fad oxidoreductase (tftc) of burkholderia cepacia ac1100.	burkholderia cepacia ac1100 completely degrades 2,4,5-trichlorophenol, in which an fadh(2)-dependent monooxygenase (tftd) and an nadh:fad oxidoreductase (tftc) catalyze the initial steps. tftd oxidizes 2,4,5-trichlorophenol (2,4,5-tcp) to 2,5-dichloro-p-benzoquinone, which is chemically reduced to 2,5-dichloro-p-hydroquinone (2,5-dichq). then, tftd oxidizes the latter to 5-chloro-2-hydroxy-p-benzoquinone. in those processes, tftc provides all the required fadh(2). we have determined the crystal ...	2010	19915006
the linkage between ribosomal crystallography, metal ions, heteropolytungstates and functional flexibility.	crystallography of ribosomes, the universal cell nucleoprotein assemblies facilitating the translation of the genetic-code into proteins, met with severe problems owing to their large size, complex structure, inherent flexibility and high conformational variability. for the case of the small ribosomal subunit, which caused extreme difficulties, post crystallization treatment by minute amounts of a heteropolytungstate cluster allowed structure determination at atomic resolution. this cluster play ...	2008	19915655
the conserved lysine69 residue plays a catalytic role in mycobacterium tuberculosis shikimate dehydrogenase.	the shikimate pathway is an attractive target for the development of antitubercular agents because it is essential in mycobacterium tuberculosis, the causative agent of tuberculosis, but absent in humans. m. tuberculosis aroe-encoded shikimate dehydrogenase catalyzes the forth reaction in the shikimate pathway. structural and functional studies indicate that lysine69 may be involved in catalysis and/or substrate binding in m. tuberculosis shikimate dehydrogenase. investigation of the kinetic pro ...	2009	19917104
unusual diheme conformation of the heme-degrading protein from mycobacterium tuberculosis.	heme degradation plays a pivotal role in the availability of the essential nutrient, iron, in pathogenic bacteria. a previously unannotated protein from mycobacterium tuberculosis, rv3592, which shares homology to heme-degrading enzymes, has been identified. biochemical analyses confirm that rv3592, which we have termed mhud (mycobacterial heme utilization, degrader), is able to bind and degrade heme. interestingly, contrary to previously reported stoichiometry for the staphylococcus aureus heme ...	2010	19917297
unusual diheme conformation of the heme-degrading protein from mycobacterium tuberculosis.	heme degradation plays a pivotal role in the availability of the essential nutrient, iron, in pathogenic bacteria. a previously unannotated protein from mycobacterium tuberculosis, rv3592, which shares homology to heme-degrading enzymes, has been identified. biochemical analyses confirm that rv3592, which we have termed mhud (mycobacterial heme utilization, degrader), is able to bind and degrade heme. interestingly, contrary to previously reported stoichiometry for the staphylococcus aureus heme ...	2010	19917297
analysis of acyclic nucleoside modifications in sirnas finds sensitivity at position 1 that is restored by 5'-terminal phosphorylation both in vitro and in vivo.	small interfering rnas (sirnas) are short, double-stranded rnas that use the endogenous rnai pathway to mediate gene silencing. phosphorylation facilitates loading of a sirna into the ago2 complex and subsequent cleavage of the target mrna. in this study, 2', 3' seco nucleoside modifications, which contain an acylic ribose ring and are commonly called unlocked nucleic acids (unas), were evaluated at all positions along the guide strand of a sirna targeting apolipoprotein b (apob). una modificati ...	2010	19917641
analysis of acyclic nucleoside modifications in sirnas finds sensitivity at position 1 that is restored by 5'-terminal phosphorylation both in vitro and in vivo.	small interfering rnas (sirnas) are short, double-stranded rnas that use the endogenous rnai pathway to mediate gene silencing. phosphorylation facilitates loading of a sirna into the ago2 complex and subsequent cleavage of the target mrna. in this study, 2', 3' seco nucleoside modifications, which contain an acylic ribose ring and are commonly called unlocked nucleic acids (unas), were evaluated at all positions along the guide strand of a sirna targeting apolipoprotein b (apob). una modificati ...	2010	19917641
molecular modeling of the bifunctional enzyme udp-glcnac 2-epimerase/mannac kinase and predictions of structural effects of mutations associated with hibm and sialuria.	the bifunctional enzyme udp-glcnac 2-epimerase/ mannac kinase (gne/mnk), encoded by the gne gene, catalyzes the first two committed, rate-limiting steps in the biosynthesis of n-acetylneuraminic acid (sialic acid). gne/mnk is feedback inhibited by binding of the downstream product, cmp-sialic acid in its allosteric site. gne mutations can result in two human disorders, hereditary inclusion body myopathy (hibm) or sialuria. so far, no active site geometry predictions or conformational transitions ...	2010	19917666
molecular modeling of the bifunctional enzyme udp-glcnac 2-epimerase/mannac kinase and predictions of structural effects of mutations associated with hibm and sialuria.	the bifunctional enzyme udp-glcnac 2-epimerase/ mannac kinase (gne/mnk), encoded by the gne gene, catalyzes the first two committed, rate-limiting steps in the biosynthesis of n-acetylneuraminic acid (sialic acid). gne/mnk is feedback inhibited by binding of the downstream product, cmp-sialic acid in its allosteric site. gne mutations can result in two human disorders, hereditary inclusion body myopathy (hibm) or sialuria. so far, no active site geometry predictions or conformational transitions ...	2010	19917666
h135a controls the redox activity of the sco copper center. kinetic and spectroscopic studies of the his135ala variant of bacillus subtilis sco.	sco-like proteins contain copper bound by two cysteines and a histidine residue. although their function is still incompletely understood, there is a clear involvement with the assembly of cytochrome oxidases that contain the cu(a) center in subunit 2, possibly mediating the transfer of copper into the cu(a) binuclear site. we are investigating the reaction chemistry of bsco, the homologue from bacillus subtilis. our studies have revealed that bsco behaves more like a redox protein than a metall ...	2009	19921776
solvent-assisted slow conversion of a dithiazole derivative produces a competitive inhibitor of peptide deformylase.	due to its potential as an antibiotic target, e. coli peptide deformylase (pdf(ec)) serves as a model enzyme system for inhibitor design. while investigating the structural-functional and inhibitory features of this enzyme, we unexpectedly discovered that 2-amino-5-mercapto-1,3,4-thiadiazole (amt) served as a slow-binding inhibitor of pdf(ec) when the above compound was dissolved only in dimethylformamide (dmf), but not in any other solvent, and allowed to age. the time dependent inhibitory pote ...	2010	19922819
solvent-assisted slow conversion of a dithiazole derivative produces a competitive inhibitor of peptide deformylase.	due to its potential as an antibiotic target, e. coli peptide deformylase (pdf(ec)) serves as a model enzyme system for inhibitor design. while investigating the structural-functional and inhibitory features of this enzyme, we unexpectedly discovered that 2-amino-5-mercapto-1,3,4-thiadiazole (amt) served as a slow-binding inhibitor of pdf(ec) when the above compound was dissolved only in dimethylformamide (dmf), but not in any other solvent, and allowed to age. the time dependent inhibitory pote ...	2010	19922819
structure of a eukaryotic nonribosomal peptide synthetase adenylation domain that activates a large hydroxamate amino acid in siderophore biosynthesis.	nonribosomal peptide synthetases (nrpss) are large, multidomain proteins that are involved in the biosynthesis of an array of secondary metabolites. we report the structure of the third adenylation domain from the siderophore-synthesizing nrps, sidn, from the endophytic fungus neotyphodium lolii. this is the first structure of a eukaryotic nrps domain, and it reveals a large binding pocket required to accommodate the unusual amino acid substrate, n(delta)-cis-anhydromevalonyl-n(delta)-hydroxy-l- ...	2010	19923209
structure of a eukaryotic nonribosomal peptide synthetase adenylation domain that activates a large hydroxamate amino acid in siderophore biosynthesis.	nonribosomal peptide synthetases (nrpss) are large, multidomain proteins that are involved in the biosynthesis of an array of secondary metabolites. we report the structure of the third adenylation domain from the siderophore-synthesizing nrps, sidn, from the endophytic fungus neotyphodium lolii. this is the first structure of a eukaryotic nrps domain, and it reveals a large binding pocket required to accommodate the unusual amino acid substrate, n(delta)-cis-anhydromevalonyl-n(delta)-hydroxy-l- ...	2010	19923209
structure of an n-terminally truncated nudix hydrolase dr2204 from deinococcus radiodurans.	nudix pyrophosphatases are a well represented protein family in the deinococcus radiodurans genome. these hydrolases, which are known to be enzymatically active towards nucleoside diphosphate derivatives, play a role in cleansing the cell pool of potentially deleterious damage products. here, the structure of dr2204, the only adp-ribose pyrophosphatase in the d. radiodurans genome that is known to be active towards flavin adenosine dinucleotide (fad), is presented at 2.0 angstrom resolution.	2009	19923723
expression, purification and crystallization of an archaeal-type phosphoenolpyruvate carboxylase.	an archaeal-type phosphoenolpyruvate carboxylase (pepca) from clostridium perfringens has been expressed in escherichia coli in a soluble form with an amino-terminal his tag. the recombinant protein is enzymatically active and two crystal forms have been obtained. complete diffraction data extending to 3.13 angstrom resolution have been measured from a crystal soaked in kau(cn)(2), using radiation at a wavelength just above the au l(iii) edge. the asymmetric unit contains two tetramers of pepca.	2009	19923749
the ligand-free state of the tpp riboswitch: a partially folded rna structure.	riboswitches are elements of mrna that regulate gene expression by undergoing structural changes upon binding of small ligands. although the structures of several riboswitches have been solved with their ligands bound, the ligand-free states of only a few riboswitches have been characterized. the ligand-free state is as important for the functionality of the riboswitch as the ligand-bound form, but the ligand-free state is often a partially folded structure of the rna, with conformational hetero ...	2009	19925806
the ligand-free state of the tpp riboswitch: a partially folded rna structure.	riboswitches are elements of mrna that regulate gene expression by undergoing structural changes upon binding of small ligands. although the structures of several riboswitches have been solved with their ligands bound, the ligand-free states of only a few riboswitches have been characterized. the ligand-free state is as important for the functionality of the riboswitch as the ligand-bound form, but the ligand-free state is often a partially folded structure of the rna, with conformational hetero ...	2009	19925806
solution nmr structures of proteins vpa0419 from vibrio parahaemolyticus and yiis from shigella flexneri provide structural coverage for protein domain family pfam 04175.		2010	19927321
solution nmr structures of proteins vpa0419 from vibrio parahaemolyticus and yiis from shigella flexneri provide structural coverage for protein domain family pfam 04175.		2010	19927321
communication between r481 and cu(b) in cytochrome bo(3) ubiquinol oxidase from escherichia coli.	the r481 residue of cytochrome bo(3) ubiquinol oxidase from e. coli is highly conserved in the heme-copper oxidase superfamily. it has been postulated to serve as part of a proton loading site that regulates proton translocation across the protein matrix of the enzyme. along these lines, proton pumping efficiency has been demonstrated to be abolished in many r481 mutants. however, r481q in bo(3) from e. coli has been shown to be fully functional, implying that the positive charge of the arginine ...	2009	19928831