Abstract:
:The sequences coding for DNA[cytosine-N4]methyltransferases MvaI (from Micrococcus varians RFL19) and Cfr9I (from Citrobacter freundii RFL9) have been determined. The predicted methylases are proteins of 454 and 300 amino acids, respectively. Primary structure comparison of M.Cfr9I and another m4C-forming methylase, M.Pvu II, revealed extended regions of homology. The sequence comparison of the three DNA[cytosine-N4]-methylases using originally developed software revealed two conserved patterns, DPF-GSGT and TSPPY, which were found similar also to those of adenine and DNA[cytosine-C5]-methylases. These data provided a basis for global alignment and classification of DNA-methylase sequences. Structural considerations led us to suggest that the first region could be the binding site of AdoMet, while the second is thought to be directly involved in the modification of the exocyclic amino group.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Klimasauskas S,Timinskas A,Menkevicius S,Butkienè D,Butkus V,Janulaitis Adoi
10.1093/nar/17.23.9823subject
Has Abstractpub_date
1989-12-11 00:00:00pages
9823-32issue
23eissn
0305-1048issn
1362-4962journal_volume
17pub_type
杂志文章abstract::A multipurpose plasmid, pUR 250, has been constructed. It contains seven unique cloning sites (Hind III, Xba I, Sal I, Acc I, Hinc II, BamH I and EcoR I) in a small region of its lac Z gene part. Insertion of foreign DNA into the plasmid can be easily detected. Plasmid DNA isolated from a clone by a rapid method can b...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.19.5765
更新日期:1982-10-11 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::The positions of the trfA and trfB promoters of broad host range IncP plasmid RK2 (identical to RP1, RP4, R68 and R18 ) were identified by RNA polymerase protection studies, and the nucleotide sequences of the promoter regions determined. A mutation within the trfA promoter sequence is associated with loss of kilD act...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.8.3619
更新日期:1984-04-25 00:00:00
abstract::MobA protein, encoded by the broad host-range plasmid R1162, is required for conjugal mobilization of this plasmid. The protein is an essential part of the relaxosome, and is also necessary for the termination of strand transfer. In vitro, MobA is a nuclease specific for one of the two DNA strands of the origin of tra...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.19.4563
更新日期:1993-09-25 00:00:00
abstract::Here, we describe two freely available web servers for molecular docking. The PatchDock method performs structure prediction of protein-protein and protein-small molecule complexes. The SymmDock method predicts the structure of a homomultimer with cyclic symmetry given the structure of the monomeric unit. The inputs t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki481
更新日期:2005-07-01 00:00:00
abstract::The efficiency of Nucleotide Excision Repair (NER)process is crucial for maintaining genomic integrity because in many organisms, including humans, it represents the only system able to repair a wide range of DNA damage. The aim of the work was to investigate whether the efficiency of the repair of photoproducts induc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv081
更新日期:2015-02-27 00:00:00
abstract::We have determined the nucleotide sequence of the major species of E. coli tRNASer and of a minor species having the same GGA anticodon. These two tRNAs should recognize the UCC and UCU codons, the most widely used codons for serine in the highly expressed genes of E. coli. The two sequences differ in only one positio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.15.5697
更新日期:1985-08-12 00:00:00
abstract::G-DNA, a polymorphic family of four-stranded DNA structures, has been proposed to play roles in a variety of biological processes including telomere function, meiotic recombination and gene regulation. Here we report the purification and cloning of TGP1, a G-DNA specific binding protein from Tetrahymena thermophila. T...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.7.1613
更新日期:1998-04-01 00:00:00
abstract::The discoidin proteins of Dictyostelium discoideum are highly expressed during development. The Disc I gamma promoter allows the regulation of heterologous protein expression by experimental conditions. We report conditions under which the promoter activity is efficiently repressed during growth in the wildtype strain...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.6.1397
更新日期:1993-03-25 00:00:00
abstract::The thymine analog 5-chlorouridine, first reported in the 1950s as anti-tumor agent, is known as an effective mutagen, clastogen and toxicant as well as an effective inducer of sister-chromatid exchange. Recently, the first microorganism with a chemically different genome was reported; the selected Escherichia coli st...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1316
更新日期:2013-02-01 00:00:00
abstract::Given the many roles proposed for Mg2+ in nucleic acids, it is essential to accurately determine their binding modes. Here, we surveyed the PDB to classify Mg2+ inner-sphere binding patterns to nucleobase imine N1/N3/N7 atoms. Among those, purine N7 atoms are considered to be the best nucleobase binding sites for diva...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1175
更新日期:2017-01-25 00:00:00
abstract::Our database on large ribosomal subunit RNA contained 334 sequences in July, 1995. All sequences in the database are aligned, taking into account secondary structure. The aligned sequences are provided, together with incorporated secondary structure information, in several computer-readable formats. These data can eas...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.1.92
更新日期:1996-01-01 00:00:00
abstract::Protein structures often show similarities to another which would not be seen at the sequence level. Given the coordinates of a protein chain, the SALAMI server at www.zbh.uni-hamburg.de/salami will search the protein data bank and return a set of similar structures without using sequence information. The results page...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp431
更新日期:2009-07-01 00:00:00
abstract::Rap1 is an essential DNA-binding factor from the yeast Saccharomyces cerevisiae involved in transcription and telomere maintenance. Its binding to DNA targets Rap1 at particular loci, and may optimize its ability to form functional macromolecular assemblies. It is a modular protein, rich in large potentially unfolded ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr1166
更新日期:2012-04-01 00:00:00
abstract::Telomeres play a central role in human cancer, cardiovascular aging and possibly longevity. However, present methods to measure telomere length are fraught with shortcomings that limit their use. Here, we describe a novel method to measure the relative telomere DNA content by dot blot analysis. In each dot, the DNA co...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr235
更新日期:2011-07-01 00:00:00
abstract::RegulonDB is a DataBase that integrates biological knowledge of the mechanisms that regulate the transcription initiation in Escherichia coli , as well as knowledge on the organization of the genes and regulatory signals into operons in the chromosome. The operon is the basic structure used in RegulonDB to describe th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.1.55
更新日期:1998-01-01 00:00:00
abstract::Transcription of transfer RNA genes by RNA polymerase III (Pol III) is controlled by general factors, TFIIIB and TFIIIC, and a negative regulator, Maf1. Here we report the interplay between TFIIIC and Maf1 in controlling Pol III activity upon the physiological switch of yeast from fermentation to respiration. TFIIIC d...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky656
更新日期:2018-10-12 00:00:00
abstract::X-linked agammaglobulinemia (XLA) is an immunodeficiency caused by mutations in the gene coding for Bruton's agammaglobulinemia tyrosine kinase (BTK). A database (BTKbase) of BTK mutations has been compiled and the recent update lists 368 entries from 318 unrelated families showing 228 unique molecular events. In addi...
journal_title:Nucleic acids research
pub_type: 杂志文章,多中心研究
doi:10.1093/nar/25.1.166
更新日期:1997-01-01 00:00:00
abstract::By successively assembling genetic parts such as BioBrick according to grammatical models, complex genetic constructs composed of dozens of functional blocks can be built. However, usually every category of genetic parts includes a few or many parts. With increasing quantity of genetic parts, the process of assembling...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx859
更新日期:2017-12-15 00:00:00
abstract::Besides orthologs of other eukaryotic mismatch-repair (MMR) proteins, plants encode MSH7, a paralog of MSH6. The Arabidopsis thaliana recognition heterodimers AtMSH2*MSH6 (AtMutSalpha) and AtMSH2*MSH3 (AtMutSbeta) were previously found to bind the same subsets of mismatches as their counterparts in other eukaryotes--r...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg780
更新日期:2003-10-15 00:00:00
abstract::We updated the plant transcription factor (TF) database to version 2.0 (PlantTFDB 2.0, http://planttfdb.cbi.pku.edu.cn) which contains 53,319 putative TFs predicted from 49 species. We made detailed annotation including general information, domain feature, gene ontology, expression pattern and ortholog groups, as well...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1141
更新日期:2011-01-01 00:00:00
abstract::The miRNA Registry provides a service for the assignment of miRNA gene names prior to publication. A comprehensive and searchable database of published miRNA sequences is accessible via a web interface (http://www.sanger.ac.uk/Software/Rfam/mirna/), and all sequence and annotation data are freely available for downloa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh023
更新日期:2004-01-01 00:00:00
abstract::This article describes recent developments of Europe PMC (http://europepmc.org), the leading database for life science literature. Formerly known as UKPMC, the service was rebranded in November 2012 as Europe PMC to reflect the scope of the funding agencies that support it. Several new developments have enriched Europ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1061
更新日期:2015-01-01 00:00:00
abstract::Rotaviruses are a major cause of acute, often fatal, gastroenteritis in infants and young children world-wide. Virions contain an 11 segment double-stranded RNA genome. Little is known about the cis-acting sequences and structural elements of the viral RNAs. Using a database of 1621 full-length sequences of mammalian ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq663
更新日期:2010-11-01 00:00:00
abstract::The transcriptional shift from repression to activation of target genes is crucial for the fidelity of Notch responses through incompletely understood mechanisms that likely involve chromatin-based control. To activate silenced genes, repressive chromatin marks are removed and active marks must be acquired. Histone H3...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw105
更新日期:2016-06-02 00:00:00
abstract::Reverse transcription of HIV-1 RNA is initiated from the 3' end of a tRNA3Lys molecule annealed to the primer binding site (PBS). An additional interaction between the anticodon loop of tRNA3Lys and a viral A-rich loop is required for efficient initiation of reverse transcription of the HIV-1 MAL isolate. In the HIV-1...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg754
更新日期:2003-10-01 00:00:00
abstract::Cells internalized synthetic oligonucleotides (oligos) in culture. The hybridization of these molecules to target RNA in the living cell was subsequently detected and characterized after fixation of the cells, with or without previous detergent extraction. Hybridized oligo was distinguished from free oligo in the cell...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.24.4946
更新日期:1995-12-25 00:00:00
abstract::A small family of DNA sequences is rearranged during the development of the somatic nucleus in Tetrahymena. The family is defined by 266 bp of highly conserved sequence which restriction mapping, hybridization and sequence analysis have shown is shared by a cloned micronuclear fragment and three sequences which consti...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.20.8007
更新日期:1986-10-24 00:00:00
abstract::The MalaCards human disease database (http://www.malacards.org/) is an integrated compendium of annotated diseases mined from 68 data sources. MalaCards has a web card for each of ∼20 000 disease entries, in six global categories. It portrays a broad array of annotation topics in 15 sections, including Summaries, Symp...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gkw1012
更新日期:2017-01-04 00:00:00
abstract::The ability of Deinococcus radiodurans to recover from extensive DNA damage is due in part to its ability to efficiently repair its genome, even following severe fragmentation by hundreds of double-strand breaks. The single-strand annealing pathway plays an important role early during the recovery process, making use ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt759
更新日期:2013-11-01 00:00:00