Abstract：
:Using the quenched flow technique the mechanism of seryl tRNA synthetase action has been investigated with respect to the presteady state kinetics of individual steps. Under conditions where the strong binding sites of the enzyme are nearly saturated and the steady state turnover number is about 1 s-1, rate constants of four different processes have been determined: steps connected with substrate associations are relatively slow (12 s-1 for the entire process); activation of serine is the rate determining step (about 1.2 s-1 in presence of tRNASer); whereas the transfer of serine onto tRNASer (35 s-1) and the dissociation of seryl tRNASer (70 s-1) are fast. Similar kinetic parameter seem to hold also for the steady state reactions. This conclusion is based on a detailed study of the substrate, product, and Mg2+ concentration dependence of the transfer reaction. The results also indicate that a second serine binding site is operative. Since the transfer of serine from a preformed adenylate complex onto tRNASer is fast, seryl adenylate seems to be a kinetically competent intermediate of the aminoacylation reaction although, of course, alternative mechanisms cannot be excluded.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Dibbelt L,Pachmann U,Zachau HGdoi
10.1093/nar/8.17.4021subject
Has Abstractpub_date
1980-09-11 00:00:00pages
4021-39issue
17eissn
0305-1048issn
1362-4962journal_volume
8pub_type
杂志文章abstract：:Polyketide synthases (PKSs) catalyze biosynthesis of a diverse family of pharmaceutically important secondary metabolites. Bioinformatics analysis of sequence and structural features of PKS proteins plays a crucial role in discovery of new natural products by genome mining, as well as in design of novel secondary meta...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq340
更新日期：2010-07-01 00:00:00
abstract：:Ovarian poly (A) + RNA from Xenopus laevis and Xenopus borealis was used to construct two cDNA libraries which were screened for histone sequences. cDNA clones to H4 mRNA were obtained from both species and an H3 cDNA clone from Xenopus laevis. The complete DNA sequences of these clones have been determined and are pr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.12.3769
更新日期：1982-06-25 00:00:00
abstract：:DrugCentral (http://drugcentral.org) is an open-access online drug compendium. DrugCentral integrates structure, bioactivity, regulatory, pharmacologic actions and indications for active pharmaceutical ingredients approved by FDA and other regulatory agencies. Monitoring of regulatory agencies for new drugs approvals ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw993
更新日期：2017-01-04 00:00:00
abstract：:Nucleic acid triplexes may regulate many important biological processes. Persistent accumulation of the oncogenic 7-kb long noncoding RNA MALAT1 is dependent on an unusually long intramolecular triple helix. This triplex structure is positioned within a conserved ENE (element for nuclear expression) motif at the lncRN...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky1171
更新日期：2019-02-20 00:00:00
abstract：:Proteomic and RNomic approaches have identified many components of different ribonucleoprotein particles (RNPs), yet still little is known about the organization and protein proximities within these heterogeneous and highly dynamic complexes. Here we describe a targeted cross-linking approach, which combines cross-lin...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv1366
更新日期：2016-02-18 00:00:00
abstract：:Metagenomics has been employed to systematically sequence, classify, analyze and manipulate the entire genetic material isolated from environmental samples. Finding genes within metagenomic sequences remains a formidable challenge, and noncoding RNA genes other than those encoding rRNA and tRNA are not well annotated ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm057
更新日期：2007-01-01 00:00:00
abstract：:As a trial practical application, we have applied optimized microfabricated electrophoresis devices, combined with enzymatic mutation detection methods, to the determination of single nucleotide polymorphism (SNP) sites in the p53 suppressor gene. Using clinical samples, we have achieved robust assays with quality fac...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.9.e43
更新日期：2000-05-01 00:00:00
abstract：:Spliceosomes are assembled in stages. The first stage forms complex E, which is characterized by the presence of U1 snRNPs base-paired to the 5' splice site, components recognizing the 3' splice site and proteins thought to connect them. The splice sites are held in close proximity and the pre-mRNA is committed to spl...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks322
更新日期：2012-08-01 00:00:00
abstract：:The gene encoding myelin basic protein (MBP) contains multiple activator sequences spanning upstream of its transcriptional initiation site which differentially promote transcription in glial cells. The proximal activator sequence, designated MB1, activates transcription in a glial cell type specific manner. This sequ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.3.545
更新日期：1992-02-11 00:00:00
abstract：:Evidence has emerged that repair of clustered DNA lesions may be compromised, possibly leading to the formation of double-strand breaks (DSB) and, thus, to deleterious events. The first repair event occurring at a multiply damaged site (MDS) is of major importance and will largely contribute to the hazardousness of MD...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm190
更新日期：2007-01-01 00:00:00
abstract：:The DNA sequence of a 225.4 kilobase segment of the Escherichia coli K-12 genome is described here, from 76.0 to 81.5 minutes on the genetic map. This brings the total of contiguous sequence from the E.coli genome project to 725.1 kb (76.0 to 92.8 minutes). We found 191 putative coding genes (ORFs) of which 72 genes w...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.13.2576
更新日期：1994-07-11 00:00:00
abstract：:Current DNA assembly methods for preparing highly purified linear subassemblies require complex and time-consuming in vitro manipulations that hinder their ability to construct megabase-sized DNAs (e.g. synthetic genomes). We have developed a new method designated 'CasHRA (Cas9-facilitated Homologous Recombination Ass...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw475
更新日期：2016-08-19 00:00:00
abstract：:The intron 2 of the murine thymidine kinase (TK) gene was observed to contain two DNase hypersensitive site. In vitro footprinting experiments indicated specific binding sites for nuclear proteins which were characterized within the sequence of intron 2. Two GC boxes (binding sites for transcription factor SP1) and tw...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.24.6805
更新日期：1991-12-25 00:00:00
abstract：:Transcription factors (TFs) regulate gene expression by binding to short DNA sequence motifs, yet their binding specificities alone cannot explain how certain TFs drive a diversity of biological processes. In order to investigate the factors that control the functions of the pleiotropic TF STAT3, we studied its genome...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks1300
更新日期：2013-02-01 00:00:00
abstract：:Endonuclease III from Escherichia coli, yeast (yNtg1p and yNtg2p) and human and E.coli endonuclease VIII have a wide substrate specificity, and recognize oxidation products of both thymine and cytosine. DNA containing single dihydrouracil (DHU) and tandem DHU lesions were used as substrates for these repair enzymes. I...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.2.407
更新日期：2001-01-15 00:00:00
abstract：:RNA pseudoknots are functional structure elements with key roles in viral and cellular processes. Prediction of a pseudoknotted minimum free energy structure is an NP-complete problem. Practical algorithms for RNA structure prediction including restricted classes of pseudoknots suffer from high runtime and poor accura...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq021
更新日期：2010-04-01 00:00:00
abstract：:Many lists containing biological identifiers, such as gene lists, have been generated in various genomics projects. Identifying the overlap among gene lists can enable us to understand the similarities and differences between the data sets. Here, we present an interactome network-based web application platform named N...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku331
更新日期：2014-07-01 00:00:00
abstract：:Enzymes of intermediary metabolism are often reported to have moonlighting functions as RNA-binding proteins and have regulatory roles beyond their primary activities. Human serine hydroxymethyltransferase (SHMT) is essential for the one-carbon metabolism, which sustains growth and proliferation in normal and tumour c...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz129
更新日期：2019-05-07 00:00:00
abstract：:The distribution patterns of shared short repetitive motifs in the expansion segments of the large subunit rRNA genes of different species show that these segments are coevolving as a set and that in two examined vertebrate species the RNA secondary structures are conserved as a consequence of runs of motifs in one re...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.20.5949
更新日期：1990-10-25 00:00:00
abstract：:The DNA-binding specificity and affinity of the dimeric human transcription factor (TF) STAT1, were assessed by total internal reflectance fluorescence protein-binding microarrays (TIRF-PBM) to evaluate the effects of protein phosphorylation, higher-order polymerization and small-molecule inhibition. Active, phosphory...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks1085
更新日期：2013-01-01 00:00:00
abstract：:Synthesis and radioiodination of a stannyl oligodeoxyribonucleotide were undertaken to evaluate a gamma ray emitting ODN ligand for thrombus imaging in vivo . Synthesis of the ODN was based on modified automatedbeta-cyanoethyl phosphoramidite chemistry with an organotin nucleoside (dU*) coupled to a thrombin binding a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.14.2897
更新日期：1997-07-15 00:00:00
abstract：:The hexamer (m5 dC-dG)3 has been synthesized and its three-dimensional structure determined by a single crystal X-ray diffraction analysis. The structure has been refined to a final R value of 15.6% at 1.3 A resolution. The molecule forms a left-handed Z-DNA helix which is similar to the unmethylated Z-DNA structure. ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.23.7879
更新日期：1982-12-11 00:00:00
abstract：:Radioactive iodine has been used to probe the relative reactivities of nucleosomal H4 tyrosine residues under various conditions of subphysiological ionic strength. We observe that tyrosine 72 of H4, which is not reactive over the range 20-150 mM NaCl, becomes the predominant site of iodination within H4 when nucleoso...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.17.4367
更新日期：1981-09-11 00:00:00
abstract：:PrankWeb is an online resource providing an interface to P2Rank, a state-of-the-art method for ligand binding site prediction. P2Rank is a template-free machine learning method based on the prediction of local chemical neighborhood ligandability centered on points placed on a solvent-accessible protein surface. Points...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz424
更新日期：2019-07-02 00:00:00
abstract：:Transcription of the human adenovirus 5 genome in transformed rat embryo cells (DFK3) was investigated using two different approaches. Preferential digestion of transcribed viral sequences by DNase I was analysed using kinetics of renaturation of 32P-labeled Ad5 HpaI restriction fragments in the presence of material w...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/5.1.1
更新日期：1978-01-01 00:00:00
abstract：:A theoretical approach for linkage mapping the genome of any higher eukaryote is described. It uses the polymerase chain reaction, oligonucleotides of random sequence and single haploid cells. Markers are defined and then the DNA of a single sperm is broken at random (eg by gamma-rays) and physically split into 3 aliq...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.17.6795
更新日期：1989-09-12 00:00:00
abstract：:Many microRNAs (miRNAs) are co-regulated during the same physiological process but the underlying cellular logic is often little understood. The conserved, immunomodulatory miRNAs miR-146 and miR-155, for instance, are co-induced in many cell types in response to microbial lipopolysaccharide (LPS) to feedback-repress ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks1030
更新日期：2013-01-07 00:00:00
abstract：:A fundamental problem with applying Consensus, Weight-Matrix or hidden Markov models as search tools for biosequences is that there is no way to know, from the model, if the modeled sequences display any dependencies between positional identities. In some instances, these dependencies are crucial in correctly acceptin...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki374
更新日期：2005-07-01 00:00:00
abstract：:The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) is Europe's primary resource for nucleotide sequence information. With the growing volume and diversity of public sequencing data comes the need for increased sophistication in data organisation, presentation and search services so as to maximise its disc...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku1129
更新日期：2015-01-01 00:00:00
abstract：:Yaf9 is an integral part of the NuA4 acetyltransferase and the SWR1 chromatin remodeling complexes. Here, we show that Yaf9 associates with acetylated histone H3 with high preference for H3K27ac. The crystal structure of the Yaf9 YEATS domain bound to the H3K27ac peptide reveals that the sequence C-terminal to K27ac s...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx1151
更新日期：2018-01-09 00:00:00
