Abstract：
:Interferon regulatory factors IRF-3 and IRF-7 are transcription factors essential in the activation of interferon-β (IFN-β) gene in response to viral infections. Although, both proteins recognize the same consensus IRF binding site AANNGAAA, they have distinct DNA binding preferences for sites in vivo. The X-ray structures of IRF-3 and IRF-7 DNA binding domains (DBDs) bound to IFN-β promoter elements revealed flexibility in the loops (L1-L3) and the residues that make contacts with the target sequence. To characterize the conformational changes that occur on DNA binding and how they differ between IRF family members, we have solved the X-ray structures of IRF-3 and IRF-7 DBDs in the absence of DNA. We found that loop L1, carrying the conserved histidine that interacts with the DNA minor groove, is disordered in apo IRF-3 but is ordered in apo IRF-7. This is reflected in differences in DNA binding affinities when the conserved histidine in loop L1 is mutated to alanine in the two proteins. The stability of loop L1 in IRF-7 derives from a unique combination of hydrophobic residues that pack against the protein core. Together, our data show that differences in flexibility of loop L1 are an important determinant of differential IRF-DNA binding.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
De Ioannes P,Escalante CR,Aggarwal AKdoi
10.1093/nar/gkr325subject
Has Abstractpub_date
2011-09-01 00:00:00pages
7300-7issue
16eissn
0305-1048issn
1362-4962pii
gkr325journal_volume
39pub_type
杂志文章abstract：:The homing endonuclease PI-SceI from Saccharo myces cerevisiae consists of two domains. The protein splicing domain I catalyzes the excision of the mature endonuclease (intein) from a precursor protein and the religation of the flanking amino acid sequences (exteins) to a functional protein. Furthermore, domain I is i...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkf523
更新日期：2002-09-15 00:00:00
abstract：:POGO-DB (http://pogo.ece.drexel.edu/) provides an easy platform for comparative microbial genomics. POGO-DB allows users to compare genomes using pre-computed metrics that were derived from extensive computationally intensive BLAST comparisons of >2000 microbes. These metrics include (i) average protein sequence ident...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt1094
更新日期：2014-01-01 00:00:00
abstract：:Previous studies have implicated the DE-1 (-111/-106) and alpha A-CRYBP1 (-66/-57) sites for activity of the mouse alpha A-crystallin promoter in transiently transfected lens cells. Here we have used the bacterial chloramphenicol acetyltransferase (CAT) reporter gene to test the functional importance of the putative D...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.11.2633
更新日期：1993-06-11 00:00:00
abstract：:Post-translational modifications contribute to the spliceosome dynamics by facilitating the physical rearrangements of the spliceosome. Here, we report USP15, a deubiquitinating enzyme, as a regulator of protein-protein interactions for the spliceosome dynamics. We show that PRP31, a component of U4 snRNP, is modified...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw1365
更新日期：2017-05-05 00:00:00
abstract：:The CRISPR system has become a powerful biological tool with a wide range of applications. However, improving targeting specificity and accurately predicting potential off-targets remains a significant goal. Here, we introduce a web-based CR: ISPR/Cas9 O: ff-target P: rediction and I: dentification T: ool (CROP-IT) th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv575
更新日期：2015-10-15 00:00:00
abstract：:The University of Minnesota Biocatalysis/Biodegradation Database (http://www.labmed.umn.edu/umbbd/ ) begins its fifth year having met its initial goals. It contains approximately 100 pathways for microbial catabolic metabolism of primarily xenobiotic organic compounds, including information on approximately 650 reacti...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.1.377
更新日期：2000-01-01 00:00:00
abstract：:Molecular dynamics simulations were performed on the duplex DNA dodecamers d(CGCGAA TT CGCG): d(CGCGAATTCGCG) and d(GCACGAA TT AAG): d(CTTAATTCGTGC), where TT denotes a cis, syn cyclobutane thymine dimer. The constant temperature and pressure algorithm of the AMBER 4.1 molecular-modeling package was used with explicit...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.7.1432
更新日期：1997-04-01 00:00:00
abstract：:Eukaryotic gene expression is regulated by enhancer-promoter interactions but the molecular mechanisms that govern specificity have remained elusive. Genome-wide studies utilizing STARR-seq identified two enhancer classes in Drosophila that interact with different core promoters: housekeeping enhancers (hkCP) and deve...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw1114
更新日期：2017-02-28 00:00:00
abstract：:It is common knowledge that conserved residues evolve slowly. We challenge generality of this central tenet of molecular biology by describing the fast evolution of a conserved nucleotide position that is located in the overlap of two open reading frames (ORFs) of polyomaviruses. The de novo ORF is expressed through e...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv378
更新日期：2015-05-26 00:00:00
abstract：:Toxicogenomics focuses on assessing the safety of compounds using gene expression profiles. Gene expression signatures from large toxicogenomics databases are expected to perform better than small databases in identifying biomarkers for the prediction and evaluation of drug safety based on a compound's toxicological m...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku955
更新日期：2015-01-01 00:00:00
abstract：:We have sequenced the Escherichia coli grpE gene and shown that it encodes a 197-amino acid residue protein of 21,668-Mr. The predicted N-terminal amino acid sequence, as well as the overall amino acid composition agree well with that of the purified protein. From Northern analysis, we have shown that transcription of...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.15.7545
更新日期：1988-08-11 00:00:00
abstract：:Approximately half of all human transcripts contain at least one upstream translational initiation site that precedes the main coding sequence (CDS) and gives rise to an upstream open reading frame (uORF). We generated uORFdb, publicly available at http://cbdm.mdc-berlin.de/tools/uorfdb, to serve as a comprehensive li...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt952
更新日期：2014-01-01 00:00:00
abstract：:With the aid of a novel poly-dA tailing-partial restriction technique and S1-protection mapping, the 5' terminal coding sequence for the 40S precursor ribosomal RNA of Xenopus laevis has been exactly identified. Since the promoter sequence for the 40S RNA should lie close to its 5' terminal coding sequence, we are abl...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/6.12.3733
更新日期：1979-08-24 00:00:00
abstract：:The hypothesis that DNA strands complementary to the coding strand contain in phase coding sequences has been investigated. Statistical analysis of the 50 genes of bacteriophage T7 shows no significant correlation between patterns of codon usage on the coding and non-coding strands. In Bacillus and yeast genes the cor...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/13.4.1389
更新日期：1985-02-25 00:00:00
abstract：:Originally identified as an RNA polymerase II interactor, Che-1/AATF (Che-1) has now been recognized as a multifunctional protein involved in cell-cycle regulation and cancer progression, as well as apoptosis inhibition and response to stress. This protein displays a peculiar nucleolar localization and it has recently...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa344
更新日期：2020-06-19 00:00:00
abstract：:The discontinuous synthesis of the complementary strands of polyoma DNA in isolated nuclei has been studied by hybridization techniques. The relative amounts of the newly synthesized complementary strands were compared by separately annealing them to denatured HpaII restriction fragments. In every case an excess (1.4-...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/4.5.1449
更新日期：1977-01-01 00:00:00
abstract：:TRF1, a duplex telomeric DNA-binding protein, plays an important role in telomere metabolism. We have previously reported that a fraction of endogenous TRF1 can stably exist free of telomere chromatin when it is phosphorylated at T371 by Cdk1; however, the role of this telomere-free (pT371)TRF1 has yet to be fully cha...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt775
更新日期：2013-12-01 00:00:00
abstract：:Programmed chromosome breakage occurs at 50-200 specific sites in the genome of Tetrahymena thermo-phila during somatic nuclear (macronuclear) differentiation. Previous studies have identified a 15 bp sequence, the Cbs (for chromosome breakage sequence), that is necessary and sufficient to specify these sites. In this...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.4.895
更新日期：2000-02-15 00:00:00
abstract：:It has recently been demonstrated that nucleobase-density profiles of typical mRNA coding sequences exhibit a complementary relationship with nucleobase-interaction propensity profiles of their cognate protein sequences. This finding supports the idea that the genetic code developed in response to direct binding inter...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv166
更新日期：2015-03-31 00:00:00
abstract：:The entire nucleotide sequence of the Ad. 2 EcoRI D fragment has been determined using the Maxam and Gilbert method. This sequence of 2678 bp contains informations relative to late mRNAs ending at position 78 and for which an AATAAA sequence corresponding to their 3' ends is found at residue number 833. Position of th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/8.10.2173
更新日期：1980-05-24 00:00:00
abstract：:We present version 2 of the SPINE system for structural proteomics. SPINE is available over the web at http://nesg.org. It serves as the central hub for the Northeast Structural Genomics Consortium, allowing collaborative structural proteomics to be carried out in a distributed fashion. The core of SPINE is a laborato...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg397
更新日期：2003-06-01 00:00:00
abstract：:The MED1/TRAP220 subunit of the Mediator plays a key role in facilitating ligand-dependent interactions of this multisubunit coactivator complex with nuclear receptors through their ligand binding domains. The isolated MED1/TRAP220 protein previously was shown to interact with glucocorticoid receptor (GR) in a ligand-...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm661
更新日期：2007-01-01 00:00:00
abstract：:The synthesis of a pentadecamer of the 5'-phosphate of the antiviral nucleoside ribavirin (1'-beta-D-ribofuranosyl-1H-1,2,4-triazole-3-carboxamide) has been achieved. This homoribopolymer is terminated at the 5'-position with an (6-aminohexyl)phosphate group to permit conjugation to a carrier and at the 3'-position by...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.5.1099
更新日期：1990-03-11 00:00:00
abstract：:Ribosome biogenesis is a dynamic multistep process, many features of which are still incompletely documented. Here, we show that changes in this pathway can be captured and annotated by means of a graphic set of pre-rRNA ratios, a technique we call Ratio Analysis of Multiple Precursors (RAMP). We find that knocking do...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku787
更新日期：2014-01-01 00:00:00
abstract：:The hammerhead self-cleaving motif occurs in a variety of RNAs that infect plants and consists of three non-conserved helices connected by a highly conserved central core. A variant hammerhead, called the extended hammerhead, is found in satellite 2 transcripts from a variety of caudate amphibians. The extended hammer...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.11.2189
更新日期：1997-06-01 00:00:00
abstract：:The Human Genome Project has facilitated the sequencing of many species, yet the current Sanger method is too expensive, labor intensive and time consuming to accomplish medical resequencing of human genomes en masse. Of the 'next-generation' technologies, cyclic reversible termination (CRT) is a promising method with...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm689
更新日期：2007-01-01 00:00:00
abstract：:PsiB protein of plasmid R6-5 inhibits the induction of the SOS pathway. The F sex factor also carries a psiB gene homologous to that of R6-5. Yet, it fails to inhibit SOS induction. In order to solve this difference, we characterized the psiB genes of R6-5 and F. We found that (i) the sequences of the two psiB genes s...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.22.10669
更新日期：1988-11-25 00:00:00
abstract：:The transcriptional regulator Spx plays a key role in maintaining the redox homeostasis of Bacillus subtilis cells exposed to disulfide stress. Defects in Spx were previously shown to lead to differential expression of numerous genes but direct and indirect regulatory effects could not be distinguished. Here we identi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks755
更新日期：2012-10-01 00:00:00
abstract：:DNA nick can be used as a design motif in programming the shape and reconfigurable deformation of synthetic DNA nanostructures, but its mechanical properties have rarely been systematically characterized at the level of base sequences. Here, we investigated sequence-dependent mechanical properties of DNA nicks through...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky1189
更新日期：2019-01-10 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
