Abstract：
:CSP41 is a ubiquitous chloroplast endoribonuclease belonging to the short chain dehydrogenase/reductase (SDR) superfamily. To help elucidate the role of CSP41 in chloroplast gene regulation, the mechanisms that determine its substrate recognition and catalytic activity were investigated. A divalent metal is required for catalysis, most probably to provide a nucleophile for cleavage 5' to the phosphodiester bond, and may also participate in cleavage site selection. This requirement distinguishes CSP41 from other Rossman fold-containing proteins from the SDR superfamily, including several RNA-binding proteins and endonucleases. CSP41 is active only in the presence of MgCl2 and CaCl2. Although Mg2+- and Ca2+-activated CSP41 cleave at identical sites in the single-stranded regions of a stem-loop-containing substrate, Mg2+-activated CSP41 was also able to cleave within the double-stranded region of the stem-loop. Mixed metal experiments with Mg2+ and Ca2+ suggest that CSP41 contains a single divalent metal-binding site which is non-selective, since Mn2+, Co2+ and Zn2+ compete with Mg2+ for binding, although there is no activity in their presence. Using site-directed mutagenesis, we identified three residues, Asn71, Asp89 and Asp103, which may form the divalent metal-binding pocket. The activation constant for Mg2+ (K(A,Mg) = 2.1 +/- 0.4 mM) is of the same order of magnitude as the stromal Mg2+ concentrations, which fluctuate between 0.5 and 10 mM as a function of light and of leaf development. These changes in stromal Mg2+ concentration may regulate CSP41 activity, and thus cpRNA stability, during plant development.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Bollenbach TJ,Stern DBdoi
10.1093/nar/gkg640keywords:
subject
Has Abstractpub_date
2003-08-01 00:00:00pages
4317-25issue
15eissn
0305-1048issn
1362-4962journal_volume
31pub_type
杂志文章abstract：:SSCP and heteroduplex analysis (HA) continue to be the most popular methods of mutation detection due to their simplicity, high sensitivity and low cost. The advantages of these methods are most clearly visible when large genes, such as BRCA1 and BRCA2, are scanned for scattered unknown mutations and/or when a large n...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.14.e71
更新日期：2001-07-15 00:00:00
abstract：:BRENDA is a comprehensive relational database on functional and molecular information of enzymes, based on primary literature. The database contains information extracted and evaluated from approximately 46 000 references, holding data of at least 40 000 different enzymes from more than 6900 different organisms, class...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/30.1.47
更新日期：2002-01-01 00:00:00
abstract：:Posttranslational modifications (PTMs) of histones represent a crucial regulatory mechanism of nucleosome and chromatin dynamics in various of DNA-based cellular processes, such as replication, transcription and DNA damage repair. Lysine succinylation (Ksucc) is a newly identified histone PTM, but its regulation and f...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa663
更新日期：2020-09-25 00:00:00
abstract：:In eukaryotes, exposure to stress conditions causes a shift from cap-dependent to cap-independent translation. In trypanosomatids, environmental switches are the driving force of a developmental program of gene expression, but it is yet unclear how their translation machinery copes with their constantly changing envir...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr555
更新日期：2011-10-01 00:00:00
abstract：:HBV genotypes differ in pathogenicity. In addition, genotype-specific differences in the regulation of transcription and virus replication exist in HBV, but the underlying mechanisms are unknown. Here, we show the presence of a G-quadruplex motif in the promoter of the preS2/S gene; this G-quadruplex is highly conserv...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx823
更新日期：2017-11-02 00:00:00
abstract：:The Mouse Genome Database (MGD, http://www.informatics.jax.org/), integrates genetic, genomic and phenotypic information about the laboratory mouse, a primary animal model for studying human biology and disease. Information in MGD is obtained from diverse sources, including the scientific literature and external datab...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn886
更新日期：2009-01-01 00:00:00
abstract：:High performance liquid chromatography analysis of imidazole open ring 7-methylguanine, 2-6 diamino-4-hydroxy-5N-methyl-formamidopyrimidine (rom7G), showed two well-separated peaks (fI and fII) of the same magnitude. Rechromatography of each isolated component indicated that they are slowly interconverted to give a 1:...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.13.5429
更新日期：1984-07-11 00:00:00
abstract：:The alternatively spliced RNA species of tumor suppressor gene p53, containing an additional 96 bases derived from intron 10, is present at approximately 25 to 30% the level of regularly spliced p53 RNA in both normal epidermal and carcinoma cells. The presence of this alternatively spliced RNA in 10T1/2 fibroblast ce...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.8.1979
更新日期：1992-04-25 00:00:00
abstract：:O-GLYCBASE is a revised database of information on glycoproteins and their O-linked glycosylation sites. Entries are compiled and revised from the literature, and from the sequence databases. Entries include information about species, sequence, glycosylation sites and glycan type and is fully cross-referenced. Compare...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.1.387
更新日期：1998-01-01 00:00:00
abstract：:Chlorella virus DNA ligase is the smallest eukaryotic ATP-dependent DNA ligase known; it suffices for yeast cell growth in lieu of the essential yeast DNA ligase Cdc9. The Chlorella virus ligase-adenylate intermediate has an intrinsic nick sensing function and its DNA footprint extends 8-9 nt on the 3'-hydroxyl (3'-OH...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg665
更新日期：2003-09-01 00:00:00
abstract：:DAXX displays complex biological functions. Remarkably, DAXX overexpression is a common feature in diverse cancers, which correlates with tumorigenesis, disease progression and treatment resistance. Structurally, DAXX is modular with an N-terminal helical bundle, a docking site for many DAXX interactors (e.g. p53 and ...
journal_title：Nucleic acids research
pub_type： 杂志文章,评审
doi：10.1093/nar/gkz634
更新日期：2019-09-05 00:00:00
abstract：:Herpes simplex virus-1 US11 is a RNA-binding protein with a novel RNA-binding domain. US11 has been reported to exhibit sequence- and conformation-specific RNA-binding, but the sequences and conformations important for binding are not known. US11 has also been described as a double-stranded RNA (dsRNA)-binding protein...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki919
更新日期：2005-10-24 00:00:00
abstract：:Sequence-specific binding of proteins to their DNA targets involves a complex spectrum of processes that often induce DNA conformational variation in the bound complex. The forces imposed by protein binding that cause the helical deformations are intimately interrelated and difficult to parse or rank in importance. To...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt492
更新日期：2013-08-01 00:00:00
abstract：:The third intron from Physarum polycephalum (Pp LSU 3) is one of the closest known relatives to the well-studied Tetrahymena group I intron. Both introns are located at the same position in the 26S rRNA gene, and with the exception of an open reading frame in Pp LSU 3, are highly homologous. While Pp LSU 3 has been sh...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.20.4315
更新日期：1994-10-11 00:00:00
abstract：:eggNOG is a public database of orthology relationships, gene evolutionary histories and functional annotations. Here, we present version 5.0, featuring a major update of the underlying genome sets, which have been expanded to 4445 representative bacteria and 168 archaea derived from 25 038 genomes, as well as 477 euka...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky1085
更新日期：2019-01-08 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：:Infrared spectroscopy was used to identify hydration-sensitive structural differences between single- stranded phosphorothioate (PS) and phosphodiester (PO) oligodeoxyribonucleotides. Spectra were recorded in the mid-infrared region, 500-1800 cm-1, at relative humidities between 0 and 98%; the PS and PO spectra are su...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.16.3261
更新日期：1996-08-15 00:00:00
abstract：:Yeast Dna2 helicase/nuclease is essential for DNA replication and assists FEN1 nuclease in processing a subset of Okazaki fragments that have long single-stranded 5' flaps. It is also involved in the maintenance of telomeres. DNA2 is a gene conserved in eukaryotes, and a putative human ortholog of yeast DNA2 (ScDNA2) ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl070
更新日期：2006-04-04 00:00:00
abstract：:Affymetrix has recently developed whole-transcript GeneChips-'Gene' and 'Exon' arrays-which interrogate exons along the length of each gene. Although each probe on these arrays is intended to hybridize perfectly to only one transcriptional target, many probes match multiple transcripts located in different parts of th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp853
更新日期：2010-01-01 00:00:00
abstract：:Four pseudorevertants of a -10 region lacP mutation were isolated. Three of these mutations were found to activate nascent promoters. These mutations were: a -2 G/C----A/T change (-2A) promoting transcription at position +11, a +1 A/T----T/A change (+1T) promoting transcription initiation at position +13, and a +10 C/...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.10.3927
更新日期：1989-05-25 00:00:00
abstract：:Extracts of the human glioma cell line A1235 (lacking O(6)-methylguanine-DNA methyltransferase) are known to restore a G:T mismatch to a normal G:C pair in a G:T-containing model (45 bp) DNA substrate. Herein we demonstrate that substitution of G:T with O(6)-methylguanine:T (m6G:T) results in extract-induced intra-str...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.11.2409
更新日期：2001-06-01 00:00:00
abstract：:Advancement in the field of computational research has made it possible for the in silico methods to offer significant benefits to both regulatory needs and requirements for risk assessments, and pharmaceutical industry to assess the safety profile of a chemical. Here, we present ProTox-II that incorporates molecular ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky318
更新日期：2018-07-02 00:00:00
abstract：:The precursor to the Euglena light harvesting chlorophyll a/b binding protein of photosystem II (LHCPII) is a polyprotein containing multiple copies of LHCPII covalently joined by a decapeptide linker. cDNA and genomic clones encoding the 5' and 3' end of a 6.6 kb LHCPII mRNA were sequenced. A 3.1 kb genomic region en...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.25.5737
更新日期：1994-12-25 00:00:00
abstract：:The Rhizobium trifolii nod genes required for host-specific nodulation of clovers are located on 14 kb of Sym (symbiotic) plasmid DNA. Analysis of the nucleotide sequence of a 3.7 kb portion of this region has revealed open reading frames corresponding to the nodABCDEF genes. A DNA sequencing technique, using primer e...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.7.2891
更新日期：1986-04-11 00:00:00
abstract：:The gene co-expression analysis toolbox (GeneCAT) introduces several novel microarray data analyzing tools. First, the multigene co-expression analysis, combined with co-expressed gene networks, provides a more powerful data mining technique than standard, single-gene co-expression analysis. Second, the high-throughpu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn292
更新日期：2008-07-01 00:00:00
abstract：:Alu elements have repeatedly been found involved in gene rearrangements in humans. Although these elements have been suggested to stimulate gene rearrangements, sparse information is available for the possible mechanism(s) of these events. Here we present a compilation of Alu elements that have been involved in recomb...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.2.256
更新日期：1995-01-25 00:00:00
abstract：:We report here the different ways in which four subunits of the basal transcription/repair factor TFIIH (XPB, XPD, p62 and p44) and the damage recognition XPC repair protein can enter the nucleus. We examined their nuclear localization by transiently expressing the gene products tagged with the enhanced green fluoresc...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.7.1574
更新日期：2001-04-01 00:00:00
abstract：:Transcription start and termination sites were mapped in the E. coli replication origin, oriC. Outward transcription from within oriC (promoters Pori-r and Pori-l) was found to start in vivo at position 178 for Pori-l and at positions 294 and 304 for Pori-r, respectively. These transcripts were terminated after 100-15...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.6.2479
更新日期：1987-03-25 00:00:00
abstract：:Sequence specific DNA methylation sometimes results in the protection of some or all of a restriction endonucleases' cleavage sites. This is usually, but not always, the result of methylation of one or both strands of DNA at the site characteristic of the corresponding "cognate" modification methylase. The known effec...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.22.5859
更新日期：1981-11-25 00:00:00
abstract：:Hepatocyte Nuclear Factor 4 (HNF-4), a liver-enriched orphan receptor of the nuclear receptor superfamily, is required for the expression of a wide variety of liver-specific genes including apoAI. To explore the possibility that site A of the apoAI gene enhancer might also be the target for HNF-4 without the interfere...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.25.5665
更新日期：1994-12-25 00:00:00
