Abstract：
:Rad18 is a ubiquitin E3 ligase that monoubiquitinates PCNA on stalled replications forks. This allows recruitment of damage-tolerant polymerases for damage bypass and DNA repair. In this activity, the Rad18 protein has to interact with Rad6, the E2 ubiquitin-conjugating enzyme, ubiquitin, PCNA and DNA. Here we analyze the biochemical interactions of specific domains of the Rad18 protein. We found that the Rad6/Rad18 complex forms stable dimers in vitro. Consistent with previous findings, both the Ring domain and a C-terminal region contribute to the Rad6 interaction, while the C-terminus is not required for the interaction with PCNA. Surprisingly we find that the C2HC zinc finger is important for interaction with ubiquitin, apparently analogous to the interactions of classical zinc fingers with ubiquitin such as found in the UBZ and UBM domains in Y-family polymerases. Finally we find that the SAP domain, but not the zinc finger domain, is capable of DNA binding in vitro.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Notenboom V,Hibbert RG,van Rossum-Fikkert SE,Olsen JV,Mann M,Sixma TKdoi
10.1093/nar/gkm615subject
Has Abstractpub_date
2007-01-01 00:00:00pages
5819-30issue
17eissn
0305-1048issn
1362-4962pii
gkm615journal_volume
35pub_type
杂志文章abstract：:LINKER was developed as an online server to assist biomedical researchers to design linker sequences for constructing functional fusion proteins. The program automatically generates a set of peptide sequences that are known to adopt extended conformations as determined by X-ray crystallography and NMR. In addition to ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh422
更新日期：2004-07-01 00:00:00
abstract：:DNA restriction fragments located 5' to the human c-myc gene display anomalous electrophoretic mobility on polyacrylamide gels. Computer modeling of the c-myc flanking DNA suggests that the slow-moving DNA fragments spanning nucleotides -1690 to -1054 (relative to c-myc promoter P1) and -718 to -452 form large left ha...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.7.2819
更新日期：1989-04-11 00:00:00
abstract：:Purified UvrA, UvrB, UvrC, UvrD, PolA and Lig proteins from Escherichia coli have been used to assess the effect of nucleotide excision repair on the conformation of native negatively supercoiled plasmid DNA in an in vitro test system. The analysis of labeled reaction products on specific gel systems suggests that the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.24.10337
更新日期：1989-12-25 00:00:00
abstract：:Mutations in human mitochondrial DNA are often associated with incurable human neuromuscular diseases. Among these mutations, an important number have been identified in tRNA genes, including 29 in the gene MT-TL1 coding for the tRNA(Leu(UUR)). The m.3243A>G mutation was described as the major cause of the MELAS syndr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr546
更新日期：2011-10-01 00:00:00
abstract：:Enzymes that form transient DNA-protein covalent complexes are targets for several potent classes of drugs used to treat infectious disease and cancer, making it important to establish robust and rapid procedures for analysis of these complexes. We report a method for isolation of DNA-protein adducts and their identif...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku490
更新日期：2014-07-01 00:00:00
abstract：:We have isolated and sequenced the complete murine I-E alpha immune response gene of the H-2db haplotype. The I-E alpha d gene consists of 5300 basepairs and is organized into five or possibly six exons that correspond to different domains of the alpha chain. The amino acid sequence deduced from the I-E alpha gene sho...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.15.5055
更新日期：1983-08-11 00:00:00
abstract：:Here, we describe the development of WikiPathways (http://www.wikipathways.org), a public wiki for pathway curation, since it was first published in 2008. New features are discussed, as well as developments in the community of contributors. New features include a zoomable pathway viewer, support for pathway ontology a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr1074
更新日期：2012-01-01 00:00:00
abstract：:Genome-wide mapping in the identification of novel candidate genes has always been the standard method in genetics and genomics to correlate a clinically interesting phenotypic trait with a genotype. However, the performance of a mapping experiment using classical microsatellite approaches can be very time consuming. ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki430
更新日期：2005-07-01 00:00:00
abstract：:The accuracy of a homology model based on the structure of a distant relative or other topologically equivalent protein is primarily limited by the quality of the alignment. Here we describe a systematic approach for sequence-to-structure alignment, called 'K*Sync', in which alignments are generated by dynamic program...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl480
更新日期：2006-01-01 00:00:00
abstract：:A simple and efficient gene replacement method, based on the recombination and repair activities of the cell, was developed. The method permits the targeted construction of markerless deletions, insertions and point mutations in the Escherichia coli chromosome. A suicide plasmid, carrying the mutant allele and the rec...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.22.4409
更新日期：1999-11-15 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：:The PriA protein was identified in Escherichia coli as a factor involved in the replication of extrachromosomal elements such as bacteriophage phiX174 and plasmid pBR322. Recent data show that PriA plays an important role in chromosomal replication, by promoting reassembly of the replication machinery during reinitiat...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/30.7.1593
更新日期：2002-04-01 00:00:00
abstract：:The functionalisation of oligodeoxynucleotides and oligoribonucleotides by incorporation of 2'-amido-2'-deoxyribonucleosides, possibly containing a reporter group via the 2'-amido bond, was examined. Therefore 2'-acetamido-ribonucleosides containing a small methyl group at the 2'-amido bond were synthesized as model c...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.1.51
更新日期：1995-01-11 00:00:00
abstract：:Among a collection of 74 aprt mutations induced by treatment of plateau phase Chinese hamster ovary CHO cells with the radiomimetic DNA double-strand cleaving agent neocarzinostatin, nine were large-scale rearrangements. Molecular analysis indicated that all nine were highly conservative, non-homologous reciprocal exc...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkf369
更新日期：2002-06-15 00:00:00
abstract：:Since 2010, the Genomicus web server is available online at http://genomicus.biologie.ens.fr/genomicus. This graphical browser provides access to comparative genomic analyses in four different phyla (Vertebrate, Plants, Fungi, and non vertebrate Metazoans). Users can analyse genomic information from extant species, as...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx1003
更新日期：2018-01-04 00:00:00
abstract：:A system for the tetracycline-inducible regulation of gene expression in mycobacteria has been developed. We have sub-cloned the tetRO region from the Corynebacterium glutamicum TetZ locus into a mycobacterial shuttle plasmid, making expression of genes cloned downstream of tetRO responsive to tetracycline. Using the ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gni023
更新日期：2005-02-01 00:00:00
abstract：:A flow-injection (FI) device is combined, through the use of a low-volume (4 microl) flow cell, with an ultrasensitive surface plasmon resonance (SPR) spectrometer equipped with a bi-cell photodiode detector. The application of this novel FI-SPR device for sequence-specific ultratrace analysis of oligodeoxynucleotides...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gnf072
更新日期：2002-07-15 00:00:00
abstract：:Bursts of free radicals produced by ionization of water in close vicinity to DNA can produce clusters of opposed DNA lesions and these are termed multiply damaged sites (MDS). How MDS are processed by the Escherichia coli DNA glycosylases, endonuclease (endo) III and endo VIII, which recognize oxidized pyrimidines, is...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.4.932
更新日期：1998-02-15 00:00:00
abstract：:Intrinsic energetic and solvation factors contributing to the unusual structural and biochemical properties of N3'-phosphoramidate DNA analogs have been re-examined using a combination of quantum mechanical and molecular dynamics methods. Evaluation of the impact of the N3'-H substitution was performed via comparison ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.15.3219
更新日期：2001-08-01 00:00:00
abstract：:PIWI-interacting RNAs (piRNAs) comprise a class of small RNAs best known for suppressing transposable elements in germline tissues. The vector mosquito Aedes aegypti encodes seven PIWI genes, four of which are somatically expressed. This somatic piRNA pathway generates piRNAs from viral RNA during infection with cytop...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky1266
更新日期：2019-03-18 00:00:00
abstract：:We present the complete nucleotide sequence of the larval beta I-globin gene of Xenopus laevis including 240 nucleotides of the 5' flanking region and 594 nucleotides beyond the polyadenylation site. The site of transcription initiation was mapped by S1 nuclease, and the site of polyadenylation was determined by compa...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.20.7705
更新日期：1984-10-25 00:00:00
abstract：:Drosophila tissue culture cells have been important in the study of homologous promoters and more recently in the study of mammalian transcriptional factors such as CTF and SP1 which bind and stimulate transcription from transfected genes. In this paper we show that a Drosophila melanogaster haploid cell line (1182-4)...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.15.6205
更新日期：1989-08-11 00:00:00
abstract：:Lateral ribosomal stalk is responsible for binding and recruiting translation factors during protein synthesis. The eukaryotic stalk consists of one P0 protein with two copies of P1•P2 heterodimers to form a P0(P1•P2)₂ pentameric P-complex. Here, we have solved the structure of full-length P1•P2 by nuclear magnetic re...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt636
更新日期：2013-10-01 00:00:00
abstract：:Bile acid biosynthesis is subjected to feedback regulation whereby bile acids down-regulate their own synthesis. The major point of this regulation is at the level of cholesterol 7alpha-hydroxylase (7alpha-hydroxylase), which controls bile acid output from the classic pathway. This regulation is at the level of transc...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.18.3587
更新日期：2000-09-15 00:00:00
abstract：:USF is a helix-loop-helix transcription factor that, like Myc, recognizes the DNA binding motif CACGTG. Two different forms of USF, characterized by apparent molecular weights of 43,000 and 44,000, were originally identified in HeLa cells by biochemical analysis. Clones for the 43-kDa USF were first characterized, but...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.3.427
更新日期：1994-02-11 00:00:00
abstract：:An adequate supply of nucleotides is essential for DNA replication and DNA repair. Moreover, inhibition of TTP synthesis can cause cell death by a poorly characterized mechanism called thymine-less death. In the yeast Saccharomyces cerevisiae, the genes encoding thymidylate synthetase (CDC21) and thymidylate kinase (C...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki219
更新日期：2005-01-28 00:00:00
abstract：:Double stranded cDNA of cucumber pale fruit viroid ( CPFV ) has been cloned by the method of Okayama and Berg (Mol.Cell.Biol.2,161-170 (1982] and the complete nucleotide sequence was established. The covalently closed circular molecules of single-stranded CPFV RNA consists of 303 nucleotides. The nucleotide sequence o...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.8.3427
更新日期：1984-04-25 00:00:00
abstract：:A type II restriction endonuclease, DraI, isolated from Deinococcus radiophilus ATCC 27603 recognises the palindromic hexanucleotide sequence (formula; see text) and cleaves it, as indicated by the arrows, to produce blunt-ended fragments. The yield of enzyme is 100 to 1000 times that of the only other known type II r...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.16.5467
更新日期：1983-08-25 00:00:00
abstract：:The Epstein-Barr virus gene BRLF1 encodes the transcription factor R, which is a sequence-specific DNA-binding protein important for the switch from latency to a productive cycle. We have defined a repertoire of specific R-binding sites using a GST-R fusion protein and a pool of 23 bp random DNA sequences. The R-bound...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.7.1172
更新日期：1994-04-11 00:00:00
abstract：:The sequence GCGCGCGCGC contains three overlapping, mutually exclusive, BssHII restriction sites, each corresponding to one of the three different reading frames. When inserted into a plasmid and digested with BssHII, the three sites in this sequence are cleaved at an approximate ratio of 2:1:2. Consequently, this sys...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.8.3107
更新日期：1989-04-25 00:00:00
