Abstract:
:PDB-REPRDB is a database of representative protein chains from the Protein Data Bank (PDB). Started at the Real World Computing Partnership (RWCP) in August 1997, it developed to the present system of PDB-REPRDB. In April 2001, the system was moved to the Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST) (http://www.cbrc.jp/); it is available at http://www.cbrc.jp/pdbreprdb/. The current database includes 33 368 protein chains from 16 682 PDB entries (1 September, 2002), from which are excluded (a) DNA and RNA data, (b) theoretically modeled data, (c) short chains (1<40 residues), or (d) data with non-standard amino acid residues at all residues. The number of entries including membrane protein structures in the PDB has increased rapidly with determination of numbers of membrane protein structures because of improved X-ray crystallography, NMR, and electron microscopic experimental techniques. Since many protein structure studies must address globular and membrane proteins separately, this new elimination factor, which excludes membrane protein chains, is introduced in the PDB-REPRDB system. Moreover, the PDB-REPRDB system for membrane protein chains begins at the same URL. The current membrane database includes 551 protein chains, including membrane domains in the SCOP database of release 1.59 (15 May, 2002).
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Noguchi T,Akiyama Ydoi
10.1093/nar/gkg022keywords:
subject
Has Abstractpub_date
2003-01-01 00:00:00pages
492-3issue
1eissn
0305-1048issn
1362-4962journal_volume
31pub_type
杂志文章abstract::The DNA sequence was determined for the narL gene of Escherichia coli. This gene is involved in global regulation of a number of nitrate controlled genes including frdABCD, tor, narGHJI, and adhE which are associated with bacterial respiration and fermentation. Comparison of the deduced amino acid sequence of narL to ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.5.1965
更新日期:1989-03-11 00:00:00
abstract::The Agrobacterium tumefaciens Ti plasmid contains at least six transcriptional units (designated vir loci) which are essential for efficient crown gall tumorigenesis. Mutations in one of these loci, virE, result in a sharply attenuated virulence phenotype. In the present communication, we have analyzed the virE operon...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.2.825
更新日期:1987-01-26 00:00:00
abstract::The database of molecular motions, MolMovDB (http://molmovdb.org), has been in existence for the past decade. It classifies macromolecular motions and provides tools to interpolate between two conformations (the Morph Server) and predict possible motions in a single structure. In 2005, we expanded the services offered...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj046
更新日期:2006-01-01 00:00:00
abstract::Functional crosstalk between histone modifications and chromatin remodeling has emerged as a key regulatory mode of transcriptional control during cell fate decisions, but the underlying mechanisms are not fully understood. Here we discover an HRP2-DPF3a-BAF epigenetic pathway that coordinates methylated histone H3 ly...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa441
更新日期:2020-07-09 00:00:00
abstract::Bacteria belonging to the class Mollicutes were among the first ones to be selected for complete genome sequencing because of the minimal size of their genomes and their pathogenicity for humans and a broad range of animals and plants. At this time six genome sequences have been publicly released (Mycoplasma genitaliu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh114
更新日期:2004-01-01 00:00:00
abstract::A complete physical map of the spinach mitochondrial genome has been established. The entire sequence content of 327 kilobase pairs (kb) is postulated to occur as a single circular molecule. Two directly repeated elements of approximately 6 kb, located on this "master chromosome", are proposed to participate in an int...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.14.5651
更新日期:1986-07-25 00:00:00
abstract::Controllable gene delivery via vector-based systems remains a formidable challenge in mammalian synthetic biology and a desirable asset in gene therapy applications. Here, we introduce a methodology to control the copies and residence time of a gene product delivered in host human cells but also selectively disrupt fr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1326
更新日期:2015-01-01 00:00:00
abstract::Key components of the translational apparatus, i.e. ribosomes, elongation factor EF-Tu and most aminoacyl-tRNA synthetases, are stereoselective and prevent incorporation of d-amino acids (d-aa) into polypeptides. The rare appearance of d-aa in natural polypeptides arises from post-translational modifications or non-ri...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv566
更新日期:2015-07-13 00:00:00
abstract::RNase P is primarily responsible for the 5΄ maturation of transfer RNAs (tRNAs) in all domains of life. Archaeal RNase P is a ribonucleoprotein made up of one catalytic RNA and five protein cofactors including L7Ae, which is known to bind the kink-turn (K-turn), an RNA structural element that causes axial bending. How...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx388
更新日期:2017-07-07 00:00:00
abstract::Conventional approaches to predict transcriptional regulatory interactions usually rely on the definition of a shared motif sequence on the target genes of a transcription factor (TF). These efforts have been frustrated by the limited availability and accuracy of TF binding site motifs, usually represented as position...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1286
更新日期:2013-02-01 00:00:00
abstract::IHF and HU are two heterodimeric nucleoid-associated proteins (NAP) that belong to the same protein family but interact differently with the DNA. IHF is a sequence-specific DNA-binding protein that bends the DNA by over 160°. HU is the most conserved NAP, which binds non-specifically to duplex DNA with a particular pr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr1236
更新日期:2012-04-01 00:00:00
abstract::The large terminase subunit is a central component of the genome packaging motor from tailed bacteriophages and herpes viruses. This two-domain enzyme has an N-terminal ATPase activity that fuels DNA translocation during packaging and a C-terminal nuclease activity required for initiation and termination of the packag...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks974
更新日期:2013-01-07 00:00:00
abstract::Neph et al. (2012) (Circuitry and dynamics of human transcription factor regulatory networks. Cell, 150: 1274-1286) reported the transcription factor (TF) regulatory networks of 41 human cell types using the DNaseI footprinting technique. This provides a valuable resource for uncovering regulation principles in differ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku923
更新日期:2014-11-10 00:00:00
abstract::DNA repair is required to maintain genome stability in stem cells and early embryos. At critical junctures, oxidative damage to DNA requires the base excision repair (BER) pathway. Since early zebrafish embryos lack the major polymerase in BER, DNA polymerase ß, repair proceeds via replicative polymerases, even though...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1142
更新日期:2011-04-01 00:00:00
abstract::Successful development of biological databases requires accommodation of the burgeoning amounts of data from high-throughput genomics pipelines. As the volume of curated data in Animal QTLdb (https://www.animalgenome.org/QTLdb) increases exponentially, the resulting challenges must be met with rapid infrastructure dev...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1084
更新日期:2019-01-08 00:00:00
abstract::Nucleotide sequences of three cloned restriction fragments of Tetrahymena mtDNA which showed hybridization with mitochondrial tRNA have been determined. EcoRI fragment 5 (4.1 kbp) contains the tRNAphe gene sequence with anticodon GAA; Hind III fragment 6 (2.0 kbp) the tRNAhis with anticodon GTG; and EcoRI fragment 7 (...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.9.3273
更新日期:1985-05-10 00:00:00
abstract::Horizontally acquired genes are typically regulated by ancestral regulators. This regulation enables expression of horizontally acquired genes to be coordinated with that of preexisting genes. Here, we report a singular example of the opposite regulation: a horizontally acquired gene that controls an ancestral regulat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa813
更新日期:2020-11-04 00:00:00
abstract::The prokaryotic beta recombinase catalyzes site-specific recombination between two directly oriented minimal six sites in chromatin-integrated substrates. Here, we demonstrate that an enhanced green fluorescent protein (EGFP)-fused version of beta recombinase (beta-EGFP) is fully active, retaining most specific activi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gnj001
更新日期:2006-01-03 00:00:00
abstract::The anti-cancer drug 2',2'-difluoro-2'-deoxycytidine (dFdC) is internally incorporated into DNA in vitro. To determine the effects of this incorporation on DNA structure and function, the beta-cyanoethyl phosphoramidite of dFdC was synthesized and oligodeoxyribonucleotides containing dFdC were made using automated sol...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.7.1763
更新日期:1992-04-11 00:00:00
abstract::Protein-protein and protein-DNA/RNA interactions play a fundamental role in a variety of biological processes. Determining the complex structures of these interactions is valuable, in which molecular docking has played an important role. To automatically make use of the binding information from the PDB in docking, her...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx407
更新日期:2017-07-03 00:00:00
abstract::DNA was purified from double minutes isolated from MTX-resistant EL4/8 mouse lymphoma cells, digested to completion with Bam H1 restriction endonuclease and cloned in lambda-1059. The properties of the library suggest that the DNA from which it was made was not detectably contaminated with non-dm chromosome material, ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.21.6597
更新日期:1982-11-11 00:00:00
abstract::Riboswitches are important gene regulatory elements frequently encountered in bacterial mRNAs. The recently discovered nadA riboswitch contains two similar, tandemly arrayed aptamer domains, with the first domain possessing high affinity for nicotinamide adenine dinucleotide (NAD+). The second domain which comprises t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa1029
更新日期:2020-12-02 00:00:00
abstract::Recently, due to the dual roles of DNA and enzyme, DNAzyme has been widely used in the field of DNA circuit, which has a wide range of applications in bio-engineered system, information processing and biocomputing. In fact, the activity of DNAzymes was regulated by subunits assembly, pH control and metal ions triggers...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1245
更新日期:2019-02-20 00:00:00
abstract::A minizyme is a hammerhead ribozyme with short oligonucleotide linkers instead of stem-loop II. In a previous study we demonstrated that a minizyme with high activity forms a dimeric structure with a common stem II. Because of their dimeric structure, minizymes are potentially capable of cleaving a substrate at two di...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.12.2302
更新日期:1996-06-15 00:00:00
abstract::A general procedure, based on a new activated alkyne linker, for the preparation of peptide-oligonucleotide conjugates (POCs) on solid support has been developed. With this linker, conjugation is effective at room temperature (RT) in millimolar concentration and submicromolar amounts. This is made possible since the u...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr603
更新日期:2011-11-01 00:00:00
abstract::Eucaryotic transcription initiation by RNA polymerase II involves protein:DNA interactions during the formation of a transcription complex. In addition to RNA polymerase II there are at least five other general transcription factors necessary for initiation with the adenovirus major late promoter. One of these, TFIIA,...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.12.3611
更新日期:1990-06-25 00:00:00
abstract::DnaD and DnaB are essential DNA-replication-initiation proteins in low-G+C content Gram-positive bacteria. Here we use sensitive Hidden Markov Model-based techniques to show that the DnaB and DnaD proteins share a common structure that is evident across all their structural domains, termed DDBH1 and DDBH2 (DnaD DnaB H...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq465
更新日期:2010-11-01 00:00:00
abstract::The recognition of human tRNA(Leu) or tRNA(Ser) by cognate aminoacyl- tRNA synthetases has distinct requirements. Only one base change (A73-->G) in tRNA(Leu) is required to generate an efficient serine acceptor in vitro, whereas several changes in three structural domains (the acceptor stem, DHU loop and long extra ar...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.3.405
更新日期:1996-02-01 00:00:00
abstract::Gene expression profiling has gradually become a routine procedure for disease diagnosis and classification. In the past decade, many computational methods have been proposed, resulting in great improvements on various levels, including feature selection and algorithms for classification and clustering. In this study,...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt343
更新日期:2013-08-01 00:00:00
abstract::Holliday junctions (four-way DNA junctions), formed during homologous recombination, are bound and resolved by junction-specific endonucleases to yield recombinant duplex DNA products. The junction-resolving enzymes are a structurally diverse class of proteins that nevertheless have many properties in common; in parti...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.24.5609
更新日期:1998-12-15 00:00:00